diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c3ec182d4..ff42532cc 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,216 +1,207 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Jun 14 2010
-# @date last modification: Wed Jan 20 2016
+# @date last modification: Tue Feb 13 2018
#
# @brief CMake file for the library
#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
+# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
#===============================================================================
# Package Management
#===============================================================================
package_get_all_source_files(
AKANTU_LIBRARY_SRCS
AKANTU_LIBRARY_PUBLIC_HDRS
AKANTU_LIBRARY_PRIVATE_HDRS
)
package_get_all_include_directories(
AKANTU_LIBRARY_INCLUDE_DIRS
)
package_get_all_external_informations(
PRIVATE_INCLUDE AKANTU_PRIVATE_EXTERNAL_INCLUDE_DIR
INTERFACE_INCLUDE AKANTU_INTERFACE_EXTERNAL_INCLUDE_DIR
LIBRARIES AKANTU_EXTERNAL_LIBRARIES
)
package_get_all_compilation_flags(CXX _cxx_flags)
set(AKANTU_EXTRA_CXX_FLAGS
"${_cxx_flags}" CACHE STRING "Extra flags defined by loaded packages" FORCE)
mark_as_advanced(AKANTU_EXTRA_CXX_FLAGS)
foreach(src_ ${AKANTU_SPIRIT_SOURCES})
set_property(SOURCE ${src_} PROPERTY COMPILE_FLAGS "-g0 -Werror")
endforeach()
#===========================================================================
# header for blas/lapack (any other fortran libraries)
#===========================================================================
package_is_activated(BLAS _blas_activated)
package_is_activated(LAPACK _lapack_activated)
if(_blas_activated OR _lapack_activated)
if(CMAKE_Fortran_COMPILER)
# ugly hack
set(CMAKE_Fortran_COMPILER_LOADED TRUE)
endif()
include(FortranCInterface)
FortranCInterface_HEADER(
"${CMAKE_CURRENT_BINARY_DIR}/aka_fortran_mangling.hh"
MACRO_NAMESPACE "AKA_FC_")
mark_as_advanced(CDEFS)
endif()
list(APPEND AKANTU_LIBRARY_INCLUDE_DIRS "${CMAKE_CURRENT_BINARY_DIR}")
set(AKANTU_INCLUDE_DIRS
${CMAKE_CURRENT_BINARY_DIR} ${AKANTU_LIBRARY_INCLUDE_DIRS}
CACHE INTERNAL "Internal include directories to link with Akantu as a subproject")
#===========================================================================
# configurations
#===========================================================================
package_get_all_material_includes(AKANTU_MATERIAL_INCLUDES)
package_get_all_material_lists(AKANTU_MATERIAL_LISTS)
configure_file(model/solid_mechanics/material_list.hh.in
"${CMAKE_CURRENT_BINARY_DIR}/material_list.hh" @ONLY)
package_get_element_lists()
configure_file(common/aka_element_classes_info.hh.in
"${CMAKE_CURRENT_BINARY_DIR}/aka_element_classes_info.hh" @ONLY)
configure_file(common/aka_config.hh.in
"${CMAKE_CURRENT_BINARY_DIR}/aka_config.hh" @ONLY)
#===============================================================================
# Debug infos
#===============================================================================
set(AKANTU_GDB_DIR ${PROJECT_SOURCE_DIR}/cmake)
if(UNIX)
string(TOUPPER "${CMAKE_BUILD_TYPE}" _u_build_type)
if(_u_build_type STREQUAL "DEBUG" OR _u_build_type STREQUAL "RELWITHDEBINFO")
configure_file(${PROJECT_SOURCE_DIR}/cmake/libakantu-gdb.py.in
"${PROJECT_BINARY_DIR}/libakantu-gdb.py"
@ONLY)
configure_file(${PROJECT_SOURCE_DIR}/cmake/akantu-debug.cc.in
"${PROJECT_BINARY_DIR}/akantu-debug.cc" @ONLY)
list(APPEND AKANTU_LIBRARY_SRCS ${PROJECT_BINARY_DIR}/akantu-debug.cc)
endif()
else()
find_program(GDB_EXECUTABLE gdb)
if(GDB_EXECUTABLE)
execute_process(COMMAND
${GDB_EXECUTABLE} --batch -x "${PROJECT_SOURCE_DIR}/cmake/gdb_python_path"
OUTPUT_VARIABLE AKANTU_PYTHON_GDB_DIR
ERROR_QUIET
RESULT_VARIABLE _res)
if(_res EQUAL 0 AND UNIX)
set(GDB_USER_CONFIG $ENV{HOME}/.gdb/auto-load)
file(MAKE_DIRECTORY ${GDB_USER_CONFIG})
configure_file(${PROJECT_SOURCE_DIR}/cmake/libakantu-gdb.py.in
"${GDB_USER_CONFIG}/${CMAKE_SHARED_LIBRARY_PREFIX}akantu${CMAKE_SHARED_LIBRARY_SUFFIX}.${AKANTU_VERSION}-gdb.py"
@ONLY)
endif()
endif()
endif()
#===============================================================================
# Library generation
#===============================================================================
add_library(akantu ${AKANTU_LIBRARY_SRCS})
target_include_directories(akantu
PRIVATE $<BUILD_INTERFACE:${AKANTU_INCLUDE_DIRS}>
INTERFACE $<INSTALL_INTERFACE:include/akantu>
)
# small trick for build includes in public
set_property(TARGET akantu APPEND PROPERTY INTERFACE_INCLUDE_DIRECTORIES
$<BUILD_INTERFACE:${AKANTU_INCLUDE_DIRS}>)
target_include_directories(akantu SYSTEM
PUBLIC ${AKANTU_INTERFACE_EXTERNAL_INCLUDE_DIR}
)
target_include_directories(akantu SYSTEM
PRIVATE ${AKANTU_PRIVATE_EXTERNAL_INCLUDE_DIR}
)
target_link_libraries(akantu ${AKANTU_EXTERNAL_LIBRARIES})
set_target_properties(akantu
PROPERTIES
${AKANTU_LIBRARY_PROPERTIES} # this contains the version
COMPILE_FLAGS "${_cxx_flags}"
)
if(NOT CMAKE_VERSION VERSION_LESS 3.1)
package_get_all_features_public(_PUBLIC_features)
package_get_all_features_private(_PRIVATE_features)
foreach(_type PRIVATE PUBLIC)
if(_${_type}_features)
target_compile_features(akantu ${_type} ${_${_type}_features})
endif()
endforeach()
else()
set_target_properties(akantu
PROPERTIES
CXX_STANDARD 14
)
endif()
package_get_all_extra_dependencies(_extra_target_dependencies)
if(_extra_target_dependencies)
# This only adding todo: find a solution for when a dependency was add the is removed...
add_dependencies(akantu ${_extra_target_dependencies})
endif()
package_get_all_export_list(AKANTU_EXPORT_LIST)
list(APPEND AKANTU_EXPORT_LIST akantu)
# TODO separate public from private headers
install(TARGETS akantu
EXPORT ${AKANTU_TARGETS_EXPORT}
LIBRARY DESTINATION lib COMPONENT lib
ARCHIVE DESTINATION lib COMPONENT lib
RUNTIME DESTINATION bin COMPONENT bin
PUBLIC_HEADER DESTINATION include/akantu/ COMPONENT dev
)
if("${AKANTU_TARGETS_EXPORT}" STREQUAL "AkantuTargets")
install(EXPORT AkantuTargets DESTINATION share/cmake/${PROJECT_NAME}
COMPONENT dev)
#Export for build tree
export(EXPORT AkantuTargets
FILE "${CMAKE_BINARY_DIR}/AkantuTargets.cmake")
export(PACKAGE Akantu)
endif()
# print out the list of materials
generate_material_list()
register_target_to_tidy(akantu)
diff --git a/src/common/aka_array.cc b/src/common/aka_array.cc
index d014ca3ab..9c273ed17 100644
--- a/src/common/aka_array.cc
+++ b/src/common/aka_array.cc
@@ -1,124 +1,123 @@
/**
* @file aka_array.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of akantu::Array
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <memory>
#include <utility>
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Functions ArrayBase */
/* -------------------------------------------------------------------------- */
ArrayBase::ArrayBase(ID id)
: id(std::move(id)), allocated_size(0), size_(0), nb_component(1),
size_of_type(0) {}
/* -------------------------------------------------------------------------- */
ArrayBase::~ArrayBase() = default;
/* -------------------------------------------------------------------------- */
void ArrayBase::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "ArrayBase [" << std::endl;
stream << space << " + size : " << size_ << std::endl;
stream << space << " + nb component : " << nb_component << std::endl;
stream << space << " + allocated size : " << allocated_size << std::endl;
Real mem_size = (allocated_size * nb_component * size_of_type) / 1024.;
stream << space << " + size of type : " << size_of_type << "B"
<< std::endl;
stream << space << " + memory allocated : " << mem_size << "kB" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <> UInt Array<Real>::find(const Real & elem) const {
AKANTU_DEBUG_IN();
Real epsilon = std::numeric_limits<Real>::epsilon();
auto it = std::find_if(begin(), end(), [&elem, &epsilon](auto && a) {
return std::abs(a - elem) <= epsilon;
});
AKANTU_DEBUG_OUT();
return (it != end()) ? end() - it : UInt(-1);
}
/* -------------------------------------------------------------------------- */
template <>
Array<ElementType> & Array<ElementType>::operator*=(__attribute__((unused))
const ElementType & alpha) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<ElementType> & Array<ElementType>::
operator-=(__attribute__((unused)) const Array<ElementType> & vect) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<ElementType> & Array<ElementType>::
operator+=(__attribute__((unused)) const Array<ElementType> & vect) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator*=(__attribute__((unused))
const char & alpha) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator-=(__attribute__((unused))
const Array<char> & vect) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator+=(__attribute__((unused))
const Array<char> & vect) {
AKANTU_TO_IMPLEMENT();
return *this;
}
} // namespace akantu
diff --git a/src/common/aka_array.hh b/src/common/aka_array.hh
index 518b2b062..a75bd18ed 100644
--- a/src/common/aka_array.hh
+++ b/src/common/aka_array.hh
@@ -1,372 +1,371 @@
/**
* @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: Fri Jan 22 2016
+ * @date last modification: Tue Jan 16 2018
*
* @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, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 <vector>
/* -------------------------------------------------------------------------- */
namespace akantu {
/// class that afford to store vectors in static memory
class ArrayBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit ArrayBase(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
UInt getSize() const __attribute__((deprecated)) { return size_; }
UInt size() const { return size_; }
/// Get the number of components
AKANTU_GET_MACRO(NbComponent, nb_component, UInt);
/// Get the name of th array
AKANTU_GET_MACRO(ID, id, const ID &);
/// Set the name of th array
AKANTU_SET_MACRO(ID, id, const ID &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the vector
ID id;
/// the size allocated
UInt allocated_size{0};
/// the size used
UInt size_{0};
/// number of components
UInt nb_component{1};
/// size of the stored type
UInt size_of_type{0};
};
/* -------------------------------------------------------------------------- */
namespace {
template <std::size_t dim, typename T> struct IteratorHelper {};
template <typename T> struct IteratorHelper<0, T> { using type = T; };
template <typename T> struct IteratorHelper<1, T> { using type = Vector<T>; };
template <typename T> struct IteratorHelper<2, T> { using type = Matrix<T>; };
template <typename T> struct IteratorHelper<3, T> {
using type = Tensor3<T>;
};
template <std::size_t dim, typename T>
using IteratorHelper_t = typename IteratorHelper<dim, T>::type;
} // namespace
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal> class Array : public ArrayBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using value_type = T;
using reference = value_type &;
using pointer_type = value_type *;
using const_reference = const value_type &;
/// Allocation of a new vector
explicit 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)
explicit Array(const std::vector<value_type> & vect);
#endif
inline ~Array() override;
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);
}
#ifndef SWIG
/* ------------------------------------------------------------------------ */
/* Iterator */
/* ------------------------------------------------------------------------ */
/// \todo protected: does not compile with intel check why
public:
template <class R, class it, class IR = R,
bool is_tensor_ = is_tensor<R>::value>
class iterator_internal;
public:
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
template <typename R = T> class const_iterator;
template <typename R = T> class iterator;
/* ------------------------------------------------------------------------ */
/// iterator for Array of nb_component = 1
using scalar_iterator = iterator<T>;
/// const_iterator for Array of nb_component = 1
using const_scalar_iterator = const_iterator<T>;
/// iterator returning Vectors of size n on entries of Array with
/// nb_component = n
using vector_iterator = iterator<Vector<T>>;
/// const_iterator returning Vectors of n size on entries of Array with
/// nb_component = n
using const_vector_iterator = const_iterator<Vector<T>>;
/// iterator returning Matrices of size (m, n) on entries of Array with
/// nb_component = m*n
using matrix_iterator = iterator<Matrix<T>>;
/// const iterator returning Matrices of size (m, n) on entries of Array with
/// nb_component = m*n
using const_matrix_iterator = const_iterator<Matrix<T>>;
/// iterator returning Tensor3 of size (m, n, k) on entries of Array with
/// nb_component = m*n*k
using tensor3_iterator = iterator<Tensor3<T>>;
/// const iterator returning Tensor3 of size (m, n, k) on entries of Array
/// with nb_component = m*n*k
using const_tensor3_iterator = const_iterator<Tensor3<T>>;
/* ------------------------------------------------------------------------ */
template <typename... Ns> inline decltype(auto) begin(Ns &&... n);
template <typename... Ns> inline decltype(auto) end(Ns &&... n);
template <typename... Ns> inline decltype(auto) begin(Ns &&... n) const;
template <typename... Ns> inline decltype(auto) end(Ns &&... n) const;
template <typename... Ns> inline decltype(auto) begin_reinterpret(Ns &&... n);
template <typename... Ns> inline decltype(auto) end_reinterpret(Ns &&... n);
template <typename... Ns>
inline decltype(auto) begin_reinterpret(Ns &&... n) const;
template <typename... Ns>
inline decltype(auto) end_reinterpret(Ns &&... n) const;
#endif // SWIG
/* ------------------------------------------------------------------------ */
/* 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[]);
#ifndef SWIG
/// append a Vector or a Matrix
template <template <typename> class C,
typename = std::enable_if_t<is_tensor<C<T>>::value>>
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);
#endif
/// changes the allocated size but not the size
virtual void reserve(UInt size);
/// change the size of the Array
virtual void resize(UInt size);
/// change the size of the Array and initialize the values
virtual void resize(UInt size, const T & val);
/// change the number of components by interlacing data
/// @param multiplicator number of interlaced components add
/// @param block_size blocks of data in the array
/// Examaple for block_size = 2, multiplicator = 2
/// array = oo oo oo -> new array = oo nn nn oo nn nn oo nn nn
void extendComponentsInterlaced(UInt multiplicator, UInt stride);
/// search elem in the vector, return the position of the first occurrence or
/// -1 if not found
UInt find(const_reference elem) const;
/// @see Array::find(const_reference elem) const
UInt find(T elem[]) const;
#ifndef SWIG
/// @see Array::find(const_reference elem) const
template <template <typename> class C,
typename = std::enable_if_t<is_tensor<C<T>>::value>>
inline UInt find(const C<T> & elem);
#endif
/// 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); }
#ifndef SWIG
/// set all tuples of the array to a given vector or matrix
/// @param vm Matrix or Vector to fill the array with
template <template <typename> class C,
typename = std::enable_if_t<is_tensor<C<T>>::value>>
inline void set(const C<T> & vm);
#endif
/// Append the content of the other array to the current one
void append(const Array<T> & other);
/// copy another Array in the current Array, the no_sanity_check allows you to
/// force the copy in cases where you know what you do with two non matching
/// Arrays in terms of n
void copy(const Array<T, is_scal> & other, bool no_sanity_check = false);
/// give the address of the memory allocated for this vector
T * storage() const { return values; };
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
protected:
/// perform the allocation for the constructors
void allocate(UInt size, UInt nb_component = 1);
/// resize initializing with uninitialized_fill if fill is set
void resizeUnitialized(UInt new_size, bool fill, const T & val = T());
/* ------------------------------------------------------------------------ */
/* 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;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// array of values
T * values; // /!\ very dangerous
};
/* -------------------------------------------------------------------------- */
/* Inline Functions Array<T, is_scal> */
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal>
inline std::ostream & operator<<(std::ostream & stream,
const Array<T, is_scal> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
/* Inline Functions ArrayBase */
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream,
const ArrayBase & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "aka_array_tmpl.hh"
#include "aka_types.hh"
#endif /* __AKANTU_VECTOR_HH__ */
diff --git a/src/common/aka_array_tmpl.hh b/src/common/aka_array_tmpl.hh
index 624536626..e5145384e 100644
--- a/src/common/aka_array_tmpl.hh
+++ b/src/common/aka_array_tmpl.hh
@@ -1,1278 +1,1278 @@
/**
* @file aka_array_tmpl.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
- * @date last modification: Fri Jan 22 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Inline functions of the classes Array<T> and ArrayBase
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* Inline Functions Array<T> */
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_ARRAY_TMPL_HH__
#define __AKANTU_AKA_ARRAY_TMPL_HH__
namespace akantu {
namespace debug {
struct ArrayException : public Exception {};
} // namespace debug
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline T & Array<T, is_scal>::operator()(UInt i, UInt j) {
AKANTU_DEBUG_ASSERT(size_ > 0, "The array \"" << id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < size_) && (j < nb_component),
"The value at position ["
<< i << "," << j << "] is out of range in array \""
<< id << "\"");
return values[i * nb_component + j];
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline const T & Array<T, is_scal>::operator()(UInt i, UInt j) const {
AKANTU_DEBUG_ASSERT(size_ > 0, "The array \"" << id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < size_) && (j < nb_component),
"The value at position ["
<< i << "," << j << "] is out of range in array \""
<< id << "\"");
return values[i * nb_component + j];
}
template <class T, bool is_scal>
inline T & Array<T, is_scal>::operator[](UInt i) {
AKANTU_DEBUG_ASSERT(size_ > 0, "The array \"" << id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < size_ * nb_component),
"The value at position ["
<< i << "] is out of range in array \"" << id
<< "\"");
return values[i];
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline const T & Array<T, is_scal>::operator[](UInt i) const {
AKANTU_DEBUG_ASSERT(size_ > 0, "The array \"" << id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < size_ * nb_component),
"The value at position ["
<< i << "] is out of range in array \"" << id
<< "\"");
return values[i];
}
/* -------------------------------------------------------------------------- */
/**
* append a tuple to the array with the value value for all components
* @param value the new last tuple or the array will contain nb_component copies
* of value
*/
template <class T, bool is_scal>
inline void Array<T, is_scal>::push_back(const T & value) {
resizeUnitialized(size_ + 1, true, value);
}
/* -------------------------------------------------------------------------- */
/**
* append a tuple to the array
* @param new_elem a C-array containing the values to be copied to the end of
* the array */
// template <class T, bool is_scal>
// inline void Array<T, is_scal>::push_back(const T new_elem[]) {
// UInt pos = size_;
// resizeUnitialized(size_ + 1, false);
// T * tmp = values + nb_component * pos;
// std::uninitialized_copy(new_elem, new_elem + nb_component, tmp);
// }
/* -------------------------------------------------------------------------- */
#ifndef SWIG
/**
* append a matrix or a vector to the array
* @param new_elem a reference to a Matrix<T> or Vector<T> */
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline void Array<T, is_scal>::push_back(const C<T> & new_elem) {
AKANTU_DEBUG_ASSERT(
nb_component == new_elem.size(),
"The vector("
<< new_elem.size()
<< ") as not a size compatible with the Array (nb_component="
<< nb_component << ").");
UInt pos = size_;
resizeUnitialized(size_ + 1, false);
T * tmp = values + nb_component * pos;
std::uninitialized_copy(new_elem.storage(), new_elem.storage() + nb_component,
tmp);
}
/* -------------------------------------------------------------------------- */
/**
* append a tuple to the array
* @param it an iterator to the tuple to be copied to the end of the array */
template <class T, bool is_scal>
template <class Ret>
inline void
Array<T, is_scal>::push_back(const Array<T, is_scal>::iterator<Ret> & it) {
UInt pos = size_;
resizeUnitialized(size_ + 1, false);
T * tmp = values + nb_component * pos;
T * new_elem = it.data();
std::uninitialized_copy(new_elem, new_elem + nb_component, tmp);
}
#endif
/* -------------------------------------------------------------------------- */
/**
* erase an element. If the erased element is not the last of the array, the
* last element is moved into the hole in order to maintain contiguity. This
* may invalidate existing iterators (For instance an iterator obtained by
* Array::end() is no longer correct) and will change the order of the
* elements.
* @param i index of element to erase
*/
template <class T, bool is_scal> inline void Array<T, is_scal>::erase(UInt i) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT((size_ > 0), "The array is empty");
AKANTU_DEBUG_ASSERT((i < size_),
"The element at position [" << i << "] is out of range ("
<< i << ">=" << size_ << ")");
if (i != (size_ - 1)) {
for (UInt j = 0; j < nb_component; ++j) {
values[i * nb_component + j] = values[(size_ - 1) * nb_component + j];
}
}
resize(size_ - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Subtract another array entry by entry from this array in place. Both arrays
* must
* have the same size and nb_component. If the arrays have different shapes,
* code compiled in debug mode will throw an expeption and optimised code
* will behave in an unpredicted manner
* @param other array to subtract from this
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> & Array<T, is_scal>::
operator-=(const Array<T, is_scal> & vect) {
AKANTU_DEBUG_ASSERT((size_ == vect.size_) &&
(nb_component == vect.nb_component),
"The too array don't have the same sizes");
T * a = values;
T * b = vect.storage();
for (UInt i = 0; i < size_ * nb_component; ++i) {
*a -= *b;
++a;
++b;
}
return *this;
}
/* -------------------------------------------------------------------------- */
/**
* Add another array entry by entry to this array in place. Both arrays must
* have the same size and nb_component. If the arrays have different shapes,
* code compiled in debug mode will throw an expeption and optimised code
* will behave in an unpredicted manner
* @param other array to add to this
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> & Array<T, is_scal>::
operator+=(const Array<T, is_scal> & vect) {
AKANTU_DEBUG_ASSERT((size_ == vect.size()) &&
(nb_component == vect.nb_component),
"The too array don't have the same sizes");
T * a = values;
T * b = vect.storage();
for (UInt i = 0; i < size_ * nb_component; ++i) {
*a++ += *b++;
}
return *this;
}
/* -------------------------------------------------------------------------- */
/**
* Multiply all entries of this array by a scalar in place
* @param alpha scalar multiplicant
* @return reference to modified this
*/
#ifndef SWIG
template <class T, bool is_scal>
Array<T, is_scal> & Array<T, is_scal>::operator*=(const T & alpha) {
T * a = values;
for (UInt i = 0; i < size_ * nb_component; ++i) {
*a++ *= alpha;
}
return *this;
}
#endif
/* -------------------------------------------------------------------------- */
/**
* Compare this array element by element to another.
* @param other array to compare to
* @return true it all element are equal and arrays have the same shape, else
* false
*/
template <class T, bool is_scal>
bool Array<T, is_scal>::operator==(const Array<T, is_scal> & array) const {
bool equal = nb_component == array.nb_component && size_ == array.size_ &&
id == array.id;
if (!equal)
return false;
if (values == array.storage())
return true;
else
return std::equal(values, values + size_ * nb_component, array.storage());
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
bool Array<T, is_scal>::operator!=(const Array<T, is_scal> & array) const {
return !operator==(array);
}
/* -------------------------------------------------------------------------- */
#ifndef SWIG
/**
* set all tuples of the array to a given vector or matrix
* @param vm Matrix or Vector to fill the array with
*/
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline void Array<T, is_scal>::set(const C<T> & vm) {
AKANTU_DEBUG_ASSERT(
nb_component == vm.size(),
"The size of the object does not match the number of components");
for (T * it = values; it < values + nb_component * size_;
it += nb_component) {
std::copy(vm.storage(), vm.storage() + nb_component, it);
}
}
#endif
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
void Array<T, is_scal>::append(const Array<T> & other) {
AKANTU_DEBUG_ASSERT(
nb_component == other.nb_component,
"Cannot append an array with a different number of component");
UInt old_size = this->size_;
this->resizeUnitialized(this->size_ + other.size(), false);
T * tmp = values + nb_component * old_size;
std::uninitialized_copy(other.storage(),
other.storage() + other.size() * nb_component, tmp);
}
/* -------------------------------------------------------------------------- */
/* Functions Array<T, is_scal> */
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const ID & id)
: ArrayBase(id), values(nullptr) {
AKANTU_DEBUG_IN();
allocate(size, nb_component);
if (!is_scal) {
T val = T();
std::uninitialized_fill(values, values + size * nb_component, val);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const T def_values[],
const ID & id)
: ArrayBase(id), values(NULL) {
AKANTU_DEBUG_IN();
allocate(size, nb_component);
T * tmp = values;
for (UInt i = 0; i < size; ++i) {
tmp = values + nb_component * i;
std::uninitialized_copy(def_values, def_values + nb_component, tmp);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const T & value,
const ID & id)
: ArrayBase(id), values(nullptr) {
AKANTU_DEBUG_IN();
allocate(size, nb_component);
std::uninitialized_fill_n(values, size * nb_component, value);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(const Array<T, is_scal> & vect, bool deep,
const ID & id)
: ArrayBase(vect) {
AKANTU_DEBUG_IN();
this->id = (id == "") ? vect.id : id;
if (deep) {
allocate(vect.size_, vect.nb_component);
T * tmp = values;
std::uninitialized_copy(vect.storage(),
vect.storage() + size_ * nb_component, tmp);
} else {
this->values = vect.storage();
this->size_ = vect.size_;
this->nb_component = vect.nb_component;
this->allocated_size = vect.allocated_size;
this->size_of_type = vect.size_of_type;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#ifndef SWIG
template <class T, bool is_scal>
Array<T, is_scal>::Array(const std::vector<T> & vect) {
AKANTU_DEBUG_IN();
this->id = "";
allocate(vect.size(), 1);
T * tmp = values;
std::uninitialized_copy(&(vect[0]), &(vect[size_ - 1]), tmp);
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal> Array<T, is_scal>::~Array() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG(dblAccessory,
"Freeing " << printMemorySize<T>(allocated_size * nb_component)
<< " (" << id << ")");
if (values) {
if (!is_scal)
for (UInt i = 0; i < size_ * nb_component; ++i) {
T * obj = values + i;
obj->~T();
}
free(values);
}
size_ = allocated_size = 0;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* perform the allocation for the constructors
* @param size is the size of the array
* @param nb_component is the number of component of the array
*/
template <class T, bool is_scal>
void Array<T, is_scal>::allocate(UInt size, UInt nb_component) {
AKANTU_DEBUG_IN();
if (size == 0) {
values = nullptr;
} else {
values = static_cast<T *>(malloc(nb_component * size * sizeof(T)));
AKANTU_DEBUG_ASSERT(values != nullptr,
"Cannot allocate "
<< printMemorySize<T>(size * nb_component) << " ("
<< id << ")");
}
if (values == nullptr) {
this->size_ = this->allocated_size = 0;
} else {
AKANTU_DEBUG(dblAccessory,
"Allocated " << printMemorySize<T>(size * nb_component) << " ("
<< id << ")");
this->size_ = this->allocated_size = size;
}
this->size_of_type = sizeof(T);
this->nb_component = nb_component;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
void Array<T, is_scal>::reserve(UInt new_size) {
UInt tmp_size = this->size_;
resizeUnitialized(new_size, false);
this->size_ = tmp_size;
}
/* -------------------------------------------------------------------------- */
/**
* change the size of the array and allocate or free memory if needed. If the
* size increases, the new tuples are filled with zeros
* @param new_size new number of tuples contained in the array */
template <class T, bool is_scal> void Array<T, is_scal>::resize(UInt new_size) {
resizeUnitialized(new_size, !is_scal);
}
/* -------------------------------------------------------------------------- */
/**
* change the size of the array and allocate or free memory if needed. If the
* size increases, the new tuples are filled with zeros
* @param new_size new number of tuples contained in the array */
template <class T, bool is_scal>
void Array<T, is_scal>::resize(UInt new_size, const T & val) {
this->resizeUnitialized(new_size, true, val);
}
/* -------------------------------------------------------------------------- */
/**
* change the size of the array and allocate or free memory if needed.
* @param new_size new number of tuples contained in the array */
template <class T, bool is_scal>
void Array<T, is_scal>::resizeUnitialized(UInt new_size, bool fill,
const T & val) {
// AKANTU_DEBUG_IN();
// free some memory
if (new_size <= allocated_size) {
if (!is_scal) {
T * old_values = values;
if (new_size < size_) {
for (UInt i = new_size * nb_component; i < size_ * nb_component; ++i) {
T * obj = old_values + i;
obj->~T();
}
}
}
if (allocated_size - new_size > AKANTU_MIN_ALLOCATION) {
AKANTU_DEBUG(dblAccessory,
"Freeing " << printMemorySize<T>((allocated_size - size_) *
nb_component)
<< " (" << id << ")");
// Normally there are no allocation problem when reducing an array
if (new_size == 0) {
free(values);
values = nullptr;
} else {
auto * tmp_ptr = static_cast<T *>(
realloc(values, new_size * nb_component * sizeof(T)));
if (tmp_ptr == nullptr) {
AKANTU_EXCEPTION("Cannot free data ("
<< id << ")"
<< " [current allocated size : " << allocated_size
<< " | "
<< "requested size : " << new_size << "]");
}
values = tmp_ptr;
}
allocated_size = new_size;
}
} else {
// allocate more memory
UInt size_to_alloc = (new_size - allocated_size < AKANTU_MIN_ALLOCATION)
? allocated_size + AKANTU_MIN_ALLOCATION
: new_size;
auto * tmp_ptr = static_cast<T *>(
realloc(values, size_to_alloc * nb_component * sizeof(T)));
AKANTU_DEBUG_ASSERT(
tmp_ptr != nullptr,
"Cannot allocate " << printMemorySize<T>(size_to_alloc * nb_component));
if (tmp_ptr == nullptr) {
AKANTU_ERROR("Cannot allocate more data ("
<< id << ")"
<< " [current allocated size : " << allocated_size << " | "
<< "requested size : " << new_size << "]");
}
AKANTU_DEBUG(dblAccessory,
"Allocating " << printMemorySize<T>(
(size_to_alloc - allocated_size) * nb_component));
allocated_size = size_to_alloc;
values = tmp_ptr;
}
if (fill && this->size_ < new_size) {
std::uninitialized_fill(values + size_ * nb_component,
values + new_size * nb_component, val);
}
size_ = new_size;
// AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* change the number of components by interlacing data
* @param multiplicator number of interlaced components add
* @param block_size blocks of data in the array
* Examaple for block_size = 2, multiplicator = 2
* array = oo oo oo -> new array = oo nn nn oo nn nn oo nn nn */
template <class T, bool is_scal>
void Array<T, is_scal>::extendComponentsInterlaced(UInt multiplicator,
UInt block_size) {
AKANTU_DEBUG_IN();
if (multiplicator == 1)
return;
AKANTU_DEBUG_ASSERT(multiplicator > 1, "invalid multiplicator");
AKANTU_DEBUG_ASSERT(nb_component % block_size == 0,
"stride must divide actual number of components");
values = static_cast<T *>(
realloc(values, nb_component * multiplicator * size_ * sizeof(T)));
UInt new_component = nb_component / block_size * multiplicator;
for (UInt i = 0, k = size_ - 1; i < size_; ++i, --k) {
for (UInt j = 0; j < new_component; ++j) {
UInt m = new_component - j - 1;
UInt n = m / multiplicator;
for (UInt l = 0, p = block_size - 1; l < block_size; ++l, --p) {
values[k * nb_component * multiplicator + m * block_size + p] =
values[k * nb_component + n * block_size + p];
}
}
}
nb_component = nb_component * multiplicator;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* search elem in the array, return the position of the first occurrence or
* -1 if not found
* @param elem the element to look for
* @return index of the first occurrence of elem or -1 if elem is not present
*/
template <class T, bool is_scal>
UInt Array<T, is_scal>::find(const T & elem) const {
AKANTU_DEBUG_IN();
auto begin = this->begin();
auto end = this->end();
auto it = std::find(begin, end, elem);
AKANTU_DEBUG_OUT();
return (it != end) ? it - begin : UInt(-1);
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal> UInt Array<T, is_scal>::find(T elem[]) const {
AKANTU_DEBUG_IN();
T * it = values;
UInt i = 0;
for (; i < size_; ++i) {
if (*it == elem[0]) {
T * cit = it;
UInt c = 0;
for (; (c < nb_component) && (*cit == elem[c]); ++c, ++cit)
;
if (c == nb_component) {
AKANTU_DEBUG_OUT();
return i;
}
}
it += nb_component;
}
return UInt(-1);
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline UInt Array<T, is_scal>::find(const C<T> & elem) {
AKANTU_DEBUG_ASSERT(elem.size() == nb_component,
"Cannot find an element with a wrong size ("
<< elem.size() << ") != " << nb_component);
return this->find(elem.storage());
}
/* -------------------------------------------------------------------------- */
/**
* copy the content of another array. This overwrites the current content.
* @param other Array to copy into this array. It has to have the same
* nb_component as this. If compiled in debug mode, an incorrect other will
* result in an exception being thrown. Optimised code may result in
* unpredicted behaviour.
*/
template <class T, bool is_scal>
void Array<T, is_scal>::copy(const Array<T, is_scal> & vect,
bool no_sanity_check) {
AKANTU_DEBUG_IN();
if (!no_sanity_check)
if (vect.nb_component != nb_component)
AKANTU_ERROR("The two arrays do not have the same number of components");
resize((vect.size_ * vect.nb_component) / nb_component);
T * tmp = values;
std::uninitialized_copy(vect.storage(), vect.storage() + size_ * nb_component,
tmp);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool is_scal> class ArrayPrintHelper {
public:
template <typename T>
static void print_content(const Array<T> & vect, std::ostream & stream,
int indent) {
if (AKANTU_DEBUG_TEST(dblDump) || AKANTU_DEBUG_LEVEL_IS_TEST()) {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << " + values : {";
for (UInt i = 0; i < vect.size(); ++i) {
stream << "{";
for (UInt j = 0; j < vect.getNbComponent(); ++j) {
stream << vect(i, j);
if (j != vect.getNbComponent() - 1)
stream << ", ";
}
stream << "}";
if (i != vect.size() - 1)
stream << ", ";
}
stream << "}" << std::endl;
}
}
};
template <> class ArrayPrintHelper<false> {
public:
template <typename T>
static void print_content(__attribute__((unused)) const Array<T> & vect,
__attribute__((unused)) std::ostream & stream,
__attribute__((unused)) int indent) {}
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
void Array<T, is_scal>::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
std::streamsize prec = stream.precision();
std::ios_base::fmtflags ff = stream.flags();
stream.setf(std::ios_base::showbase);
stream.precision(2);
stream << space << "Array<" << debug::demangle(typeid(T).name()) << "> ["
<< std::endl;
stream << space << " + id : " << this->id << std::endl;
stream << space << " + size : " << this->size_ << std::endl;
stream << space << " + nb_component : " << this->nb_component << std::endl;
stream << space << " + allocated size : " << this->allocated_size
<< std::endl;
stream << space << " + memory size : "
<< printMemorySize<T>(allocated_size * nb_component) << std::endl;
if (!AKANTU_DEBUG_LEVEL_IS_TEST())
stream << space << " + address : " << std::hex << this->values
<< std::dec << std::endl;
stream.precision(prec);
stream.flags(ff);
ArrayPrintHelper<is_scal>::print_content(*this, stream, indent);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/* Inline Functions ArrayBase */
/* -------------------------------------------------------------------------- */
inline UInt ArrayBase::getMemorySize() const {
return allocated_size * nb_component * size_of_type;
}
inline void ArrayBase::empty() { size_ = 0; }
#ifndef SWIG
/* -------------------------------------------------------------------------- */
/* Iterators */
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <class R, class daughter, class IR, bool is_tensor>
class Array<T, is_scal>::iterator_internal {
public:
using value_type = R;
using pointer = R *;
using reference = R &;
using proxy = typename R::proxy;
using const_proxy = const typename R::proxy;
using const_reference = const R &;
using internal_value_type = IR;
using internal_pointer = IR *;
using difference_type = std::ptrdiff_t;
using iterator_category = std::random_access_iterator_tag;
public:
iterator_internal() = default;
iterator_internal(pointer_type data, UInt _offset)
: _offset(_offset), initial(data), ret(nullptr), ret_ptr(data) {
AKANTU_ERROR(
"The constructor should never be called it is just an ugly trick...");
}
iterator_internal(std::unique_ptr<internal_value_type> && wrapped)
: _offset(wrapped->size()), initial(wrapped->storage()),
ret(std::move(wrapped)), ret_ptr(ret->storage()) {}
iterator_internal(const iterator_internal & it) {
if (this != &it) {
this->_offset = it._offset;
this->initial = it.initial;
this->ret_ptr = it.ret_ptr;
this->ret = std::make_unique<internal_value_type>(*it.ret, false);
}
}
iterator_internal(iterator_internal && it) = default;
virtual ~iterator_internal() = default;
inline iterator_internal & operator=(const iterator_internal & it) {
if (this != &it) {
this->_offset = it._offset;
this->initial = it.initial;
this->ret_ptr = it.ret_ptr;
if (this->ret)
this->ret->shallowCopy(*it.ret);
else
this->ret = std::make_unique<internal_value_type>(*it.ret, false);
}
return *this;
}
UInt getCurrentIndex() {
return (this->ret_ptr - this->initial) / this->_offset;
};
inline reference operator*() {
ret->values = ret_ptr;
return *ret;
};
inline const_reference operator*() const {
ret->values = ret_ptr;
return *ret;
};
inline pointer operator->() {
ret->values = ret_ptr;
return ret.get();
};
inline daughter & operator++() {
ret_ptr += _offset;
return static_cast<daughter &>(*this);
};
inline daughter & operator--() {
ret_ptr -= _offset;
return static_cast<daughter &>(*this);
};
inline daughter & operator+=(const UInt n) {
ret_ptr += _offset * n;
return static_cast<daughter &>(*this);
}
inline daughter & operator-=(const UInt n) {
ret_ptr -= _offset * n;
return static_cast<daughter &>(*this);
}
inline proxy operator[](const UInt n) {
ret->values = ret_ptr + n * _offset;
return proxy(*ret);
}
inline const_proxy operator[](const UInt n) const {
ret->values = ret_ptr + n * _offset;
return const_proxy(*ret);
}
inline bool operator==(const iterator_internal & other) const {
return this->ret_ptr == other.ret_ptr;
}
inline bool operator!=(const iterator_internal & other) const {
return this->ret_ptr != other.ret_ptr;
}
inline bool operator<(const iterator_internal & other) const {
return this->ret_ptr < other.ret_ptr;
}
inline bool operator<=(const iterator_internal & other) const {
return this->ret_ptr <= other.ret_ptr;
}
inline bool operator>(const iterator_internal & other) const {
return this->ret_ptr > other.ret_ptr;
}
inline bool operator>=(const iterator_internal & other) const {
return this->ret_ptr >= other.ret_ptr;
}
inline daughter operator+(difference_type n) {
daughter tmp(static_cast<daughter &>(*this));
tmp += n;
return tmp;
}
inline daughter operator-(difference_type n) {
daughter tmp(static_cast<daughter &>(*this));
tmp -= n;
return tmp;
}
inline difference_type operator-(const iterator_internal & b) {
return (this->ret_ptr - b.ret_ptr) / _offset;
}
inline pointer_type data() const { return ret_ptr; }
inline difference_type offset() const { return _offset; }
protected:
UInt _offset{0};
pointer_type initial{nullptr};
std::unique_ptr<internal_value_type> ret{nullptr};
pointer_type ret_ptr{nullptr};
};
/* -------------------------------------------------------------------------- */
/**
* Specialization for scalar types
*/
template <class T, bool is_scal>
template <class R, class daughter, class IR>
class Array<T, is_scal>::iterator_internal<R, daughter, IR, false> {
public:
using value_type = R;
using pointer = R *;
using reference = R &;
using const_reference = const R &;
using internal_value_type = IR;
using internal_pointer = IR *;
using difference_type = std::ptrdiff_t;
using iterator_category = std::random_access_iterator_tag;
public:
iterator_internal(pointer data = nullptr) : ret(data), initial(data){};
iterator_internal(const iterator_internal & it) = default;
iterator_internal(iterator_internal && it) = default;
virtual ~iterator_internal() = default;
inline iterator_internal & operator=(const iterator_internal & it) = default;
UInt getCurrentIndex() { return (this->ret - this->initial); };
inline reference operator*() { return *ret; };
inline const_reference operator*() const { return *ret; };
inline pointer operator->() { return ret; };
inline daughter & operator++() {
++ret;
return static_cast<daughter &>(*this);
};
inline daughter & operator--() {
--ret;
return static_cast<daughter &>(*this);
};
inline daughter & operator+=(const UInt n) {
ret += n;
return static_cast<daughter &>(*this);
}
inline daughter & operator-=(const UInt n) {
ret -= n;
return static_cast<daughter &>(*this);
}
inline reference operator[](const UInt n) { return ret[n]; }
inline bool operator==(const iterator_internal & other) const {
return ret == other.ret;
}
inline bool operator!=(const iterator_internal & other) const {
return ret != other.ret;
}
inline bool operator<(const iterator_internal & other) const {
return ret < other.ret;
}
inline bool operator<=(const iterator_internal & other) const {
return ret <= other.ret;
}
inline bool operator>(const iterator_internal & other) const {
return ret > other.ret;
}
inline bool operator>=(const iterator_internal & other) const {
return ret >= other.ret;
}
inline daughter operator-(difference_type n) { return daughter(ret - n); }
inline daughter operator+(difference_type n) { return daughter(ret + n); }
inline difference_type operator-(const iterator_internal & b) {
return ret - b.ret;
}
inline pointer data() const { return ret; }
protected:
pointer ret{nullptr};
pointer initial{nullptr};
};
/* -------------------------------------------------------------------------- */
/* Begin/End functions implementation */
/* -------------------------------------------------------------------------- */
namespace detail {
template <class Tuple, size_t... Is>
constexpr auto take_front_impl(Tuple && t, std::index_sequence<Is...>) {
return std::make_tuple(std::get<Is>(std::forward<Tuple>(t))...);
}
template <size_t N, class Tuple> constexpr auto take_front(Tuple && t) {
return take_front_impl(std::forward<Tuple>(t),
std::make_index_sequence<N>{});
}
template <typename... V> constexpr auto product_all(V &&... v) {
std::common_type_t<int, V...> result = 1;
(void)std::initializer_list<int>{(result *= v, 0)...};
return result;
}
template <typename... T> std::string to_string_all(T &&... t) {
if (sizeof...(T) == 0)
return "";
std::stringstream ss;
bool noComma = true;
ss << "(";
(void)std::initializer_list<bool>{
(ss << (noComma ? "" : ", ") << t, noComma = false)...};
ss << ")";
return ss.str();
}
template <std::size_t N> struct InstantiationHelper {
template <typename type, typename T, typename... Ns>
static auto instantiate(T && data, Ns... ns) {
return std::make_unique<type>(data, ns...);
}
};
template <> struct InstantiationHelper<0> {
template <typename type, typename T> static auto instantiate(T && data) {
return data;
}
};
template <typename Arr, typename T, typename... Ns>
decltype(auto) get_iterator(Arr && array, T * data, Ns &&... ns) {
using type = IteratorHelper_t<sizeof...(Ns) - 1, T>;
using array_type = std::decay_t<Arr>;
using iterator =
std::conditional_t<std::is_const<std::remove_reference_t<Arr>>::value,
typename array_type::template const_iterator<type>,
typename array_type::template iterator<type>>;
static_assert(sizeof...(Ns), "You should provide a least one size");
if (array.getNbComponent() * array.size() !=
product_all(std::forward<Ns>(ns)...)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::ArrayException(),
"The iterator on "
<< debug::demangle(typeid(Arr).name())
<< to_string_all(array.size(), array.getNbComponent())
<< "is not compatible with the type "
<< debug::demangle(typeid(type).name()) << to_string_all(ns...));
}
auto && wrapped = aka::apply(
[&](auto... n) {
return InstantiationHelper<sizeof...(n)>::template instantiate<type>(
data, n...);
},
take_front<sizeof...(Ns) - 1>(std::make_tuple(ns...)));
return iterator(std::move(wrapped));
}
} // namespace detail
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin(Ns &&... ns) {
return detail::get_iterator(*this, values, std::forward<Ns>(ns)..., size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end(Ns &&... ns) {
return detail::get_iterator(*this, values + nb_component * size_,
std::forward<Ns>(ns)..., size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin(Ns &&... ns) const {
return detail::get_iterator(*this, values, std::forward<Ns>(ns)..., size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end(Ns &&... ns) const {
return detail::get_iterator(*this, values + nb_component * size_,
std::forward<Ns>(ns)..., size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin_reinterpret(Ns &&... ns) {
return detail::get_iterator(*this, values, std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end_reinterpret(Ns &&... ns) {
return detail::get_iterator(
*this, values + detail::product_all(std::forward<Ns>(ns)...),
std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin_reinterpret(Ns &&... ns) const {
return detail::get_iterator(*this, values, std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end_reinterpret(Ns &&... ns) const {
return detail::get_iterator(
*this, values + detail::product_all(std::forward<Ns>(ns)...),
std::forward<Ns>(ns)...);
}
/* -------------------------------------------------------------------------- */
/* Views */
/* -------------------------------------------------------------------------- */
namespace detail {
template <typename Array, typename... Ns> class ArrayView {
using tuple = std::tuple<Ns...>;
public:
ArrayView(Array && array, Ns... ns)
: array(std::forward<Array>(array)), sizes(std::move(ns)...) {}
ArrayView(ArrayView && array_view) = default;
ArrayView & operator=(const ArrayView & array_view) = default;
ArrayView & operator=(ArrayView && array_view) = default;
decltype(auto) begin() {
return aka::apply(
[&](auto &&... ns) { return array.begin_reinterpret(ns...); }, sizes);
}
decltype(auto) begin() const {
return aka::apply(
[&](auto &&... ns) { return array.begin_reinterpret(ns...); }, sizes);
}
decltype(auto) end() {
return aka::apply(
[&](auto &&... ns) { return array.end_reinterpret(ns...); }, sizes);
}
decltype(auto) end() const {
return aka::apply(
[&](auto &&... ns) { return array.end_reinterpret(ns...); }, sizes);
}
decltype(auto) size() const {
return std::get<std::tuple_size<tuple>::value - 1>(sizes);
}
decltype(auto) dims() const { return std::tuple_size<tuple>::value - 1; }
private:
Array array;
tuple sizes;
};
} // namespace detail
/* -------------------------------------------------------------------------- */
template <typename Array, typename... Ns>
decltype(auto) make_view(Array && array, Ns... ns) {
static_assert(aka::conjunction<std::is_integral<std::decay_t<Ns>>...>::value,
"Ns should be integral types");
auto size = std::forward<decltype(array)>(array).size() *
std::forward<decltype(array)>(array).getNbComponent() /
detail::product_all(ns...);
return detail::ArrayView<Array, std::common_type_t<size_t, Ns>...,
std::common_type_t<size_t, decltype(size)>>(
std::forward<Array>(array), std::move(ns)..., size);
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename R>
class Array<T, is_scal>::const_iterator
: public iterator_internal<const R, Array<T, is_scal>::const_iterator<R>,
R> {
public:
using parent = iterator_internal<const R, const_iterator, R>;
using value_type = typename parent::value_type;
using pointer = typename parent::pointer;
using reference = typename parent::reference;
using difference_type = typename parent::difference_type;
using iterator_category = typename parent::iterator_category;
public:
const_iterator() : parent(){};
// const_iterator(pointer_type data, UInt offset) : parent(data, offset) {}
// const_iterator(pointer warped) : parent(warped) {}
// const_iterator(const parent & it) : parent(it) {}
const_iterator(const const_iterator & it) = default;
const_iterator(const_iterator && it) = default;
template <typename P, typename = std::enable_if_t<not is_tensor<P>::value>>
const_iterator(P * data) : parent(data) {}
template <typename UP_P,
typename =
std::enable_if_t<is_tensor<typename UP_P::element_type>::value>>
const_iterator(UP_P && tensor) : parent(std::forward<UP_P>(tensor)) {}
const_iterator & operator=(const const_iterator & it) = default;
};
template <class T, class R, bool is_tensor_ = is_tensor<R>::value>
struct ConstConverterIteratorHelper {
using const_iterator = typename Array<T>::template const_iterator<R>;
using iterator = typename Array<T>::template iterator<R>;
static inline const_iterator convert(const iterator & it) {
return const_iterator(std::unique_ptr<R>(new R(*it, false)));
}
};
template <class T, class R> struct ConstConverterIteratorHelper<T, R, false> {
using const_iterator = typename Array<T>::template const_iterator<R>;
using iterator = typename Array<T>::template iterator<R>;
static inline const_iterator convert(const iterator & it) {
return const_iterator(it.data());
}
};
template <class T, bool is_scal>
template <typename R>
class Array<T, is_scal>::iterator
: public iterator_internal<R, Array<T, is_scal>::iterator<R>> {
public:
using parent = iterator_internal<R, iterator>;
using value_type = typename parent::value_type;
using pointer = typename parent::pointer;
using reference = typename parent::reference;
using difference_type = typename parent::difference_type;
using iterator_category = typename parent::iterator_category;
public:
iterator() : parent(){};
iterator(const iterator & it) = default;
iterator(iterator && it) = default;
template <typename P, typename = std::enable_if_t<not is_tensor<P>::value>>
iterator(P * data) : parent(data) {}
template <typename UP_P,
typename =
std::enable_if_t<is_tensor<typename UP_P::element_type>::value>>
iterator(UP_P && tensor) : parent(std::forward<UP_P>(tensor)) {}
iterator & operator=(const iterator & it) = default;
operator const_iterator<R>() {
return ConstConverterIteratorHelper<T, R>::convert(*this);
}
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename R>
inline typename Array<T, is_scal>::template iterator<R>
Array<T, is_scal>::erase(const iterator<R> & it) {
T * curr = it.data();
UInt pos = (curr - values) / nb_component;
erase(pos);
iterator<R> rit = it;
return --rit;
}
#endif
} // namespace akantu
#endif /* __AKANTU_AKA_ARRAY_TMPL_HH__ */
diff --git a/src/common/aka_blas_lapack.hh b/src/common/aka_blas_lapack.hh
index 55ba9a8c4..76a244310 100644
--- a/src/common/aka_blas_lapack.hh
+++ b/src/common/aka_blas_lapack.hh
@@ -1,343 +1,343 @@
/**
* @file aka_blas_lapack.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 06 2013
- * @date last modification: Mon Jan 18 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Interface of the Fortran BLAS/LAPACK libraries
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_BLAS_LAPACK_HH__
#define __AKANTU_AKA_BLAS_LAPACK_HH__
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_BLAS
#include "aka_fortran_mangling.hh"
extern "C" {
/* ------------------------------------------------------------------------ */
/* Double precision */
/* ------------------------------------------------------------------------ */
// LEVEL 1
double AKA_FC_GLOBAL(ddot, DDOT)(int *, double *, int *, double *, int *);
void AKA_FC_GLOBAL(daxpy, DAXPY)(int *, double *, double *, int *, double *,
int *);
// LEVEL 2
void AKA_FC_GLOBAL(dgemv, DGEMV)(char *, int *, int *, double *, double *,
int *, double *, int *, double *, double *,
int *);
// LEVEL 3
void AKA_FC_GLOBAL(dgemm, DGEMM)(char *, char *, int *, int *, int *, double *,
double *, int *, double *, int *, double *,
double *, int *);
/* ------------------------------------------------------------------------ */
/* Simple precision */
/* ------------------------------------------------------------------------ */
// LEVEL 1
float AKA_FC_GLOBAL(sdot, SDOT)(int *, float *, int *, float *, int *);
void AKA_FC_GLOBAL(saxpy, SAXPY)(int *, float *, float *, int *, float *,
int *);
// LEVEL 2
void AKA_FC_GLOBAL(sgemv, SGEMV)(char *, int *, int *, float *, float *, int *,
float *, int *, float *, float *, int *);
// LEVEL 3
void AKA_FC_GLOBAL(sgemm, SGEMM)(char *, char *, int *, int *, int *, float *,
float *, int *, float *, int *, float *,
float *, int *);
}
#endif
namespace akantu {
#define AKANTU_WARNING_IGNORE_UNUSED_PARAMETER
#include "aka_warning.hh"
/// Wrapper around the S/DDOT BLAS function that returns the dot product of two
/// vectors
template <typename T>
inline T aka_dot(int * n, T * x, int * incx, T * y, int * incy) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DAXPY BLAS function that computes \f$y := \alpha x +
/// y\f$
template <typename T>
inline void aka_axpy(int * n, T * alpha, T * x, int * incx, T * y, int * incy) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DGEMV BLAS function that computes matrix-vector product
/// \f$y := \alpha A^{(T)}x + \beta y \f$
template <typename T>
inline void aka_gemv(char * trans, int * m, int * n, T * alpha, T * a,
int * lda, T * x, int * incx, T * beta, T * y,
int * incy) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DGEMM BLAS function that computes the product of two
/// matrices \f$C := \alpha A^{(T)} B^{(T)} + \beta C \f$
template <typename T>
inline void aka_gemm(char * transa, char * transb, int * m, int * n, int * k,
T * alpha, T * a, int * lda, T * b, int * ldb, T * beta,
T * c, int * ldc) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
#if defined(AKANTU_USE_BLAS)
template <>
inline double aka_dot<double>(int * n, double * x, int * incx, double * y,
int * incy) {
return AKA_FC_GLOBAL(ddot, DDOT)(n, x, incx, y, incy);
}
template <>
inline void aka_axpy(int * n, double * alpha, double * x, int * incx,
double * y, int * incy) {
return AKA_FC_GLOBAL(daxpy, DAXPY)(n, alpha, x, incx, y, incy);
}
template <>
inline void aka_gemv<double>(char * trans, int * m, int * n, double * alpha,
double * a, int * lda, double * x, int * incx,
double * beta, double * y, int * incy) {
return AKA_FC_GLOBAL(dgemv, DGEMV)(trans, m, n, alpha, a, lda, x, incx, beta,
y, incy);
}
template <>
inline void aka_gemm<double>(char * transa, char * transb, int * m, int * n,
int * k, double * alpha, double * a, int * lda,
double * b, int * ldb, double * beta, double * c,
int * ldc) {
AKA_FC_GLOBAL(dgemm, DGEMM)
(transa, transb, m, n, k, alpha, a, lda, b, ldb, beta, c, ldc);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <>
inline float aka_dot<float>(int * n, float * x, int * incx, float * y,
int * incy) {
return AKA_FC_GLOBAL(sdot, SDOT)(n, x, incx, y, incy);
}
template <>
inline void aka_axpy(int * n, float * alpha, float * x, int * incx, float * y,
int * incy) {
return AKA_FC_GLOBAL(daxpy, DAXPY)(n, alpha, x, incx, y, incy);
}
template <>
inline void aka_gemv<float>(char * trans, int * m, int * n, float * alpha,
float * a, int * lda, float * x, int * incx,
float * beta, float * y, int * incy) {
AKA_FC_GLOBAL(sgemv, SGEMV)
(trans, m, n, alpha, a, lda, x, incx, beta, y, incy);
}
template <>
inline void aka_gemm<float>(char * transa, char * transb, int * m, int * n,
int * k, float * alpha, float * a, int * lda,
float * b, int * ldb, float * beta, float * c,
int * ldc) {
AKA_FC_GLOBAL(sgemm, SGEMM)
(transa, transb, m, n, k, alpha, a, lda, b, ldb, beta, c, ldc);
}
#endif
} // akantu
#ifdef AKANTU_USE_LAPACK
#include "aka_fortran_mangling.hh"
extern "C" {
/* ------------------------------------------------------------------------ */
/* Double general matrix */
/* ------------------------------------------------------------------------ */
/// compute the eigenvalues/vectors
void AKA_FC_GLOBAL(dgeev, DGEEV)(char * jobvl, char * jobvr, int * n,
double * a, int * lda, double * wr,
double * wi, double * vl, int * ldvl,
double * vr, int * ldvr, double * work,
int * lwork, int * info);
/// LU decomposition of a general matrix
void AKA_FC_GLOBAL(dgetrf, DGETRF)(int * m, int * n, double * a, int * lda,
int * ipiv, int * info);
/// generate inverse of a matrix given its LU decomposition
void AKA_FC_GLOBAL(dgetri, DGETRI)(int * n, double * a, int * lda, int * ipiv,
double * work, int * lwork, int * info);
/// solving A x = b using a LU factorization
void AKA_FC_GLOBAL(dgetrs, DGETRS)(char * trans, int * n, int * nrhs,
double * A, int * lda, int * ipiv,
double * b, int * ldb, int * info);
/* ------------------------------------------------------------------------ */
/* Simple general matrix */
/* ------------------------------------------------------------------------ */
/// compute the eigenvalues/vectors
void AKA_FC_GLOBAL(sgeev, SGEEV)(char * jobvl, char * jobvr, int * n, float * a,
int * lda, float * wr, float * wi, float * vl,
int * ldvl, float * vr, int * ldvr,
float * work, int * lwork, int * info);
/// LU decomposition of a general matrix
void AKA_FC_GLOBAL(sgetrf, SGETRF)(int * m, int * n, float * a, int * lda,
int * ipiv, int * info);
/// generate inverse of a matrix given its LU decomposition
void AKA_FC_GLOBAL(sgetri, SGETRI)(int * n, float * a, int * lda, int * ipiv,
float * work, int * lwork, int * info);
/// solving A x = b using a LU factorization
void AKA_FC_GLOBAL(sgetrs, SGETRS)(char * trans, int * n, int * nrhs, float * A,
int * lda, int * ipiv, float * b, int * ldb,
int * info);
}
#endif // AKANTU_USE_LAPACK
namespace akantu {
/// Wrapper around the S/DGEEV BLAS function that computes the eigenvalues and
/// eigenvectors of a matrix
template <typename T>
inline void aka_geev(char * jobvl, char * jobvr, int * n, T * a, int * lda,
T * wr, T * wi, T * vl, int * ldvl, T * vr, int * ldvr,
T * work, int * lwork, int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRF BLAS function that computes the LU decomposition
/// of a matrix
template <typename T>
inline void aka_getrf(int * m, int * n, T * a, int * lda, int * ipiv,
int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRI BLAS function that computes the inverse of a
/// matrix given its LU decomposition
template <typename T>
inline void aka_getri(int * n, T * a, int * lda, int * ipiv, T * work,
int * lwork, int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRS BLAS function that solves \f$A^{(T)}x = b\f$
/// using LU decomposition
template <typename T>
inline void aka_getrs(char * trans, int * n, int * nrhs, T * A, int * lda,
int * ipiv, T * b, int * ldb, int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
#include "aka_warning_restore.hh"
#ifdef AKANTU_USE_LAPACK
template <>
inline void aka_geev<double>(char * jobvl, char * jobvr, int * n, double * a,
int * lda, double * wr, double * wi, double * vl,
int * ldvl, double * vr, int * ldvr, double * work,
int * lwork, int * info) {
AKA_FC_GLOBAL(dgeev, DGEEV)
(jobvl, jobvr, n, a, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
}
template <>
inline void aka_getrf<double>(int * m, int * n, double * a, int * lda,
int * ipiv, int * info) {
AKA_FC_GLOBAL(dgetrf, DGETRF)(m, n, a, lda, ipiv, info);
}
template <>
inline void aka_getri<double>(int * n, double * a, int * lda, int * ipiv,
double * work, int * lwork, int * info) {
AKA_FC_GLOBAL(dgetri, DGETRI)(n, a, lda, ipiv, work, lwork, info);
}
template <>
inline void aka_getrs<double>(char * trans, int * n, int * nrhs, double * A,
int * lda, int * ipiv, double * b, int * ldb,
int * info) {
AKA_FC_GLOBAL(dgetrs, DGETRS)(trans, n, nrhs, A, lda, ipiv, b, ldb, info);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <>
inline void aka_geev<float>(char * jobvl, char * jobvr, int * n, float * a,
int * lda, float * wr, float * wi, float * vl,
int * ldvl, float * vr, int * ldvr, float * work,
int * lwork, int * info) {
AKA_FC_GLOBAL(sgeev, SGEEV)
(jobvl, jobvr, n, a, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
}
template <>
inline void aka_getrf<float>(int * m, int * n, float * a, int * lda, int * ipiv,
int * info) {
AKA_FC_GLOBAL(sgetrf, SGETRF)(m, n, a, lda, ipiv, info);
}
template <>
inline void aka_getri<float>(int * n, float * a, int * lda, int * ipiv,
float * work, int * lwork, int * info) {
AKA_FC_GLOBAL(sgetri, SGETRI)(n, a, lda, ipiv, work, lwork, info);
}
template <>
inline void aka_getrs<float>(char * trans, int * n, int * nrhs, float * A,
int * lda, int * ipiv, float * b, int * ldb,
int * info) {
AKA_FC_GLOBAL(sgetrs, SGETRS)(trans, n, nrhs, A, lda, ipiv, b, ldb, info);
}
#endif
} // akantu
#endif /* __AKANTU_AKA_BLAS_LAPACK_HH__ */
diff --git a/src/common/aka_circular_array.hh b/src/common/aka_circular_array.hh
index 7b9972b38..442967ff9 100644
--- a/src/common/aka_circular_array.hh
+++ b/src/common/aka_circular_array.hh
@@ -1,130 +1,129 @@
/**
* @file aka_circular_array.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Sun Aug 13 2017
*
* @brief class of circular array
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_CIRCULAR_ARRAY_HH__
#define __AKANTU_AKA_CIRCULAR_ARRAY_HH__
/* -------------------------------------------------------------------------- */
#include <typeinfo>
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <class T> class CircularArray : protected Array<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef typename Array<T>::value_type value_type;
typedef typename Array<T>::reference reference;
typedef typename Array<T>::pointer_type pointer_type;
typedef typename Array<T>::const_reference const_reference;
/// Allocation of a new array with a default value
CircularArray(UInt size, UInt nb_component = 1,
const_reference value = value_type(), const ID & id = "")
: Array<T>(size, nb_component, value, id), start_position(0),
end_position(size - 1) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
virtual ~CircularArray() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
advance start and end position by one:
the first element is now at the end of the array
**/
inline void makeStep();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
private:
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
inline reference operator()(UInt i, UInt j = 0);
inline const_reference operator()(UInt i, UInt j = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
UInt size() const { return this->size_; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// indice of first element in this circular array
UInt start_position;
/// indice of last element in this circular array
UInt end_position;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "aka_circular_array_inline_impl.cc"
#endif
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const CircularArray<T> & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#endif /* __AKANTU_AKA_CIRCULAR_ARRAY_HH__ */
diff --git a/src/common/aka_circular_array_inline_impl.cc b/src/common/aka_circular_array_inline_impl.cc
index 8ebf880dc..98be1e402 100644
--- a/src/common/aka_circular_array_inline_impl.cc
+++ b/src/common/aka_circular_array_inline_impl.cc
@@ -1,99 +1,98 @@
/**
* @file aka_circular_array_inline_impl.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Nov 11 2011
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Feb 03 2016
*
* @brief implementation of circular array
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* Inline Functions Array<T> */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <class T>
inline typename CircularArray<T>::reference CircularArray<T>::
operator()(UInt i, UInt j) {
AKANTU_DEBUG_ASSERT(end_position != start_position,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT(
(i < (end_position - start_position + this->allocated_size) %
this->allocated_size +
1) &&
(j < this->nb_component),
"The value at position [" << i << "," << j
<< "] is out of range in array \"" << this->id
<< "\"");
return this->values[((i + start_position) % this->allocated_size) *
this->nb_component +
j];
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline typename CircularArray<T>::const_reference CircularArray<T>::
operator()(UInt i, UInt j) const {
AKANTU_DEBUG_ASSERT(end_position != start_position,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT(
(i < (end_position - start_position + this->allocated_size) %
this->allocated_size +
1) &&
(j < this->nb_component),
"The value at position [" << i << "," << j
<< "] is out of range in array \"" << this->id
<< "\"");
return this->values[((i + start_position) % this->allocated_size) *
this->nb_component +
j];
}
/* -------------------------------------------------------------------------- */
template <class T> inline void CircularArray<T>::makeStep() {
AKANTU_DEBUG_IN();
start_position = (start_position + 1) % this->allocated_size;
end_position = (end_position + 1) % this->allocated_size;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T>
void CircularArray<T>::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "CircularArray<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
stream << space << " + start_position : " << this->start_position
<< std::endl;
stream << space << " + end_position : " << this->end_position << std::endl;
Array<T>::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
diff --git a/src/common/aka_common.cc b/src/common/aka_common.cc
index 4449190bc..9faaab7c6 100644
--- a/src/common/aka_common.cc
+++ b/src/common/aka_common.cc
@@ -1,153 +1,152 @@
/**
* @file aka_common.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Mon Feb 05 2018
*
* @brief Initialization of global variables
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "aka_static_memory.hh"
#include "communicator.hh"
#include "cppargparse.hh"
#include "parser.hh"
#include "communication_tag.hh"
/* -------------------------------------------------------------------------- */
#include <ctime>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void initialize(int & argc, char **& argv) {
AKANTU_DEBUG_IN();
initialize("", argc, argv);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void initialize(const std::string & input_file, int & argc, char **& argv) {
AKANTU_DEBUG_IN();
StaticMemory::getStaticMemory();
Communicator & comm = Communicator::getStaticCommunicator(argc, argv);
Tag::setMaxTag(comm.getMaxTag());
debug::debugger.setParallelContext(comm.whoAmI(), comm.getNbProc());
debug::setDebugLevel(dblError);
static_argparser.setParallelContext(comm.whoAmI(), comm.getNbProc());
static_argparser.setExternalExitFunction(debug::exit);
static_argparser.addArgument("--aka_input_file", "Akantu's input file", 1,
cppargparse::_string, std::string());
static_argparser.addArgument(
"--aka_debug_level",
std::string("Akantu's overall debug level") +
std::string(" (0: error, 1: exceptions, 4: warnings, 5: info, ..., "
"100: dump") +
std::string(" more info on levels can be foind in aka_error.hh)"),
1, cppargparse::_integer, int(dblWarning));
static_argparser.addArgument(
"--aka_print_backtrace",
"Should Akantu print a backtrace in case of error", 0,
cppargparse::_boolean, false, true);
static_argparser.parse(argc, argv, cppargparse::_remove_parsed);
std::string infile = static_argparser["aka_input_file"];
if (infile == "")
infile = input_file;
debug::debugger.printBacktrace(static_argparser["aka_print_backtrace"]);
if ("" != infile) {
readInputFile(infile);
}
long int seed;
try {
seed = static_parser.getParameter("seed", _ppsc_current_scope);
} catch (debug::Exception &) {
seed = time(nullptr);
}
seed *= (comm.whoAmI() + 1);
RandomGenerator<UInt>::seed(seed);
int dbl_level = static_argparser["aka_debug_level"];
debug::setDebugLevel(DebugLevel(dbl_level));
AKANTU_DEBUG_INFO("Random seed set to " << seed);
std::atexit(finalize);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void finalize() {
AKANTU_DEBUG_IN();
// if (StaticCommunicator::isInstantiated()) {
// StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
// delete &comm;
// }
if (StaticMemory::isInstantiated()) {
delete &(StaticMemory::getStaticMemory());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void readInputFile(const std::string & input_file) {
static_parser.parse(input_file);
}
/* -------------------------------------------------------------------------- */
cppargparse::ArgumentParser & getStaticArgumentParser() {
return static_argparser;
}
/* -------------------------------------------------------------------------- */
Parser & getStaticParser() { return static_parser; }
/* -------------------------------------------------------------------------- */
const ParserSection & getUserParser() {
return *(static_parser.getSubSections(ParserType::_user).first);
}
std::unique_ptr<Communicator> Communicator::static_communicator;
} // akantu
diff --git a/src/common/aka_common.hh b/src/common/aka_common.hh
index 09bcf4b14..37aaded5b 100644
--- a/src/common/aka_common.hh
+++ b/src/common/aka_common.hh
@@ -1,519 +1,519 @@
/**
* @file aka_common.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Mon Feb 12 2018
*
* @brief common type descriptions for akantu
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COMMON_HH__
#define __AKANTU_COMMON_HH__
#include "aka_compatibilty_with_cpp_standard.hh"
/* -------------------------------------------------------------------------- */
#define __BEGIN_AKANTU_DUMPER__ namespace dumper {
#define __END_AKANTU_DUMPER__ }
/* -------------------------------------------------------------------------- */
#if defined(WIN32)
#define __attribute__(x)
#endif
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
#include "aka_error.hh"
#include "aka_safe_enum.hh"
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
#include <limits>
#include <list>
#include <string>
#include <type_traits>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Common types */
/* -------------------------------------------------------------------------- */
using ID = std::string;
#ifdef AKANTU_NDEBUG
static const Real REAL_INIT_VALUE = Real(0.);
#else
static const Real REAL_INIT_VALUE = std::numeric_limits<Real>::quiet_NaN();
#endif
/* -------------------------------------------------------------------------- */
/* Memory types */
/* -------------------------------------------------------------------------- */
using MemoryID = UInt;
// using Surface = std::string;
// using SurfacePair= std::pair<Surface, Surface>;
// using SurfacePairList = std::list<SurfacePair>;
/* -------------------------------------------------------------------------- */
extern const UInt _all_dimensions;
#define AKANTU_PP_ENUM(s, data, i, elem) \
BOOST_PP_TUPLE_REM() \
elem BOOST_PP_COMMA_IF(BOOST_PP_NOT_EQUAL(i, BOOST_PP_DEC(data)))
} // namespace akantu
#if (defined(__GNUC__) || defined(__GNUG__))
#define AKA_GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if AKA_GCC_VERSION < 60000
#define AKANTU_ENUM_HASH(type_name) \
namespace std { \
template <> struct hash<::akantu::type_name> { \
using argument_type = ::akantu::type_name; \
size_t operator()(const argument_type & e) const noexcept { \
auto ue = underlying_type_t<argument_type>(e); \
return uh(ue); \
} \
\
private: \
const hash<underlying_type_t<argument_type>> uh{}; \
}; \
}
#else
#define AKANTU_ENUM_HASH(type_name)
#endif // AKA_GCC_VERSION
#endif // GNU
#include "aka_element_classes_info.hh"
namespace akantu {
#define AKANTU_PP_CAT(s, data, elem) BOOST_PP_CAT(data, elem)
#define AKANTU_PP_TYPE_TO_STR(s, data, elem) \
({BOOST_PP_CAT(data::_, elem), BOOST_PP_STRINGIZE(elem)})
#define AKANTU_PP_STR_TO_TYPE(s, data, elem) \
({BOOST_PP_STRINGIZE(elem), BOOST_PP_CAT(data::_, elem)})
#define AKANTU_ENUM_DECLARE(type_name, list) \
enum class type_name { \
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_CAT, _, list)) \
};
#define AKANTU_ENUM_OUTPUT_STREAM(type_name, list) \
} \
AKANTU_ENUM_HASH(type_name) \
namespace aka { \
inline std::string to_string(const ::akantu::type_name & type) { \
static std::unordered_map<::akantu::type_name, std::string> convert{ \
BOOST_PP_SEQ_FOR_EACH_I( \
AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(list), \
BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_TYPE_TO_STR, \
::akantu::type_name, list))}; \
return convert.at(type); \
} \
} \
namespace akantu { \
inline std::ostream & operator<<(std::ostream & stream, \
const type_name & type) { \
stream << aka::to_string(type); \
return stream; \
}
#define AKANTU_ENUM_INPUT_STREAM(type_name, list) \
inline std::istream & operator>>(std::istream & stream, type_name & type) { \
std::string str; \
stream >> str; \
static std::unordered_map<std::string, type_name> convert{ \
BOOST_PP_SEQ_FOR_EACH_I( \
AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(list), \
BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_STR_TO_TYPE, type_name, list))}; \
type = convert.at(str); \
return stream; \
}
/* -------------------------------------------------------------------------- */
/* Mesh/FEM/Model types */
/* -------------------------------------------------------------------------- */
/// small help to use names for directions
enum SpacialDirection { _x = 0, _y = 1, _z = 2 };
/// enum MeshIOType type of mesh reader/writer
enum MeshIOType {
_miot_auto, ///< Auto guess of the reader to use based on the extension
_miot_gmsh, ///< Gmsh files
_miot_gmsh_struct, ///< Gsmh reader with reintpretation of elements has
/// structures elements
_miot_diana, ///< TNO Diana mesh format
_miot_abaqus ///< Abaqus mesh format
};
/// enum MeshEventHandlerPriority defines relative order of execution of events
enum EventHandlerPriority {
_ehp_highest = 0,
_ehp_mesh = 5,
_ehp_fe_engine = 9,
_ehp_synchronizer = 10,
_ehp_dof_manager = 20,
_ehp_model = 94,
_ehp_non_local_manager = 100,
_ehp_lowest = 100
};
#ifndef SWIG
// clang-format off
#define AKANTU_MODEL_TYPES \
(model) \
(solid_mechanics_model) \
(solid_mechanics_model_cohesive) \
(heat_transfer_model) \
(structural_mechanics_model) \
(embedded_model)
// clang-format on
/// enum ModelType defines which type of physics is solved
AKANTU_ENUM_DECLARE(ModelType, AKANTU_MODEL_TYPES)
AKANTU_ENUM_OUTPUT_STREAM(ModelType, AKANTU_MODEL_TYPES)
AKANTU_ENUM_INPUT_STREAM(ModelType, AKANTU_MODEL_TYPES)
#else
enum class ModelType {
_model,
_solid_mechanics_model,
_solid_mechanics_model_cohesive,
_heat_transfer_model,
_structural_mechanics_model,
_embedded_model
};
#endif
/// enum AnalysisMethod type of solving method used to solve the equation of
/// motion
enum AnalysisMethod {
_static = 0,
_implicit_dynamic = 1,
_explicit_lumped_mass = 2,
_explicit_lumped_capacity = 2,
_explicit_consistent_mass = 3
};
/// enum DOFSupportType defines which kind of dof that can exists
enum DOFSupportType { _dst_nodal, _dst_generic };
/// Type of non linear resolution available in akantu
enum NonLinearSolverType {
_nls_linear, ///< No non linear convergence loop
_nls_newton_raphson, ///< Regular Newton-Raphson
_nls_newton_raphson_modified, ///< Newton-Raphson with initial tangent
_nls_lumped, ///< Case of lumped mass or equivalent matrix
_nls_auto ///< This will take a default value that make sense in case of
/// model::getNewSolver
};
/// Define the node/dof type
enum NodeType : Int { _nt_pure_gost = -3, _nt_master = -2, _nt_normal = -1 };
/// Type of time stepping solver
enum TimeStepSolverType {
_tsst_static, ///< Static solution
_tsst_dynamic, ///< Dynamic solver
_tsst_dynamic_lumped, ///< Dynamic solver with lumped mass
_tsst_not_defined, ///< For not defined cases
};
/// Type of integration scheme
enum IntegrationSchemeType {
_ist_pseudo_time, ///< Pseudo Time
_ist_forward_euler, ///< GeneralizedTrapezoidal(0)
_ist_trapezoidal_rule_1, ///< GeneralizedTrapezoidal(1/2)
_ist_backward_euler, ///< GeneralizedTrapezoidal(1)
_ist_central_difference, ///< NewmarkBeta(0, 1/2)
_ist_fox_goodwin, ///< NewmarkBeta(1/6, 1/2)
_ist_trapezoidal_rule_2, ///< NewmarkBeta(1/2, 1/2)
_ist_linear_acceleration, ///< NewmarkBeta(1/3, 1/2)
_ist_newmark_beta, ///< generic NewmarkBeta with user defined
/// alpha and beta
_ist_generalized_trapezoidal ///< generic GeneralizedTrapezoidal with user
/// defined alpha
};
/// enum SolveConvergenceCriteria different convergence criteria
enum SolveConvergenceCriteria {
_scc_residual, ///< Use residual to test the convergence
_scc_solution, ///< Use solution to test the convergence
_scc_residual_mass_wgh ///< Use residual weighted by inv. nodal mass to testb
};
/// enum CohesiveMethod type of insertion of cohesive elements
enum CohesiveMethod { _intrinsic, _extrinsic };
/// @enum SparseMatrixType type of sparse matrix used
enum MatrixType { _unsymmetric, _symmetric, _mt_not_defined };
/* -------------------------------------------------------------------------- */
/* Ghosts handling */
/* -------------------------------------------------------------------------- */
/// @enum CommunicatorType type of communication method to use
enum CommunicatorType { _communicator_mpi, _communicator_dummy };
/// @enum SynchronizationTag type of synchronizations
enum SynchronizationTag {
//--- Generic tags ---
_gst_whatever,
_gst_update,
_gst_size,
//--- SolidMechanicsModel tags ---
_gst_smm_mass, ///< synchronization of the SolidMechanicsModel.mass
_gst_smm_for_gradu, ///< synchronization of the
/// SolidMechanicsModel.displacement
_gst_smm_boundary, ///< synchronization of the boundary, forces, velocities
/// and displacement
_gst_smm_uv, ///< synchronization of the nodal velocities and displacement
_gst_smm_res, ///< synchronization of the nodal residual
_gst_smm_init_mat, ///< synchronization of the data to initialize materials
_gst_smm_stress, ///< synchronization of the stresses to compute the internal
/// forces
_gst_smmc_facets, ///< synchronization of facet data to setup facet synch
_gst_smmc_facets_conn, ///< synchronization of facet global connectivity
_gst_smmc_facets_stress, ///< synchronization of facets' stress to setup facet
/// synch
_gst_smmc_damage, ///< synchronization of damage
// --- GlobalIdsUpdater tags ---
_gst_giu_global_conn, ///< synchronization of global connectivities
// --- CohesiveElementInserter tags ---
_gst_ce_groups, ///< synchronization of cohesive element insertion depending
/// on facet groups
// --- GroupManager tags ---
_gst_gm_clusters, ///< synchronization of clusters
// --- HeatTransfer tags ---
_gst_htm_capacity, ///< synchronization of the nodal heat capacity
_gst_htm_temperature, ///< synchronization of the nodal temperature
_gst_htm_gradient_temperature, ///< synchronization of the element gradient
/// temperature
// --- LevelSet tags ---
_gst_htm_phi, ///< synchronization of the nodal level set value phi
_gst_htm_gradient_phi, ///< synchronization of the element gradient phi
//--- Material non local ---
_gst_mnl_for_average, ///< synchronization of data to average in non local
/// material
_gst_mnl_weight, ///< synchronization of data for the weight computations
// --- NeighborhoodSynchronization tags ---
_gst_nh_criterion,
// --- General tags ---
_gst_test, ///< Test tag
_gst_user_1, ///< tag for user simulations
_gst_user_2, ///< tag for user simulations
_gst_material_id, ///< synchronization of the material ids
_gst_for_dump, ///< everything that needs to be synch before dump
// --- Contact & Friction ---
_gst_cf_nodal, ///< synchronization of disp, velo, and current position
_gst_cf_incr, ///< synchronization of increment
// --- Solver tags ---
_gst_solver_solution ///< synchronization of the solution obained with the
/// PETSc solver
};
/// standard output stream operator for SynchronizationTag
inline std::ostream & operator<<(std::ostream & stream,
SynchronizationTag type);
/// @enum GhostType type of ghost
enum GhostType {
_not_ghost = 0,
_ghost = 1,
_casper // not used but a real cute ghost
};
}
#ifndef SWIG
AKANTU_ENUM_HASH(GhostType)
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
struct GhostType_def {
using type = GhostType;
static const type _begin_ = _not_ghost;
static const type _end_ = _casper;
};
using ghost_type_t = safe_enum<GhostType_def>;
extern ghost_type_t ghost_types;
/// standard output stream operator for GhostType
inline std::ostream & operator<<(std::ostream & stream, GhostType type);
/* -------------------------------------------------------------------------- */
/* Global defines */
/* -------------------------------------------------------------------------- */
#define AKANTU_MIN_ALLOCATION 2000
#define AKANTU_INDENT " "
#define AKANTU_INCLUDE_INLINE_IMPL
/* -------------------------------------------------------------------------- */
/* Type traits */
/* -------------------------------------------------------------------------- */
struct TensorTrait {};
/* -------------------------------------------------------------------------- */
template <typename T> using is_tensor = std::is_base_of<TensorTrait, T>;
/* -------------------------------------------------------------------------- */
template <typename T> using is_scalar = std::is_arithmetic<T>;
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#define AKANTU_SET_MACRO(name, variable, type) \
inline void set##name(type variable) { this->variable = variable; }
#define AKANTU_GET_MACRO(name, variable, type) \
inline type get##name() const { return variable; }
#define AKANTU_GET_MACRO_NOT_CONST(name, variable, type) \
inline type get##name() { return variable; }
#define AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, support, con) \
inline con Array<type> & get##name( \
const support & el_type, const GhostType & ghost_type = _not_ghost) \
con { \
return variable(el_type, ghost_type); \
}
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, )
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, const)
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, )
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, const)
/* -------------------------------------------------------------------------- */
/// initialize the static part of akantu
void initialize(int & argc, char **& argv);
/// initialize the static part of akantu and read the global input_file
void initialize(const std::string & input_file, int & argc, char **& argv);
/* -------------------------------------------------------------------------- */
/// finilize correctly akantu and clean the memory
void finalize();
/* -------------------------------------------------------------------------- */
/// Read an new input file
void readInputFile(const std::string & input_file);
/* -------------------------------------------------------------------------- */
/*
* For intel compiler annoying remark
*/
// #if defined(__INTEL_COMPILER)
// /// remark #981: operands are evaluated in unspecified order
// #pragma warning(disable : 981)
// /// remark #383: value copied to temporary, reference to temporary used
// #pragma warning(disable : 383)
// #endif // defined(__INTEL_COMPILER)
/* -------------------------------------------------------------------------- */
/* string manipulation */
/* -------------------------------------------------------------------------- */
inline std::string to_lower(const std::string & str);
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim);
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/// give a string representation of the a human readable size in bit
template <typename T> std::string printMemorySize(UInt size);
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "aka_fwd.hh"
namespace akantu {
/// get access to the internal argument parser
cppargparse::ArgumentParser & getStaticArgumentParser();
/// get access to the internal input file parser
Parser & getStaticParser();
/// get access to the user part of the internal input file parser
const ParserSection & getUserParser();
} // namespace akantu
#include "aka_common_inline_impl.cc"
/* -------------------------------------------------------------------------- */
#if AKANTU_INTEGER_SIZE == 4
#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b9
#elif AKANTU_INTEGER_SIZE == 8
#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b97f4a7c13LL
#endif
namespace std {
/**
* Hashing function for pairs based on hash_combine from boost The magic number
* is coming from the golden number @f[\phi = \frac{1 + \sqrt5}{2}@f]
* @f[\frac{2^32}{\phi} = 0x9e3779b9@f]
* http://stackoverflow.com/questions/4948780/magic-number-in-boosthash-combine
* http://burtleburtle.net/bob/hash/doobs.html
*/
template <typename a, typename b> struct hash<std::pair<a, b>> {
hash() = default;
size_t operator()(const std::pair<a, b> & p) const {
size_t seed = ah(p.first);
return bh(p.second) + AKANTU_HASH_COMBINE_MAGIC_NUMBER + (seed << 6) +
(seed >> 2);
}
private:
const hash<a> ah{};
const hash<b> bh{};
};
} // namespace std
#endif /* __AKANTU_COMMON_HH__ */
diff --git a/src/common/aka_common_inline_impl.cc b/src/common/aka_common_inline_impl.cc
index a16615d07..9f2a34849 100644
--- a/src/common/aka_common_inline_impl.cc
+++ b/src/common/aka_common_inline_impl.cc
@@ -1,459 +1,458 @@
/**
* @file aka_common_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief inline implementations of common akantu type descriptions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 "aka_common.hh"
#include <algorithm>
#include <cctype>
#include <iomanip>
#include <iostream>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_COMMON_INLINE_IMPL_CC__
#define __AKANTU_AKA_COMMON_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
/// standard output stream operator for GhostType
inline std::ostream & operator<<(std::ostream & stream, GhostType type) {
switch (type) {
case _not_ghost:
stream << "not_ghost";
break;
case _ghost:
stream << "ghost";
break;
case _casper:
stream << "Casper the friendly ghost";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for TimeStepSolverType
inline std::ostream & operator<<(std::ostream & stream,
const TimeStepSolverType & type) {
switch (type) {
case _tsst_static:
stream << "static";
break;
case _tsst_dynamic:
stream << "dynamic";
break;
case _tsst_dynamic_lumped:
stream << "dynamic_lumped";
break;
case _tsst_not_defined:
stream << "not defined time step solver";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard input stream operator for TimeStepSolverType
inline std::istream & operator>>(std::istream & stream,
TimeStepSolverType & type) {
std::string str;
stream >> str;
if (str == "static")
type = _tsst_static;
else if (str == "dynamic")
type = _tsst_dynamic;
else if (str == "dynamic_lumped")
type = _tsst_dynamic_lumped;
else {
AKANTU_ERROR("The type " << str
<< " is not a recognized TimeStepSolverType");
stream.setstate(std::ios::failbit);
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for NonLinearSolverType
inline std::ostream & operator<<(std::ostream & stream,
const NonLinearSolverType & type) {
switch (type) {
case _nls_linear:
stream << "linear";
break;
case _nls_newton_raphson:
stream << "newton_raphson";
break;
case _nls_newton_raphson_modified:
stream << "newton_raphson_modified";
break;
case _nls_lumped:
stream << "lumped";
break;
case _nls_auto:
stream << "auto";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard input stream operator for NonLinearSolverType
inline std::istream & operator>>(std::istream & stream,
NonLinearSolverType & type) {
std::string str;
stream >> str;
if (str == "linear")
type = _nls_linear;
else if (str == "newton_raphson")
type = _nls_newton_raphson;
else if (str == "newton_raphson_modified")
type = _nls_newton_raphson_modified;
else if (str == "lumped")
type = _nls_lumped;
else if (str == "auto")
type = _nls_auto;
else
type = _nls_auto;
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for IntegrationSchemeType
inline std::ostream & operator<<(std::ostream & stream,
const IntegrationSchemeType & type) {
switch (type) {
case _ist_pseudo_time:
stream << "pseudo_time";
break;
case _ist_forward_euler:
stream << "forward_euler";
break;
case _ist_trapezoidal_rule_1:
stream << "trapezoidal_rule_1";
break;
case _ist_backward_euler:
stream << "backward_euler";
break;
case _ist_central_difference:
stream << "central_difference";
break;
case _ist_fox_goodwin:
stream << "fox_goodwin";
break;
case _ist_trapezoidal_rule_2:
stream << "trapezoidal_rule_2";
break;
case _ist_linear_acceleration:
stream << "linear_acceleration";
break;
case _ist_newmark_beta:
stream << "newmark_beta";
break;
case _ist_generalized_trapezoidal:
stream << "generalized_trapezoidal";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard input stream operator for IntegrationSchemeType
inline std::istream & operator>>(std::istream & stream,
IntegrationSchemeType & type) {
std::string str;
stream >> str;
if (str == "pseudo_time")
type = _ist_pseudo_time;
else if (str == "forward_euler")
type = _ist_forward_euler;
else if (str == "trapezoidal_rule_1")
type = _ist_trapezoidal_rule_1;
else if (str == "backward_euler")
type = _ist_backward_euler;
else if (str == "central_difference")
type = _ist_central_difference;
else if (str == "fox_goodwin")
type = _ist_fox_goodwin;
else if (str == "trapezoidal_rule_2")
type = _ist_trapezoidal_rule_2;
else if (str == "linear_acceleration")
type = _ist_linear_acceleration;
else if (str == "newmark_beta")
type = _ist_newmark_beta;
else if (str == "generalized_trapezoidal")
type = _ist_generalized_trapezoidal;
else {
AKANTU_ERROR("The type " << str
<< " is not a recognized IntegrationSchemeType");
stream.setstate(std::ios::failbit);
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for SynchronizationTag
inline std::ostream & operator<<(std::ostream & stream,
SynchronizationTag type) {
switch (type) {
case _gst_whatever:
stream << "_gst_whatever";
break;
case _gst_update:
stream << "_gst_update";
break;
case _gst_size:
stream << "_gst_size";
break;
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_giu_global_conn:
stream << "_gst_giu_global_conn";
break;
case _gst_ce_groups:
stream << "_gst_ce_groups";
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_nh_criterion:
stream << "_gst_nh_criterion";
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_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,
const SolveConvergenceCriteria & criteria) {
switch (criteria) {
case _scc_residual:
stream << "_scc_residual";
break;
case _scc_solution:
stream << "_scc_solution";
break;
case _scc_residual_mass_wgh:
stream << "_scc_residual_mass_wgh";
break;
}
return stream;
}
inline std::istream & operator>>(std::istream & stream,
SolveConvergenceCriteria & criteria) {
std::string str;
stream >> str;
if (str == "residual")
criteria = _scc_residual;
else if (str == "solution")
criteria = _scc_solution;
else if (str == "residual_mass_wgh")
criteria = _scc_residual_mass_wgh;
else {
stream.setstate(std::ios::failbit);
}
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;
}
} // akantu
#include <cmath>
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> std::string printMemorySize(UInt size) {
Real real_size = size * sizeof(T);
UInt mult = 0;
if (real_size != 0)
mult = (std::log(real_size) / std::log(2)) / 10;
std::stringstream sstr;
real_size /= Real(1 << (10 * mult));
sstr << std::setprecision(2) << std::fixed << real_size;
std::string size_prefix;
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_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();
}
} // akantu
#endif /* __AKANTU_AKA_COMMON_INLINE_IMPL_CC__ */
diff --git a/src/common/aka_compatibilty_with_cpp_standard.hh b/src/common/aka_compatibilty_with_cpp_standard.hh
index ebc6b3795..35fefe790 100644
--- a/src/common/aka_compatibilty_with_cpp_standard.hh
+++ b/src/common/aka_compatibilty_with_cpp_standard.hh
@@ -1,147 +1,150 @@
/**
* @file aka_compatibilty_with_cpp_standard.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Wed Oct 25 2017
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 10 2018
*
- * @brief The content of this file is taken from the possible implementations on
+ * @brief The content of this file is taken from the possible implementations
+ * on
* http://en.cppreference.com
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
/* -------------------------------------------------------------------------- */
#include <tuple>
#include <type_traits>
#include <utility>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_COMPATIBILTY_WITH_CPP_STANDARD_HH__
#define __AKANTU_AKA_COMPATIBILTY_WITH_CPP_STANDARD_HH__
namespace aka {
// Part taken from C++14
#if __cplusplus < 201402L
template <bool B, class T = void>
using enable_if_t = typename enable_if<B, T>::type;
#else
template <bool B, class T = void> using enable_if_t = std::enable_if_t<B, T>;
#endif
// Part taken from C++17
#if __cplusplus < 201703L
// bool_constant
template <bool B> using bool_constant = std::integral_constant<bool, B>;
namespace {
template <bool B> constexpr bool bool_constant_v = bool_constant<B>::value;
}
/* -------------------------------------------------------------------------- */
// conjunction
template <class...> struct conjunction : std::true_type {};
template <class B1> struct conjunction<B1> : B1 {};
template <class B1, class... Bn>
struct conjunction<B1, Bn...>
: std::conditional_t<bool(B1::value), conjunction<Bn...>, B1> {};
/* -------------------------------------------------------------------------- */
// negations
template <class B> struct negation : bool_constant<!bool(B::value)> {};
/* -------------------------------------------------------------------------- */
namespace detail {
template <class T> struct is_reference_wrapper : std::false_type {};
template <class U>
struct is_reference_wrapper<std::reference_wrapper<U>> : std::true_type {};
// template <class T>
// constexpr bool is_reference_wrapper_v = is_reference_wrapper<T>::value;
// template <class T, class Type, class T1, class... Args>
// decltype(auto) INVOKE(Type T::*f, T1 && t1, Args &&... args) {
// static_assert(std::is_member_function_pointer<decltype(f)>{} and
// std::is_base_of<T, std::decay_t<T1>>{},
// "Does not know what to do with this types");
// return (std::forward<T1>(t1).*f)(std::forward<Args>(args)...);
// }
template <class T, class Type, class T1, class... Args>
decltype(auto) INVOKE(Type T::*f, T1 && t1, Args &&... args) {
static_if(std::is_member_function_pointer<decltype(f)>{})
.then_([&](auto && f) {
static_if(std::is_base_of<T, std::decay_t<T1>>{})
.then_([&](auto && f) {
return (std::forward<T1>(t1).*f)(std::forward<Args>(args)...);
})
.elseif(is_reference_wrapper<std::decay_t<T1>>{})([&](auto && f) {
return (t1.get().*f)(std::forward<Args>(args)...);
})
.else_([&](auto && f) {
return ((*std::forward<T1>(t1)).*
f)(std::forward<Args>(args)...);
})(std::forward<decltype(f)>(f));
})
.else_([&](auto && f) {
static_assert(std::is_member_object_pointer<decltype(f)>::value,
"f is not a member object");
static_assert(sizeof...(args) == 0, "f takes arguments");
static_if(std::is_base_of<T, std::decay_t<T1>>{})
.then_([&](auto && f) { return std::forward<T1>(t1).*f; })
.elseif(std::is_base_of<T, std::decay_t<T1>>{})(
[&](auto && f) { return t1.get().*f; })
.else_([&](auto && f) { return (*std::forward<T1>(t1)).*f; })(
std::forward<decltype(f)>(f));
})(std::forward<decltype(f)>(f));
}
template <class F, class... Args>
decltype(auto) INVOKE(F && f, Args &&... args) {
return std::forward<F>(f)(std::forward<Args>(args)...);
}
} // namespace detail
template <class F, class... Args>
decltype(auto) invoke(F && f, Args &&... args) {
return detail::INVOKE(std::forward<F>(f), std::forward<Args>(args)...);
}
namespace detail {
template <class F, class Tuple, std::size_t... Is>
constexpr decltype(auto) apply_impl(F && f, Tuple && t,
std::index_sequence<Is...>) {
return invoke(std::forward<F>(f), std::get<Is>(std::forward<Tuple>(t))...);
}
} // namespace detail
template <class F, class Tuple>
constexpr decltype(auto) apply(F && f, Tuple && t) {
return detail::apply_impl(
std::forward<F>(f), std::forward<Tuple>(t),
std::make_index_sequence<std::tuple_size<std::decay_t<Tuple>>::value>{});
}
#endif
} // namespace aka
#endif /* __AKANTU_AKA_COMPATIBILTY_WITH_CPP_STANDARD_HH__ */
diff --git a/src/common/aka_config.hh.in b/src/common/aka_config.hh.in
index ecbec6274..321a236e4 100644
--- a/src/common/aka_config.hh.in
+++ b/src/common/aka_config.hh.in
@@ -1,103 +1,94 @@
/**
* @file aka_config.hh.in
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Thu Jan 25 2018
*
* @brief Compilation time configuration of Akantu
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
*
- * You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_CONFIG_HH__
#define __AKANTU_AKA_CONFIG_HH__
#define AKANTU_VERSION_MAJOR @AKANTU_MAJOR_VERSION@
#define AKANTU_VERSION_MINOR @AKANTU_MINOR_VERSION@
#define AKANTU_VERSION_PATCH @AKANTU_PATCH_VERSION@
#define AKANTU_VERSION (AKANTU_VERSION_MAJOR * 10000 \
+ AKANTU_VERSION_MINOR * 100 \
+ AKANTU_VERSION_PATCH)
@AKANTU_TYPES_EXTRA_INCLUDES@
namespace akantu {
using Real = @AKANTU_FLOAT_TYPE@;
using Int = @AKANTU_SIGNED_INTEGER_TYPE@;
using UInt = @AKANTU_UNSIGNED_INTEGER_TYPE@;
} // akantu
#define AKANTU_INTEGER_SIZE @AKANTU_INTEGER_SIZE@
#define AKANTU_FLOAT_SIZE @AKANTU_FLOAT_SIZE@
#cmakedefine AKANTU_HAS_STRDUP
#cmakedefine AKANTU_USE_BLAS
#cmakedefine AKANTU_USE_LAPACK
#cmakedefine AKANTU_PARALLEL
#cmakedefine AKANTU_USE_MPI
#cmakedefine AKANTU_USE_SCOTCH
#cmakedefine AKANTU_USE_PTSCOTCH
#cmakedefine AKANTU_SCOTCH_NO_EXTERN
#cmakedefine AKANTU_IMPLICIT
#cmakedefine AKANTU_USE_MUMPS
#cmakedefine AKANTU_USE_PETSC
#cmakedefine AKANTU_USE_IOHELPER
#cmakedefine AKANTU_USE_QVIEW
#cmakedefine AKANTU_USE_BLACKDYNAMITE
#cmakedefine AKANTU_USE_PYBIND11
#cmakedefine AKANTU_USE_OBSOLETE_GETTIMEOFDAY
#cmakedefine AKANTU_EXTRA_MATERIALS
#cmakedefine AKANTU_STUDENTS_EXTRA_PACKAGE
#cmakedefine AKANTU_DAMAGE_NON_LOCAL
#cmakedefine AKANTU_SOLID_MECHANICS
#cmakedefine AKANTU_STRUCTURAL_MECHANICS
#cmakedefine AKANTU_HEAT_TRANSFER
#cmakedefine AKANTU_PYTHON_INTERFACE
#cmakedefine AKANTU_COHESIVE_ELEMENT
#cmakedefine AKANTU_PARALLEL_COHESIVE_ELEMENT
#cmakedefine AKANTU_IGFEM
#cmakedefine AKANTU_USE_CGAL
#cmakedefine AKANTU_EMBEDDED
// Debug tools
//#cmakedefine AKANTU_NDEBUG
#cmakedefine AKANTU_DEBUG_TOOLS
#cmakedefine READLINK_COMMAND @READLINK_COMMAND@
#cmakedefine ADDR2LINE_COMMAND @ADDR2LINE_COMMAND@
#define __aka_inline__ inline
#endif /* __AKANTU_AKA_CONFIG_HH__ */
diff --git a/src/common/aka_csr.hh b/src/common/aka_csr.hh
index 632b20219..7227cceee 100644
--- a/src/common/aka_csr.hh
+++ b/src/common/aka_csr.hh
@@ -1,259 +1,258 @@
/**
* @file aka_csr.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 20 2011
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Sun Dec 03 2017
*
* @brief A compresed sparse row structure based on akantu Arrays
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_CSR_HH__
#define __AKANTU_AKA_CSR_HH__
namespace akantu {
/**
* This class can be used to store the structure of a sparse matrix or for
* vectors with variable number of component per element
*
* @param nb_rows number of rows of a matrix or size of a vector.
*/
template <typename T> class CSR {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit CSR(UInt nb_rows = 0)
: nb_rows(nb_rows), rows_offsets(nb_rows + 1, 1, "rows_offsets"),
rows(0, 1, "rows") {
rows_offsets.clear();
};
virtual ~CSR() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// does nothing
inline void beginInsertions(){};
/// insert a new entry val in row row
inline UInt insertInRow(UInt row, const T & val) {
UInt pos = rows_offsets(row)++;
rows(pos) = val;
return pos;
}
/// access an element of the matrix
inline const T & operator()(UInt row, UInt col) const {
AKANTU_DEBUG_ASSERT(rows_offsets(row + 1) - rows_offsets(row) > col,
"This element is not present in this CSR");
return rows(rows_offsets(row) + col);
}
/// access an element of the matrix
inline T & operator()(UInt row, UInt col) {
AKANTU_DEBUG_ASSERT(rows_offsets(row + 1) - rows_offsets(row) > col,
"This element is not present in this CSR");
return rows(rows_offsets(row) + col);
}
inline void endInsertions() {
for (UInt i = nb_rows; i > 0; --i)
rows_offsets(i) = rows_offsets(i - 1);
rows_offsets(0) = 0;
}
inline void countToCSR() {
for (UInt i = 1; i < nb_rows; ++i)
rows_offsets(i) += rows_offsets(i - 1);
for (UInt i = nb_rows; i >= 1; --i)
rows_offsets(i) = rows_offsets(i - 1);
rows_offsets(0) = 0;
}
inline void clearRows() {
rows_offsets.clear();
rows.resize(0);
};
inline void resizeRows(UInt nb_rows) {
this->nb_rows = nb_rows;
rows_offsets.resize(nb_rows + 1);
rows_offsets.clear();
}
inline void resizeCols() { rows.resize(rows_offsets(nb_rows)); }
inline void copy(Array<UInt> & offsets, Array<T> & values) {
offsets.copy(rows_offsets);
values.copy(rows);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// returns the number of rows
inline UInt getNbRows() const { return rows_offsets.size() - 1; };
/// returns the number of non-empty columns in a given row
inline UInt getNbCols(UInt row) const {
return rows_offsets(row + 1) - rows_offsets(row);
};
/// returns the offset (start of columns) for a given row
inline UInt & rowOffset(UInt row) { return rows_offsets(row); };
/// iterator on a row
template <class R>
class iterator_internal
: public std::iterator<std::bidirectional_iterator_tag, R> {
public:
using _parent = std::iterator<std::bidirectional_iterator_tag, R>;
using pointer = typename _parent::pointer;
using reference = typename _parent::reference;
explicit iterator_internal(pointer x = nullptr) : pos(x){};
iterator_internal(const iterator_internal & it) : pos(it.pos){};
iterator_internal & operator++() {
++pos;
return *this;
};
iterator_internal operator++(int) {
iterator tmp(*this);
operator++();
return tmp;
};
iterator_internal & operator--() {
--pos;
return *this;
};
iterator_internal operator--(int) {
iterator_internal tmp(*this);
operator--();
return tmp;
};
bool operator==(const iterator_internal & rhs) { return pos == rhs.pos; };
bool operator!=(const iterator_internal & rhs) { return pos != rhs.pos; };
reference operator*() { return *pos; };
pointer operator->() const { return pos; };
private:
pointer pos;
};
using iterator = iterator_internal<T>;
using const_iterator = iterator_internal<const T>;
inline iterator begin(UInt row) {
return iterator(rows.storage() + rows_offsets(row));
};
inline iterator end(UInt row) {
return iterator(rows.storage() + rows_offsets(row + 1));
};
inline const_iterator begin(UInt row) const {
return const_iterator(rows.storage() + rows_offsets(row));
};
inline const_iterator end(UInt row) const {
return const_iterator(rows.storage() + rows_offsets(row + 1));
};
inline iterator rbegin(UInt row) {
return iterator(rows.storage() + rows_offsets(row + 1) - 1);
};
inline iterator rend(UInt row) {
return iterator(rows.storage() + rows_offsets(row) - 1);
};
inline const Array<UInt> & getRowsOffset() const { return rows_offsets; };
inline const Array<T> & getRows() const { return rows; };
inline Array<T> & getRows() { return rows; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
UInt nb_rows;
/// array of size nb_rows containing the offset where the values are stored in
Array<UInt> rows_offsets;
/// compressed row values, values of row[i] are stored between rows_offsets[i]
/// and rows_offsets[i+1]
Array<T> rows;
};
/* -------------------------------------------------------------------------- */
/* Data CSR */
/* -------------------------------------------------------------------------- */
/**
* Inherits from CSR<UInt> and can contain information such as matrix values
* where the mother class would be a CSR structure for row and cols
*
* @return nb_rows
*/
template <class T> class DataCSR : public CSR<UInt> {
public:
DataCSR(UInt nb_rows = 0) : CSR<UInt>(nb_rows), data(0, 1){};
inline void resizeCols() {
CSR<UInt>::resizeCols();
data.resize(rows_offsets(nb_rows));
}
inline const Array<T> & getData() const { return data; };
private:
Array<T> data;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "aka_csr_inline_impl.cc"
/// standard output stream operator
// inline std::ostream & operator <<(std::ostream & stream, const CSR & _this)
// {
// _this.printself(stream);
// return stream;
// }
} // akantu
#endif /* __AKANTU_AKA_CSR_HH__ */
diff --git a/src/common/aka_element_classes_info.hh.in b/src/common/aka_element_classes_info.hh.in
index 1fbdeadf1..a1b6651e1 100644
--- a/src/common/aka_element_classes_info.hh.in
+++ b/src/common/aka_element_classes_info.hh.in
@@ -1,217 +1,209 @@
/**
* @file aka_element_classes_info.hh.in
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Jul 19 2015
- * @date last modification: Fri Oct 16 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Declaration of the enums for the element classes
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
*
- * You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_ELEMENT_CLASSES_INFO_HH__
#define __AKANTU_AKA_ELEMENT_CLASSES_INFO_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Element Types */
/* -------------------------------------------------------------------------- */
/// @enum ElementType type of elements
enum ElementType {
_not_defined,
@AKANTU_ELEMENT_TYPES_ENUM@
_max_element_type
};
@AKANTU_ELEMENT_TYPES_BOOST_SEQ@
@AKANTU_ALL_ELEMENT_BOOST_SEQ@
/* -------------------------------------------------------------------------- */
/* Element Kinds */
/* -------------------------------------------------------------------------- */
@AKANTU_ELEMENT_KINDS_BOOST_SEQ@
@AKANTU_ELEMENT_KIND_BOOST_SEQ@
#ifndef SWIG
enum ElementKind {
BOOST_PP_SEQ_ENUM(AKANTU_ELEMENT_KIND),
_ek_not_defined
};
/* -------------------------------------------------------------------------- */
struct ElementKind_def {
using type = ElementKind;
static const type _begin_ = BOOST_PP_SEQ_HEAD(AKANTU_ELEMENT_KIND);
static const type _end_ = _ek_not_defined;
};
using element_kind_t = safe_enum<ElementKind_def> ;
#else
enum ElementKind;
#endif
/* -------------------------------------------------------------------------- */
/// @enum GeometricalType type of element potentially contained in a Mesh
enum GeometricalType {
@AKANTU_GEOMETRICAL_TYPES_ENUM@
_gt_not_defined
};
/* -------------------------------------------------------------------------- */
/* Interpolation Types */
/* -------------------------------------------------------------------------- */
@AKANTU_INTERPOLATION_TYPES_BOOST_SEQ@
#ifndef SWIG
/// @enum InterpolationType type of elements
enum InterpolationType {
BOOST_PP_SEQ_ENUM(AKANTU_INTERPOLATION_TYPES),
_itp_not_defined
};
#else
enum InterpolationType;
#endif
/* -------------------------------------------------------------------------- */
/* Some sub types less probable to change */
/* -------------------------------------------------------------------------- */
/// @enum GeometricalShapeType types of shapes to define the contains
/// function in the element classes
enum GeometricalShapeType {
@AKANTU_GEOMETRICAL_SHAPES_ENUM@
_gst_not_defined
};
/* -------------------------------------------------------------------------- */
/// @enum GaussIntegrationType classes of types using common
/// description of the gauss point position and weights
enum GaussIntegrationType {
@AKANTU_GAUSS_INTEGRATION_TYPES_ENUM@
_git_not_defined
};
/* -------------------------------------------------------------------------- */
/// @enum InterpolationKind the family of interpolation types
enum InterpolationKind {
@AKANTU_INTERPOLATION_KIND_ENUM@
_itk_not_defined
};
/* -------------------------------------------------------------------------- */
// BOOST PART: TOUCH ONLY IF YOU KNOW WHAT YOU ARE DOING
#define AKANTU_BOOST_CASE_MACRO(r, macro, _type) \
case _type: { \
macro(_type); \
break; \
}
#define AKANTU_BOOST_LIST_SWITCH(macro1, list1, var) \
do { \
switch (var) { \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, macro1, list1) \
default: { \
AKANTU_ERROR("Type (" << var << ") not handled by this function"); \
} \
} \
} while (0)
#define AKANTU_BOOST_LIST_SWITCH_NO_DEFAULT(macro1, list1, var) \
do { \
switch (var) { \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, macro1, list1) \
case _not_defined: \
break; \
case _max_element_type: \
break; \
} \
} while (0)
#define AKANTU_BOOST_ELEMENT_SWITCH(macro1, list1) \
AKANTU_BOOST_LIST_SWITCH(macro1, list1, type)
#define AKANTU_BOOST_ELEMENT_SWITCH_NO_DEFAULT(macro1, list1) \
AKANTU_BOOST_LIST_SWITCH_NO_DEFAULT(macro1, list1, type)
#define AKANTU_BOOST_ALL_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_BOOST_ALL_ELEMENT_SWITCH_NO_DEFAULT(macro) \
AKANTU_BOOST_ELEMENT_SWITCH_NO_DEFAULT(macro, AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_BOOST_LIST_MACRO(r, macro, type) macro(type)
#define AKANTU_BOOST_APPLY_ON_LIST(macro, list) \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_GET_ELEMENT_LIST(kind) AKANTU##kind##_ELEMENT_TYPE
#define AKANTU_BOOST_KIND_ELEMENT_SWITCH(macro, kind) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, AKANTU_GET_ELEMENT_LIST(kind))
// BOOST_PP_SEQ_TO_LIST does not exists in Boost < 1.49
#define AKANTU_GENERATE_KIND_LIST(seq) \
BOOST_PP_TUPLE_TO_LIST(BOOST_PP_SEQ_SIZE(seq), BOOST_PP_SEQ_TO_TUPLE(seq))
#define AKANTU_ELEMENT_KIND_BOOST_LIST \
AKANTU_GENERATE_KIND_LIST(AKANTU_ELEMENT_KIND)
#define AKANTU_BOOST_ALL_KIND_LIST(macro, list) \
BOOST_PP_LIST_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_KIND(macro) \
AKANTU_BOOST_ALL_KIND_LIST(macro, AKANTU_ELEMENT_KIND_BOOST_LIST)
#define AKANTU_BOOST_ALL_KIND_SWITCH(macro) \
AKANTU_BOOST_LIST_SWITCH(macro, AKANTU_ELEMENT_KIND, kind)
@AKANTU_ELEMENT_KINDS_BOOST_MACROS@
// /// define kept for compatibility reasons (they are most probably not needed
// /// anymore) \todo check if they can be removed
// #define AKANTU_REGULAR_ELEMENT_TYPE AKANTU_ek_regular_ELEMENT_TYPE
// #define AKANTU_COHESIVE_ELEMENT_TYPE AKANTU_ek_cohesive_ELEMENT_TYPE
// #define AKANTU_STRUCTURAL_ELEMENT_TYPE AKANTU_ek_structural_ELEMENT_TYPE
// #define AKANTU_IGFEM_ELEMENT_TYPE AKANTU_ek_igfem_ELEMENT_TYPE
/* -------------------------------------------------------------------------- */
/* Lists of interests for FEEngineTemplate functions */
/* -------------------------------------------------------------------------- */
@AKANTU_FE_ENGINE_LISTS@
} // akantu
#endif /* __AKANTU_AKA_ELEMENT_CLASSES_INFO_HH__ */
#include "aka_element_classes_info_inline_impl.cc"
diff --git a/src/common/aka_element_classes_info_inline_impl.cc b/src/common/aka_element_classes_info_inline_impl.cc
index 6bac2c4ee..871c7d2b6 100644
--- a/src/common/aka_element_classes_info_inline_impl.cc
+++ b/src/common/aka_element_classes_info_inline_impl.cc
@@ -1,113 +1,114 @@
/**
* @file aka_element_classes_info_inline_impl.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 18 2015
- * @date last modification: Sun Jul 19 2015
+ * @date last modification: Wed Jan 10 2018
*
* @brief Implementation of the streaming fonction for the element classes
* enums
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_CC__
#define __AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_CC__
AKANTU_ENUM_HASH(ElementType)
#define AKANTU_PP_ELEMTYPE_TO_STR(s, data, elem) \
({akantu::elem, BOOST_PP_STRINGIZE(elem)})
#define AKANTU_PP_STR_TO_ELEMTYPE(s, data, elem) \
({BOOST_PP_STRINGIZE(elem), akantu::elem})
namespace aka {
inline std::string to_string(const akantu::ElementType & type) {
static std::unordered_map<akantu::ElementType, std::string> convert{
BOOST_PP_SEQ_FOR_EACH_I(
AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(AKANTU_ALL_ELEMENT_TYPE),
BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_ELEMTYPE_TO_STR, _,
AKANTU_ALL_ELEMENT_TYPE)),
{akantu::_not_defined, "_not_defined"},
{akantu::_max_element_type, "_max_element_type"}};
return convert.at(type);
}
}
namespace akantu {
#define STRINGIFY(type) stream << BOOST_PP_STRINGIZE(type)
/* -------------------------------------------------------------------------- */
//! standard output stream operator for ElementType
inline std::ostream & operator<<(std::ostream & stream,
const ElementType & type) {
stream << aka::to_string(type);
return stream;
}
/* -------------------------------------------------------------------------- */
//! standard input stream operator for ElementType
inline std::istream & operator>>(std::istream & stream, ElementType & type) {
std::string str;
stream >> str;
static std::unordered_map<std::string, ElementType> convert{
BOOST_PP_SEQ_FOR_EACH_I(
AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(AKANTU_ALL_ELEMENT_TYPE),
BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_STR_TO_ELEMTYPE, _,
AKANTU_ALL_ELEMENT_TYPE))};
type = convert.at(str);
return stream;
}
/* -------------------------------------------------------------------------- */
//! standard output stream operator for ElementType
inline std::ostream & operator<<(std::ostream & stream, ElementKind kind) {
AKANTU_BOOST_ALL_KIND_SWITCH(STRINGIFY);
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for InterpolationType
inline std::ostream & operator<<(std::ostream & stream,
InterpolationType type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, STRINGIFY,
AKANTU_INTERPOLATION_TYPES)
case _itp_not_defined:
stream << "_itp_not_defined";
break;
}
return stream;
}
#undef STRINGIFY
} // akantu
#endif /* __AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_CC__ */
diff --git a/src/common/aka_error.cc b/src/common/aka_error.cc
index bbe935cb2..1afca6656 100644
--- a/src/common/aka_error.cc
+++ b/src/common/aka_error.cc
@@ -1,360 +1,359 @@
/**
* @file aka_error.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 06 2010
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Sun Dec 03 2017
*
* @brief handling of errors
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_error.hh"
#include "aka_common.hh"
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include <csignal>
#include <iostream>
#if (defined(READLINK_COMMAND) || defined(ADDR2LINE_COMMAND)) && \
(not defined(_WIN32))
#include <execinfo.h>
#include <sys/wait.h>
#endif
#include <cmath>
#include <cstring>
#include <cxxabi.h>
#include <fstream>
#include <iomanip>
#include <map>
#include <sys/types.h>
#include <unistd.h>
#if defined(AKANTU_CORE_CXX11)
#include <chrono>
#elif defined(AKANTU_USE_OBSOLETE_GETTIMEOFDAY)
#include <sys/time.h>
#else
#include <time.h>
#endif
#ifdef AKANTU_USE_MPI
#include <mpi.h>
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace debug {
static void printBacktraceAndExit(int) { std::terminate(); }
/* ------------------------------------------------------------------------ */
void initSignalHandler() { std::signal(SIGSEGV, &printBacktraceAndExit); }
/* ------------------------------------------------------------------------ */
std::string demangle(const char * symbol) {
int status;
std::string result;
char * demangled_name;
if ((demangled_name = abi::__cxa_demangle(symbol, nullptr, nullptr,
&status)) != nullptr) {
result = demangled_name;
free(demangled_name);
} else {
result = symbol;
}
return result;
}
/* ------------------------------------------------------------------------ */
#if (defined(READLINK_COMMAND) || defined(ADDR2LINK_COMMAND)) && \
(not defined(_WIN32))
std::string exec(const std::string & cmd) {
FILE * pipe = popen(cmd.c_str(), "r");
if (!pipe)
return "";
char buffer[1024];
std::string result = "";
while (!feof(pipe)) {
if (fgets(buffer, 128, pipe) != nullptr)
result += buffer;
}
result = result.substr(0, result.size() - 1);
pclose(pipe);
return result;
}
#endif
/* ------------------------------------------------------------------------ */
void printBacktrace(__attribute__((unused)) int sig) {
AKANTU_DEBUG_INFO("Caught signal " << sig << "!");
#if not defined(_WIN32)
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
std::string me = "";
char buf[1024];
/* The manpage says it won't null terminate. Let's zero the buffer. */
memset(buf, 0, sizeof(buf));
/* Note we use sizeof(buf)-1 since we may need an extra char for NUL. */
if (readlink("/proc/self/exe", buf, sizeof(buf) - 1))
me = std::string(buf);
std::ifstream inmaps;
inmaps.open("/proc/self/maps");
std::map<std::string, size_t> addr_map;
std::string line;
while (inmaps.good()) {
std::getline(inmaps, line);
std::stringstream sstr(line);
size_t first = line.find('-');
std::stringstream sstra(line.substr(0, first));
size_t addr;
sstra >> std::hex >> addr;
std::string lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
if (lib != "" && addr_map.find(lib) == addr_map.end()) {
addr_map[lib] = addr;
}
}
if (me != "")
addr_map[me] = 0;
#endif
/// \todo for windows this part could be coded using CaptureStackBackTrace
/// and SymFromAddr
const size_t max_depth = 100;
size_t stack_depth;
void * stack_addrs[max_depth];
char ** stack_strings;
size_t i;
stack_depth = backtrace(stack_addrs, max_depth);
stack_strings = backtrace_symbols(stack_addrs, stack_depth);
std::cerr << "BACKTRACE : " << stack_depth << " stack frames."
<< std::endl;
auto w = size_t(std::floor(log(double(stack_depth)) / std::log(10.)) + 1);
/// -1 to remove the call to the printBacktrace function
for (i = 1; i < stack_depth; i++) {
std::cerr << std::dec << " [" << std::setw(w) << i << "] ";
std::string bt_line(stack_strings[i]);
size_t first, second;
if ((first = bt_line.find('(')) != std::string::npos &&
(second = bt_line.find('+')) != std::string::npos) {
std::string location = bt_line.substr(0, first);
#if defined(READLINK_COMMAND)
std::string location_cmd =
std::string(BOOST_PP_STRINGIZE(READLINK_COMMAND)) +
std::string(" -f ") + location;
location = exec(location_cmd);
#endif
std::string call =
demangle(bt_line.substr(first + 1, second - first - 1).c_str());
size_t f = bt_line.find('[');
size_t s = bt_line.find(']');
std::string address = bt_line.substr(f + 1, s - f - 1);
std::stringstream sstra(address);
size_t addr;
sstra >> std::hex >> addr;
std::cerr << location << " [" << call << "]";
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
auto it = addr_map.find(location);
if (it != addr_map.end()) {
std::stringstream syscom;
syscom << BOOST_PP_STRINGIZE(ADDR2LINE_COMMAND) << " 0x" << std::hex
<< (addr - it->second) << " -i -e " << location;
std::string line = exec(syscom.str());
std::cerr << " (" << line << ")" << std::endl;
} else {
#endif
std::cerr << " (0x" << std::hex << addr << ")" << std::endl;
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
}
#endif
} else {
std::cerr << bt_line << std::endl;
}
}
free(stack_strings);
std::cerr << "END BACKTRACE" << std::endl;
#endif
}
/* ------------------------------------------------------------------------ */
namespace {
void terminate_handler() {
auto eptr = std::current_exception();
auto t = abi::__cxa_current_exception_type();
auto name = t ? demangle(t->name()) : std::string("unknown");
try {
if (eptr)
std::rethrow_exception(eptr);
else
std::cerr << "!! Execution terminated for unknown reasons !!"
<< std::endl;
} catch (std::exception & e) {
std::cerr << "!! Uncaught exception of type " << name
<< " !!\nwhat(): \"" << e.what() << "\"" << std::endl;
} catch (...) {
std::cerr << "!! Something strange of type \"" << name
<< "\" was thrown.... !!" << std::endl;
}
if (debugger.printBacktrace())
printBacktrace(15);
}
} // namespace
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
Debugger::Debugger() {
cout = &std::cerr;
level = dblWarning;
parallel_context = "";
file_open = false;
print_backtrace = false;
initSignalHandler();
std::set_terminate(terminate_handler);
}
/* ------------------------------------------------------------------------ */
Debugger::~Debugger() {
if (file_open) {
dynamic_cast<std::ofstream *>(cout)->close();
delete cout;
}
}
/* ------------------------------------------------------------------------ */
void Debugger::exit(int status) {
if (status != 0)
std::terminate();
std::exit(0);
}
/*------------------------------------------------------------------------- */
void Debugger::throwException(const std::string & info,
const std::string & file, unsigned int line,
__attribute__((unused)) bool silent,
__attribute__((unused))
const std::string & location) const
noexcept(false) {
#if !defined(AKANTU_NDEBUG)
if (!silent) {
printMessage("###", dblWarning, info + location);
}
#endif
debug::Exception ex(info, file, line);
throw ex;
}
/* ------------------------------------------------------------------------ */
void Debugger::printMessage(const std::string & prefix,
const DebugLevel & level,
const std::string & info) const {
if (this->level >= level) {
#if defined(AKANTU_CORE_CXX11)
double timestamp =
std::chrono::duration_cast<std::chrono::duration<double, std::micro>>(
std::chrono::system_clock::now().time_since_epoch())
.count();
#elif defined(AKANTU_USE_OBSOLETE_GETTIMEOFDAY)
struct timeval time;
gettimeofday(&time, NULL);
double timestamp = time.tv_sec * 1e6 + time.tv_usec; /*in us*/
#else
struct timespec time;
clock_gettime(CLOCK_REALTIME_COARSE, &time);
double timestamp = time.tv_sec * 1e6 + time.tv_nsec * 1e-3; /*in us*/
#endif
*(cout) << parallel_context << "{" << (size_t)timestamp << "} " << prefix
<< " " << info << std::endl;
}
}
/* ------------------------------------------------------------------------ */
void Debugger::setDebugLevel(const DebugLevel & level) {
this->level = level;
}
/* ------------------------------------------------------------------------ */
const DebugLevel & Debugger::getDebugLevel() const { return this->level; }
/* ------------------------------------------------------------------------ */
void Debugger::setLogFile(const std::string & filename) {
if (file_open) {
dynamic_cast<std::ofstream *>(cout)->close();
delete cout;
}
auto * fileout = new std::ofstream(filename.c_str());
file_open = true;
cout = fileout;
}
std::ostream & Debugger::getOutputStream() { return *cout; }
/* ------------------------------------------------------------------------ */
void Debugger::setParallelContext(int rank, int size) {
std::stringstream sstr;
UInt pad = std::ceil(std::log10(size));
sstr << "<" << getpid() << ">[R" << std::setfill(' ') << std::right
<< std::setw(pad) << rank << "|S" << size << "] ";
parallel_context = sstr.str();
}
void setDebugLevel(const DebugLevel & level) {
debugger.setDebugLevel(level);
}
const DebugLevel & getDebugLevel() { return debugger.getDebugLevel(); }
/* --------------------------------------------------------------------------
*/
void exit(int status) { debugger.exit(status); }
} // namespace debug
} // namespace akantu
diff --git a/src/common/aka_error.hh b/src/common/aka_error.hh
index d06b8bb97..cf737bbc8 100644
--- a/src/common/aka_error.hh
+++ b/src/common/aka_error.hh
@@ -1,339 +1,339 @@
/**
* @file aka_error.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Mon Jul 13 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief error management and internal exceptions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include <sstream>
#include <typeinfo>
#include <utility>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ERROR_HH__
#define __AKANTU_ERROR_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
enum DebugLevel {
dbl0 = 0,
dblError = 0,
dblAssert = 0,
dbl1 = 1,
dblException = 1,
dblCritical = 1,
dbl2 = 2,
dblMajor = 2,
dbl3 = 3,
dblCall = 3,
dblSecondary = 3,
dblHead = 3,
dbl4 = 4,
dblWarning = 4,
dbl5 = 5,
dblInfo = 5,
dbl6 = 6,
dblIn = 6,
dblOut = 6,
dbl7 = 7,
dbl8 = 8,
dblTrace = 8,
dbl9 = 9,
dblAccessory = 9,
dbl10 = 10,
dblDebug = 42,
dbl100 = 100,
dblDump = 100,
dblTest = 1337
};
/* -------------------------------------------------------------------------- */
#define AKANTU_LOCATION \
"(" << __func__ << "(): " << __FILE__ << ":" << __LINE__ << ")"
/* -------------------------------------------------------------------------- */
namespace debug {
void setDebugLevel(const DebugLevel & level);
const DebugLevel & getDebugLevel();
void initSignalHandler();
std::string demangle(const char * symbol);
#ifndef SWIG
std::string exec(const std::string & cmd);
#endif
void printBacktrace(int sig);
void exit(int status) __attribute__((noreturn));
/* ------------------------------------------------------------------------ */
/// exception class that can be thrown by akantu
class Exception : public std::exception {
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
protected:
explicit Exception(std::string info = "")
: _info(std::move(info)), _file("") {}
public:
//! full constructor
Exception(std::string info, std::string file, unsigned int line)
: _info(std::move(info)), _file(std::move(file)), _line(line) {}
//! destructor
~Exception() noexcept override = default;
/* ---------------------------------------------------------------------- */
/* Methods */
/* ---------------------------------------------------------------------- */
public:
const char * what() const noexcept override { return _info.c_str(); }
virtual const std::string info() const noexcept {
std::stringstream stream;
stream << debug::demangle(typeid(*this).name()) << " : " << _info << " ["
<< _file << ":" << _line << "]";
return stream.str();
}
public:
void setInfo(const std::string & info) { _info = info; }
void setFile(const std::string & file) { _file = file; }
void setLine(unsigned int line) { _line = line; }
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
protected:
/// exception description and additionals
std::string _info;
private:
/// file it is thrown from
std::string _file;
/// ligne it is thrown from
unsigned int _line{0};
};
class CriticalError : public Exception {};
class AssertException : public Exception {};
class NotImplementedException : public Exception {};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Exception & _this) {
stream << _this.what();
return stream;
}
/* --------------------------------------------------------------------------
*/
class Debugger {
public:
Debugger();
virtual ~Debugger();
Debugger(const Debugger &) = default;
Debugger & operator=(const Debugger &) = default;
void exit(int status) __attribute__((noreturn));
void throwException(const std::string & info, const std::string & file,
unsigned int line, bool, const std::string &) const
noexcept(false) __attribute__((noreturn));
/*----------------------------------------------------------------------- */
template <class Except>
void throwCustomException(const Except & ex, const std::string & info,
const std::string & file, unsigned int line) const
noexcept(false) __attribute__((noreturn));
/*----------------------------------------------------------------------- */
template <class Except>
void throwCustomException(const Except & ex, const std::string & file,
unsigned int line) const noexcept(false)
__attribute__((noreturn));
void printMessage(const std::string & prefix, const DebugLevel & level,
const std::string & info) const;
void setOutStream(std::ostream & out) { cout = &out; }
std::ostream & getOutStream() { return *cout; }
public:
void setParallelContext(int rank, int size);
void setDebugLevel(const DebugLevel & level);
const DebugLevel & getDebugLevel() const;
void setLogFile(const std::string & filename);
std::ostream & getOutputStream();
inline bool testLevel(const DebugLevel & level) const {
return (this->level >= (level));
}
void printBacktrace(bool on_off) { this->print_backtrace = on_off; }
bool printBacktrace() { return this->print_backtrace; }
private:
std::string parallel_context;
std::ostream * cout;
bool file_open;
DebugLevel level;
bool print_backtrace;
};
extern Debugger debugger;
} // namespace debug
/* -------------------------------------------------------------------------- */
#define AKANTU_STRINGSTREAM_IN(_str, _sstr) \
; \
do { \
std::stringstream _dbg_s_info; \
_dbg_s_info << _sstr; \
_str = _dbg_s_info.str(); \
} while (false)
/* -------------------------------------------------------------------------- */
#define AKANTU_EXCEPTION(info) AKANTU_EXCEPTION_(info, false)
#define AKANTU_SILENT_EXCEPTION(info) AKANTU_EXCEPTION_(info, true)
#define AKANTU_EXCEPTION_(info, silent) \
do { \
std::stringstream _dbg_str; \
_dbg_str << info; \
std::stringstream _dbg_loc; \
_dbg_loc << AKANTU_LOCATION; \
::akantu::debug::debugger.throwException( \
_dbg_str.str(), __FILE__, __LINE__, silent, _dbg_loc.str()); \
} while (false)
#define AKANTU_CUSTOM_EXCEPTION_INFO(ex, info) \
do { \
std::stringstream _dbg_str; \
_dbg_str << info; \
::akantu::debug::debugger.throwCustomException(ex, _dbg_str.str(), \
__FILE__, __LINE__); \
} while (false)
#define AKANTU_CUSTOM_EXCEPTION(ex) \
do { \
::akantu::debug::debugger.throwCustomException(ex, __FILE__, __LINE__); \
} while (false)
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_NDEBUG
#define AKANTU_DEBUG_TEST(level) (false)
#define AKANTU_DEBUG_LEVEL_IS_TEST() \
(::akantu::debug::debugger.testLevel(dblTest))
#define AKANTU_DEBUG(level, info)
#define AKANTU_DEBUG_(pref, level, info)
#define AKANTU_DEBUG_IN()
#define AKANTU_DEBUG_OUT()
#define AKANTU_DEBUG_INFO(info)
#define AKANTU_DEBUG_WARNING(info)
#define AKANTU_DEBUG_TRACE(info)
#define AKANTU_DEBUG_ASSERT(test, info)
#define AKANTU_ERROR(info) \
AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::CriticalError(), info)
/* -------------------------------------------------------------------------- */
#else
#define AKANTU_DEBUG(level, info) AKANTU_DEBUG_(" ", level, info)
#define AKANTU_DEBUG_(pref, level, info) \
do { \
std::string _dbg_str; \
AKANTU_STRINGSTREAM_IN(_dbg_str, info << " " << AKANTU_LOCATION); \
::akantu::debug::debugger.printMessage(pref, level, _dbg_str); \
} while (false)
#define AKANTU_DEBUG_TEST(level) (::akantu::debug::debugger.testLevel(level))
#define AKANTU_DEBUG_LEVEL_IS_TEST() \
(::akantu::debug::debugger.testLevel(dblTest))
#define AKANTU_DEBUG_IN() \
AKANTU_DEBUG_("==>", ::akantu::dblIn, __func__ << "()")
#define AKANTU_DEBUG_OUT() \
AKANTU_DEBUG_("<==", ::akantu::dblOut, __func__ << "()")
#define AKANTU_DEBUG_INFO(info) AKANTU_DEBUG_("---", ::akantu::dblInfo, info)
#define AKANTU_DEBUG_WARNING(info) \
AKANTU_DEBUG_("/!\\", ::akantu::dblWarning, info)
#define AKANTU_DEBUG_TRACE(info) AKANTU_DEBUG_(">>>", ::akantu::dblTrace, info)
#define AKANTU_DEBUG_ASSERT(test, info) \
do { \
if (not(test)) \
AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::AssertException(), \
"assert [" << #test << "] " << info); \
} while (false)
#define AKANTU_ERROR(info) \
do { \
AKANTU_DEBUG_("!!! ", ::akantu::dblError, info); \
AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::CriticalError(), info); \
} while (false)
#endif // AKANTU_NDEBUG
#define AKANTU_TO_IMPLEMENT() \
AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::NotImplementedException(), \
__func__ << " : not implemented yet !")
/* -------------------------------------------------------------------------- */
namespace debug {
/* ------------------------------------------------------------------------ */
template <class Except>
void Debugger::throwCustomException(const Except & ex,
const std::string & info,
const std::string & file,
unsigned int line) const noexcept(false) {
auto & nc_ex = const_cast<Except &>(ex);
nc_ex.setInfo(info);
nc_ex.setFile(file);
nc_ex.setLine(line);
throw ex;
}
/* ------------------------------------------------------------------------ */
template <class Except>
void Debugger::throwCustomException(const Except & ex,
const std::string & file,
unsigned int line) const noexcept(false) {
auto & nc_ex = const_cast<Except &>(ex);
nc_ex.setFile(file);
nc_ex.setLine(line);
throw ex;
}
} // namespace debug
} // namespace akantu
#endif /* __AKANTU_ERROR_HH__ */
diff --git a/src/common/aka_event_handler_manager.hh b/src/common/aka_event_handler_manager.hh
index 5fd229933..043493feb 100644
--- a/src/common/aka_event_handler_manager.hh
+++ b/src/common/aka_event_handler_manager.hh
@@ -1,126 +1,125 @@
/**
* @file aka_event_handler_manager.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Dec 16 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Base of Event Handler classes
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_EVENT_HANDLER_MANAGER_HH__
#define __AKANTU_AKA_EVENT_HANDLER_MANAGER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <list>
/* -------------------------------------------------------------------------- */
namespace akantu {
template <class EventHandler> class EventHandlerManager {
private:
using priority_value = std::pair<EventHandlerPriority, EventHandler *>;
using priority_list = std::list<priority_value>;
struct KeyComp {
bool operator()(const priority_value & a, const priority_value & b) const {
return (a.first < b.first);
}
bool operator()(const priority_value & a, UInt b) const {
return (a.first < b);
}
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
virtual ~EventHandlerManager() { event_handlers.clear(); }
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register a new EventHandler to the Manager. The register object
/// will then be informed about the events the manager observes.
void registerEventHandler(EventHandler & event_handler,
EventHandlerPriority priority = _ehp_highest) {
auto it = this->searchEventHandler(event_handler);
if (it != this->event_handlers.end()) {
AKANTU_EXCEPTION("This event handler was already registered (priority: "
<< priority << ")");
}
auto pos =
std::lower_bound(this->event_handlers.begin(),
this->event_handlers.end(), priority, KeyComp());
this->event_handlers.insert(pos, std::make_pair(priority, &event_handler));
}
/// unregister a EventHandler object. This object will not be
/// notified anymore about the events this manager observes.
void unregisterEventHandler(EventHandler & event_handler) {
auto it = this->searchEventHandler(event_handler);
if (it == this->event_handlers.end()) {
AKANTU_EXCEPTION("This event handler is not registered");
}
this->event_handlers.erase(it);
}
/// Notify all the registered EventHandlers about the event that just occured.
template <class Event> void sendEvent(const Event & event) {
for (auto & pair : this->event_handlers)
pair.second->sendEvent(event);
}
private:
typename priority_list::iterator searchEventHandler(EventHandler & handler) {
auto it = this->event_handlers.begin();
auto end = this->event_handlers.end();
for (; it != end && it->second != &handler; ++it)
;
return it;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// list of the event handlers
priority_list event_handlers;
};
} // namespace akantu
#endif /* __AKANTU_AKA_EVENT_HANDLER_MANAGER_HH__ */
diff --git a/src/common/aka_extern.cc b/src/common/aka_extern.cc
index 78ae76cfa..f6fb3c004 100644
--- a/src/common/aka_extern.cc
+++ b/src/common/aka_extern.cc
@@ -1,109 +1,108 @@
/**
* @file aka_extern.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Thu Nov 19 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief initialisation of all global variables
* to insure the order of creation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_math.hh"
#include "aka_named_argument.hh"
#include "aka_random_generator.hh"
#include "communication_tag.hh"
#include "cppargparse.hh"
#include "parser.hh"
#include "solid_mechanics_model.hh"
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "solid_mechanics_model_cohesive.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
/* error.hpp variables */
/* -------------------------------------------------------------------------- */
namespace debug {
/** \todo write function to get this
* values from the environment or a config file
*/
/// standard output for debug messages
std::ostream * _akantu_debug_cout = &std::cerr;
/// standard output for normal messages
std::ostream & _akantu_cout = std::cout;
/// parallel context used in debug messages
std::string _parallel_context = "";
Debugger debugger;
#if defined(AKANTU_DEBUG_TOOLS)
DebugElementManager element_manager;
#endif
} // namespace debug
/* -------------------------------------------------------------------------- */
/// list of ghost iterable types
ghost_type_t ghost_types(_casper);
/* -------------------------------------------------------------------------- */
/// Paser for commandline arguments
::cppargparse::ArgumentParser static_argparser;
/// Parser containing the information parsed by the input file given to initFull
Parser static_parser;
bool Parser::permissive_parser = false;
/* -------------------------------------------------------------------------- */
Real Math::tolerance = 1e2 * std::numeric_limits<Real>::epsilon();
/* -------------------------------------------------------------------------- */
const UInt _all_dimensions = UInt(-1);
/* -------------------------------------------------------------------------- */
const Array<UInt> empty_filter(0, 1, "empty_filter");
/* -------------------------------------------------------------------------- */
template <> long int RandomGenerator<UInt>::_seed = 5489u;
template <> std::default_random_engine RandomGenerator<UInt>::generator(5489u);
/* -------------------------------------------------------------------------- */
int Tag::max_tag = 0;
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/common/aka_factory.hh b/src/common/aka_factory.hh
index 64bd867f6..a278ef69d 100644
--- a/src/common/aka_factory.hh
+++ b/src/common/aka_factory.hh
@@ -1,83 +1,85 @@
/**
* @file aka_factory.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Thu Jul 06 2017
+ * @date creation: Sun Jul 09 2017
+ * @date last modification: Fri Dec 08 2017
*
- * @brief This is a generic factory
+ * @brief This is a generic factory
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
#include <map>
#include <memory>
#include <string>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_FACTORY_HH__
#define __AKANTU_AKA_FACTORY_HH__
namespace akantu {
template <class Base, class T = ID, class... Args> class Factory {
using allocator_t = std::function<std::unique_ptr<Base>(Args...)>;
private:
Factory() = default;
public:
Factory(const Factory &) = delete;
Factory & operator=(const Factory &) = delete;
static Factory & getInstance() {
static Factory instance;
return instance;
}
/* ------------------------------------------------------------------------ */
bool registerAllocator(const T & id, const allocator_t & allocator) {
if (allocators.find(id) != allocators.end())
AKANTU_EXCEPTION("The id " << id << " is already registered in the "
<< debug::demangle(typeid(Base).name())
<< " factory");
allocators[id] = allocator;
return true;
}
template <typename... AArgs>
std::unique_ptr<Base> allocate(const T & id, AArgs &&... args) const {
if (allocators.find(id) == allocators.end())
AKANTU_EXCEPTION("The id " << id << " is not registered in the "
<< debug::demangle(typeid(Base).name())
<< " factory.");
return std::forward<std::unique_ptr<Base>>(
allocators.at(id)(std::forward<AArgs>(args)...));
}
private:
std::map<T, allocator_t> allocators;
};
} // namespace akantu
#endif /* __AKANTU_AKA_FACTORY_HH__ */
diff --git a/src/common/aka_fwd.hh b/src/common/aka_fwd.hh
index 9055e696b..0ec003f5a 100644
--- a/src/common/aka_fwd.hh
+++ b/src/common/aka_fwd.hh
@@ -1,72 +1,72 @@
/**
* @file aka_fwd.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Wed Oct 25 2017
*
* @brief File containing forward declarations in akantu.
* This file helps if circular #include would be needed because two classes
* refer both to each other. This file usually does not need any modification.
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_FWD_HH__
#define __AKANTU_FWD_HH__
namespace cppargparse {
class ArgumentParser;
}
namespace akantu {
// forward declaration
template <int dim, class model_type> struct ContactData;
template <typename T> class Matrix;
template <typename T> class Vector;
template <typename T> class Tensor3;
template <typename T, bool is_scal = is_scalar<T>::value> class Array;
template <typename T, typename SupportType = ElementType>
class ElementTypeMapArray;
template <class T> class SpatialGrid;
// Model element
template <class ModelPolicy> class ModelElement;
extern const Array<UInt> empty_filter;
class Parser;
class ParserSection;
extern Parser static_parser;
extern cppargparse::ArgumentParser static_argparser;
class Mesh;
class SparseMatrix;
} // namespace akantu
#endif /* __AKANTU_FWD_HH__ */
diff --git a/src/common/aka_grid_dynamic.hh b/src/common/aka_grid_dynamic.hh
index f43007915..d717b12c8 100644
--- a/src/common/aka_grid_dynamic.hh
+++ b/src/common/aka_grid_dynamic.hh
@@ -1,512 +1,512 @@
/**
* @file aka_grid_dynamic.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Sat Sep 26 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Grid that is auto balanced
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_types.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_GRID_DYNAMIC_HH__
#define __AKANTU_AKA_GRID_DYNAMIC_HH__
namespace akantu {
class Mesh;
template <typename T> class SpatialGrid {
public:
explicit SpatialGrid(UInt dimension)
: dimension(dimension), spacing(dimension), center(dimension),
lower(dimension), upper(dimension), empty_cell() {}
SpatialGrid(UInt dimension, const Vector<Real> & spacing,
const Vector<Real> & center)
: dimension(dimension), spacing(spacing), center(center),
lower(dimension), upper(dimension), empty_cell() {
for (UInt i = 0; i < dimension; ++i) {
lower(i) = std::numeric_limits<Real>::max();
upper(i) = -std::numeric_limits<Real>::max();
}
}
virtual ~SpatialGrid() = default;
class neighbor_cells_iterator;
class cells_iterator;
class CellID {
public:
CellID() : ids() {}
explicit CellID(UInt dimention) : ids(dimention) {}
void setID(UInt dir, Int id) { ids(dir) = id; }
Int getID(UInt dir) const { return ids(dir); }
bool operator<(const CellID & id) const {
return std::lexicographical_compare(
ids.storage(), ids.storage() + ids.size(), id.ids.storage(),
id.ids.storage() + id.ids.size());
}
bool operator==(const CellID & id) const {
return std::equal(ids.storage(), ids.storage() + ids.size(),
id.ids.storage());
}
bool operator!=(const CellID & id) const { return !(operator==(id)); }
class neighbor_cells_iterator
: private std::iterator<std::forward_iterator_tag, UInt> {
public:
neighbor_cells_iterator(const CellID & cell_id, bool end)
: cell_id(cell_id), position(cell_id.ids.size(), end ? 1 : -1) {
this->updateIt();
if (end)
this->it++;
}
neighbor_cells_iterator & operator++() {
UInt i = 0;
for (; i < position.size() && position(i) == 1; ++i)
;
if (i == position.size()) {
++it;
return *this;
}
for (UInt j = 0; j < i; ++j)
position(j) = -1;
position(i)++;
updateIt();
return *this;
}
neighbor_cells_iterator operator++(int) {
neighbor_cells_iterator tmp(*this);
operator++();
return tmp;
};
bool operator==(const neighbor_cells_iterator & rhs) const {
return cell_id == rhs.cell_id && it == rhs.it;
};
bool operator!=(const neighbor_cells_iterator & rhs) const {
return !operator==(rhs);
};
CellID operator*() const {
CellID cur_cell_id(cell_id);
cur_cell_id.ids += position;
return cur_cell_id;
};
private:
void updateIt() {
it = 0;
for (UInt i = 0; i < position.size(); ++i)
it = it * 3 + (position(i) + 1);
}
private:
/// central cell id
const CellID & cell_id;
// number representing the current neighbor in base 3;
UInt it;
// current cell shift
Vector<Int> position;
};
class Neighbors {
public:
explicit Neighbors(const CellID & cell_id) : cell_id(cell_id) {}
decltype(auto) begin() { return neighbor_cells_iterator(cell_id, false); }
decltype(auto) end() { return neighbor_cells_iterator(cell_id, true); }
private:
const CellID & cell_id;
};
decltype(auto) neighbors() { return Neighbors(*this); }
private:
friend class cells_iterator;
Vector<Int> ids;
};
/* ------------------------------------------------------------------------ */
class Cell {
public:
using iterator = typename std::vector<T>::iterator;
using const_iterator = typename std::vector<T>::const_iterator;
Cell() : id(), data() {}
explicit Cell(const CellID & cell_id) : id(cell_id), data() {}
bool operator==(const Cell & cell) const { return id == cell.id; }
bool operator!=(const Cell & cell) const { return id != cell.id; }
Cell & add(const T & d) {
data.push_back(d);
return *this;
}
iterator begin() { return data.begin(); }
const_iterator begin() const { return data.begin(); }
iterator end() { return data.end(); }
const_iterator end() const { return data.end(); }
private:
CellID id;
std::vector<T> data;
};
private:
using cells_container = std::map<CellID, Cell>;
public:
const Cell & getCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
if (it != cells.end())
return it->second;
return empty_cell;
}
decltype(auto) beginCell(const CellID & cell_id) {
auto it = cells.find(cell_id);
if (it != cells.end())
return it->second.begin();
return empty_cell.begin();
}
decltype(auto) endCell(const CellID & cell_id) {
auto it = cells.find(cell_id);
if (it != cells.end())
return it->second.end();
return empty_cell.end();
}
decltype(auto) beginCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
if (it != cells.end())
return it->second.begin();
return empty_cell.begin();
}
decltype(auto) endCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
if (it != cells.end())
return it->second.end();
return empty_cell.end();
}
/* ------------------------------------------------------------------------ */
class cells_iterator
: private std::iterator<std::forward_iterator_tag, CellID> {
public:
explicit cells_iterator(typename std::map<CellID, Cell>::const_iterator it)
: it(it) {}
cells_iterator & operator++() {
this->it++;
return *this;
}
cells_iterator operator++(int) {
cells_iterator tmp(*this);
operator++();
return tmp;
};
bool operator==(const cells_iterator & rhs) const { return it == rhs.it; };
bool operator!=(const cells_iterator & rhs) const {
return !operator==(rhs);
};
CellID operator*() const {
CellID cur_cell_id(this->it->first);
return cur_cell_id;
};
private:
/// map iterator
typename std::map<CellID, Cell>::const_iterator it;
};
public:
template <class vector_type>
Cell & insert(const T & d, const vector_type & position) {
auto && cell_id = getCellID(position);
auto && it = cells.find(cell_id);
if (it == cells.end()) {
Cell cell(cell_id);
auto & tmp = (cells[cell_id] = cell).add(d);
for (UInt i = 0; i < dimension; ++i) {
Real posl = center(i) + cell_id.getID(i) * spacing(i);
Real posu = posl + spacing(i);
if (posl < lower(i))
lower(i) = posl;
if (posu > upper(i))
upper(i) = posu;
}
return tmp;
} else {
return it->second.add(d);
}
}
/* ------------------------------------------------------------------------ */
inline decltype(auto) begin() const {
auto begin = this->cells.begin();
return cells_iterator(begin);
}
inline decltype(auto) end() const {
auto end = this->cells.end();
return cells_iterator(end);
}
template <class vector_type>
CellID getCellID(const vector_type & position) const {
CellID cell_id(dimension);
for (UInt i = 0; i < dimension; ++i) {
cell_id.setID(i, getCellID(position(i), i));
}
return cell_id;
}
void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
std::streamsize prec = stream.precision();
std::ios_base::fmtflags ff = stream.flags();
stream.setf(std::ios_base::showbase);
stream.precision(5);
stream << space << "SpatialGrid<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
stream << space << " + dimension : " << this->dimension << std::endl;
stream << space << " + lower bounds : {";
for (UInt i = 0; i < lower.size(); ++i) {
if (i != 0)
stream << ", ";
stream << lower(i);
};
stream << "}" << std::endl;
stream << space << " + upper bounds : {";
for (UInt i = 0; i < upper.size(); ++i) {
if (i != 0)
stream << ", ";
stream << upper(i);
};
stream << "}" << std::endl;
stream << space << " + spacing : {";
for (UInt i = 0; i < spacing.size(); ++i) {
if (i != 0)
stream << ", ";
stream << spacing(i);
};
stream << "}" << std::endl;
stream << space << " + center : {";
for (UInt i = 0; i < center.size(); ++i) {
if (i != 0)
stream << ", ";
stream << center(i);
};
stream << "}" << std::endl;
stream << space << " + nb_cells : " << this->cells.size() << "/";
Vector<Real> dist(this->dimension);
dist = upper;
dist -= lower;
for (UInt i = 0; i < this->dimension; ++i) {
dist(i) /= spacing(i);
}
UInt nb_cells = std::ceil(dist(0));
for (UInt i = 1; i < this->dimension; ++i) {
nb_cells *= std::ceil(dist(i));
}
stream << nb_cells << std::endl;
stream << space << "]" << std::endl;
stream.precision(prec);
stream.flags(ff);
}
void saveAsMesh(Mesh & mesh) const;
private:
/* --------------------------------------------------------------------------
*/
inline UInt getCellID(Real position, UInt direction) const {
AKANTU_DEBUG_ASSERT(direction < center.size(),
"The direction asked (" << direction
<< ") is out of range "
<< center.size());
Real dist_center = position - center(direction);
Int id = std::floor(dist_center / spacing(direction));
// if(dist_center < 0) id--;
return id;
}
friend class GridSynchronizer;
public:
AKANTU_GET_MACRO(LowerBounds, lower, const Vector<Real> &);
AKANTU_GET_MACRO(UpperBounds, upper, const Vector<Real> &);
AKANTU_GET_MACRO(Spacing, spacing, const Vector<Real> &);
protected:
UInt dimension;
cells_container cells;
Vector<Real> spacing;
Vector<Real> center;
Vector<Real> lower;
Vector<Real> upper;
Cell empty_cell;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const SpatialGrid<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "mesh.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> void SpatialGrid<T>::saveAsMesh(Mesh & mesh) const {
auto & nodes = const_cast<Array<Real> &>(mesh.getNodes());
ElementType type;
switch (dimension) {
case 1:
type = _segment_2;
break;
case 2:
type = _quadrangle_4;
break;
case 3:
type = _hexahedron_8;
break;
}
mesh.addConnectivityType(type);
auto & connectivity = const_cast<Array<UInt> &>(mesh.getConnectivity(type));
auto & uint_data = mesh.getDataPointer<UInt>("tag_1", type);
Vector<Real> pos(dimension);
UInt global_id = 0;
for (auto & cell_pair : cells) {
UInt cur_node = nodes.size();
UInt cur_elem = connectivity.size();
const CellID & cell_id = cell_pair.first;
for (UInt i = 0; i < dimension; ++i)
pos(i) = center(i) + cell_id.getID(i) * spacing(i);
nodes.push_back(pos);
for (UInt i = 0; i < dimension; ++i)
pos(i) += spacing(i);
nodes.push_back(pos);
connectivity.push_back(cur_node);
switch (dimension) {
case 1:
connectivity(cur_elem, 1) = cur_node + 1;
break;
case 2:
pos(0) -= spacing(0);
nodes.push_back(pos);
pos(0) += spacing(0);
pos(1) -= spacing(1);
nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 3;
connectivity(cur_elem, 2) = cur_node + 1;
connectivity(cur_elem, 3) = cur_node + 2;
break;
case 3:
pos(1) -= spacing(1);
pos(2) -= spacing(2);
nodes.push_back(pos);
pos(1) += spacing(1);
nodes.push_back(pos);
pos(0) -= spacing(0);
nodes.push_back(pos);
pos(1) -= spacing(1);
pos(2) += spacing(2);
nodes.push_back(pos);
pos(0) += spacing(0);
nodes.push_back(pos);
pos(0) -= spacing(0);
pos(1) += spacing(1);
nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 2;
connectivity(cur_elem, 2) = cur_node + 3;
connectivity(cur_elem, 3) = cur_node + 4;
connectivity(cur_elem, 4) = cur_node + 5;
connectivity(cur_elem, 5) = cur_node + 6;
connectivity(cur_elem, 6) = cur_node + 1;
connectivity(cur_elem, 7) = cur_node + 7;
break;
}
uint_data.push_back(global_id);
++global_id;
}
}
} // namespace akantu
#endif /* __AKANTU_AKA_GRID_DYNAMIC_HH__ */
diff --git a/src/common/aka_iterators.hh b/src/common/aka_iterators.hh
index 7eed4b058..b9a33e8b1 100644
--- a/src/common/aka_iterators.hh
+++ b/src/common/aka_iterators.hh
@@ -1,352 +1,354 @@
/**
* @file aka_iterators.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Wed Jul 19 2017
+ * @date creation: Fri Aug 11 2017
+ * @date last modification: Mon Jan 29 2018
*
- * @brief iterator interfaces
+ * @brief iterator interfaces
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include <tuple>
#include <utility>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_ITERATORS_HH__
#define __AKANTU_AKA_ITERATORS_HH__
namespace akantu {
namespace tuple {
/* ------------------------------------------------------------------------ */
namespace details {
template <size_t N> struct Foreach {
template <class Tuple>
static inline bool not_equal(Tuple && a, Tuple && b) {
if (std::get<N - 1>(std::forward<Tuple>(a)) ==
std::get<N - 1>(std::forward<Tuple>(b)))
return false;
return Foreach<N - 1>::not_equal(std::forward<Tuple>(a),
std::forward<Tuple>(b));
}
};
/* ---------------------------------------------------------------------- */
template <> struct Foreach<0> {
template <class Tuple>
static inline bool not_equal(Tuple && a, Tuple && b) {
return std::get<0>(std::forward<Tuple>(a)) !=
std::get<0>(std::forward<Tuple>(b));
}
};
template <typename... Ts>
decltype(auto) make_tuple_no_decay(Ts &&... args) {
return std::tuple<Ts...>(std::forward<Ts>(args)...);
}
template <class F, class Tuple, size_t... Is>
void foreach_impl(F && func, Tuple && tuple,
std::index_sequence<Is...> &&) {
(void)std::initializer_list<int>{
(std::forward<F>(func)(std::get<Is>(std::forward<Tuple>(tuple))),
0)...};
}
template <class F, class Tuple, size_t... Is>
decltype(auto) transform_impl(F && func, Tuple && tuple,
std::index_sequence<Is...> &&) {
return make_tuple_no_decay(
std::forward<F>(func)(std::get<Is>(std::forward<Tuple>(tuple)))...);
}
} // namespace details
/* ------------------------------------------------------------------------ */
template <class Tuple> bool are_not_equal(Tuple && a, Tuple && b) {
return details::Foreach<std::tuple_size<std::decay_t<Tuple>>::value>::
not_equal(std::forward<Tuple>(a), std::forward<Tuple>(b));
}
template <class F, class Tuple> void foreach (F && func, Tuple && tuple) {
return details::foreach_impl(
std::forward<F>(func), std::forward<Tuple>(tuple),
std::make_index_sequence<
std::tuple_size<std::decay_t<Tuple>>::value>{});
}
template <class F, class Tuple>
decltype(auto) transform(F && func, Tuple && tuple) {
return details::transform_impl(
std::forward<F>(func), std::forward<Tuple>(tuple),
std::make_index_sequence<
std::tuple_size<std::decay_t<Tuple>>::value>{});
}
} // namespace tuple
/* -------------------------------------------------------------------------- */
namespace iterators {
namespace {
template <typename It, typename category>
struct is_at_least_category
: std::is_same<std::common_type_t<
typename std::iterator_traits<It>::iterator_category,
category>,
category> {};
}
template <class... Iterators> class ZipIterator {
public:
using value_type =
std::tuple<typename std::iterator_traits<Iterators>::value_type...>;
using difference_type = std::common_type_t<
typename std::iterator_traits<Iterators>::difference_type...>;
using pointer =
std::tuple<typename std::iterator_traits<Iterators>::pointer...>;
using reference =
std::tuple<typename std::iterator_traits<Iterators>::reference...>;
using iterator_category = std::input_iterator_tag;
// std::common_type_t<typename
// std::iterator_traits<Iterators>::iterator_category...>;
private:
using tuple_t = std::tuple<Iterators...>;
public:
explicit ZipIterator(tuple_t iterators) : iterators(std::move(iterators)) {}
// input iterator ++it
ZipIterator & operator++() {
tuple::foreach ([](auto && it) { ++it; }, iterators);
return *this;
}
// input iterator it++
ZipIterator operator++(int) {
auto cpy = *this;
tuple::foreach ([](auto && it) { ++it; }, iterators);
return cpy;
}
// input iterator it != other_it
bool operator!=(const ZipIterator & other) const {
return tuple::are_not_equal(iterators, other.iterators);
}
// input iterator dereference *it
decltype(auto) operator*() {
return tuple::transform([](auto && it) -> decltype(auto) { return *it; },
iterators);
}
bool operator==(const ZipIterator & other) const {
return not tuple::are_not_equal(iterators, other.iterators);
}
private:
tuple_t iterators;
};
} // namespace iterators
/* -------------------------------------------------------------------------- */
template <class... Iterators>
decltype(auto) zip_iterator(std::tuple<Iterators...> && iterators_tuple) {
auto zip = iterators::ZipIterator<Iterators...>(
std::forward<decltype(iterators_tuple)>(iterators_tuple));
return zip;
}
/* -------------------------------------------------------------------------- */
namespace containers {
template <class... Containers> class ZipContainer {
using containers_t = std::tuple<Containers...>;
public:
explicit ZipContainer(Containers &&... containers)
: containers(std::forward<Containers>(containers)...) {}
decltype(auto) begin() const {
return zip_iterator(
tuple::transform([](auto && c) { return c.begin(); },
std::forward<containers_t>(containers)));
}
decltype(auto) end() const {
return zip_iterator(
tuple::transform([](auto && c) { return c.end(); },
std::forward<containers_t>(containers)));
}
decltype(auto) begin() {
return zip_iterator(
tuple::transform([](auto && c) { return c.begin(); },
std::forward<containers_t>(containers)));
}
decltype(auto) end() {
return zip_iterator(
tuple::transform([](auto && c) { return c.end(); },
std::forward<containers_t>(containers)));
}
private:
containers_t containers;
};
template <class Iterator> class Range {
public:
explicit Range(Iterator && it1, Iterator && it2)
: iterators(std::forward<Iterator>(it1), std::forward<Iterator>(it2)) {}
decltype(auto) begin() const { return std::get<0>(iterators); }
decltype(auto) begin() { return std::get<0>(iterators); }
decltype(auto) end() const { return std::get<1>(iterators); }
decltype(auto) end() { return std::get<1>(iterators); }
private:
std::tuple<Iterator, Iterator> iterators;
};
} // namespace containers
/* -------------------------------------------------------------------------- */
template <class... Containers> decltype(auto) zip(Containers &&... conts) {
return containers::ZipContainer<Containers...>(
std::forward<Containers>(conts)...);
}
template <class Iterator>
decltype(auto) range(Iterator && it1, Iterator && it2) {
return containers::Range<Iterator>(std::forward<Iterator>(it1),
std::forward<Iterator>(it2));
}
/* -------------------------------------------------------------------------- */
/* Arange */
/* -------------------------------------------------------------------------- */
namespace iterators {
template <class T> class ArangeIterator {
public:
using value_type = T;
using pointer = T *;
using reference = T &;
using difference_type = size_t;
using iterator_category = std::input_iterator_tag;
constexpr ArangeIterator(T value, T step) : value(value), step(step) {}
constexpr ArangeIterator(const ArangeIterator &) = default;
constexpr ArangeIterator & operator++() {
value += step;
return *this;
}
constexpr T operator*() const { return value; }
constexpr bool operator==(const ArangeIterator & other) const {
return (value == other.value) and (step == other.step);
}
constexpr bool operator!=(const ArangeIterator & other) const {
return not operator==(other);
}
private:
T value{0};
const T step{1};
};
} // namespace iterators
namespace containers {
template <class T> class ArangeContainer {
public:
using iterator = iterators::ArangeIterator<T>;
constexpr ArangeContainer(T start, T stop, T step = 1)
: start(start), stop((stop - start) % step == 0
? stop
: start + (1 + (stop - start) / step) * step),
step(step) {}
explicit constexpr ArangeContainer(T stop) : ArangeContainer(0, stop, 1) {}
constexpr T operator[](size_t i) {
T val = start + i * step;
assert(val < stop && "i is out of range");
return val;
}
constexpr T size() { return (stop - start) / step; }
constexpr iterator begin() { return iterator(start, step); }
constexpr iterator end() { return iterator(stop, step); }
private:
const T start{0}, stop{0}, step{1};
};
} // namespace containers
template <class T,
typename = std::enable_if_t<std::is_integral<std::decay_t<T>>::value>>
inline decltype(auto) arange(const T & stop) {
return containers::ArangeContainer<T>(stop);
}
template <class T1, class T2,
typename = std::enable_if_t<
std::is_integral<std::common_type_t<T1, T2>>::value>>
inline constexpr decltype(auto) arange(const T1 & start, const T2 & stop) {
return containers::ArangeContainer<std::common_type_t<T1, T2>>(start, stop);
}
template <class T1, class T2, class T3,
typename = std::enable_if_t<
std::is_integral<std::common_type_t<T1, T2, T3>>::value>>
inline constexpr decltype(auto) arange(const T1 & start, const T2 & stop,
const T3 & step) {
return containers::ArangeContainer<std::common_type_t<T1, T2, T3>>(
start, stop, step);
}
/* -------------------------------------------------------------------------- */
template <class Container>
inline constexpr decltype(auto) enumerate(Container && container,
size_t start_ = 0) {
auto stop = std::forward<Container>(container).size();
decltype(stop) start = start_;
return zip(arange(start, stop), std::forward<Container>(container));
}
} // namespace akantu
namespace std {
template <typename... Its>
struct iterator_traits<::akantu::iterators::ZipIterator<Its...>> {
using iterator_category = forward_iterator_tag;
using value_type =
typename ::akantu::iterators::ZipIterator<Its...>::value_type;
using difference_type =
typename ::akantu::iterators::ZipIterator<Its...>::difference_type;
using pointer = typename ::akantu::iterators::ZipIterator<Its...>::pointer;
using reference =
typename ::akantu::iterators::ZipIterator<Its...>::reference;
};
}
#endif /* __AKANTU_AKA_ITERATORS_HH__ */
diff --git a/src/common/aka_math.cc b/src/common/aka_math.cc
index 09ad498d8..09bd4270d 100644
--- a/src/common/aka_math.cc
+++ b/src/common/aka_math.cc
@@ -1,251 +1,250 @@
/**
* @file aka_math.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Fri May 15 2015
+ * @date last modification: Sun Aug 13 2017
*
* @brief Implementation of the math toolbox
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_math.hh"
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void Math::matrix_vector(UInt m, UInt n, const Array<Real> & A,
const Array<Real> & x, Array<Real> & y, Real alpha) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(A.size() == x.size(),
"The vector A(" << A.getID() << ") and the vector x("
<< x.getID()
<< ") must have the same size");
AKANTU_DEBUG_ASSERT(A.getNbComponent() == m * n,
"The vector A(" << A.getID()
<< ") has the good number of component.");
AKANTU_DEBUG_ASSERT(
x.getNbComponent() == n,
"The vector x(" << x.getID() << ") do not the good number of component.");
AKANTU_DEBUG_ASSERT(
y.getNbComponent() == n,
"The vector y(" << y.getID() << ") do not the good number of component.");
UInt nb_element = A.size();
UInt offset_A = A.getNbComponent();
UInt offset_x = x.getNbComponent();
y.resize(nb_element);
Real * A_val = A.storage();
Real * x_val = x.storage();
Real * y_val = y.storage();
for (UInt el = 0; el < nb_element; ++el) {
matrix_vector(m, n, A_val, x_val, y_val, alpha);
A_val += offset_A;
x_val += offset_x;
y_val += offset_x;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Math::matrix_matrix(UInt m, UInt n, UInt k, const Array<Real> & A,
const Array<Real> & B, Array<Real> & C, Real alpha) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(A.size() == B.size(),
"The vector A(" << A.getID() << ") and the vector B("
<< B.getID()
<< ") must have the same size");
AKANTU_DEBUG_ASSERT(A.getNbComponent() == m * k,
"The vector A(" << A.getID()
<< ") has the good number of component.");
AKANTU_DEBUG_ASSERT(
B.getNbComponent() == k * n,
"The vector B(" << B.getID() << ") do not the good number of component.");
AKANTU_DEBUG_ASSERT(
C.getNbComponent() == m * n,
"The vector C(" << C.getID() << ") do not the good number of component.");
UInt nb_element = A.size();
UInt offset_A = A.getNbComponent();
UInt offset_B = B.getNbComponent();
UInt offset_C = C.getNbComponent();
C.resize(nb_element);
Real * A_val = A.storage();
Real * B_val = B.storage();
Real * C_val = C.storage();
for (UInt el = 0; el < nb_element; ++el) {
matrix_matrix(m, n, k, A_val, B_val, C_val, alpha);
A_val += offset_A;
B_val += offset_B;
C_val += offset_C;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Math::matrix_matrixt(UInt m, UInt n, UInt k, const Array<Real> & A,
const Array<Real> & B, Array<Real> & C, Real alpha) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(A.size() == B.size(),
"The vector A(" << A.getID() << ") and the vector B("
<< B.getID()
<< ") must have the same size");
AKANTU_DEBUG_ASSERT(A.getNbComponent() == m * k,
"The vector A(" << A.getID()
<< ") has the good number of component.");
AKANTU_DEBUG_ASSERT(
B.getNbComponent() == k * n,
"The vector B(" << B.getID() << ") do not the good number of component.");
AKANTU_DEBUG_ASSERT(
C.getNbComponent() == m * n,
"The vector C(" << C.getID() << ") do not the good number of component.");
UInt nb_element = A.size();
UInt offset_A = A.getNbComponent();
UInt offset_B = B.getNbComponent();
UInt offset_C = C.getNbComponent();
C.resize(nb_element);
Real * A_val = A.storage();
Real * B_val = B.storage();
Real * C_val = C.storage();
for (UInt el = 0; el < nb_element; ++el) {
matrix_matrixt(m, n, k, A_val, B_val, C_val, alpha);
A_val += offset_A;
B_val += offset_B;
C_val += offset_C;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Math::compute_tangents(const Array<Real> & normals,
Array<Real> & tangents) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = normals.getNbComponent();
UInt tangent_components = spatial_dimension * (spatial_dimension - 1);
AKANTU_DEBUG_ASSERT(
tangent_components == tangents.getNbComponent(),
"Cannot compute the tangents, the storage array for tangents"
<< " does not have the good amount of components.");
UInt nb_normals = normals.size();
tangents.resize(nb_normals);
Real * normal_it = normals.storage();
Real * tangent_it = tangents.storage();
/// compute first tangent
for (UInt q = 0; q < nb_normals; ++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 = tangents.storage();
for (UInt q = 0; q < nb_normals; ++q) {
Math::normal3(normal_it, tangent_it, tangent_it + spatial_dimension);
normal_it += spatial_dimension;
tangent_it += tangent_components;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real Math::reduce(Array<Real> & array) {
UInt nb_values = array.size();
if (nb_values == 0)
return 0.;
UInt nb_values_to_sum = nb_values >> 1;
std::sort(array.begin(), array.end());
// as long as the half is not empty
while (nb_values_to_sum) {
UInt remaining = (nb_values - 2 * nb_values_to_sum);
if (remaining)
array(nb_values - 2) += array(nb_values - 1);
// sum to consecutive values and store the sum in the first half
for (UInt i = 0; i < nb_values_to_sum; ++i) {
array(i) = array(2 * i) + array(2 * i + 1);
}
nb_values = nb_values_to_sum;
nb_values_to_sum >>= 1;
}
return array(0);
}
} // akantu
diff --git a/src/common/aka_math.hh b/src/common/aka_math.hh
index 3a38dfd1a..6973b22b1 100644
--- a/src/common/aka_math.hh
+++ b/src/common/aka_math.hh
@@ -1,292 +1,291 @@
/**
* @file aka_math.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Fri May 15 2015
+ * @date last modification: Mon Sep 11 2017
*
* @brief mathematical operations
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_MATH_H__
#define __AKANTU_AKA_MATH_H__
/* -------------------------------------------------------------------------- */
#include <utility>
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal> class Array;
class Math {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Matrix algebra */
/* ------------------------------------------------------------------------ */
/// @f$ y = A*x @f$
static void matrix_vector(UInt m, UInt n, const Array<Real, true> & A,
const Array<Real, true> & x, Array<Real, true> & y,
Real alpha = 1.);
/// @f$ y = A*x @f$
static inline void matrix_vector(UInt m, UInt n, Real * A, Real * x, Real * y,
Real alpha = 1.);
/// @f$ y = A^t*x @f$
static inline void matrixt_vector(UInt m, UInt n, Real * A, Real * x,
Real * y, Real alpha = 1.);
/// @f$ C = A*B @f$
static void matrix_matrix(UInt m, UInt n, UInt k, const Array<Real, true> & A,
const Array<Real, true> & B, Array<Real, true> & C,
Real alpha = 1.);
/// @f$ C = A*B^t @f$
static void matrix_matrixt(UInt m, UInt n, UInt k,
const Array<Real, true> & A,
const Array<Real, true> & B, Array<Real, true> & C,
Real alpha = 1.);
/// @f$ C = A*B @f$
static inline void matrix_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
/// @f$ C = A^t*B @f$
static inline void matrixt_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
/// @f$ C = A*B^t @f$
static inline void matrix_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
/// @f$ C = A^t*B^t @f$
static inline void matrixt_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
template <bool tr_A, bool tr_B>
static inline void matMul(UInt m, UInt n, UInt k, Real alpha, Real * A,
Real * B, Real beta, Real * C);
template <bool tr_A>
static inline void matVectMul(UInt m, UInt n, Real alpha, Real * A, Real * x,
Real beta, Real * y);
static inline void aXplusY(UInt n, Real alpha, Real * x, Real * y);
static inline void matrix33_eigenvalues(Real * A, Real * Adiag);
static inline void matrix22_eigenvalues(Real * A, Real * Adiag);
template <UInt dim> static inline void eigenvalues(Real * A, Real * d);
/// solve @f$ A x = \Lambda x @f$ and return d and V such as @f$ A V[i:] =
/// d[i] V[i:]@f$
template <typename T>
static void matrixEig(UInt n, T * A, T * d, T * V = nullptr);
/// determinent of a 2x2 matrix
static inline Real det2(const Real * mat);
/// determinent of a 3x3 matrix
static inline Real det3(const Real * mat);
/// determinent of a nxn matrix
template <UInt n> static inline Real det(const Real * mat);
/// determinent of a nxn matrix
template <typename T> static inline T det(UInt n, const T * mat);
/// inverse a nxn matrix
template <UInt n> static inline void inv(const Real * mat, Real * inv);
/// inverse a nxn matrix
template <typename T> static inline void inv(UInt n, const T * mat, T * inv);
/// inverse a 3x3 matrix
static inline void inv3(const Real * mat, Real * inv);
/// inverse a 2x2 matrix
static inline void inv2(const Real * mat, Real * inv);
/// solve A x = b using a LU factorization
template <typename T>
static inline void solve(UInt n, const T * A, T * x, const T * b);
/// return the double dot product between 2 tensors in 2d
static inline Real matrixDoubleDot22(Real * A, Real * B);
/// return the double dot product between 2 tensors in 3d
static inline Real matrixDoubleDot33(Real * A, Real * B);
/// extension of the double dot product to two 2nd order tensor in dimension n
static inline Real matrixDoubleDot(UInt n, Real * A, Real * B);
/* ------------------------------------------------------------------------ */
/* Array algebra */
/* ------------------------------------------------------------------------ */
/// vector cross product
static inline void vectorProduct3(const Real * v1, const Real * v2,
Real * res);
/// normalize a vector
static inline void normalize2(Real * v);
/// normalize a vector
static inline void normalize3(Real * v);
/// return norm of a 2-vector
static inline Real norm2(const Real * v);
/// return norm of a 3-vector
static inline Real norm3(const Real * v);
/// return norm of a vector
static inline Real norm(UInt n, const Real * v);
/// return the dot product between 2 vectors in 2d
static inline Real vectorDot2(const Real * v1, const Real * v2);
/// return the dot product between 2 vectors in 3d
static inline Real vectorDot3(const Real * v1, const Real * v2);
/// return the dot product between 2 vectors
static inline Real vectorDot(Real * v1, Real * v2, UInt n);
/* ------------------------------------------------------------------------ */
/* Geometry */
/* ------------------------------------------------------------------------ */
/// compute normal a normal to a vector
static inline void normal2(const Real * v1, Real * res);
/// compute normal a normal to a vector
static inline void normal3(const Real * v1, const Real * v2, Real * res);
/// compute the tangents to an array of normal vectors
static void compute_tangents(const Array<Real> & normals,
Array<Real> & tangents);
/// distance in 2D between x and y
static inline Real distance_2d(const Real * x, const Real * y);
/// distance in 3D between x and y
static inline Real distance_3d(const Real * x, const Real * y);
/// radius of the in-circle of a triangle
static inline Real triangle_inradius(const Real * coord1, const Real * coord2,
const Real * coord3);
/// radius of the in-circle of a tetrahedron
static inline Real tetrahedron_inradius(const Real * coord1,
const Real * coord2,
const Real * coord3,
const Real * coord4);
/// volume of a tetrahedron
static inline Real tetrahedron_volume(const Real * coord1,
const Real * coord2,
const Real * coord3,
const Real * coord4);
/// compute the barycenter of n points
static inline void barycenter(const Real * coord, UInt nb_points,
UInt spatial_dimension, Real * barycenter);
/// vector between x and y
static inline void vector_2d(const Real * x, const Real * y, Real * vec);
/// vector pointing from x to y in 3 spatial dimension
static inline void vector_3d(const Real * x, const Real * y, Real * vec);
/// test if two scalar are equal within a given tolerance
static inline bool are_float_equal(Real x, Real y);
/// test if two vectors are equal within a given tolerance
static inline bool are_vector_equal(UInt n, Real * x, Real * y);
#ifdef isnan
#error \
"You probably included <math.h> which is incompatible with aka_math please use\
<cmath> or add a \"#undef isnan\" before akantu includes"
#endif
/// test if a real is a NaN
static inline bool isnan(Real x);
/// test if the line x and y intersects each other
static inline bool intersects(Real x_min, Real x_max, Real y_min, Real y_max);
/// test if a is in the range [x_min, x_max]
static inline bool is_in_range(Real a, Real x_min, Real x_max);
static inline Real getTolerance() { return tolerance; };
static inline void setTolerance(Real tol) { tolerance = tol; };
template <UInt p, typename T> static inline T pow(T x);
/// reduce all the values of an array, the summation is done in place and the
/// array is modified
static Real reduce(Array<Real> & array);
class NewtonRaphson {
public:
NewtonRaphson(Real tolerance, Real max_iteration)
: tolerance(tolerance), max_iteration(max_iteration) {}
template <class Functor> Real solve(const Functor & funct, Real x_0);
private:
Real tolerance;
Real max_iteration;
};
struct NewtonRaphsonFunctor {
explicit NewtonRaphsonFunctor(std::string name) : name(std::move(name)) {}
virtual ~NewtonRaphsonFunctor() = default;
virtual Real f(Real x) const = 0;
virtual Real f_prime(Real x) const = 0;
std::string name;
};
private:
/// tolerance for functions that need one
static Real tolerance;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "aka_math_tmpl.hh"
} // akantu
#endif /* __AKANTU_AKA_MATH_H__ */
diff --git a/src/common/aka_math_tmpl.hh b/src/common/aka_math_tmpl.hh
index 2e0bdb5a7..599e21b3b 100644
--- a/src/common/aka_math_tmpl.hh
+++ b/src/common/aka_math_tmpl.hh
@@ -1,784 +1,783 @@
/**
* @file aka_math_tmpl.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Mathilde Radiguet <mathilde.radiguet@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Wed Oct 21 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the inline functions of the math toolkit
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
} // akantu
#include <cmath>
#include <cstring>
#include <typeinfo>
#include "aka_blas_lapack.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void Math::matrix_vector(UInt im, UInt in, Real * A, Real * x, Real * y,
Real alpha) {
#ifdef AKANTU_USE_BLAS
/// y = alpha*op(A)*x + beta*y
char tran_A = 'N';
int incx = 1;
int incy = 1;
double beta = 0.;
int m = im;
int n = in;
aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
#else
memset(y, 0, im * sizeof(Real));
for (UInt i = 0; i < im; ++i) {
for (UInt j = 0; j < in; ++j) {
y[i] += A[i + j * im] * x[j];
}
y[i] *= alpha;
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrixt_vector(UInt im, UInt in, Real * A, Real * x, Real * y,
Real alpha) {
#ifdef AKANTU_USE_BLAS
/// y = alpha*op(A)*x + beta*y
char tran_A = 'T';
int incx = 1;
int incy = 1;
double beta = 0.;
int m = im;
int n = in;
aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
#else
memset(y, 0, in * sizeof(Real));
for (UInt i = 0; i < im; ++i) {
for (UInt j = 0; j < in; ++j) {
y[j] += A[j * im + i] * x[i];
}
y[i] *= alpha;
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrix_matrix(UInt im, UInt in, UInt ik, Real * A, Real * B,
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'N';
char trans_b = 'N';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &k, &beta, C, &m);
#else
memset(C, 0, im * in * sizeof(Real));
for (UInt j = 0; j < in; ++j) {
UInt _jb = j * ik;
UInt _jc = j * im;
for (UInt i = 0; i < im; ++i) {
for (UInt l = 0; l < ik; ++l) {
UInt _la = l * im;
C[i + _jc] += A[i + _la] * B[l + _jb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrixt_matrix(UInt im, UInt in, UInt ik, Real * A, Real * B,
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'T';
char trans_b = 'N';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &k, &beta, C, &m);
#else
memset(C, 0, im * in * sizeof(Real));
for (UInt j = 0; j < in; ++j) {
UInt _jc = j * im;
UInt _jb = j * ik;
for (UInt i = 0; i < im; ++i) {
UInt _ia = i * ik;
for (UInt l = 0; l < ik; ++l) {
C[i + _jc] += A[l + _ia] * B[l + _jb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrix_matrixt(UInt im, UInt in, UInt ik, Real * A, Real * B,
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'N';
char trans_b = 'T';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &n, &beta, C, &m);
#else
memset(C, 0, im * in * sizeof(Real));
for (UInt j = 0; j < in; ++j) {
UInt _jc = j * im;
for (UInt i = 0; i < im; ++i) {
for (UInt l = 0; l < ik; ++l) {
UInt _la = l * im;
UInt _lb = l * in;
C[i + _jc] += A[i + _la] * B[j + _lb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrixt_matrixt(UInt im, UInt in, UInt ik, Real * A, Real * B,
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'T';
char trans_b = 'T';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &n, &beta, C, &m);
#else
memset(C, 0, im * in * sizeof(Real));
for (UInt j = 0; j < in; ++j) {
UInt _jc = j * im;
for (UInt i = 0; i < im; ++i) {
UInt _ia = i * ik;
for (UInt l = 0; l < ik; ++l) {
UInt _lb = l * in;
C[i + _jc] += A[l + _ia] * B[j + _lb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::aXplusY(UInt n, Real alpha, Real * x, Real * y) {
#ifdef AKANTU_USE_BLAS
/// y := alpha x + y
int incx = 1, incy = 1;
aka_axpy(&n, &alpha, x, &incx, y, &incy);
#else
for (UInt i = 0; i < n; ++i)
*(y++) += alpha * *(x++);
#endif
}
/* -------------------------------------------------------------------------- */
inline Real Math::vectorDot(Real * v1, Real * v2, UInt in) {
#ifdef AKANTU_USE_BLAS
/// d := v1 . v2
int incx = 1, incy = 1, n = in;
Real d = aka_dot(&n, v1, &incx, v2, &incy);
#else
Real d = 0;
for (UInt i = 0; i < in; ++i) {
d += v1[i] * v2[i];
}
#endif
return d;
}
/* -------------------------------------------------------------------------- */
template <bool tr_A, bool tr_B>
inline void Math::matMul(UInt m, UInt n, UInt k, Real alpha, Real * A, Real * B,
__attribute__((unused)) Real beta, Real * C) {
if (tr_A) {
if (tr_B)
matrixt_matrixt(m, n, k, A, B, C, alpha);
else
matrixt_matrix(m, n, k, A, B, C, alpha);
} else {
if (tr_B)
matrix_matrixt(m, n, k, A, B, C, alpha);
else
matrix_matrix(m, n, k, A, B, C, alpha);
}
}
/* -------------------------------------------------------------------------- */
template <bool tr_A>
inline void Math::matVectMul(UInt m, UInt n, Real alpha, Real * A, Real * x,
__attribute__((unused)) Real beta, Real * y) {
if (tr_A) {
matrixt_vector(m, n, A, x, y, alpha);
} else {
matrix_vector(m, n, A, x, y, alpha);
}
}
/* -------------------------------------------------------------------------- */
template <typename T> inline void Math::matrixEig(UInt n, T * A, T * d, T * V) {
// Matrix A is row major, so the lapack function in fortran will process
// A^t. Asking for the left eigenvectors of A^t will give the transposed right
// eigenvectors of A so in the C++ code the right eigenvectors.
char jobvr, jobvl;
if (V != nullptr)
jobvr = 'V'; // compute left eigenvectors
else
jobvr = 'N'; // compute left eigenvectors
jobvl = 'N'; // compute right eigenvectors
auto * di = new T[n]; // imaginary part of the eigenvalues
int info;
int N = n;
T wkopt;
int lwork = -1;
// query and allocate the optimal workspace
aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, nullptr, &N, V, &N, &wkopt,
&lwork, &info);
lwork = int(wkopt);
auto * work = new T[lwork];
// solve the eigenproblem
aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, nullptr, &N, V, &N, work,
&lwork, &info);
AKANTU_DEBUG_ASSERT(
info == 0,
"Problem computing eigenvalues/vectors. DGEEV exited with the value "
<< info);
delete[] work;
delete[] di; // I hope for you that there was no complex eigenvalues !!!
}
/* -------------------------------------------------------------------------- */
inline void Math::matrix22_eigenvalues(Real * A, Real * Adiag) {
/// d = determinant of Matrix A
Real d = det2(A);
/// b = trace of Matrix A
Real b = A[0] + A[3];
Real c = sqrt(b * b - 4 * d);
Adiag[0] = .5 * (b + c);
Adiag[1] = .5 * (b - c);
}
/* -------------------------------------------------------------------------- */
inline void Math::matrix33_eigenvalues(Real * A, Real * Adiag) {
matrixEig(3, A, Adiag);
}
/* -------------------------------------------------------------------------- */
template <UInt dim> inline void Math::eigenvalues(Real * A, Real * d) {
if (dim == 1) {
d[0] = A[0];
} else if (dim == 2) {
matrix22_eigenvalues(A, d);
}
// else if(dim == 3) { matrix33_eigenvalues(A, d); }
else
matrixEig(dim, A, d);
}
/* -------------------------------------------------------------------------- */
inline Real Math::det2(const Real * mat) {
return mat[0] * mat[3] - mat[1] * mat[2];
}
/* -------------------------------------------------------------------------- */
inline Real Math::det3(const Real * mat) {
return mat[0] * (mat[4] * mat[8] - mat[7] * mat[5]) -
mat[3] * (mat[1] * mat[8] - mat[7] * mat[2]) +
mat[6] * (mat[1] * mat[5] - mat[4] * mat[2]);
}
/* -------------------------------------------------------------------------- */
template <UInt n> inline Real Math::det(const Real * mat) {
if (n == 1)
return *mat;
else if (n == 2)
return det2(mat);
else if (n == 3)
return det3(mat);
else
return det(n, mat);
}
/* -------------------------------------------------------------------------- */
template <typename T> inline T Math::det(UInt n, const T * A) {
int N = n;
int info;
auto * ipiv = new int[N + 1];
auto * LU = new T[N * N];
std::copy(A, A + N * N, LU);
// LU factorization of A
aka_getrf(&N, &N, LU, &N, ipiv, &info);
if (info > 0) {
AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
<< " )");
}
// det(A) = det(L) * det(U) = 1 * det(U) = product_i U_{ii}
T det = 1.;
for (int i = 0; i < N; ++i)
det *= (2 * (ipiv[i] == i) - 1) * LU[i * n + i];
delete[] ipiv;
delete[] LU;
return det;
}
/* -------------------------------------------------------------------------- */
inline void Math::normal2(const Real * vec, Real * normal) {
normal[0] = vec[1];
normal[1] = -vec[0];
Math::normalize2(normal);
}
/* -------------------------------------------------------------------------- */
inline void Math::normal3(const Real * vec1, const Real * vec2, Real * normal) {
Math::vectorProduct3(vec1, vec2, normal);
Math::normalize3(normal);
}
/* -------------------------------------------------------------------------- */
inline void Math::normalize2(Real * vec) {
Real norm = Math::norm2(vec);
vec[0] /= norm;
vec[1] /= norm;
}
/* -------------------------------------------------------------------------- */
inline void Math::normalize3(Real * vec) {
Real norm = Math::norm3(vec);
vec[0] /= norm;
vec[1] /= norm;
vec[2] /= norm;
}
/* -------------------------------------------------------------------------- */
inline Real Math::norm2(const Real * vec) {
return sqrt(vec[0] * vec[0] + vec[1] * vec[1]);
}
/* -------------------------------------------------------------------------- */
inline Real Math::norm3(const Real * vec) {
return sqrt(vec[0] * vec[0] + vec[1] * vec[1] + vec[2] * vec[2]);
}
/* -------------------------------------------------------------------------- */
inline Real Math::norm(UInt n, const Real * vec) {
Real norm = 0.;
for (UInt i = 0; i < n; ++i) {
norm += vec[i] * vec[i];
}
return sqrt(norm);
}
/* -------------------------------------------------------------------------- */
inline void Math::inv2(const Real * mat, Real * inv) {
Real det_mat = det2(mat);
inv[0] = mat[3] / det_mat;
inv[1] = -mat[1] / det_mat;
inv[2] = -mat[2] / det_mat;
inv[3] = mat[0] / det_mat;
}
/* -------------------------------------------------------------------------- */
inline void Math::inv3(const Real * mat, Real * inv) {
Real det_mat = det3(mat);
inv[0] = (mat[4] * mat[8] - mat[7] * mat[5]) / det_mat;
inv[1] = (mat[2] * mat[7] - mat[8] * mat[1]) / det_mat;
inv[2] = (mat[1] * mat[5] - mat[4] * mat[2]) / det_mat;
inv[3] = (mat[5] * mat[6] - mat[8] * mat[3]) / det_mat;
inv[4] = (mat[0] * mat[8] - mat[6] * mat[2]) / det_mat;
inv[5] = (mat[2] * mat[3] - mat[5] * mat[0]) / det_mat;
inv[6] = (mat[3] * mat[7] - mat[6] * mat[4]) / det_mat;
inv[7] = (mat[1] * mat[6] - mat[7] * mat[0]) / det_mat;
inv[8] = (mat[0] * mat[4] - mat[3] * mat[1]) / det_mat;
}
/* -------------------------------------------------------------------------- */
template <UInt n> inline void Math::inv(const Real * A, Real * Ainv) {
if (n == 1)
*Ainv = 1. / *A;
else if (n == 2)
inv2(A, Ainv);
else if (n == 3)
inv3(A, Ainv);
else
inv(n, A, Ainv);
}
/* -------------------------------------------------------------------------- */
template <typename T> inline void Math::inv(UInt n, const T * A, T * invA) {
int N = n;
int info;
auto * ipiv = new int[N + 1];
int lwork = N * N;
auto * work = new T[lwork];
std::copy(A, A + n * n, invA);
aka_getrf(&N, &N, invA, &N, ipiv, &info);
if (info > 0) {
AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
<< " )");
}
aka_getri(&N, invA, &N, ipiv, work, &lwork, &info);
if (info != 0) {
AKANTU_ERROR("Cannot invert the matrix (info: " << info << " )");
}
delete[] ipiv;
delete[] work;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Math::solve(UInt n, const T * A, T * x, const T * b) {
int N = n;
int info;
auto * ipiv = new int[N];
auto * lu_A = new T[N * N];
std::copy(A, A + N * N, lu_A);
aka_getrf(&N, &N, lu_A, &N, ipiv, &info);
if (info > 0) {
AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
<< " )");
}
char trans = 'N';
int nrhs = 1;
std::copy(b, b + N, x);
aka_getrs(&trans, &N, &nrhs, lu_A, &N, ipiv, x, &N, &info);
if (info != 0) {
AKANTU_ERROR("Cannot solve the system (info: " << info << " )");
}
delete[] ipiv;
delete[] lu_A;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
inline Real Math::matrixDoubleDot22(Real * A, Real * B) {
Real d;
d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3];
return d;
}
/* -------------------------------------------------------------------------- */
inline Real Math::matrixDoubleDot33(Real * A, Real * B) {
Real d;
d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3] + A[4] * B[4] +
A[5] * B[5] + A[6] * B[6] + A[7] * B[7] + A[8] * B[8];
return d;
}
/* -------------------------------------------------------------------------- */
inline Real Math::matrixDoubleDot(UInt n, Real * A, Real * B) {
Real d = 0.;
for (UInt i = 0; i < n; ++i) {
for (UInt j = 0; j < n; ++j) {
d += A[i * n + j] * B[i * n + j];
}
}
return d;
}
/* -------------------------------------------------------------------------- */
inline void Math::vectorProduct3(const Real * v1, const Real * v2, Real * res) {
res[0] = v1[1] * v2[2] - v1[2] * v2[1];
res[1] = v1[2] * v2[0] - v1[0] * v2[2];
res[2] = v1[0] * v2[1] - v1[1] * v2[0];
}
/* -------------------------------------------------------------------------- */
inline Real Math::vectorDot2(const Real * v1, const Real * v2) {
return (v1[0] * v2[0] + v1[1] * v2[1]);
}
/* -------------------------------------------------------------------------- */
inline Real Math::vectorDot3(const Real * v1, const Real * v2) {
return (v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2]);
}
/* -------------------------------------------------------------------------- */
inline Real Math::distance_2d(const Real * x, const Real * y) {
return sqrt((y[0] - x[0]) * (y[0] - x[0]) + (y[1] - x[1]) * (y[1] - x[1]));
}
/* -------------------------------------------------------------------------- */
inline Real Math::triangle_inradius(const Real * coord1, const Real * coord2,
const Real * coord3) {
/**
* @f{eqnarray*}{
* r &=& A / s \\
* A &=& 1/4 * \sqrt{(a + b + c) * (a - b + c) * (a + b - c) (-a + b + c)} \\
* s &=& \frac{a + b + c}{2}
* @f}
*/
Real a, b, c;
a = distance_2d(coord1, coord2);
b = distance_2d(coord2, coord3);
c = distance_2d(coord1, coord3);
Real s;
s = (a + b + c) * 0.5;
return sqrt((s - a) * (s - b) * (s - c) / s);
}
/* -------------------------------------------------------------------------- */
inline Real Math::distance_3d(const Real * x, const Real * y) {
return sqrt((y[0] - x[0]) * (y[0] - x[0]) + (y[1] - x[1]) * (y[1] - x[1]) +
(y[2] - x[2]) * (y[2] - x[2]));
}
/* -------------------------------------------------------------------------- */
inline Real Math::tetrahedron_volume(const Real * coord1, const Real * coord2,
const Real * coord3, const Real * coord4) {
Real xx[9], vol;
xx[0] = coord2[0];
xx[1] = coord2[1];
xx[2] = coord2[2];
xx[3] = coord3[0];
xx[4] = coord3[1];
xx[5] = coord3[2];
xx[6] = coord4[0];
xx[7] = coord4[1];
xx[8] = coord4[2];
vol = det3(xx);
xx[0] = coord1[0];
xx[1] = coord1[1];
xx[2] = coord1[2];
xx[3] = coord3[0];
xx[4] = coord3[1];
xx[5] = coord3[2];
xx[6] = coord4[0];
xx[7] = coord4[1];
xx[8] = coord4[2];
vol -= det3(xx);
xx[0] = coord1[0];
xx[1] = coord1[1];
xx[2] = coord1[2];
xx[3] = coord2[0];
xx[4] = coord2[1];
xx[5] = coord2[2];
xx[6] = coord4[0];
xx[7] = coord4[1];
xx[8] = coord4[2];
vol += det3(xx);
xx[0] = coord1[0];
xx[1] = coord1[1];
xx[2] = coord1[2];
xx[3] = coord2[0];
xx[4] = coord2[1];
xx[5] = coord2[2];
xx[6] = coord3[0];
xx[7] = coord3[1];
xx[8] = coord3[2];
vol -= det3(xx);
vol /= 6;
return vol;
}
/* -------------------------------------------------------------------------- */
inline Real Math::tetrahedron_inradius(const Real * coord1, const Real * coord2,
const Real * coord3,
const Real * coord4) {
Real l12, l13, l14, l23, l24, l34;
l12 = distance_3d(coord1, coord2);
l13 = distance_3d(coord1, coord3);
l14 = distance_3d(coord1, coord4);
l23 = distance_3d(coord2, coord3);
l24 = distance_3d(coord2, coord4);
l34 = distance_3d(coord3, coord4);
Real s1, s2, s3, s4;
s1 = (l12 + l23 + l13) * 0.5;
s1 = sqrt(s1 * (s1 - l12) * (s1 - l23) * (s1 - l13));
s2 = (l12 + l24 + l14) * 0.5;
s2 = sqrt(s2 * (s2 - l12) * (s2 - l24) * (s2 - l14));
s3 = (l23 + l34 + l24) * 0.5;
s3 = sqrt(s3 * (s3 - l23) * (s3 - l34) * (s3 - l24));
s4 = (l13 + l34 + l14) * 0.5;
s4 = sqrt(s4 * (s4 - l13) * (s4 - l34) * (s4 - l14));
Real volume = Math::tetrahedron_volume(coord1, coord2, coord3, coord4);
return 3 * volume / (s1 + s2 + s3 + s4);
}
/* -------------------------------------------------------------------------- */
inline void Math::barycenter(const Real * coord, UInt nb_points,
UInt spatial_dimension, Real * barycenter) {
memset(barycenter, 0, spatial_dimension * sizeof(Real));
for (UInt n = 0; n < nb_points; ++n) {
UInt offset = n * spatial_dimension;
for (UInt i = 0; i < spatial_dimension; ++i) {
barycenter[i] += coord[offset + i] / (Real)nb_points;
}
}
}
/* -------------------------------------------------------------------------- */
inline void Math::vector_2d(const Real * x, const Real * y, Real * res) {
res[0] = y[0] - x[0];
res[1] = y[1] - x[1];
}
/* -------------------------------------------------------------------------- */
inline void Math::vector_3d(const Real * x, const Real * y, Real * res) {
res[0] = y[0] - x[0];
res[1] = y[1] - x[1];
res[2] = y[2] - x[2];
}
/* -------------------------------------------------------------------------- */
/// Combined absolute and relative tolerance test proposed in
/// Real-time collision detection by C. Ericson (2004)
inline bool Math::are_float_equal(const Real x, const Real y) {
Real abs_max = std::max(std::abs(x), std::abs(y));
abs_max = std::max(abs_max, Real(1.));
return std::abs(x - y) <= (tolerance * abs_max);
}
/* -------------------------------------------------------------------------- */
inline bool Math::isnan(Real x) {
#if defined(__INTEL_COMPILER)
#pragma warning(push)
#pragma warning(disable : 1572)
#endif // defined(__INTEL_COMPILER)
// x = x return false means x = quiet_NaN
return !(x == x);
#if defined(__INTEL_COMPILER)
#pragma warning(pop)
#endif // defined(__INTEL_COMPILER)
}
/* -------------------------------------------------------------------------- */
inline bool Math::are_vector_equal(UInt n, Real * x, Real * y) {
bool test = true;
for (UInt i = 0; i < n; ++i) {
test &= are_float_equal(x[i], y[i]);
}
return test;
}
/* -------------------------------------------------------------------------- */
inline bool Math::intersects(Real x_min, Real x_max, Real y_min, Real y_max) {
return !((x_max <= y_min) || (x_min >= y_max));
}
/* -------------------------------------------------------------------------- */
inline bool Math::is_in_range(Real a, Real x_min, Real x_max) {
return ((a >= x_min) && (a <= x_max));
}
/* -------------------------------------------------------------------------- */
template <UInt p, typename T> inline T Math::pow(T x) {
return (pow<p - 1, T>(x) * x);
}
template <> inline UInt Math::pow<0, UInt>(__attribute__((unused)) UInt x) {
return (1);
}
template <> inline Real Math::pow<0, Real>(__attribute__((unused)) Real x) {
return (1.);
}
/* -------------------------------------------------------------------------- */
template <class Functor>
Real Math::NewtonRaphson::solve(const Functor & funct, Real x_0) {
Real x = x_0;
Real f_x = funct.f(x);
UInt iter = 0;
while (std::abs(f_x) > this->tolerance && iter < this->max_iteration) {
x -= f_x / funct.f_prime(x);
f_x = funct.f(x);
iter++;
}
AKANTU_DEBUG_ASSERT(iter < this->max_iteration,
"Newton Raphson ("
<< funct.name << ") solve did not converge in "
<< this->max_iteration << " iterations (tolerance: "
<< this->tolerance << ")");
return x;
}
diff --git a/src/common/aka_memory.cc b/src/common/aka_memory.cc
index 006134ced..ed6c70903 100644
--- a/src/common/aka_memory.cc
+++ b/src/common/aka_memory.cc
@@ -1,64 +1,63 @@
/**
* @file aka_memory.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief static memory wrapper
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <utility>
#include "aka_memory.hh"
#include "aka_static_memory.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Memory::Memory(ID id, MemoryID memory_id)
: static_memory(StaticMemory::getStaticMemory()), id(std::move(id)),
memory_id(memory_id) {}
/* -------------------------------------------------------------------------- */
Memory::~Memory() {
if (StaticMemory::isInstantiated()) {
std::list<ID>::iterator it;
for (it = handeld_vectors_id.begin(); it != handeld_vectors_id.end();
++it) {
AKANTU_DEBUG(dblAccessory, "Deleting the vector " << *it);
static_memory.sfree(memory_id, *it);
}
static_memory.destroy();
}
handeld_vectors_id.clear();
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/common/aka_memory.hh b/src/common/aka_memory.hh
index a5db23abb..d2e030a1e 100644
--- a/src/common/aka_memory.hh
+++ b/src/common/aka_memory.hh
@@ -1,115 +1,114 @@
/**
* @file aka_memory.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief wrapper for the static_memory, all object which wants
* to access the static_memory as to inherit from the class memory
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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_MEMORY_HH__
#define __AKANTU_MEMORY_HH__
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_static_memory.hh"
/* -------------------------------------------------------------------------- */
#include <list>
/* -------------------------------------------------------------------------- */
namespace akantu {
class Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
protected:
Memory(ID id, MemoryID memory_id = 0);
virtual ~Memory();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// malloc
template <class T>
inline Array<T> & alloc(const ID & name, UInt size, UInt nb_component);
/// malloc
template <class T>
inline Array<T> & alloc(const ID & name, UInt size, UInt nb_component,
const T & init_value);
/* ------------------------------------------------------------------------ */
/// free an array
inline void dealloc(const ID & name);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
template <typename T> inline Array<T> & getArray(const ID & name);
template <typename T> inline const Array<T> & getArray(const ID & name) const;
public:
AKANTU_GET_MACRO(MemoryID, memory_id, const MemoryID &);
AKANTU_GET_MACRO(ID, id, const ID &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the static memory instance
StaticMemory & static_memory;
/// list of allocated vectors id
std::list<ID> handeld_vectors_id;
protected:
ID id;
/// the id registred in the static memory
MemoryID memory_id;
};
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "aka_memory_inline_impl.cc"
#endif
} // akantu
#endif /* __AKANTU_MEMORY_HH__ */
diff --git a/src/common/aka_memory_inline_impl.cc b/src/common/aka_memory_inline_impl.cc
index eec8da71a..70cb0e538 100644
--- a/src/common/aka_memory_inline_impl.cc
+++ b/src/common/aka_memory_inline_impl.cc
@@ -1,66 +1,65 @@
/**
* @file aka_memory_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the inline functions of the class Memory
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 <class T>
inline Array<T> & Memory::alloc(const ID & name, UInt size, UInt nb_component) {
handeld_vectors_id.push_back(name);
return static_memory.smalloc<T>(memory_id, name, size, nb_component);
}
/* -------------------------------------------------------------------------- */
template <class T>
inline Array<T> & Memory::alloc(const ID & name, UInt size, UInt nb_component,
const T & init_value) {
handeld_vectors_id.push_back(name);
return static_memory.smalloc<T>(memory_id, name, size, nb_component,
init_value);
}
/* -------------------------------------------------------------------------- */
inline void Memory::dealloc(const ID & name) {
AKANTU_DEBUG(dblAccessory, "Deleting the vector " << name);
static_memory.sfree(memory_id, name);
handeld_vectors_id.remove(name);
}
/* -------------------------------------------------------------------------- */
template <class T> inline Array<T> & Memory::getArray(const ID & name) {
return static_cast<Array<T> &>(
const_cast<ArrayBase &>(static_memory.getArray(memory_id, name)));
}
/* -------------------------------------------------------------------------- */
template <class T>
inline const Array<T> & Memory::getArray(const ID & name) const {
return static_cast<Array<T> &>(
const_cast<ArrayBase &>(static_memory.getArray(memory_id, name)));
}
diff --git a/src/common/aka_named_argument.hh b/src/common/aka_named_argument.hh
index 2f8f8f3d7..53a366d15 100644
--- a/src/common/aka_named_argument.hh
+++ b/src/common/aka_named_argument.hh
@@ -1,164 +1,194 @@
+/**
+ * @file aka_named_argument.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Fri Jun 16 2017
+ * @date last modification: Wed Dec 06 2017
+ *
+ * @brief tool to use named arguments in functions
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/**
* @file aka_named_argument.hh
*
* @author Marco Arena
*
* @date creation Fri Jun 16 2017
*
* @brief A Documented file.
*
* @section LICENSE
*
* Public Domain ? https://gist.github.com/ilpropheta/7576dce4c3249df89f85
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_compatibilty_with_cpp_standard.hh"
/* -------------------------------------------------------------------------- */
#include <tuple>
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_NAMED_ARGUMENT_HH__
#define __AKANTU_AKA_NAMED_ARGUMENT_HH__
namespace akantu {
namespace named_argument {
struct param_t_trait {};
/* -- Pack utils (proxy version) ------------------------------------------ */
/// Proxy containing [tag, value]
template <typename tag, typename type> struct param_t : param_t_trait {
using _tag = tag;
using _type = type;
template <typename T>
explicit param_t(T && value) : _value(std::forward<T>(value)) {}
type _value;
};
/*
* Tagged proxy that allows syntax _name = value
* operator=(T&&) returns a param_t instance
**/
template <typename tag> struct param_proxy {
using _tag = tag;
template <typename T> decltype(auto) operator=(T && value) {
return param_t<tag, decltype(value)>{std::forward<T>(value)};
}
};
/* Same as type_at but it's supposed to be used by passing
a pack of param_t (_tag is looked for instead of a
plain type). This and type_at should be refactored.
*/
template <typename T, typename head, typename... tail> struct type_at_p {
enum {
_tmp = (std::is_same<T, typename std::decay_t<head>::_tag>::value)
? 0
: type_at_p<T, tail...>::_pos
};
enum { _pos = _tmp == -1 ? -1 : 1 + _tmp };
};
template <typename T, typename head> struct type_at_p<T, head> {
enum {
_pos =
(std::is_same<T, typename std::decay<head>::type::_tag>::value ? 1
: -1)
};
};
template <typename... Ts> struct type_at {
enum { _pos = -1 };
};
template <typename T, typename head, typename... tail>
struct type_at<T, head, tail...> {
enum { _tmp = type_at_p<T, head, tail...>::_pos };
enum { _pos = _tmp == 1 ? 0 : (_tmp == -1 ? -1 : _tmp - 1) };
};
/* Same as get_at but it's supposed to be used by passing
a pack of param_t (_type is retrieved instead)
This and get_at should be refactored.
*/
template <int pos, int curr> struct get_at {
static_assert(pos >= 0, "Required parameter");
template <typename head, typename... tail>
static decltype(auto) get(head &&, tail &&... t) {
return get_at<pos, curr + 1>::get(std::forward<tail>(t)...);
}
};
template <int pos> struct get_at<pos, pos> {
static_assert(pos >= 0, "Required parameter");
template <typename head, typename... tail>
static decltype(auto) get(head && h, tail &&...) {
return std::forward<decltype(h._value)>(h._value);
}
};
// Optional version
template <int pos, int curr> struct get_optional {
template <typename T, typename... pack>
static decltype(auto) get(T &&, pack &&... _pack) {
return get_at<pos, curr>::get(std::forward<pack>(_pack)...);
}
};
template <int curr> struct get_optional<-1, curr> {
template <typename T, typename... pack>
static decltype(auto) get(T && _default, pack &&...) {
return std::forward<T>(_default);
}
};
} // namespace named_argument
// CONVENIENCE MACROS FOR CLASS DESIGNERS ==========
#define TAG_OF_ARGUMENT(_name) p_##_name
#define TAG_OF_ARGUMENT_WNS(_name) TAG_OF_ARGUMENT(_name)
#define REQUIRED_NAMED_ARG(_name) \
named_argument::get_at< \
named_argument::type_at<TAG_OF_ARGUMENT_WNS(_name), pack...>::_pos, \
0>::get(std::forward<pack>(_pack)...)
#define REQUIRED_NAMED_ARG(_name) \
named_argument::get_at< \
named_argument::type_at<TAG_OF_ARGUMENT_WNS(_name), pack...>::_pos, \
0>::get(std::forward<pack>(_pack)...)
#define OPTIONAL_NAMED_ARG(_name, _defaultVal) \
named_argument::get_optional< \
named_argument::type_at<TAG_OF_ARGUMENT_WNS(_name), pack...>::_pos, \
0>::get(_defaultVal, std::forward<pack>(_pack)...)
#define DECLARE_NAMED_ARGUMENT(name) \
struct TAG_OF_ARGUMENT(name) {}; \
named_argument::param_proxy<TAG_OF_ARGUMENT_WNS(name)> _##name \
__attribute__((unused))
namespace {
struct use_named_args_t {};
use_named_args_t use_named_args __attribute__((unused));
} // namespace
template <typename T> struct is_named_argument : public std::false_type {};
template <typename... type>
struct is_named_argument<named_argument::param_t<type...>>
: public std::true_type {};
template <typename... pack>
using are_named_argument =
aka::conjunction<is_named_argument<std::decay_t<pack>>...>;
} // namespace akantu
#endif /* __AKANTU_AKA_NAMED_ARGUMENT_HH__ */
diff --git a/src/common/aka_random_generator.hh b/src/common/aka_random_generator.hh
index 7cda1a505..5bbb5a501 100644
--- a/src/common/aka_random_generator.hh
+++ b/src/common/aka_random_generator.hh
@@ -1,268 +1,268 @@
/**
* @file aka_random_generator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Wed Nov 11 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief generic random generator
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <random>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_RANDOM_GENERATOR_HH__
#define __AKANTU_AKA_RANDOM_GENERATOR_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* List of available distributions */
/* -------------------------------------------------------------------------- */
// clang-format off
#define AKANTU_RANDOM_DISTRIBUTION_TYPES \
((uniform , std::uniform_real_distribution )) \
((exponential , std::exponential_distribution )) \
((gamma , std::gamma_distribution )) \
((weibull , std::weibull_distribution )) \
((extreme_value, std::extreme_value_distribution)) \
((normal , std::normal_distribution )) \
((lognormal , std::lognormal_distribution )) \
((chi_squared , std::chi_squared_distribution )) \
((cauchy , std::cauchy_distribution )) \
((fisher_f , std::fisher_f_distribution )) \
((student_t , std::student_t_distribution ))
// clang-format on
#define AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(elem) BOOST_PP_CAT(_rdt_, elem)
#define AKANTU_RANDOM_DISTRIBUTION_PREFIX(s, data, elem) \
AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(BOOST_PP_TUPLE_ELEM(2, 0, elem))
enum RandomDistributionType {
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_RANDOM_DISTRIBUTION_PREFIX, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)),
_rdt_not_defined
};
/* -------------------------------------------------------------------------- */
/* Generator */
/* -------------------------------------------------------------------------- */
template <typename T> class RandomGenerator {
/* ------------------------------------------------------------------------ */
public:
inline T operator()() { return generator(); }
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int) const {
stream << "RandGenerator [seed=" << _seed << "]";
}
/* ------------------------------------------------------------------------ */
public:
static void seed(long int s) {
_seed = s;
generator.seed(_seed);
}
static long int seed() { return _seed; }
static constexpr T min() { return generator.min(); }
static constexpr T max() { return generator.max(); }
/* ------------------------------------------------------------------------ */
private:
static long int _seed;
static std::default_random_engine generator;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#undef AKANTU_RANDOM_DISTRIBUTION_PREFIX
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE(r, data, elem) \
case AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem)): { \
stream << BOOST_PP_STRINGIZE(AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem))); \
break; \
}
inline std::ostream & operator<<(std::ostream & stream,
RandomDistributionType type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
default:
stream << UInt(type) << " not a RandomDistributionType";
break;
}
return stream;
}
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE
/* -------------------------------------------------------------------------- */
/* Some Helper */
/* -------------------------------------------------------------------------- */
template <typename T, class Distribution> class RandomDistributionTypeHelper {
enum { value = _rdt_not_defined };
};
/* -------------------------------------------------------------------------- */
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE(r, data, elem) \
template <typename T> \
struct RandomDistributionTypeHelper< \
T, BOOST_PP_TUPLE_ELEM(2, 1, elem) < T>> { \
enum { \
value = AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem)) \
}; \
\
static void printself(std::ostream & stream) { \
stream << BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 0, elem)); \
} \
};
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE
/* -------------------------------------------------------------------------- */
template <class T> class RandomDistribution {
public:
virtual ~RandomDistribution() = default;
virtual T operator()(RandomGenerator<UInt> & gen) = 0;
virtual std::unique_ptr<RandomDistribution<T>> make_unique() const = 0;
virtual void printself(std::ostream & stream, int = 0) const = 0;
};
template <class T, class Distribution>
class RandomDistributionProxy : public RandomDistribution<T> {
public:
explicit RandomDistributionProxy(Distribution dist)
: distribution(std::move(dist)) {}
T operator()(RandomGenerator<UInt> & gen) override {
return distribution(gen);
}
std::unique_ptr<RandomDistribution<T>> make_unique() const override {
return std::make_unique<RandomDistributionProxy<T, Distribution>>(
distribution);
}
void printself(std::ostream & stream, int = 0) const override {
RandomDistributionTypeHelper<T, Distribution>::printself(stream);
stream << " [ " << distribution << " ]";
}
private:
Distribution distribution;
};
/* -------------------------------------------------------------------------- */
/* RandomParameter */
/* -------------------------------------------------------------------------- */
template <typename T> class RandomParameter {
public:
template <class Distribution>
explicit RandomParameter(T base_value, Distribution dist)
: base_value(base_value),
type(RandomDistributionType(
RandomDistributionTypeHelper<T, Distribution>::value)),
distribution_proxy(
std::make_unique<RandomDistributionProxy<T, Distribution>>(
std::move(dist))) {}
explicit RandomParameter(T base_value)
: base_value(base_value),
type(RandomDistributionType(
RandomDistributionTypeHelper<
T, std::uniform_real_distribution<T>>::value)),
distribution_proxy(
std::make_unique<
RandomDistributionProxy<T, std::uniform_real_distribution<T>>>(
std::uniform_real_distribution<T>(0., 0.))) {}
RandomParameter(const RandomParameter & other)
: base_value(other.base_value), type(other.type),
distribution_proxy(other.distribution_proxy->make_unique()) {}
RandomParameter & operator=(const RandomParameter & other) {
distribution_proxy = other.distribution_proxy->make_unique();
base_value = other.base_value;
type = other.type;
return *this;
}
virtual ~RandomParameter() = default;
inline void setBaseValue(const T & value) { this->base_value = value; }
inline T getBaseValue() const { return this->base_value; }
template <template <typename> class Generator, class iterator>
void setValues(iterator it, iterator end) {
RandomGenerator<UInt> gen;
for (; it != end; ++it)
*it = this->base_value + (*distribution_proxy)(gen);
}
virtual void printself(std::ostream & stream,
__attribute__((unused)) int indent = 0) const {
stream << base_value;
stream << " + " << *distribution_proxy;
}
private:
/// Value with no random variations
T base_value;
/// Random distribution type
RandomDistributionType type;
/// Proxy to store a std random distribution
std::unique_ptr<RandomDistribution<T>> distribution_proxy;
};
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
RandomDistribution<T> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
RandomParameter<T> & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#endif /* __AKANTU_AKA_RANDOM_GENERATOR_HH__ */
diff --git a/src/common/aka_safe_enum.hh b/src/common/aka_safe_enum.hh
index b27885dd1..2fd2a57bb 100644
--- a/src/common/aka_safe_enum.hh
+++ b/src/common/aka_safe_enum.hh
@@ -1,86 +1,86 @@
/**
* @file aka_safe_enum.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Tue Nov 07 2017
*
* @brief Safe enums type (see More C++ Idioms/Type Safe Enum on Wikibooks
* http://en.wikibooks.org/wiki/More_C%2B%2B_Idioms/Type_Safe_Enum)
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_SAFE_ENUM_HH__
#define __AKANTU_AKA_SAFE_ENUM_HH__
namespace akantu {
/// Safe enumerated type
template <typename def, typename inner = typename def::type>
class safe_enum : public def {
using type = typename def::type;
public:
explicit safe_enum(type v = def::_end_) : val(v) {}
safe_enum(safe_enum && other) = default;
safe_enum & operator=(safe_enum && other) = default;
inner underlying() const { return val; }
bool operator==(const safe_enum & s) const { return this->val == s.val; }
bool operator!=(const safe_enum & s) const { return this->val != s.val; }
bool operator<(const safe_enum & s) const { return this->val < s.val; }
bool operator<=(const safe_enum & s) const { return this->val <= s.val; }
bool operator>(const safe_enum & s) const { return this->val > s.val; }
bool operator>=(const safe_enum & s) const { return this->val >= s.val; }
operator inner() { return val; };
public:
// Works only if enumerations are contiguous.
class iterator {
public:
explicit iterator(type v) : it(v) {}
iterator & operator++() {
++it;
return *this;
}
safe_enum operator*() { return safe_enum(static_cast<type>(it)); }
bool operator!=(iterator const & it) { return it.it != this->it; }
private:
int it;
};
static iterator begin() { return iterator(def::_begin_); }
static iterator end() { return iterator(def::_end_); }
protected:
inner val;
};
} // akantu
#endif /* __AKANTU_AKA_SAFE_ENUM_HH__ */
diff --git a/src/common/aka_static_if.hh b/src/common/aka_static_if.hh
index 29a9bae34..cc77f848d 100644
--- a/src/common/aka_static_if.hh
+++ b/src/common/aka_static_if.hh
@@ -1,94 +1,29 @@
-// Copyright (c) 2016 Vittorio Romeo
-// License: AFL 3.0 | https://opensource.org/licenses/AFL-3.0
-// http://vittorioromeo.info | vittorio.romeo@outlook.com
-
-#ifndef __AKANTU_AKA_STATIC_IF_HH__
-#define __AKANTU_AKA_STATIC_IF_HH__
-
-#include <utility>
-
-#define FWD(...) ::std::forward<decltype(__VA_ARGS__)>(__VA_ARGS__)
-
-namespace akantu {
-
-template <typename TPredicate> auto static_if(TPredicate) noexcept;
-
-namespace impl {
- template <bool TPredicateResult> struct static_if_impl;
-
- template <typename TFunctionToCall> struct static_if_result;
-
- template <typename TF> auto make_static_if_result(TF && f) noexcept;
-
- template <> struct static_if_impl<true> {
- template <typename TF> auto & else_(TF &&) noexcept {
- // Ignore `else_`, as the predicate is true.
- return *this;
- }
-
- template <typename TPredicate> auto & else_if(TPredicate) noexcept {
- // Ignore `else_if`, as the predicate is true.
- return *this;
- }
-
- template <typename TF> auto then(TF && f) noexcept {
- // We found a matching branch, just make a result and
- // ignore everything else.
- return make_static_if_result(FWD(f));
- }
- };
-
- template <> struct static_if_impl<false> {
- template <typename TF> auto & then(TF &&) noexcept {
- // Ignore `then`, as the predicate is false.
- return *this;
- }
-
- template <typename TF> auto else_(TF && f) noexcept {
- // (Assuming that `else_` is after all `else_if` calls.)
-
- // We found a matching branch, just make a result and
- // ignore everything else.
-
- return make_static_if_result(FWD(f));
- }
-
- template <typename TPredicate> auto else_if(TPredicate) noexcept {
- return static_if(TPredicate{});
- }
-
- template <typename... Ts> auto operator()(Ts &&...) noexcept {
- // If there are no `else` branches, we must ignore calls
- // to a failed `static_if` matching.
- }
- };
-
- template <typename TFunctionToCall>
- struct static_if_result : TFunctionToCall {
- // Perfect-forward the function in the result instance.
- template <typename TFFwd>
- explicit static_if_result(TFFwd && f) noexcept : TFunctionToCall(FWD(f)) {}
-
- // Ignore everything, we found a result.
- template <typename TF> auto & then(TF &&) noexcept { return *this; }
-
- template <typename TPredicate> auto & else_if(TPredicate) noexcept {
- return *this;
- }
-
- template <typename TF> auto & else_(TF &&) noexcept { return *this; }
- };
-
- template <typename TF> auto make_static_if_result(TF && f) noexcept {
- return static_if_result<TF>{FWD(f)};
- }
-} // namespace impl
-
-template <typename TPredicate> auto static_if(TPredicate) noexcept {
- return impl::static_if_impl<TPredicate{}>{};
-}
-
-#undef FWD
-} // namespace akantu
-
-#endif /* __AKANTU_AKA_STATIC_IF_HH__ */
+/**
+ * @file aka_static_if.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Sun Aug 13 2017
+ * @date last modification: Wed Oct 25 2017
+ *
+ * @brief if constexpr equivalent in c++14
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
diff --git a/src/common/aka_static_memory.cc b/src/common/aka_static_memory.cc
index a3a18b7aa..b1e9d8efa 100644
--- a/src/common/aka_static_memory.cc
+++ b/src/common/aka_static_memory.cc
@@ -1,161 +1,160 @@
/**
* @file aka_static_memory.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Jan 06 2016
+ * @date last modification: Wed Nov 08 2017
*
* @brief Memory management
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include <stdexcept>
/* -------------------------------------------------------------------------- */
#include "aka_static_memory.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
bool StaticMemory::is_instantiated = false;
StaticMemory * StaticMemory::single_static_memory = nullptr;
UInt StaticMemory::nb_reference = 0;
/* -------------------------------------------------------------------------- */
StaticMemory & StaticMemory::getStaticMemory() {
if (!single_static_memory) {
single_static_memory = new StaticMemory();
is_instantiated = true;
}
nb_reference++;
return *single_static_memory;
}
/* -------------------------------------------------------------------------- */
void StaticMemory::destroy() {
nb_reference--;
if (nb_reference == 0) {
delete single_static_memory;
}
}
/* -------------------------------------------------------------------------- */
StaticMemory::~StaticMemory() {
AKANTU_DEBUG_IN();
MemoryMap::iterator memory_it;
for (memory_it = memories.begin(); memory_it != memories.end(); ++memory_it) {
ArrayMap::iterator vector_it;
for (vector_it = (memory_it->second).begin();
vector_it != (memory_it->second).end(); ++vector_it) {
delete vector_it->second;
}
(memory_it->second).clear();
}
memories.clear();
is_instantiated = false;
StaticMemory::single_static_memory = nullptr;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StaticMemory::sfree(const MemoryID & memory_id, const ID & name) {
AKANTU_DEBUG_IN();
try {
auto & vectors = const_cast<ArrayMap &>(getMemory(memory_id));
ArrayMap::iterator vector_it;
vector_it = vectors.find(name);
if (vector_it != vectors.end()) {
AKANTU_DEBUG_INFO("Array " << name
<< " removed from the static memory number "
<< memory_id);
delete vector_it->second;
vectors.erase(vector_it);
AKANTU_DEBUG_OUT();
return;
}
} catch (debug::Exception e) {
AKANTU_EXCEPTION("The memory "
<< memory_id << " does not exist (perhaps already freed) ["
<< e.what() << "]");
AKANTU_DEBUG_OUT();
return;
}
AKANTU_DEBUG_INFO("The vector " << name
<< " does not exist (perhaps already freed)");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StaticMemory::printself(std::ostream & stream, int indent) const {
std::string space = "";
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
std::streamsize prec = stream.precision();
stream.precision(2);
stream << space << "StaticMemory [" << std::endl;
UInt nb_memories = memories.size();
stream << space << " + nb memories : " << nb_memories << std::endl;
Real tot_size = 0;
MemoryMap::const_iterator memory_it;
for (memory_it = memories.begin(); memory_it != memories.end(); ++memory_it) {
Real mem_size = 0;
stream << space << AKANTU_INDENT << "Memory [" << std::endl;
UInt mem_id = memory_it->first;
stream << space << AKANTU_INDENT << " + memory id : " << mem_id
<< std::endl;
UInt nb_vectors = (memory_it->second).size();
stream << space << AKANTU_INDENT << " + nb vectors : " << nb_vectors
<< std::endl;
stream.precision(prec);
ArrayMap::const_iterator vector_it;
for (vector_it = (memory_it->second).begin();
vector_it != (memory_it->second).end(); ++vector_it) {
(vector_it->second)->printself(stream, indent + 2);
mem_size += (vector_it->second)->getMemorySize();
}
stream << space << AKANTU_INDENT
<< " + total size : " << printMemorySize<char>(mem_size)
<< std::endl;
stream << space << AKANTU_INDENT << "]" << std::endl;
tot_size += mem_size;
}
stream << space << " + total size : " << printMemorySize<char>(tot_size)
<< std::endl;
stream << space << "]" << std::endl;
stream.precision(prec);
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/common/aka_static_memory.hh b/src/common/aka_static_memory.hh
index 3fddb5de0..e80897c65 100644
--- a/src/common/aka_static_memory.hh
+++ b/src/common/aka_static_memory.hh
@@ -1,157 +1,156 @@
/**
* @file aka_static_memory.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Sun Dec 03 2017
*
* @brief Memory management
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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
*
* The class handling the memory, allocation/reallocation/desallocation
* The objects can register their array and ask for allocation or realocation
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STATIC_MEMORY_HH__
#define __AKANTU_STATIC_MEMORY_HH__
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
using ArrayMap = std::map<ID, ArrayBase *>;
using MemoryMap = std::map<MemoryID, ArrayMap>;
/**
* @class StaticMemory
* @brief Class for memory management common to all objects (this class as to
* be accessed by an interface class memory)
*/
class StaticMemory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
/// Default constructor
StaticMemory() = default;
public:
virtual ~StaticMemory();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the global instance of the StaticMemory
static StaticMemory & getStaticMemory();
static bool isInstantiated() { return is_instantiated; };
/// remove a reference on the static memory
void destroy();
/// access to an Array
inline const ArrayBase & getArray(const MemoryID & memory_id,
const ID & name) const;
/// get all vectors of a memory
inline const ArrayMap & getMemory(const MemoryID & memory_id) const;
/* ------------------------------------------------------------------------ */
/* Class Methods */
/* ------------------------------------------------------------------------ */
public:
/**
* Allocation of an array of type
*
* @param memory_id the id of the memory accessing to the static memory
* @param name name of the array (for example connectivity)
* @param size number of size (for example number of nodes)
* @param nb_component number of component (for example spatial dimension)
* @param type the type code of the array to be allocated
*
* @return pointer to an array of size nb_tupes * nb_component * sizeof(T)
*/
template <typename T>
Array<T> & smalloc(const MemoryID & memory_id, const ID & name, UInt size,
UInt nb_component);
template <typename T>
Array<T> & smalloc(const MemoryID & memory_id, const ID & name, UInt size,
UInt nb_component, const T & init_value);
/**
* free the memory associated to the array name
*
* @param memory_id the id of the memory accessing to the static memory
* @param name the name of an existing array
*/
void sfree(const MemoryID & memory_id, const ID & name);
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// is the static memory instantiated
static bool is_instantiated;
/// unique instance of the StaticMemory
static StaticMemory * single_static_memory;
/// map of all allocated arrays, indexed by their names
MemoryMap memories;
/// number of references on the static memory
static UInt nb_reference;
};
#include "aka_static_memory_inline_impl.cc"
#include "aka_static_memory_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const StaticMemory & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* __AKANTU_STATIC_MEMORY_HH__ */
diff --git a/src/common/aka_static_memory_inline_impl.cc b/src/common/aka_static_memory_inline_impl.cc
index cc245ebaf..a0cc61fab 100644
--- a/src/common/aka_static_memory_inline_impl.cc
+++ b/src/common/aka_static_memory_inline_impl.cc
@@ -1,65 +1,64 @@
/**
* @file aka_static_memory_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
- * @date last modification: Fri May 22 2015
+ * @date last modification: Wed Feb 03 2016
*
* @brief Implementation of inline functions of the class StaticMemory
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 const ArrayMap &
StaticMemory::getMemory(const MemoryID & memory_id) const {
AKANTU_DEBUG_IN();
MemoryMap::const_iterator memory_it;
memory_it = memories.find(memory_id);
if (memory_it == memories.end()) {
AKANTU_SILENT_EXCEPTION("StaticMemory as no memory with ID " << memory_id);
}
AKANTU_DEBUG_OUT();
return memory_it->second;
}
/* -------------------------------------------------------------------------- */
inline const ArrayBase & StaticMemory::getArray(const MemoryID & memory_id,
const ID & name) const {
AKANTU_DEBUG_IN();
const ArrayMap & vectors = getMemory(memory_id);
ArrayMap::const_iterator vectors_it;
vectors_it = vectors.find(name);
if (vectors_it == vectors.end()) {
AKANTU_SILENT_EXCEPTION("StaticMemory as no array named "
<< name << " for the Memory " << memory_id);
}
AKANTU_DEBUG_OUT();
return *(vectors_it->second);
}
/* -------------------------------------------------------------------------- */
diff --git a/src/common/aka_static_memory_tmpl.hh b/src/common/aka_static_memory_tmpl.hh
index 484f7f125..b938bed9d 100644
--- a/src/common/aka_static_memory_tmpl.hh
+++ b/src/common/aka_static_memory_tmpl.hh
@@ -1,87 +1,86 @@
/**
* @file aka_static_memory_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Tue Feb 20 2018
*
* @brief template part of the StaticMemory
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 <typename T>
Array<T> & StaticMemory::smalloc(const MemoryID & memory_id, const ID & name,
UInt size, UInt nb_component) {
AKANTU_DEBUG_IN();
MemoryMap::iterator memory_it;
memory_it = memories.find(memory_id);
if (memory_it == memories.end()) {
memories[memory_id] = ArrayMap();
memory_it = memories.find(memory_id);
}
if ((memory_it->second).find(name) != (memory_it->second).end()) {
AKANTU_ERROR("The vector \"" << name
<< "\" is already registred in the memory "
<< memory_id);
}
auto * tmp_vect = new Array<T>(size, nb_component, name);
(memory_it->second)[name] = tmp_vect;
AKANTU_DEBUG_OUT();
return *tmp_vect;
}
/* -------------------------------------------------------------------------- */
template <typename T>
Array<T> & StaticMemory::smalloc(const MemoryID & memory_id, const ID & name,
UInt size, UInt nb_component,
const T & init_value) {
AKANTU_DEBUG_IN();
MemoryMap::iterator memory_it;
memory_it = memories.find(memory_id);
if (memory_it == memories.end()) {
memories[memory_id] = ArrayMap();
memory_it = memories.find(memory_id);
}
if ((memory_it->second).find(name) != (memory_it->second).end()) {
AKANTU_ERROR("The vector \"" << name
<< "\" is already registred in the memory "
<< memory_id);
}
auto * tmp_vect = new Array<T>(size, nb_component, init_value, name);
(memory_it->second)[name] = tmp_vect;
AKANTU_DEBUG_OUT();
return *tmp_vect;
}
/* -------------------------------------------------------------------------- */
diff --git a/src/common/aka_typelist.hh b/src/common/aka_typelist.hh
index 1eb75cdfe..aa295594d 100644
--- a/src/common/aka_typelist.hh
+++ b/src/common/aka_typelist.hh
@@ -1,155 +1,155 @@
/**
* @file aka_typelist.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Mon Jun 19 2017
*
* @brief Objects that support the visitor design pattern
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TYPELIST_HH__
#define __AKANTU_TYPELIST_HH__
#include "aka_common.hh"
namespace akantu {
struct Empty_type {};
class Null_type {};
template <class T, class U> struct Typelist {
typedef T Head;
typedef U Tail;
};
template <typename T1 = Null_type, typename T2 = Null_type,
typename T3 = Null_type, typename T4 = Null_type,
typename T5 = Null_type, typename T6 = Null_type,
typename T7 = Null_type, typename T8 = Null_type,
typename T9 = Null_type, typename T10 = Null_type,
typename T11 = Null_type, typename T12 = Null_type,
typename T13 = Null_type, typename T14 = Null_type,
typename T15 = Null_type, typename T16 = Null_type,
typename T17 = Null_type, typename T18 = Null_type,
typename T19 = Null_type, typename T20 = Null_type>
struct MakeTypelist {
private:
typedef typename MakeTypelist<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
T13, T14, T15, T16, T17, T18, T19, T20>::Result
TailResult;
public:
typedef Typelist<T1, TailResult> Result;
};
template <> struct MakeTypelist<> { typedef Null_type Result; };
////////////////////////////////////////////////////////////////////////////////
// class template Length
// Computes the length of a typelist
// Invocation (TList is a typelist):
// Length<TList>::value
// returns a compile-time constant containing the length of TList, not counting
// the end terminator (which by convention is Null_type)
////////////////////////////////////////////////////////////////////////////////
template <class TList> struct Length;
template <> struct Length<Null_type> {
enum { value = 0 };
};
template <class T, class U> struct Length<Typelist<T, U>> {
enum { value = 1 + Length<U>::value };
};
////////////////////////////////////////////////////////////////////////////////
// class template TypeAt
// Finds the type at a given index in a typelist
// Invocation (TList is a typelist and index is a compile-time integral
// constant):
// TypeAt<TList, index>::Result
// returns the type in position 'index' in TList
// If you pass an out-of-bounds index, the result is a compile-time error
////////////////////////////////////////////////////////////////////////////////
template <class TList, unsigned int index> struct TypeAt;
template <class Head, class Tail> struct TypeAt<Typelist<Head, Tail>, 0> {
typedef Head Result;
};
template <class Head, class Tail, unsigned int i>
struct TypeAt<Typelist<Head, Tail>, i> {
typedef typename TypeAt<Tail, i - 1>::Result Result;
};
////////////////////////////////////////////////////////////////////////////////
// class template Erase
// Erases the first occurence, if any, of a type in a typelist
// Invocation (TList is a typelist and T is a type):
// Erase<TList, T>::Result
// returns a typelist that is TList without the first occurence of T
////////////////////////////////////////////////////////////////////////////////
template <class TList, class T> struct Erase;
template <class T> // Specialization 1
struct Erase<Null_type, T> {
typedef Null_type Result;
};
template <class T, class Tail> // Specialization 2
struct Erase<Typelist<T, Tail>, T> {
typedef Tail Result;
};
template <class Head, class Tail, class T> // Specialization 3
struct Erase<Typelist<Head, Tail>, T> {
typedef Typelist<Head, typename Erase<Tail, T>::Result> Result;
};
template <class TList, class T> struct IndexOf;
template <class T> struct IndexOf<Null_type, T> {
enum { value = -1 };
};
template <class T, class Tail> struct IndexOf<Typelist<T, Tail>, T> {
enum { value = 0 };
};
template <class Head, class Tail, class T>
struct IndexOf<Typelist<Head, Tail>, T> {
private:
enum { temp = IndexOf<Tail, T>::value };
public:
enum { value = (temp == -1 ? -1 : 1 + temp) };
};
} // akantu
#endif /* __AKANTU_TYPELIST_HH__ */
diff --git a/src/common/aka_types.hh b/src/common/aka_types.hh
index 09c422ee7..33e1d3aaf 100644
--- a/src/common/aka_types.hh
+++ b/src/common/aka_types.hh
@@ -1,1302 +1,1301 @@
/**
* @file aka_types.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 17 2011
- * @date last modification: Fri Jan 22 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief description of the "simple" types
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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 <initializer_list>
#include <iomanip>
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_TYPES_HH__
#define __AKANTU_AKA_TYPES_HH__
namespace akantu {
enum NormType { L_1 = 1, L_2 = 2, L_inf = UInt(-1) };
/**
* DimHelper is a class to generalize the setup of a dim array from 3
* values. This gives a common interface in the TensorStorage class
* independently of its derived inheritance (Vector, Matrix, Tensor3)
* @tparam dim
*/
template <UInt dim> struct DimHelper {
static inline void setDims(UInt m, UInt n, UInt p, 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;
/* -------------------------------------------------------------------------- */
/* Proxy classes */
/* -------------------------------------------------------------------------- */
namespace tensors {
template <class A, class B> struct is_copyable {
enum : bool { value = false };
};
template <class A> struct is_copyable<A, A> {
enum : bool { value = true };
};
template <class A> struct is_copyable<A, typename A::RetType> {
enum : bool { value = true };
};
template <class A> struct is_copyable<A, typename A::RetType::proxy> {
enum : bool { value = true };
};
} // namespace tensors
/**
* @class TensorProxy aka_types.hh
* @desc The TensorProxy class is a proxy class to the TensorStorage it handles
* the
* wrapped case. That is to say if an accessor should give access to a Tensor
* wrapped on some data, like the Array<T>::iterator they can return a
* TensorProxy that will be automatically transformed as a TensorStorage wrapped
* on the same data
* @tparam T stored type
* @tparam ndim order of the tensor
* @tparam RetType real derived type
*/
template <typename T, UInt ndim, class _RetType> class TensorProxy {
protected:
using RetTypeProxy = typename _RetType::proxy;
constexpr TensorProxy(T * data, UInt m, UInt n, UInt p) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->values = data;
}
#ifndef SWIG
template <class Other,
typename = std::enable_if_t<
tensors::is_copyable<TensorProxy, Other>::value>>
explicit TensorProxy(const Other & other) {
this->values = other.storage();
for (UInt i = 0; i < ndim; ++i)
this->n[i] = other.size(i);
}
#endif
public:
using RetType = _RetType;
UInt size(UInt i) const {
AKANTU_DEBUG_ASSERT(i < ndim,
"This tensor has only " << ndim << " dimensions, not "
<< (i + 1));
return n[i];
}
inline UInt size() const {
UInt _size = 1;
for (UInt d = 0; d < ndim; ++d)
_size *= this->n[d];
return _size;
}
T * storage() const { return values; }
#ifndef SWIG
template <class Other,
typename = std::enable_if_t<
tensors::is_copyable<TensorProxy, Other>::value>>
inline TensorProxy & operator=(const Other & other) {
AKANTU_DEBUG_ASSERT(
other.size() == this->size(),
"You are trying to copy two tensors with different sizes");
memcpy(this->values, other.storage(), this->size() * sizeof(T));
return *this;
}
#endif
// template <class Other, typename = std::enable_if_t<
// tensors::is_copyable<TensorProxy, Other>::value>>
// inline TensorProxy & operator=(const Other && other) {
// AKANTU_DEBUG_ASSERT(
// other.size() == this->size(),
// "You are trying to copy two tensors with different sizes");
// memcpy(this->values, other.storage(), this->size() * sizeof(T));
// return *this;
// }
template <typename O> inline RetTypeProxy & operator*=(const O & o) {
RetType(*this) *= o;
return static_cast<RetTypeProxy &>(*this);
}
template <typename O> inline RetTypeProxy & operator/=(const O & o) {
RetType(*this) /= o;
return static_cast<RetTypeProxy &>(*this);
}
protected:
T * values;
UInt n[ndim];
};
/* -------------------------------------------------------------------------- */
template <typename T> class VectorProxy : public TensorProxy<T, 1, Vector<T>> {
using parent = TensorProxy<T, 1, Vector<T>>;
using type = Vector<T>;
public:
constexpr VectorProxy(T * data, UInt n) : parent(data, n, 0, 0) {}
template <class Other> explicit VectorProxy(Other & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline VectorProxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
// inline VectorProxy<T> & operator=(const VectorProxy && other) {
// parent::operator=(other);
// return *this;
// }
/* ------------------------------------------------------------------------ */
T & operator()(UInt index) { return this->values[index]; };
const T & operator()(UInt index) const { return this->values[index]; };
};
template <typename T> class MatrixProxy : public TensorProxy<T, 2, Matrix<T>> {
using parent = TensorProxy<T, 2, Matrix<T>>;
using type = Matrix<T>;
public:
MatrixProxy(T * data, UInt m, UInt n) : parent(data, m, n, 0) {}
template <class Other> explicit MatrixProxy(Other & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline MatrixProxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
};
template <typename T>
class Tensor3Proxy : public TensorProxy<T, 3, Tensor3<T>> {
using parent = TensorProxy<T, 3, Tensor3<T>>;
using type = Tensor3<T>;
public:
Tensor3Proxy(const T * data, UInt m, UInt n, UInt k)
: parent(data, m, n, k) {}
Tensor3Proxy(const Tensor3Proxy & src) : parent(src) {}
Tensor3Proxy(const Tensor3<T> & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline Tensor3Proxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
};
/* -------------------------------------------------------------------------- */
/* Tensor base class */
/* -------------------------------------------------------------------------- */
template <typename T, UInt ndim, class RetType>
class TensorStorage : public TensorTrait {
public:
using value_type = T;
friend class Array<T>;
protected:
template <class TensorType> void copySize(const TensorType & src) {
for (UInt d = 0; d < ndim; ++d)
this->n[d] = src.size(d);
this->_size = src.size();
}
TensorStorage() : values(nullptr) {
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;
}
public:
TensorStorage(const TensorStorage & src) = delete;
TensorStorage(const TensorStorage & src, bool deep_copy) : values(nullptr) {
if (deep_copy)
this->deepCopy(src);
else
this->shallowCopy(src);
}
protected:
TensorStorage(UInt m, UInt n, UInt p, const T & def) {
static_assert(std::is_trivially_constructible<T>{},
"Cannot create a tensor on non trivial types");
DimHelper<ndim>::setDims(m, n, p, this->n);
this->computeSize();
this->values = new T[this->_size];
this->set(def);
this->wrapped = false;
}
TensorStorage(T * data, UInt m, UInt n, UInt p) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->computeSize();
this->values = data;
this->wrapped = true;
}
public:
/* ------------------------------------------------------------------------ */
template <class TensorType> inline void shallowCopy(const TensorType & src) {
this->copySize(src);
if (!this->wrapped)
delete[] this->values;
this->values = src.storage();
this->wrapped = true;
}
/* ------------------------------------------------------------------------ */
template <class TensorType> inline void deepCopy(const TensorType & src) {
this->copySize(src);
if (!this->wrapped)
delete[] this->values;
static_assert(std::is_trivially_constructible<T>{},
"Cannot create a tensor on non trivial types");
this->values = new T[this->_size];
static_assert(std::is_trivially_copyable<T>{},
"Cannot copy a tensor on non trivial types");
memcpy((void *)this->values, (void *)src.storage(),
this->_size * sizeof(T));
this->wrapped = false;
}
virtual ~TensorStorage() {
if (!this->wrapped)
delete[] this->values;
}
/* ------------------------------------------------------------------------ */
inline TensorStorage & operator=(const TensorStorage & src) {
return this->operator=(dynamic_cast<RetType &>(src));
}
/* ------------------------------------------------------------------------ */
inline TensorStorage & operator=(const RetType & src) {
if (this != &src) {
if (this->wrapped) {
static_assert(std::is_trivially_copyable<T>{},
"Cannot copy a tensor on non trivial types");
// this test is not sufficient for Tensor of order higher than 1
AKANTU_DEBUG_ASSERT(this->_size == src.size(),
"Tensors of different size");
memcpy((void *)this->values, (void *)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));
}
/// Y = \alpha X + Y
inline RetType & aXplusY(const TensorStorage & other, const T & alpha = 1.) {
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
Math::aXplusY(this->_size, alpha, other.storage(), this->storage());
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
T * storage() const { return values; }
UInt size() const { return _size; }
UInt size(UInt i) const {
AKANTU_DEBUG_ASSERT(i < ndim,
"This tensor has only " << ndim << " dimensions, not "
<< (i + 1));
return n[i];
};
/* ------------------------------------------------------------------------ */
inline void 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));
}
bool isWrapped() const { return this->wrapped; }
protected:
inline void computeSize() {
_size = 1;
for (UInt d = 0; d < ndim; ++d)
_size *= this->n[d];
}
protected:
template <typename R, NormType norm_type> struct NormHelper {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
for (; it < end; ++it)
_norm += std::pow(std::abs(*it), norm_type);
return std::pow(_norm, 1. / norm_type);
}
};
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{false};
};
/* -------------------------------------------------------------------------- */
/* Vector */
/* -------------------------------------------------------------------------- */
template <typename T> class Vector : public TensorStorage<T, 1, Vector<T>> {
using parent = TensorStorage<T, 1, Vector<T>>;
public:
using value_type = typename parent::value_type;
using proxy = VectorProxy<T>;
public:
Vector() : parent() {}
explicit Vector(UInt n, const T & def = T()) : parent(n, 0, 0, def) {}
Vector(T * data, UInt n) : parent(data, n, 0, 0) {}
Vector(const Vector & src, bool deep_copy = true) : parent(src, deep_copy) {}
Vector(const TensorProxy<T, 1, Vector> & src) : parent(src) {}
Vector(std::initializer_list<T> list) : parent(list.size(), 0, 0, T()) {
UInt i = 0;
for (auto val : list) {
operator()(i++) = val;
}
}
public:
~Vector() override = default;
/* ------------------------------------------------------------------------ */
inline Vector & operator=(const Vector & src) {
parent::operator=(src);
return *this;
}
/* ------------------------------------------------------------------------ */
inline T & operator()(UInt i) {
AKANTU_DEBUG_ASSERT((i < this->n[0]),
"Access out of the vector! "
<< "Index (" << i
<< ") is out of the vector of size (" << this->n[0]
<< ")");
return *(this->values + i);
}
inline const T & operator()(UInt i) const {
AKANTU_DEBUG_ASSERT((i < this->n[0]),
"Access out of the vector! "
<< "Index (" << i
<< ") is out of the vector of size (" << this->n[0]
<< ")");
return *(this->values + i);
}
inline T & operator[](UInt i) { return this->operator()(i); }
inline const T & operator[](UInt i) const { return this->operator()(i); }
/* ------------------------------------------------------------------------ */
inline Vector<T> & operator*=(Real x) { return parent::operator*=(x); }
inline Vector<T> & operator/=(Real x) { return parent::operator/=(x); }
/* ------------------------------------------------------------------------ */
inline Vector<T> & operator*=(const Vector<T> & vect) {
T * a = this->storage();
T * b = vect.storage();
for (UInt i = 0; i < this->_size; ++i)
*(a++) *= *(b++);
return *this;
}
/* ------------------------------------------------------------------------ */
inline Real dot(const Vector<T> & vect) const {
return Math::vectorDot(this->values, vect.storage(), this->_size);
}
/* ------------------------------------------------------------------------ */
inline Real mean() const {
Real mean = 0;
T * a = this->storage();
for (UInt i = 0; i < this->_size; ++i)
mean += *(a++);
return mean / this->_size;
}
/* ------------------------------------------------------------------------ */
inline Vector & crossProduct(const Vector<T> & v1, const Vector<T> & v2) {
AKANTU_DEBUG_ASSERT(this->size() == 3,
"crossProduct is only defined in 3D (n=" << this->size()
<< ")");
AKANTU_DEBUG_ASSERT(
this->size() == v1.size() && this->size() == v2.size(),
"crossProduct is not a valid operation non matching size vectors");
Math::vectorProduct3(v1.storage(), v2.storage(), this->values);
return *this;
}
inline Vector crossProduct(const Vector<T> & v) {
Vector<T> tmp(this->size());
tmp.crossProduct(*this, v);
return tmp;
}
/* ------------------------------------------------------------------------ */
inline void solve(const Matrix<T> & A, const Vector<T> & b) {
AKANTU_DEBUG_ASSERT(
this->size() == A.rows() && this->_size == A.cols(),
"The size of the solution vector mismatches the size of the matrix");
AKANTU_DEBUG_ASSERT(
this->_size == b._size,
"The rhs vector has a mismatch in size with the matrix");
Math::solve(this->_size, A.storage(), this->values, b.storage());
}
/* ------------------------------------------------------------------------ */
template <bool tr_A>
inline void mul(const Matrix<T> & A, const Vector<T> & x, 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 Vector<Real> & normalize() {
Real n = norm();
operator/=(n);
return *this;
}
/* ------------------------------------------------------------------------ */
/// norm of (*this - x)
inline Real distance(const Vector<T> & y) const {
Real * vx = this->values;
Real * vy = y.storage();
Real sum_2 = 0;
for (UInt i = 0; i < this->_size; ++i, ++vx, ++vy)
sum_2 += (*vx - *vy) * (*vx - *vy);
return sqrt(sum_2);
}
/* ------------------------------------------------------------------------ */
inline bool equal(const Vector<T> & v,
Real tolerance = Math::getTolerance()) const {
T * a = this->storage();
T * b = v.storage();
UInt i = 0;
while (i < this->_size && (std::abs(*(a++) - *(b++)) < tolerance))
++i;
return i == this->_size;
}
/* ------------------------------------------------------------------------ */
inline short compare(const Vector<T> & v,
Real tolerance = Math::getTolerance()) const {
T * a = this->storage();
T * b = v.storage();
for (UInt i(0); i < this->_size; ++i, ++a, ++b) {
if (std::abs(*a - *b) > tolerance)
return (((*a - *b) > tolerance) ? 1 : -1);
}
return 0;
}
/* ------------------------------------------------------------------------ */
inline bool operator==(const Vector<T> & v) const { return equal(v); }
inline bool operator!=(const Vector<T> & v) const { return !operator==(v); }
inline bool operator<(const Vector<T> & v) const { return compare(v) == -1; }
inline bool operator>(const Vector<T> & v) const { return compare(v) == 1; }
/* ------------------------------------------------------------------------ */
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << "[";
for (UInt i = 0; i < this->_size; ++i) {
if (i != 0)
stream << ", ";
stream << this->values[i];
}
stream << "]";
}
// friend class ::akantu::Array<T>;
};
using RVector = Vector<Real>;
/* ------------------------------------------------------------------------ */
template <>
inline bool Vector<UInt>::equal(const Vector<UInt> & v,
__attribute__((unused)) Real tolerance) const {
UInt * a = this->storage();
UInt * b = v.storage();
UInt i = 0;
while (i < this->_size && (*(a++) == *(b++)))
++i;
return i == this->_size;
}
/* ------------------------------------------------------------------------ */
/* Matrix */
/* ------------------------------------------------------------------------ */
template <typename T> class Matrix : public TensorStorage<T, 2, Matrix<T>> {
using parent = TensorStorage<T, 2, Matrix<T>>;
public:
using value_type = typename parent::value_type;
using proxy = MatrixProxy<T>;
public:
Matrix() : parent() {}
Matrix(UInt m, UInt n, const T & def = T()) : parent(m, n, 0, def) {}
Matrix(T * data, UInt m, UInt n) : parent(data, m, n, 0) {}
Matrix(const Matrix & src, bool deep_copy = true) : parent(src, deep_copy) {}
Matrix(const MatrixProxy<T> & src) : parent(src) {}
Matrix(std::initializer_list<std::initializer_list<T>> list) {
static_assert(std::is_trivially_copyable<T>{},
"Cannot create a tensor on non trivial types");
std::size_t n = 0;
std::size_t m = list.size();
for (auto row : list) {
n = std::max(n, row.size());
}
DimHelper<2>::setDims(m, n, 0, this->n);
this->computeSize();
this->values = new T[this->_size];
this->set(0);
UInt i = 0, j = 0;
for (auto & row : list) {
for (auto & val : row) {
at(i, j++) = val;
}
++i;
j = 0;
}
}
~Matrix() override = default;
/* ------------------------------------------------------------------------ */
inline Matrix & operator=(const Matrix & src) {
parent::operator=(src);
return *this;
}
public:
/* ---------------------------------------------------------------------- */
UInt rows() const { return this->n[0]; }
UInt cols() const { return this->n[1]; }
/* ---------------------------------------------------------------------- */
inline T & at(UInt i, UInt j) {
AKANTU_DEBUG_ASSERT(((i < this->n[0]) && (j < this->n[1])),
"Access out of the matrix! "
<< "Index (" << i << ", " << j
<< ") is out of the matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return *(this->values + i + j * this->n[0]);
}
inline const T & at(UInt i, UInt j) const {
AKANTU_DEBUG_ASSERT(((i < this->n[0]) && (j < this->n[1])),
"Access out of the matrix! "
<< "Index (" << i << ", " << j
<< ") is out of the matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return *(this->values + i + j * this->n[0]);
}
/* ------------------------------------------------------------------------ */
inline T & operator()(UInt i, UInt j) { return this->at(i, j); }
inline const T & operator()(UInt i, UInt j) const { return this->at(i, j); }
/// give a line vector wrapped on the column i
inline VectorProxy<T> operator()(UInt j) {
AKANTU_DEBUG_ASSERT(j < this->n[1],
"Access out of the matrix! "
<< "You are trying to access the column vector "
<< j << " in a matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return VectorProxy<T>(this->values + j * this->n[0], this->n[0]);
}
inline const VectorProxy<T> operator()(UInt j) const {
AKANTU_DEBUG_ASSERT(j < this->n[1],
"Access out of the matrix! "
<< "You are trying to access the column vector "
<< j << " in a matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return VectorProxy<T>(this->values + j * this->n[0], this->n[0]);
}
inline void block(const Matrix & block, UInt pos_i, UInt pos_j) {
AKANTU_DEBUG_ASSERT(pos_i + block.rows() <= rows(),
"The block size or position are not correct");
AKANTU_DEBUG_ASSERT(pos_i + block.cols() <= cols(),
"The block size or position are not correct");
for (UInt i = 0; i < block.rows(); ++i)
for (UInt j = 0; j < block.cols(); ++j)
this->at(i + pos_i, j + pos_j) = block(i, j);
}
inline Matrix block(UInt pos_i, UInt pos_j, UInt block_rows,
UInt block_cols) const {
AKANTU_DEBUG_ASSERT(pos_i + block_rows <= rows(),
"The block size or position are not correct");
AKANTU_DEBUG_ASSERT(pos_i + block_cols <= cols(),
"The block size or position are not correct");
Matrix block(block_rows, block_cols);
for (UInt i = 0; i < block_rows; ++i)
for (UInt j = 0; j < block_cols; ++j)
block(i, j) = this->at(i + pos_i, j + pos_j);
return block;
}
inline T & operator[](UInt idx) { return *(this->values + idx); };
inline const T & operator[](UInt idx) const { return *(this->values + idx); };
/* ---------------------------------------------------------------------- */
inline Matrix operator*(const Matrix & B) {
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() != nullptr)
AKANTU_DEBUG_ASSERT((eigenvectors.rows() == eigenvectors.cols()) &&
(eigenvectors.rows() == this->cols()),
"Eigenvectors needs to be a square matrix of size "
<< this->cols() << " x " << this->cols() << ".");
#endif
Matrix<T> tmp = *this;
Vector<T> tmp_eigs(eigenvalues.size());
Matrix<T> tmp_eig_vects(eigenvectors.rows(), eigenvectors.cols());
if (tmp_eig_vects.rows() == 0 || tmp_eig_vects.cols() == 0)
Math::matrixEig(tmp.cols(), tmp.storage(), tmp_eigs.storage());
else
Math::matrixEig(tmp.cols(), tmp.storage(), tmp_eigs.storage(),
tmp_eig_vects.storage());
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 Matrix inverse() {
Matrix inv(this->rows(), this->cols());
inv.inverse(*this);
return inv;
}
/* --------------------------------------------------------------------- */
inline T det() const {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"inv is not a valid operation on a rectangular matrix");
if (this->cols() == 1)
return *(this->values);
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_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 << "[";
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>> {
using parent = TensorStorage<T, 3, Tensor3<T>>;
public:
using value_type = typename parent::value_type;
using proxy = Tensor3Proxy<T>;
public:
Tensor3() : parent(){};
Tensor3(UInt m, UInt n, UInt p, const T & def = T()) : parent(m, n, p, def) {}
Tensor3(T * data, UInt m, UInt n, UInt p) : parent(data, m, n, p) {}
Tensor3(const Tensor3 & src, bool deep_copy = true)
: parent(src, deep_copy) {}
Tensor3(const proxy & src) : parent(src) {}
public:
/* ------------------------------------------------------------------------ */
inline Tensor3 & operator=(const Tensor3 & src) {
parent::operator=(src);
return *this;
}
/* ---------------------------------------------------------------------- */
inline T & operator()(UInt i, UInt j, UInt k) {
AKANTU_DEBUG_ASSERT(
(i < this->n[0]) && (j < this->n[1]) && (k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the element "
<< "(" << i << ", " << j << ", " << k << ") in a tensor of size ("
<< this->n[0] << ", " << this->n[1] << ", " << this->n[2] << ")");
return *(this->values + (k * this->n[0] + i) * this->n[1] + j);
}
inline const T & operator()(UInt i, UInt j, UInt k) const {
AKANTU_DEBUG_ASSERT(
(i < this->n[0]) && (j < this->n[1]) && (k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the element "
<< "(" << i << ", " << j << ", " << k << ") in a tensor of size ("
<< this->n[0] << ", " << this->n[1] << ", " << this->n[2] << ")");
return *(this->values + (k * this->n[0] + i) * this->n[1] + j);
}
inline MatrixProxy<T> operator()(UInt k) {
AKANTU_DEBUG_ASSERT((k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the slice " << k
<< " in a tensor3 of size (" << this->n[0] << ", "
<< this->n[1] << ", " << this->n[2] << ")");
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline const MatrixProxy<T> operator()(UInt k) const {
AKANTU_DEBUG_ASSERT((k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the slice " << k
<< " in a tensor3 of size (" << this->n[0] << ", "
<< this->n[1] << ", " << this->n[2] << ")");
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline MatrixProxy<T> operator[](UInt k) {
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline 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]);
}
};
/* -------------------------------------------------------------------------- */
// support operations for the creation of other vectors
/* -------------------------------------------------------------------------- */
template <typename T>
Vector<T> operator*(const T & scalar, const Vector<T> & a) {
Vector<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Vector<T> operator*(const Vector<T> & a, const T & scalar) {
Vector<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Vector<T> operator/(const Vector<T> & a, const T & scalar) {
Vector<T> r(a);
r /= scalar;
return r;
}
template <typename T>
Vector<T> operator*(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r *= b;
return r;
}
template <typename T>
Vector<T> operator+(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r += b;
return r;
}
template <typename T>
Vector<T> operator-(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r -= b;
return r;
}
template <typename T>
Vector<T> operator*(const Matrix<T> & A, const Vector<T> & b) {
Vector<T> r(b.size());
r.template mul<false>(A, b);
return r;
}
/* -------------------------------------------------------------------------- */
template <typename T>
Matrix<T> operator*(const T & scalar, const Matrix<T> & a) {
Matrix<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Matrix<T> operator*(const Matrix<T> & a, const T & scalar) {
Matrix<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Matrix<T> operator/(const Matrix<T> & a, const T & scalar) {
Matrix<T> r(a);
r /= scalar;
return r;
}
template <typename T>
Matrix<T> operator+(const Matrix<T> & a, const Matrix<T> & b) {
Matrix<T> r(a);
r += b;
return r;
}
template <typename T>
Matrix<T> operator-(const Matrix<T> & a, const Matrix<T> & b) {
Matrix<T> r(a);
r -= b;
return r;
}
} // namespace akantu
#endif /* __AKANTU_AKA_TYPES_HH__ */
diff --git a/src/common/aka_visitor.hh b/src/common/aka_visitor.hh
index b16fe120e..ad43690ff 100644
--- a/src/common/aka_visitor.hh
+++ b/src/common/aka_visitor.hh
@@ -1,164 +1,164 @@
/**
* @file aka_visitor.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Mon Jun 19 2017
*
* @brief Objects that support the visitor design pattern
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_VISITOR_HH__
#define __AKANTU_VISITOR_HH__
#include "aka_typelist.hh"
namespace akantu {
///////////////////////////////////////////////////////////////////////////
// visitor class template, adapted from the Andrei Alexandrescu's
// "Modern C++ Design"
enum Visit_type { Mutable, Immutable };
template <class T, typename R = void, Visit_type = Mutable> class StrictVisitor;
template <class T, typename R> class StrictVisitor<T, R, Mutable> {
public:
typedef R ReturnType;
typedef T ParamType;
virtual ~StrictVisitor() {}
virtual ReturnType Visit(ParamType &) = 0;
};
template <class T, typename R> class StrictVisitor<T, R, Immutable> {
public:
typedef R ReturnType;
typedef const T ParamType;
virtual ~StrictVisitor() {}
virtual ReturnType Visit(ParamType &) = 0;
};
/// class template StrictVisitor (specialization)
template <class Head, class Tail, typename R>
class StrictVisitor<Typelist<Head, Tail>, R, Mutable>
: public StrictVisitor<Head, R, Mutable>,
public StrictVisitor<Tail, R, Mutable> {
public:
typedef R ReturnType;
typedef Head ParamType;
// using StrictVisitor<Head, R>::Visit;
// using StrictVisitor<Tail, R>::Visit;
};
template <class Head, typename R>
class StrictVisitor<Typelist<Head, Null_type>, R, Mutable>
: public StrictVisitor<Head, R, Mutable> {
public:
typedef R ReturnType;
typedef Head ParamType;
using StrictVisitor<Head, R, Mutable>::Visit;
};
template <class Head, class Tail, typename R>
class StrictVisitor<Typelist<Head, Tail>, R, Immutable>
: public StrictVisitor<Head, R, Immutable>,
public StrictVisitor<Tail, R, Immutable> {
public:
typedef R ReturnType;
typedef Head ParamType;
// using StrictVisitor<Head, R>::Visit;
// using StrictVisitor<Tail, R>::Visit;
};
template <class Head, typename R>
class StrictVisitor<Typelist<Head, Null_type>, R, Immutable>
: public StrictVisitor<Head, R, Immutable> {
public:
typedef R ReturnType;
typedef Head ParamType;
using StrictVisitor<Head, R, Immutable>::Visit;
};
////////////////////////////////////////////////////////////////////////////////
// class template NonStrictVisitor
// Implements non-strict visitation (you can implement only part of the Visit
// functions)
//
template <class R> struct DefaultFunctor {
template <class T> R operator()(T &) { return R(); }
};
template <class T, typename R = void, Visit_type V = Mutable,
class F = DefaultFunctor<R>>
class BaseVisitorImpl;
template <class Head, class Tail, typename R, Visit_type V, class F>
class BaseVisitorImpl<Typelist<Head, Tail>, R, V, F>
: public StrictVisitor<Head, R, V>, public BaseVisitorImpl<Tail, R, V, F> {
public:
typedef typename StrictVisitor<Head, R, V>::ParamType ParamType;
virtual R Visit(ParamType & h) { return F()(h); }
};
template <class Head, typename R, Visit_type V, class F>
class BaseVisitorImpl<Typelist<Head, Null_type>, R, V, F>
: public StrictVisitor<Head, R, V> {
public:
typedef typename StrictVisitor<Head, R, V>::ParamType ParamType;
virtual R Visit(ParamType & h) { return F()(h); }
};
/// Visitor
template <class R> struct Strict {};
template <typename R, class TList, Visit_type V = Mutable,
template <class> class FunctorPolicy = DefaultFunctor>
class Visitor : public BaseVisitorImpl<TList, R, V, FunctorPolicy<R>> {
public:
typedef R ReturnType;
template <class Visited> ReturnType GenericVisit(Visited & host) {
StrictVisitor<Visited, ReturnType, V> & subObj = *this;
return subObj.Visit(host);
}
};
template <typename R, class TList, Visit_type V>
class Visitor<R, TList, V, Strict> : public StrictVisitor<TList, R, V> {
public:
typedef R ReturnType;
template <class Visited> ReturnType GenericVisit(Visited & host) {
StrictVisitor<Visited, ReturnType, V> & subObj = *this;
return subObj.Visit(host);
}
};
} // akantu
#endif /* __AKANTU_VISITOR_HH__ */
diff --git a/src/common/aka_voigthelper.cc b/src/common/aka_voigthelper.cc
index 13bdbbb3b..ddf66d62e 100644
--- a/src/common/aka_voigthelper.cc
+++ b/src/common/aka_voigthelper.cc
@@ -1,68 +1,68 @@
/**
* @file aka_voigthelper.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 20 2013
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Mon Jun 19 2017
*
* @brief Voigt indices
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_voigthelper.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* clang-format off */
template <> const UInt VoigtHelper<1>::mat[][1] = {{0}};
template <> const UInt VoigtHelper<2>::mat[][2] = {{0, 2},
{3, 1}};
template <> const UInt VoigtHelper<3>::mat[][3] = {{0, 5, 4},
{8, 1, 3},
{7, 6, 2}};
template <> const UInt VoigtHelper<1>::vec[][2] = {{0, 0}};
template <> const UInt VoigtHelper<2>::vec[][2] = {{0, 0},
{1, 1},
{0, 1},
{1, 0}};
template <> const UInt VoigtHelper<3>::vec[][2] = {{0, 0},
{1, 1},
{2, 2},
{1, 2},
{0, 2},
{0, 1},
{2, 1},
{2, 0},
{1, 0}};
template <> const Real VoigtHelper<1>::factors[] = {1.};
template <> const Real VoigtHelper<2>::factors[] = {1., 1., 2.};
template <> const Real VoigtHelper<3>::factors[] = {1., 1., 1.,
2., 2., 2.};
/* clang-format on */
} // akantu
diff --git a/src/common/aka_voigthelper.hh b/src/common/aka_voigthelper.hh
index 25a0cd79b..ac3dfd893 100644
--- a/src/common/aka_voigthelper.hh
+++ b/src/common/aka_voigthelper.hh
@@ -1,79 +1,79 @@
-
/**
* @file aka_voigthelper.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 20 2013
- * @date last modification: Fri Jan 22 2016
+ * @date last modification: Mon Jan 29 2018
*
* @brief Helper file for Voigt notation
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKA_VOIGTHELPER_HH__
#define __AKA_VOIGTHELPER_HH__
#include "aka_common.hh"
#include "aka_types.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim> class VoigtHelper {
static_assert(dim != 0, "Cannot be 0D");
public:
/// transfer the B matrix to a Voigt notation B matrix
inline static void transferBMatrixToSymVoigtBMatrix(
const Matrix<Real> & B, Matrix<Real> & Bvoigt, UInt nb_nodes_per_element);
/// transfer the BNL matrix to a Voigt notation B matrix (See Bathe et al.
/// IJNME vol 9, 1975)
inline static void transferBMatrixToBNL(const Matrix<Real> & B,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element);
/// transfer the BL2 matrix to a Voigt notation B matrix (See Bathe et al.
/// IJNME vol 9, 1975)
inline static void transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element);
public:
static constexpr UInt size{(dim * (dim - 1)) / 2 + dim};
// matrix of vector index I as function of tensor indices i,j
static const UInt mat[dim][dim];
// array of matrix indices ij as function of vector index I
static const UInt vec[dim * dim][2];
// factors to multiply the strain by for voigt notation
static const Real factors[size];
};
} // akantu
#include "aka_voigthelper_tmpl.hh"
#endif
diff --git a/src/common/aka_voigthelper_tmpl.hh b/src/common/aka_voigthelper_tmpl.hh
index 1c7cec16d..0582da0b8 100644
--- a/src/common/aka_voigthelper_tmpl.hh
+++ b/src/common/aka_voigthelper_tmpl.hh
@@ -1,149 +1,179 @@
+/**
+ * @file aka_voigthelper_tmpl.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Fri Dec 20 2013
+ * @date last modification: Wed Dec 06 2017
+ *
+ * @brief implementation of the voight helper
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/**
* @file aka_voigthelper_tmpl.hh
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @date Wed Nov 16 12:22:58 2016
*/
/* -------------------------------------------------------------------------- */
#include "aka_voigthelper.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_VOIGTHELPER_TMPL_HH__
#define __AKANTU_AKA_VOIGTHELPER_TMPL_HH__
namespace akantu {
template <UInt dim> constexpr UInt VoigtHelper<dim>::size;
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
const Matrix<Real> & B, Matrix<Real> & Bvoigt, UInt nb_nodes_per_element) {
Bvoigt.clear();
for (UInt i = 0; i < dim; ++i)
for (UInt n = 0; n < nb_nodes_per_element; ++n)
Bvoigt(i, i + n * dim) = B(i, n);
if (dim == 2) {
/// in 2D, fill the @f$ [\frac{\partial N_i}{\partial x}, \frac{\partial
/// N_i}{\partial y}]@f$ row
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Bvoigt(2, 1 + n * 2) = B(0, n);
Bvoigt(2, 0 + n * 2) = B(1, n);
}
}
if (dim == 3) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Real dndx = B(0, n);
Real dndy = B(1, n);
Real dndz = B(2, n);
/// in 3D, fill the @f$ [0, \frac{\partial N_i}{\partial y},
/// \frac{N_i}{\partial z}]@f$ row
Bvoigt(3, 1 + n * 3) = dndz;
Bvoigt(3, 2 + n * 3) = dndy;
/// in 3D, fill the @f$ [\frac{\partial N_i}{\partial x}, 0,
/// \frac{N_i}{\partial z}]@f$ row
Bvoigt(4, 0 + n * 3) = dndz;
Bvoigt(4, 2 + n * 3) = dndx;
/// in 3D, fill the @f$ [\frac{\partial N_i}{\partial x},
/// \frac{N_i}{\partial y}, 0]@f$ row
Bvoigt(5, 0 + n * 3) = dndy;
Bvoigt(5, 1 + n * 3) = dndx;
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void VoigtHelper<dim>::transferBMatrixToBNL(const Matrix<Real> & B,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
Bvoigt.clear();
// see Finite element formulations for large deformation dynamic analysis,
// Bathe et al. IJNME vol 9, 1975, page 364 B_{NL}
for (UInt i = 0; i < dim; ++i) {
for (UInt m = 0; m < nb_nodes_per_element; ++m) {
for (UInt n = 0; n < dim; ++n) {
// std::cout << B(n, m) << std::endl;
Bvoigt(i * dim + n, m * dim + i) = B(n, m);
}
}
}
// TODO: Verify the 2D and 1D case
}
/* -------------------------------------------------------------------------- */
template <>
inline void VoigtHelper<1>::transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
Bvoigt.clear();
for (UInt j = 0; j < nb_nodes_per_element; ++j)
for (UInt k = 0; k < 2; ++k)
Bvoigt(0, j * 2 + k) = grad_u(k, 0) * B(0, j);
}
/* -------------------------------------------------------------------------- */
template <>
inline void VoigtHelper<3>::transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
Bvoigt.clear();
for (UInt i = 0; i < 3; ++i)
for (UInt j = 0; j < nb_nodes_per_element; ++j)
for (UInt k = 0; k < 3; ++k)
Bvoigt(i, j * 3 + k) = grad_u(k, i) * B(i, j);
for (UInt i = 3; i < 6; ++i) {
for (UInt j = 0; j < nb_nodes_per_element; ++j) {
for (UInt k = 0; k < 3; ++k) {
UInt aux = i - 3;
for (UInt m = 0; m < 3; ++m) {
if (m != aux) {
UInt index1 = m;
UInt index2 = 3 - m - aux;
Bvoigt(i, j * 3 + k) += grad_u(k, index1) * B(index2, j);
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void VoigtHelper<2>::transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
Bvoigt.clear();
for (UInt i = 0; i < 2; ++i)
for (UInt j = 0; j < nb_nodes_per_element; ++j)
for (UInt k = 0; k < 2; ++k)
Bvoigt(i, j * 2 + k) = grad_u(k, i) * B(i, j);
for (UInt j = 0; j < nb_nodes_per_element; ++j) {
for (UInt k = 0; k < 2; ++k) {
for (UInt m = 0; m < 2; ++m) {
UInt index1 = m;
UInt index2 = (2 - 1) - m;
Bvoigt(2, j * 2 + k) += grad_u(k, index1) * B(index2, j);
}
}
}
}
} // akantu
#endif /* __AKANTU_AKA_VOIGTHELPER_TMPL_HH__ */
diff --git a/src/common/aka_warning.hh b/src/common/aka_warning.hh
index 21db7d188..13dd7c52e 100644
--- a/src/common/aka_warning.hh
+++ b/src/common/aka_warning.hh
@@ -1,25 +1,55 @@
+/**
+ * @file aka_warning.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Mon Nov 14 2016
+ * @date last modification: Fri Dec 02 2016
+ *
+ * @brief file to include to remove some warnings
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
// Intel warnings
#if defined(__INTEL_COMPILER)
#if defined(AKANTU_WARNING_IGNORE_UNUSED_PARAMETER)
#endif
// Clang Warnings
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
- // is only gnu
+// is only gnu
#pragma clang diagnostic push
#if defined(AKANTU_WARNING_IGNORE_UNUSED_PARAMETER)
#pragma clang diagnostic ignored "-Wunused-parameter"
#endif
// GCC warnings
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#if defined(AKANTU_WARNING_IGNORE_UNUSED_PARAMETER)
#pragma GCC diagnostic ignored "-Wunused-parameter"
#endif
#endif
diff --git a/src/common/aka_warning_restore.hh b/src/common/aka_warning_restore.hh
index 6f123debb..0d142a18f 100644
--- a/src/common/aka_warning_restore.hh
+++ b/src/common/aka_warning_restore.hh
@@ -1,16 +1,46 @@
+/**
+ * @file aka_warning_restore.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Mon Nov 14 2016
+ * @date last modification: Fri Dec 02 2016
+ *
+ * @brief file to include to reactivate the previously deactivatied warnings
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
- // is only gnu
+// is only gnu
#pragma clang diagnostic pop
#elif defined(__GNUG__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic pop
#else
#if defined(AKANTU_WARNING_IGNORE_UNUSED_PARAMETER)
#pragma GCC diagnostic warning "-Wunused-parameter"
#endif
#endif
#endif
#undef AKANTU_WARNING_IGNORE_UNUSED_PARAMETER
diff --git a/src/fe_engine/cohesive_element.hh b/src/fe_engine/cohesive_element.hh
index e6ab33817..143bf3fe9 100644
--- a/src/fe_engine/cohesive_element.hh
+++ b/src/fe_engine/cohesive_element.hh
@@ -1,91 +1,90 @@
/**
* @file cohesive_element.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 22 2015
+ * @date last modification: Wed Oct 11 2017
*
* @brief Generates the cohesive element structres (defined in
* element_class.hh)
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_ELEMENT_HH__
#define __AKANTU_COHESIVE_ELEMENT_HH__
namespace akantu {
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_2d_4, _gt_cohesive_2d_4,
_itp_lagrange_segment_2, _ek_cohesive, 2,
_git_segment, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_2d_6, _gt_cohesive_2d_6,
_itp_lagrange_segment_3, _ek_cohesive, 2,
_git_segment, 3);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_1d_2, _gt_cohesive_1d_2,
_itp_lagrange_point_1, _ek_cohesive, 1,
_git_point, 1);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_6, _gt_cohesive_3d_6,
_itp_lagrange_triangle_3, _ek_cohesive, 3,
_git_triangle, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_12, _gt_cohesive_3d_12,
_itp_lagrange_triangle_6, _ek_cohesive, 3,
_git_triangle, 3);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_8, _gt_cohesive_3d_8,
_itp_lagrange_quadrangle_4, _ek_cohesive,
3, _git_segment, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_16, _gt_cohesive_3d_16,
_itp_serendip_quadrangle_8, _ek_cohesive,
3, _git_segment, 3);
template <ElementType> struct CohesiveFacetProperty {
static const ElementType cohesive_type = _not_defined;
};
#define AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(ftype, ctype) \
template <> struct CohesiveFacetProperty<ftype> { \
static const ElementType cohesive_type = ctype; \
}
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_point_1, _cohesive_1d_2);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_segment_2, _cohesive_2d_4);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_segment_3, _cohesive_2d_6);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_triangle_3, _cohesive_3d_6);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_triangle_6, _cohesive_3d_12);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_quadrangle_4, _cohesive_3d_8);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_quadrangle_8, _cohesive_3d_16);
} // namespace akantu
#endif /* __AKANTU_COHESIVE_ELEMENT_HH__ */
diff --git a/src/fe_engine/element.hh b/src/fe_engine/element.hh
index fd5f4d668..02b8796a4 100644
--- a/src/fe_engine/element.hh
+++ b/src/fe_engine/element.hh
@@ -1,112 +1,113 @@
/**
* @file element.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Sat Jul 11 2015
+ * @date last modification: Tue Jan 23 2018
*
* @brief Element helper class
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_HH__
#define __AKANTU_ELEMENT_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Element */
/* -------------------------------------------------------------------------- */
class Element {
public:
ElementType type;
UInt element;
GhostType ghost_type;
// ElementKind kind;
// ElementType type{_not_defined};
// UInt element{0};
// GhostType ghost_type{_not_ghost};
// ElementKind kind{_ek_regular};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline ElementKind kind() const;
inline bool operator==(const Element & elem) const {
return std::tie(type, element, ghost_type) ==
std::tie(elem.type, elem.element, elem.ghost_type);
}
inline bool operator!=(const Element & elem) const {
return std::tie(type, element, ghost_type) !=
std::tie(elem.type, elem.element, elem.ghost_type);
}
// inline bool operator==(const Element & elem) const {
// return ((element == elem.element) && (type == elem.type) &&
// (ghost_type == elem.ghost_type) && (kind == elem.kind));
// }
// inline bool operator!=(const Element & elem) const {
// return ((element != elem.element) || (type != elem.type) ||
// (ghost_type != elem.ghost_type) || (kind != elem.kind));
// }
inline bool operator<(const Element & rhs) const;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Element & _this) {
stream << "Element [" << _this.type << ", " << _this.element << ", "
<< _this.ghost_type << "]";
return stream;
}
namespace {
const Element ElementNull{_not_defined, UInt(-1), _casper};
// Element{_not_defined, 0, _casper, _ek_not_defined};
}
/* -------------------------------------------------------------------------- */
inline bool Element::operator<(const Element & rhs) const {
// bool res =
// (rhs == ElementNull) ||
// ((this->kind < rhs.kind) ||
// ((this->kind == rhs.kind) &&
// ((this->ghost_type < rhs.ghost_type) ||
// ((this->ghost_type == rhs.ghost_type) &&
// ((this->type < rhs.type) ||
// ((this->type == rhs.type) && (this->element < rhs.element)))))));
return ((rhs == ElementNull) ||
std::tie(ghost_type, type, element) <
std::tie(rhs.ghost_type, rhs.type, rhs.element));
}
} // namespace akantu
#endif /* __AKANTU_ELEMENT_HH__ */
diff --git a/src/fe_engine/element_class.hh b/src/fe_engine/element_class.hh
index fb89b5709..feddcdc69 100644
--- a/src/fe_engine/element_class.hh
+++ b/src/fe_engine/element_class.hh
@@ -1,401 +1,400 @@
/**
* @file element_class.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Declaration of the ElementClass main class and the
* Integration and Interpolation elements
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_CLASS_HH__
#define __AKANTU_ELEMENT_CLASS_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/// default element class structure
template <ElementType element_type> struct ElementClassProperty {
static const GeometricalType geometrical_type{_gt_not_defined};
static const InterpolationType interpolation_type{_itp_not_defined};
static const ElementKind element_kind{_ek_regular};
static const UInt spatial_dimension{0};
static const GaussIntegrationType gauss_integration_type{_git_not_defined};
static const UInt polynomial_degree{0};
};
/// Macro to generate the element class structures for different element types
#define AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(elem_type, geom_type, \
interp_type, elem_kind, sp, \
gauss_int_type, min_int_order) \
template <> struct ElementClassProperty<elem_type> { \
static const GeometricalType geometrical_type{geom_type}; \
static const InterpolationType interpolation_type{interp_type}; \
static const ElementKind element_kind{elem_kind}; \
static const UInt spatial_dimension{sp}; \
static const GaussIntegrationType gauss_integration_type{gauss_int_type}; \
static const UInt polynomial_degree{min_int_order}; \
}
/* -------------------------------------------------------------------------- */
/* Geometry */
/* -------------------------------------------------------------------------- */
/// Default GeometricalShape structure
template <GeometricalType geometrical_type> struct GeometricalShape {
static const GeometricalShapeType shape{_gst_point};
};
/// Templated GeometricalShape with function contains
template <GeometricalShapeType shape> struct GeometricalShapeContains {
/// Check if the point (vector in 2 and 3D) at natural coordinate coor
template <class vector_type>
static inline bool contains(const vector_type & coord);
};
/// Macro to generate the GeometricalShape structures for different geometrical
/// types
#define AKANTU_DEFINE_SHAPE(geom_type, geom_shape) \
template <> struct GeometricalShape<geom_type> { \
static const GeometricalShapeType shape{geom_shape}; \
}
AKANTU_DEFINE_SHAPE(_gt_hexahedron_20, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_hexahedron_8, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_pentahedron_15, _gst_prism);
AKANTU_DEFINE_SHAPE(_gt_pentahedron_6, _gst_prism);
AKANTU_DEFINE_SHAPE(_gt_point, _gst_point);
AKANTU_DEFINE_SHAPE(_gt_quadrangle_4, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_quadrangle_8, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_segment_2, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_segment_3, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_tetrahedron_10, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_tetrahedron_4, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_triangle_3, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_triangle_6, _gst_triangle);
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type>
struct GeometricalElementProperty {};
template <ElementType element_type>
struct ElementClassExtraGeometryProperties {};
/* -------------------------------------------------------------------------- */
/// Templated GeometricalElement with function getInradius
template <GeometricalType geometrical_type,
GeometricalShapeType shape =
GeometricalShape<geometrical_type>::shape>
class GeometricalElement {
using geometrical_property = GeometricalElementProperty<geometrical_type>;
public:
/// compute the in-radius
static inline Real getInradius(__attribute__((unused))
const Matrix<Real> & coord) {
AKANTU_TO_IMPLEMENT();
}
/// true if the natural coordinates are in the element
template <class vector_type>
static inline bool contains(const vector_type & coord);
public:
static AKANTU_GET_MACRO_NOT_CONST(SpatialDimension,
geometrical_property::spatial_dimension,
UInt);
static AKANTU_GET_MACRO_NOT_CONST(NbNodesPerElement,
geometrical_property::nb_nodes_per_element,
UInt);
static inline constexpr auto getNbFacetTypes() {
return geometrical_property::nb_facet_types;
};
static inline UInt getNbFacetsPerElement(UInt t);
static inline UInt getNbFacetsPerElement();
static inline constexpr auto getFacetLocalConnectivityPerElement(UInt t = 0);
};
/* -------------------------------------------------------------------------- */
/* Interpolation */
/* -------------------------------------------------------------------------- */
/// default InterpolationProperty structure
template <InterpolationType interpolation_type> struct InterpolationProperty {};
/// Macro to generate the InterpolationProperty structures for different
/// interpolation types
#define AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(itp_type, itp_kind, \
nb_nodes, ndim) \
template <> struct InterpolationProperty<itp_type> { \
static constexpr InterpolationKind kind{itp_kind}; \
static constexpr UInt nb_nodes_per_element{nb_nodes}; \
static constexpr UInt natural_space_dimension{ndim}; \
}
/* -------------------------------------------------------------------------- */
/// Generic (templated by the enum InterpolationType which specifies the order
/// and the dimension of the interpolation) class handling the elemental
/// interpolation
template <InterpolationType interpolation_type,
InterpolationKind kind =
InterpolationProperty<interpolation_type>::kind>
class InterpolationElement {
public:
using interpolation_property = InterpolationProperty<interpolation_type>;
/// compute the shape values for a given set of points in natural coordinates
static inline void computeShapes(const Matrix<Real> & natural_coord,
Matrix<Real> & N);
/// compute the shape values for a given point in natural coordinates
template <class vector_type>
static inline void computeShapes(const vector_type &, vector_type &) {
AKANTU_TO_IMPLEMENT();
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with variation of natural coordinates on a given set
* of points in natural coordinates
*/
static inline void computeDNDS(const Matrix<Real> & natural_coord,
Tensor3<Real> & dnds);
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with
* variation of natural coordinates on a given point in natural
* coordinates
*/
template <class vector_type, class matrix_type>
static inline void computeDNDS(const vector_type &, matrix_type &) {
AKANTU_TO_IMPLEMENT();
}
/// compute jacobian (or integration variable change factor) for a given point
/// in the case of spatial_dimension != natural_space_dimension
static inline void computeSpecialJacobian(const Matrix<Real> &, Real &) {
AKANTU_TO_IMPLEMENT();
}
/// interpolate a field given (arbitrary) natural coordinates
static inline void
interpolateOnNaturalCoordinates(const Vector<Real> & natural_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated);
/// interpolate a field given the shape functions on the interpolation point
static inline void interpolate(const Matrix<Real> & nodal_values,
const Vector<Real> & shapes,
Vector<Real> & interpolated);
/// interpolate a field given the shape functions on the interpolations points
static inline void interpolate(const Matrix<Real> & nodal_values,
const Matrix<Real> & shapes,
Matrix<Real> & interpolated);
/// compute the gradient of a given field on the given natural coordinates
static inline void
gradientOnNaturalCoordinates(const Vector<Real> & natural_coords,
const Matrix<Real> & f, Matrix<Real> & gradient);
public:
static AKANTU_GET_MACRO_NOT_CONST(
ShapeSize,
InterpolationProperty<interpolation_type>::nb_nodes_per_element, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
ShapeDerivativesSize,
(InterpolationProperty<interpolation_type>::nb_nodes_per_element *
InterpolationProperty<interpolation_type>::natural_space_dimension),
UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NaturalSpaceDimension,
InterpolationProperty<interpolation_type>::natural_space_dimension, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NbNodesPerInterpolationElement,
InterpolationProperty<interpolation_type>::nb_nodes_per_element, UInt);
};
/* -------------------------------------------------------------------------- */
/* Integration */
/* -------------------------------------------------------------------------- */
template <GaussIntegrationType git_class, UInt nb_points>
struct GaussIntegrationTypeData {
/// quadrature points in natural coordinates
static Real quad_positions[];
/// weights for the Gauss integration
static Real quad_weights[];
};
template <ElementType type,
UInt n = ElementClassProperty<type>::polynomial_degree>
class GaussIntegrationElement {
public:
static UInt getNbQuadraturePoints();
static const Matrix<Real> getQuadraturePoints();
static const Vector<Real> getWeights();
};
/* -------------------------------------------------------------------------- */
/* ElementClass */
/* -------------------------------------------------------------------------- */
template <ElementType element_type,
ElementKind element_kind =
ElementClassProperty<element_type>::element_kind>
class ElementClass
: public GeometricalElement<
ElementClassProperty<element_type>::geometrical_type>,
public InterpolationElement<
ElementClassProperty<element_type>::interpolation_type> {
protected:
using geometrical_element =
GeometricalElement<ElementClassProperty<element_type>::geometrical_type>;
using interpolation_element = InterpolationElement<
ElementClassProperty<element_type>::interpolation_type>;
using element_property = ElementClassProperty<element_type>;
using interpolation_property =
typename interpolation_element::interpolation_property;
public:
/**
* compute @f$ J = \frac{\partial x_j}{\partial s_i} @f$ the variation of real
* coordinates along with variation of natural coordinates on a given point in
* natural coordinates
*/
static inline void computeJMat(const Matrix<Real> & dnds,
const Matrix<Real> & node_coords,
Matrix<Real> & J);
/**
* compute the Jacobian matrix by computing the variation of real coordinates
* along with variation of natural coordinates on a given set of points in
* natural coordinates
*/
static inline void computeJMat(const Tensor3<Real> & dnds,
const Matrix<Real> & node_coords,
Tensor3<Real> & J);
/// compute the jacobians of a serie of natural coordinates
static inline void computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians);
/// compute jacobian (or integration variable change factor) for a set of
/// points
static inline void computeJacobian(const Tensor3<Real> & J,
Vector<Real> & jacobians);
/// compute jacobian (or integration variable change factor) for a given point
static inline void computeJacobian(const Matrix<Real> & J, Real & jacobians);
/// compute shape derivatives (input is dxds) for a set of points
static inline void computeShapeDerivatives(const Tensor3<Real> & J,
const Tensor3<Real> & dnds,
Tensor3<Real> & shape_deriv);
/// compute shape derivatives (input is dxds) for a given point
static inline void computeShapeDerivatives(const Matrix<Real> & J,
const Matrix<Real> & dnds,
Matrix<Real> & shape_deriv);
/// compute the normal of a surface defined by the function f
static inline void
computeNormalsOnNaturalCoordinates(const Matrix<Real> & coord,
Matrix<Real> & f, Matrix<Real> & normals);
/// get natural coordinates from real coordinates
static inline void inverseMap(const Vector<Real> & real_coords,
const Matrix<Real> & node_coords,
Vector<Real> & natural_coords,
Real tolerance = 1e-10);
/// get natural coordinates from real coordinates
static inline void inverseMap(const Matrix<Real> & real_coords,
const Matrix<Real> & node_coords,
Matrix<Real> & natural_coords,
Real tolerance = 1e-10);
public:
static AKANTU_GET_MACRO_NOT_CONST(Kind, element_kind, ElementKind);
static constexpr AKANTU_GET_MACRO_NOT_CONST(
SpatialDimension, ElementClassProperty<element_type>::spatial_dimension,
UInt);
using element_class_extra_geom_property =
ElementClassExtraGeometryProperties<element_type>;
static constexpr auto getP1ElementType() {
return element_class_extra_geom_property::p1_type;
}
static constexpr auto getFacetType(UInt t = 0) {
return element_class_extra_geom_property::facet_type[t];
}
static constexpr auto getFacetTypes();
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "geometrical_element_property.hh"
#include "interpolation_element_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "element_class_tmpl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
#include "element_class_pentahedron_6_inline_impl.cc"
/* keep order */
#include "element_class_hexahedron_20_inline_impl.cc"
#include "element_class_hexahedron_8_inline_impl.cc"
#include "element_class_pentahedron_15_inline_impl.cc"
#include "element_class_point_1_inline_impl.cc"
#include "element_class_quadrangle_4_inline_impl.cc"
#include "element_class_quadrangle_8_inline_impl.cc"
#include "element_class_segment_2_inline_impl.cc"
#include "element_class_segment_3_inline_impl.cc"
#include "element_class_tetrahedron_10_inline_impl.cc"
#include "element_class_tetrahedron_4_inline_impl.cc"
#include "element_class_triangle_3_inline_impl.cc"
#include "element_class_triangle_6_inline_impl.cc"
} // namespace akantu
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "element_class_structural.hh"
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "cohesive_element.hh"
#endif
#if defined(AKANTU_IGFEM)
#include "element_class_igfem.hh"
#endif
#endif /* __AKANTU_ELEMENT_CLASS_HH__ */
diff --git a/src/fe_engine/element_class_structural.hh b/src/fe_engine/element_class_structural.hh
index 0af2d1891..d719c6e11 100644
--- a/src/fe_engine/element_class_structural.hh
+++ b/src/fe_engine/element_class_structural.hh
@@ -1,252 +1,254 @@
/**
* @file element_class_structural.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Thu Oct 22 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Specialization of the element classes for structural elements
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_CLASS_STRUCTURAL_HH__
#define __AKANTU_ELEMENT_CLASS_STRUCTURAL_HH__
namespace akantu {
/// Macro to generate the InterpolationProperty structures for different
/// interpolation types
#define AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY( \
itp_type, itp_geom_type, ndof, nb_stress, nb_dnds_cols) \
template <> struct InterpolationProperty<itp_type> { \
static const InterpolationKind kind{_itk_structural}; \
static const UInt nb_nodes_per_element{ \
InterpolationProperty<itp_geom_type>::nb_nodes_per_element}; \
static const InterpolationType itp_geometry_type{itp_geom_type}; \
static const UInt natural_space_dimension{ \
InterpolationProperty<itp_geom_type>::natural_space_dimension}; \
static const UInt nb_degree_of_freedom{ndof}; \
static const UInt nb_stress_components{nb_stress}; \
static const UInt dnds_columns{nb_dnds_cols}; \
}
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type>
class InterpolationElement<interpolation_type, _itk_structural> {
public:
using interpolation_property = InterpolationProperty<interpolation_type>;
/// compute the shape values for a given set of points in natural coordinates
static inline void computeShapes(const Matrix<Real> & natural_coord,
const Matrix<Real> & real_coord,
Tensor3<Real> & N) {
for (UInt i = 0; i < natural_coord.cols(); ++i) {
Matrix<Real> n_t = N(i);
computeShapes(natural_coord(i), real_coord, n_t);
}
}
/// compute the shape values for a given point in natural coordinates
static inline void computeShapes(const Vector<Real> & natural_coord,
const Matrix<Real> & real_coord,
Matrix<Real> & N);
/// compute shape derivatives (input is dxds) for a set of points
static inline void computeShapeDerivatives(const Tensor3<Real> & Js,
const Tensor3<Real> & DNDSs,
const Matrix<Real> & R,
Tensor3<Real> & Bs) {
for (UInt i = 0; i < Js.size(2); ++i) {
Matrix<Real> J = Js(i);
Matrix<Real> DNDS = DNDSs(i);
Matrix<Real> DNDX(DNDS.rows(), DNDS.cols());
auto inv_J = J.inverse();
DNDX.mul<false, false>(inv_J, DNDS);
Matrix<Real> B_R = Bs(i);
Matrix<Real> B(B_R.rows(), B_R.cols());
arrangeInVoigt(DNDX, B);
B_R.mul<false, false>(B, R);
}
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with variation of natural coordinates on a given set
* of points in natural coordinates
*/
static inline void computeDNDS(const Matrix<Real> & natural_coord,
const Matrix<Real> & real_coord,
Tensor3<Real> & dnds) {
for (UInt i = 0; i < natural_coord.cols(); ++i) {
Matrix<Real> dnds_t = dnds(i);
computeDNDS(natural_coord(i), real_coord, dnds_t);
}
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with
* variation of natural coordinates on a given point in natural
* coordinates
*/
static inline void computeDNDS(const Vector<Real> & natural_coord,
const Matrix<Real> & real_coord,
Matrix<Real> & dnds);
/**
* arrange B in Voigt notation from DNDS
*/
static inline void arrangeInVoigt(const Matrix<Real> & dnds,
Matrix<Real> & B) {
// Default implementation assumes dnds is already in Voigt notation
B.deepCopy(dnds);
}
public:
static inline constexpr auto getNbNodesPerInterpolationElement() {
return interpolation_property::nb_nodes_per_element;
}
static inline constexpr auto getShapeSize() {
return interpolation_property::nb_nodes_per_element *
interpolation_property::nb_degree_of_freedom *
interpolation_property::nb_degree_of_freedom;
}
static inline constexpr auto getShapeDerivativesSize() {
return interpolation_property::nb_nodes_per_element *
interpolation_property::nb_degree_of_freedom *
interpolation_property::nb_stress_components;
}
static inline constexpr auto getNaturalSpaceDimension() {
return interpolation_property::natural_space_dimension;
}
static inline constexpr auto getNbDegreeOfFreedom() {
return interpolation_property::nb_degree_of_freedom;
}
static inline constexpr auto getNbStressComponents() {
return interpolation_property::nb_stress_components;
}
};
/// Macro to generate the element class structures for different structural
/// element types
/* -------------------------------------------------------------------------- */
#define AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY( \
elem_type, geom_type, interp_type, parent_el_type, elem_kind, sp, \
gauss_int_type, min_int_order) \
template <> struct ElementClassProperty<elem_type> { \
static const GeometricalType geometrical_type{geom_type}; \
static const InterpolationType interpolation_type{interp_type}; \
static const ElementType parent_element_type{parent_el_type}; \
static const ElementKind element_kind{elem_kind}; \
static const UInt spatial_dimension{sp}; \
static const GaussIntegrationType gauss_integration_type{gauss_int_type}; \
static const UInt polynomial_degree{min_int_order}; \
}
/* -------------------------------------------------------------------------- */
/* ElementClass for structural elements */
/* -------------------------------------------------------------------------- */
template <ElementType element_type>
class ElementClass<element_type, _ek_structural>
: public GeometricalElement<
ElementClassProperty<element_type>::geometrical_type>,
public InterpolationElement<
ElementClassProperty<element_type>::interpolation_type> {
protected:
using geometrical_element =
GeometricalElement<ElementClassProperty<element_type>::geometrical_type>;
using interpolation_element = InterpolationElement<
ElementClassProperty<element_type>::interpolation_type>;
using parent_element =
ElementClass<ElementClassProperty<element_type>::parent_element_type>;
public:
static inline void
computeRotationMatrix(Matrix<Real> & /*R*/, const Matrix<Real> & /*X*/,
const Vector<Real> & /*extra_normal*/) {
AKANTU_TO_IMPLEMENT();
}
/// compute jacobian (or integration variable change factor) for a given point
static inline void computeJMat(const Vector<Real> & natural_coords,
const Matrix<Real> & Xs, Matrix<Real> & J) {
Matrix<Real> dnds(Xs.rows(), Xs.cols());
parent_element::computeDNDS(natural_coords, dnds);
J.mul<false, true>(dnds, Xs);
}
static inline void computeJMat(const Matrix<Real> & natural_coords,
const Matrix<Real> & Xs, Tensor3<Real> & Js) {
for (UInt i = 0; i < natural_coords.cols(); ++i) {
// because non-const l-value reference does not bind to r-value
Matrix<Real> J = Js(i);
computeJMat(Vector<Real>(natural_coords(i)), Xs, J);
}
}
static inline void computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians) {
using itp = typename interpolation_element::interpolation_property;
Tensor3<Real> Js(itp::natural_space_dimension, itp::natural_space_dimension,
natural_coords.cols());
computeJMat(natural_coords, node_coords, Js);
for (UInt i = 0; i < natural_coords.cols(); ++i) {
Matrix<Real> J = Js(i);
jacobians(i) = J.det();
}
}
static inline void computeRotation(const Matrix<Real> & node_coords,
Matrix<Real> & rotation);
public:
static AKANTU_GET_MACRO_NOT_CONST(Kind, _ek_structural, ElementKind);
static AKANTU_GET_MACRO_NOT_CONST(P1ElementType, _not_defined, ElementType);
static AKANTU_GET_MACRO_NOT_CONST(FacetType, _not_defined, ElementType);
static constexpr auto getFacetType(__attribute__((unused)) UInt t = 0) {
return _not_defined;
}
static constexpr AKANTU_GET_MACRO_NOT_CONST(
SpatialDimension, ElementClassProperty<element_type>::spatial_dimension,
UInt);
static constexpr auto getFacetTypes() {
return ElementClass<_not_defined>::getFacetTypes();
}
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "element_classes/element_class_hermite_inline_impl.cc"
/* keep order */
#include "element_classes/element_class_bernoulli_beam_inline_impl.cc"
#include "element_classes/element_class_kirchhoff_shell_inline_impl.cc"
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_ELEMENT_CLASS_STRUCTURAL_HH__ */
diff --git a/src/fe_engine/element_class_tmpl.hh b/src/fe_engine/element_class_tmpl.hh
index b58d164f1..4b8701579 100644
--- a/src/fe_engine/element_class_tmpl.hh
+++ b/src/fe_engine/element_class_tmpl.hh
@@ -1,531 +1,531 @@
/**
* @file element_class_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Thu Oct 22 2015
+ * @date last modification: Wed Nov 29 2017
*
* @brief Implementation of the inline templated function of the element class
* descriptions
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "gauss_integration_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_CLASS_TMPL_HH__
#define __AKANTU_ELEMENT_CLASS_TMPL_HH__
namespace akantu {
template <ElementType element_type, ElementKind element_kind>
inline constexpr auto
ElementClass<element_type, element_kind>::getFacetTypes() {
return VectorProxy<const ElementType>(
element_class_extra_geom_property::facet_type.data(),
geometrical_element::getNbFacetTypes());
}
/* -------------------------------------------------------------------------- */
/* GeometricalElement */
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline constexpr auto
GeometricalElement<geometrical_type,
shape>::getFacetLocalConnectivityPerElement(UInt t) {
int pos = 0;
for (UInt i = 0; i < t; ++i) {
pos += geometrical_property::nb_facets[i] *
geometrical_property::nb_nodes_per_facet[i];
}
return MatrixProxy<const UInt>(
geometrical_property::facet_connectivity_vect.data() + pos,
geometrical_property::nb_facets[t],
geometrical_property::nb_nodes_per_facet[t]);
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement() {
UInt total_nb_facets = 0;
for (UInt n = 0; n < geometrical_property::nb_facet_types; ++n) {
total_nb_facets += geometrical_property::nb_facets[n];
}
return total_nb_facets;
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement(UInt t) {
return geometrical_property::nb_facets[t];
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
template <class vector_type>
inline bool GeometricalElement<geometrical_type, shape>::contains(
const vector_type & coords) {
return GeometricalShapeContains<shape>::contains(coords);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_point>::contains(const vector_type & coords) {
return (coords(0) < std::numeric_limits<Real>::epsilon());
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_square>::contains(const vector_type & coords) {
bool in = true;
for (UInt i = 0; i < coords.size() && in; ++i)
in &= ((coords(i) >= -(1. + std::numeric_limits<Real>::epsilon())) &&
(coords(i) <= (1. + std::numeric_limits<Real>::epsilon())));
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_triangle>::contains(const vector_type & coords) {
bool in = true;
Real sum = 0;
for (UInt i = 0; (i < coords.size()) && in; ++i) {
in &= ((coords(i) >= -(Math::getTolerance())) &&
(coords(i) <= (1. + Math::getTolerance())));
sum += coords(i);
}
if (in)
return (in && (sum <= (1. + Math::getTolerance())));
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_prism>::contains(const vector_type & coords) {
bool in = ((coords(0) >= -1.) && (coords(0) <= 1.)); // x in segment [-1, 1]
// y and z in triangle
in &= ((coords(1) >= 0) && (coords(1) <= 1.));
in &= ((coords(2) >= 0) && (coords(2) <= 1.));
Real sum = coords(1) + coords(2);
return (in && (sum <= 1));
}
/* -------------------------------------------------------------------------- */
/* InterpolationElement */
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeShapes(
const Matrix<Real> & natural_coord, Matrix<Real> & N) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(N(p));
Vector<Real> ncoord_p(natural_coord(p));
computeShapes(ncoord_p, Np);
}
}
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeDNDS(
const Matrix<Real> & natural_coord, Tensor3<Real> & dnds) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> dnds_p(dnds(p));
Vector<Real> ncoord_p(natural_coord(p));
computeDNDS(ncoord_p, dnds_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on a point a field for which values are given on the
* node of the element using the shape functions at this interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Vector<Real> & shapes,
Vector<Real> & interpolated) {
Matrix<Real> interpm(interpolated.storage(), nodal_values.rows(), 1);
Matrix<Real> shapesm(
shapes.storage(),
InterpolationProperty<interpolation_type>::nb_nodes_per_element, 1);
interpm.mul<false, false>(nodal_values, shapesm);
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on several points a field for which values are given on the
* node of the element using the shape functions at the interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated values of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Matrix<Real> & shapes,
Matrix<Real> & interpolated) {
UInt nb_points = shapes.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(shapes(p));
Vector<Real> interpolated_p(interpolated(p));
interpolate(nodal_values, Np, interpolated_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate the field on a point given in natural coordinates the field which
* values are given on the node of the element
*
* @param natural_coords natural coordinates of point where to interpolate \xi
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::interpolateOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & nodal_values,
Vector<Real> & interpolated) {
Vector<Real> shapes(
InterpolationProperty<interpolation_type>::nb_nodes_per_element);
computeShapes(natural_coords, shapes);
interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
/// @f$ gradient_{ij} = \frac{\partial f_j}{\partial s_i} = \sum_k
/// \frac{\partial N_k}{\partial s_i}f_{j n_k} @f$
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::gradientOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & f,
Matrix<Real> & gradient) {
Matrix<Real> dnds(
InterpolationProperty<interpolation_type>::natural_space_dimension,
InterpolationProperty<interpolation_type>::nb_nodes_per_element);
computeDNDS(natural_coords, dnds);
gradient.mul<false, true>(f, dnds);
}
/* -------------------------------------------------------------------------- */
/* ElementClass */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Tensor3<Real> & dnds,
const Matrix<Real> & node_coords,
Tensor3<Real> & J) {
UInt nb_points = dnds.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> J_p(J(p));
Matrix<Real> dnds_p(dnds(p));
computeJMat(dnds_p, node_coords, J_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Matrix<Real> & dnds,
const Matrix<Real> & node_coords,
Matrix<Real> & J) {
/// @f$ J = dxds = dnds * x @f$
J.mul<false, true>(dnds, node_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians) {
UInt nb_points = natural_coords.cols();
Matrix<Real> dnds(interpolation_property::natural_space_dimension,
interpolation_property::nb_nodes_per_element);
Matrix<Real> J(natural_coords.rows(), node_coords.rows());
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> ncoord_p(natural_coords(p));
interpolation_element::computeDNDS(ncoord_p, dnds);
computeJMat(dnds, node_coords, J);
computeJacobian(J, jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Tensor3<Real> & J,
Vector<Real> & jacobians) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
computeJacobian(J(p), jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeJacobian(const Matrix<Real> & J,
Real & jacobians) {
if (J.rows() == J.cols()) {
jacobians = Math::det<element_property::spatial_dimension>(J.storage());
} else {
interpolation_element::computeSpecialJacobian(J, jacobians);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Tensor3<Real> & J,
const Tensor3<Real> & dnds,
Tensor3<Real> & shape_deriv) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> shape_deriv_p(shape_deriv(p));
computeShapeDerivatives(J(p), dnds(p), shape_deriv_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Matrix<Real> & J,
const Matrix<Real> & dnds,
Matrix<Real> & shape_deriv) {
Matrix<Real> inv_J(J.rows(), J.cols());
Math::inv<element_property::spatial_dimension>(J.storage(), inv_J.storage());
shape_deriv.mul<false, false>(inv_J, dnds);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeNormalsOnNaturalCoordinates(
const Matrix<Real> & coord, Matrix<Real> & f, Matrix<Real> & normals) {
UInt dimension = normals.rows();
UInt nb_points = coord.cols();
AKANTU_DEBUG_ASSERT((dimension - 1) ==
interpolation_property::natural_space_dimension,
"cannot extract a normal because of dimension mismatch "
<< dimension - 1 << " "
<< interpolation_property::natural_space_dimension);
Matrix<Real> J(dimension, interpolation_property::natural_space_dimension);
for (UInt p = 0; p < nb_points; ++p) {
interpolation_element::gradientOnNaturalCoordinates(coord(p), f, J);
if (dimension == 2) {
Math::normal2(J.storage(), normals(p).storage());
}
if (dimension == 3) {
Math::normal3(J(0).storage(), J(1).storage(), normals(p).storage());
}
}
}
/* ------------------------------------------------------------------------- */
/**
* In the non linear cases we need to iterate to find the natural coordinates
*@f$\xi@f$
* provided real coordinates @f$x@f$.
*
* We want to solve: @f$ x- \phi(\xi) = 0@f$ with @f$\phi(\xi) = \sum_I N_I(\xi)
*x_I@f$
* the mapping function which uses the nodal coordinates @f$x_I@f$.
*
* To that end we use the Newton method and the following series:
*
* @f$ \frac{\partial \phi(x_k)}{\partial \xi} \left( \xi_{k+1} - \xi_k \right)
*= x - \phi(x_k)@f$
*
* When we consider elements embedded in a dimension higher than them (2D
*triangle in a 3D space for example)
* @f$ J = \frac{\partial \phi(\xi_k)}{\partial \xi}@f$ is of dimension
*@f$dim_{space} \times dim_{elem}@f$ which
* is not invertible in most cases. Rather we can solve the problem:
*
* @f$ J^T J \left( \xi_{k+1} - \xi_k \right) = J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that
*
* @f$ d\xi = \xi_{k+1} - \xi_k = (J^T J)^{-1} J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that if the series converges we have:
*
* @f$ 0 = J^T \left( \phi(\xi_\infty) - x \right) @f$
*
* And we see that this is ill-posed only if @f$ J^T x = 0@f$ which means that
*the vector provided
* is normal to any tangent which means it is outside of the element itself.
*
* @param real_coords: the real coordinates the natural coordinates are sought
*for
* @param node_coords: the coordinates of the nodes forming the element
* @param natural_coords: output->the sought natural coordinates
* @param spatial_dimension: spatial dimension of the problem
*
**/
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Vector<Real> & real_coords, const Matrix<Real> & node_coords,
Vector<Real> & natural_coords, Real tolerance) {
UInt spatial_dimension = real_coords.size();
UInt dimension = natural_coords.size();
// matrix copy of the real_coords
Matrix<Real> mreal_coords(real_coords.storage(), spatial_dimension, 1);
// initial guess
// Matrix<Real> natural_guess(natural_coords.storage(), dimension, 1);
natural_coords.clear();
// real space coordinates provided by initial guess
Matrix<Real> physical_guess(dimension, 1);
// objective function f = real_coords - physical_guess
Matrix<Real> f(dimension, 1);
// dnds computed on the natural_guess
// Matrix<Real> dnds(interpolation_element::nb_nodes_per_element,
// spatial_dimension);
// J Jacobian matrix computed on the natural_guess
Matrix<Real> J(spatial_dimension, dimension);
// G = J^t * J
Matrix<Real> G(spatial_dimension, spatial_dimension);
// Ginv = G^{-1}
Matrix<Real> Ginv(spatial_dimension, spatial_dimension);
// J = Ginv * J^t
Matrix<Real> F(spatial_dimension, dimension);
// dxi = \xi_{k+1} - \xi in the iterative process
Matrix<Real> dxi(spatial_dimension, 1);
/* --------------------------- */
/* init before iteration loop */
/* --------------------------- */
// do interpolation
auto update_f = [&f, &physical_guess, &natural_coords, &node_coords,
&mreal_coords, dimension]() {
Vector<Real> physical_guess_v(physical_guess.storage(), dimension);
interpolation_element::interpolateOnNaturalCoordinates(
natural_coords, node_coords, physical_guess_v);
// compute initial objective function value f = real_coords - physical_guess
f = mreal_coords;
f -= physical_guess;
// compute initial error
auto error = f.norm<L_2>();
return error;
};
auto inverse_map_error = update_f();
/* --------------------------- */
/* iteration loop */
/* --------------------------- */
while (tolerance < inverse_map_error) {
// compute J^t
interpolation_element::gradientOnNaturalCoordinates(natural_coords,
node_coords, J);
// compute G
G.mul<true, false>(J, J);
// inverse G
Ginv.inverse(G);
// compute F
F.mul<false, true>(Ginv, J);
// compute increment
dxi.mul<false, false>(F, f);
// update our guess
natural_coords += Vector<Real>(dxi(0));
inverse_map_error = update_f();
}
// memcpy(natural_coords.storage(), natural_guess.storage(), sizeof(Real) *
// natural_coords.size());
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Matrix<Real> & real_coords, const Matrix<Real> & node_coords,
Matrix<Real> & natural_coords, Real tolerance) {
UInt nb_points = real_coords.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> X(real_coords(p));
Vector<Real> ncoord_p(natural_coords(p));
inverseMap(X, node_coords, ncoord_p, tolerance);
}
}
} // namespace akantu
#endif /* __AKANTU_ELEMENT_CLASS_TMPL_HH__ */
diff --git a/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.cc b/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.cc
index 407cb0af0..417f631c6 100644
--- a/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.cc
@@ -1,222 +1,223 @@
/**
* @file element_class_bernoulli_beam_inline_impl.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jul 15 2011
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Mon Feb 19 2018
*
* @brief Specialization of the element_class class for the type
- _bernoulli_beam_2
+ * _bernoulli_beam_2
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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
*
* @verbatim
--x-----q1----|----q2-----x---> x
-1 0 1
@endverbatim
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
#include "element_class_structural.hh"
//#include "aka_element_classes_info.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_CC__
#define __AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(_itp_bernoulli_beam_2,
_itp_lagrange_segment_2, 3,
2, 6);
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(_itp_bernoulli_beam_3,
_itp_lagrange_segment_2, 6,
4, 6);
AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY(_bernoulli_beam_2,
_gt_segment_2,
_itp_bernoulli_beam_2,
_segment_2, _ek_structural, 2,
_git_segment, 3);
AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY(_bernoulli_beam_3,
_gt_segment_2,
_itp_bernoulli_beam_3,
_segment_2, _ek_structural, 3,
_git_segment, 3);
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::computeShapes(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
Vector<Real> L(2);
InterpolationElement<_itp_lagrange_segment_2, _itk_lagrangian>::computeShapes(
natural_coords, L);
Matrix<Real> H(2, 4);
InterpolationElement<_itp_hermite_2, _itk_structural>::computeShapes(
natural_coords, real_coord, H);
// clang-format off
// u1 v1 t1 u2 v2 t2
N = {{L(0), 0 , 0 , L(1), 0 , 0 }, // u
{0 , H(0, 0), H(0, 1), 0 , H(0, 2), H(0, 3)}, // v
{0 , H(1, 0), H(1, 1), 0 , H(1, 2), H(1, 3)}}; // theta
// clang-format on
}
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::computeShapes(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
Vector<Real> L(2);
InterpolationElement<_itp_lagrange_segment_2, _itk_lagrangian>::computeShapes(
natural_coords, L);
Matrix<Real> H(2, 4);
InterpolationElement<_itp_hermite_2, _itk_structural>::computeShapes(
natural_coords, real_coord, H);
// clang-format off
// u1 v1 w1 x1 y1 z1 u2 v2 w2 x2 y2 z2
N = {{L(0), 0 , 0 , 0 , 0 , 0 , L(1), 0 , 0 , 0 , 0 , 0 }, // u
{0 , H(0, 0), 0 , 0 , H(0, 1), 0 , 0 , H(0, 2), 0 , 0 , H(0, 3), 0 }, // v
{0 , 0 , H(0, 0), 0 , 0 , H(0, 1), 0 , 0 , H(0, 2), 0 , 0 , H(0, 3)}, // w
{0 , 0 , 0 , L(0), 0 , 0 , 0 , 0 , 0 , L(1), 0 , 0 }, // thetax
{0 , H(1, 0), 0 , 0 , H(1, 1), 0 , 0 , H(1, 2), 0 , 0 , H(1, 3), 0 }, // thetay
{0 , 0 , H(1, 0), 0 , 0 , H(1, 1), 0 , 0 , H(1, 2), 0 , 0 , H(1, 3)}}; // thetaz
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & dnds) {
Matrix<Real> L(1, 2);
InterpolationElement<_itp_lagrange_segment_2, _itk_lagrangian>::computeDNDS(
natural_coords, L);
Matrix<Real> H(1, 4);
InterpolationElement<_itp_hermite_2, _itk_structural>::computeDNDS(
natural_coords, real_coord, H);
// Storing the derivatives in dnds
dnds.block(L, 0, 0);
dnds.block(H, 0, 2);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::arrangeInVoigt(
const Matrix<Real> & dnds, Matrix<Real> & B) {
auto L = dnds.block(0, 0, 1, 2); // Lagrange shape derivatives
auto H = dnds.block(0, 2, 1, 4); // Hermite shape derivatives
// clang-format off
// u1 v1 t1 u2 v2 t2
B = {{L(0, 0), 0, 0, L(0, 1), 0, 0 },
{0, H(0, 0), H(0, 1), 0, H(0, 2), H(0, 3)}};
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & dnds) {
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::computeDNDS(
natural_coords, real_coord, dnds);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::arrangeInVoigt(
const Matrix<Real> & dnds, Matrix<Real> & B) {
auto L = dnds.block(0, 0, 1, 2); // Lagrange shape derivatives
auto H = dnds.block(0, 2, 1, 4); // Hermite shape derivatives
// clang-format off
// u1 v1 w1 x1 y1 z1 u2 v2 w2 x2 y2 z2
B = {{L(0, 0), 0 , 0 , 0 , 0 , 0 , L(0, 1), 0 , 0 , 0 , 0 , 0 }, // eps
{0 , H(0, 0), 0 , 0 , 0 , H(0, 1), 0 , H(0, 2), 0 , 0 , 0 , H(0, 3)}, // chi strong axis
{0 , 0 ,-H(0, 0), 0 , H(0, 1), 0 , 0 , 0 ,-H(0, 2), 0 , H(0, 3), 0 }, // chi weak axis
{0 , 0 , 0 , L(0, 0), 0 , 0 , 0 , 0 , 0 , L(0, 1), 0 , 0 }}; // chi torsion
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void ElementClass<_bernoulli_beam_2>::computeRotationMatrix(
Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> &) {
Vector<Real> x2 = X(1); // X2
Vector<Real> x1 = X(0); // X1
auto cs = (x2 - x1);
cs.normalize();
auto c = cs(0);
auto s = cs(1);
// clang-format off
/// Definition of the rotation matrix
R = {{ c, s, 0.},
{-s, c, 0.},
{ 0., 0., 1.}};
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void ElementClass<_bernoulli_beam_3>::computeRotationMatrix(
Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> & n) {
Vector<Real> x2 = X(1); // X2
Vector<Real> x1 = X(0); // X1
auto dim = X.rows();
auto x = (x2 - x1);
x.normalize();
auto x_n = x.crossProduct(n);
Matrix<Real> Pe = {{1., 0., 0.}, {0., -1., 0.}, {0., 0., 1.}};
Matrix<Real> Pg(dim, dim);
Pg(0) = x;
Pg(1) = x_n;
Pg(2) = n;
Pe *= Pg.inverse();
R.clear();
/// Definition of the rotation matrix
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
R(i + dim, j + dim) = R(i, j) = Pe(i, j);
}
} // namespace akantu
#endif /* __AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_CC__ */
diff --git a/src/fe_engine/element_classes/element_class_hermite_inline_impl.cc b/src/fe_engine/element_classes/element_class_hermite_inline_impl.cc
index 03972b2a0..33ac526aa 100644
--- a/src/fe_engine/element_classes/element_class_hermite_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_hermite_inline_impl.cc
@@ -1,179 +1,179 @@
/**
* @file element_class_hermite_inline_impl.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
- * @author Lucas Frérot <lucas.frerot@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
*
- * @date creation: Fri Jul 15 2011
- * @date last modification: Sun Oct 19 2014
+ * @date creation: Fri Nov 10 2017
+ * @date last modification: Mon Feb 19 2018
*
* @brief Specialization of the element_class class for the type
- _hermite
+ * _hermite
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
--x-----q1----|----q2-----x---> x
-1 0 1
@endverbatim
*
* @subsection shapes Shape functions
* @f[
* \begin{array}{ll}
* M_1(\xi) &= 1/4(\xi^{3}/-3\xi+2)\\
* M_2(\xi) &= -1/4(\xi^{3}-3\xi-2)
* \end{array}
*
* \begin{array}{ll}
* L_1(\xi) &= 1/4(\xi^{3}-\xi^{2}-\xi+1)\\
* L_2(\xi) &= 1/4(\xi^{3}+\xi^{2}-\xi-1)
* \end{array}
*
* \begin{array}{ll}
* M'_1(\xi) &= 3/4(\xi^{2}-1)\\
* M'_2(\xi) &= -3/4(\xi^{2}-1)
* \end{array}
*
* \begin{array}{ll}
* L'_1(\xi) &= 1/4(3\xi^{2}-2\xi-1)\\
* L'_2(\xi) &= 1/4(3\xi^{2}+2\xi-1)
* \end{array}
*@f]
*
* @subsection dnds Shape derivatives
*
*@f[
* \begin{array}{ll}
* N'_1(\xi) &= -1/2\\
* N'_2(\xi) &= 1/2
* \end{array}]
*
* \begin{array}{ll}
* -M''_1(\xi) &= -3\xi/2\\
* -M''_2(\xi) &= 3\xi/2\\
* \end{array}
*
* \begin{array}{ll}
* -L''_1(\xi) &= -1/2a(3\xi/a-1)\\
* -L''_2(\xi) &= -1/2a(3\xi/a+1)
* \end{array}
*@f]
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
#include "element_class_structural.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_CC__
#define __AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(_itp_hermite_2,
_itp_lagrange_segment_2, 2,
1, 4);
/* -------------------------------------------------------------------------- */
namespace {
namespace details {
inline Real computeLength(const Matrix<Real> & real_coord) {
Vector<Real> x1 = real_coord(0);
Vector<Real> x2 = real_coord(1);
return x1.distance(x2);
}
inline void computeShapes(const Vector<Real> & natural_coords, Real a,
Matrix<Real> & N) {
/// natural coordinate
Real xi = natural_coords(0);
// Cubic Hermite splines interpolating displacement
auto M1 = 1. / 4. * Math::pow<2>(xi - 1) * (xi + 2);
auto M2 = 1. / 4. * Math::pow<2>(xi + 1) * (2 - xi);
auto L1 = a / 4. * Math::pow<2>(xi - 1) * (xi + 1);
auto L2 = a / 4. * Math::pow<2>(xi + 1) * (xi - 1);
#if 1 // Version where we also interpolate the rotations
// Derivatives (with respect to x) of previous functions interpolating
// rotations
auto M1_ = 3. / (4. * a) * (xi * xi - 1);
auto M2_ = 3. / (4. * a) * (1 - xi * xi);
auto L1_ = 1 / 4. * (3 * xi * xi - 2 * xi - 1);
auto L2_ = 1 / 4. * (3 * xi * xi + 2 * xi - 1);
// clang-format off
// v1 t1 v2 t2
N = {{M1 , L1 , M2 , L2}, // displacement interpolation
{M1_, L1_, M2_, L2_}}; // rotation interpolation
// clang-format on
#else // Version where we only interpolate displacements
// clang-format off
// v1 t1 v2 t2
N = {{M1, L1, M2, L2}};
// clang-format on
#endif
}
/* ---------------------------------------------------------------------- */
inline void computeDNDS(const Vector<Real> & natural_coords, Real a,
Matrix<Real> & B) {
// natural coordinate
Real xi = natural_coords(0);
// Derivatives with respect to xi for rotations
auto M1__ = 3. / 2. * xi;
auto M2__ = 3. / 2. * (-xi);
auto L1__ = a / 2. * (3 * xi - 1);
auto L2__ = a / 2. * (3 * xi + 1);
// v1 t1 v2 t2
B = {{M1__, L1__, M2__, L2__}}; // computing curvature : {chi} = [B]{d}
B /= a; // to account for first order deriv w/r to x
}
} // namespace details
} // namespace
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_hermite_2, _itk_structural>::computeShapes(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
auto L = details::computeLength(real_coord);
details::computeShapes(natural_coords, L / 2, N);
}
/* -------------------------------------------------------------------------- */
template <>
inline void InterpolationElement<_itp_hermite_2, _itk_structural>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & B) {
auto L = details::computeLength(real_coord);
details::computeDNDS(natural_coords, L / 2, B);
}
} // namespace akantu
#endif /* __AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_CC__ */
diff --git a/src/fe_engine/element_classes/element_class_hexahedron_20_inline_impl.cc b/src/fe_engine/element_classes/element_class_hexahedron_20_inline_impl.cc
index da0c877fc..0906a90be 100644
--- a/src/fe_engine/element_classes/element_class_hexahedron_20_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_hexahedron_20_inline_impl.cc
@@ -1,259 +1,259 @@
/**
* @file element_class_hexahedron_20_inline_impl.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Sacha Laffely <sacha.laffely@epfl.ch>
* @author Damien Scantamburlo <damien.scantamburlo@epfl.ch>
*
* @date creation: Tue Mar 31 2015
- * @date last modification: Thu Jul 16 2015
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _hexahedron_20
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+terms of the GNU Lesser General Public License as published by the Free
+Software Foundation, either version 3 of the License, or (at your option) any
+later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
\y
\z /
| /
7-----|18--------6
/| | / /|
/ | | / / |
19 | | / 17 |
/ 15 | / / 14
/ | | / / |
4-------16---/---5 |
| | +----|------------\x
| 3-------10-|-----2
| / | /
12 / 13 /
| 11 | 9
| / | /
|/ |/
0--------8-------1
x y z
* N0 -1 -1 -1
* N1 1 -1 -1
* N2 1 1 -1
* N3 -1 1 -1
* N4 -1 -1 1
* N5 1 -1 1
* N6 1 1 1
* N7 -1 1 1
* N8 0 -1 -1
* N9 1 0 -1
* N10 0 1 -1
* N11 -1 0 -1
* N12 -1 -1 0
* N13 1 -1 0
* N14 1 1 0
* N15 -1 1 0
* N16 0 -1 1
* N17 1 0 1
* N18 0 1 1
* N19 -1 0 1
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_hexahedron_20, _gt_hexahedron_20,
_itp_serendip_hexahedron_20, _ek_regular,
3, _git_segment, 3);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_serendip_hexahedron_20>::computeShapes(
const vector_type & c, vector_type & N) {
// Shape function , Natural coordinates
N(0) =
0.125 * (1 - c(0)) * (1 - c(1)) * (1 - c(2)) * (-2 - c(0) - c(1) - c(2));
N(1) =
0.125 * (1 + c(0)) * (1 - c(1)) * (1 - c(2)) * (-2 + c(0) - c(1) - c(2));
N(2) =
0.125 * (1 + c(0)) * (1 + c(1)) * (1 - c(2)) * (-2 + c(0) + c(1) - c(2));
N(3) =
0.125 * (1 - c(0)) * (1 + c(1)) * (1 - c(2)) * (-2 - c(0) + c(1) - c(2));
N(4) =
0.125 * (1 - c(0)) * (1 - c(1)) * (1 + c(2)) * (-2 - c(0) - c(1) + c(2));
N(5) =
0.125 * (1 + c(0)) * (1 - c(1)) * (1 + c(2)) * (-2 + c(0) - c(1) + c(2));
N(6) =
0.125 * (1 + c(0)) * (1 + c(1)) * (1 + c(2)) * (-2 + c(0) + c(1) + c(2));
N(7) =
0.125 * (1 - c(0)) * (1 + c(1)) * (1 + c(2)) * (-2 - c(0) + c(1) + c(2));
N(8) = 0.25 * (1 - c(0) * c(0)) * (1 - c(1)) * (1 - c(2));
N(9) = 0.25 * (1 - c(1) * c(1)) * (1 + c(0)) * (1 - c(2));
N(10) = 0.25 * (1 - c(0) * c(0)) * (1 + c(1)) * (1 - c(2));
N(11) = 0.25 * (1 - c(1) * c(1)) * (1 - c(0)) * (1 - c(2));
N(12) = 0.25 * (1 - c(2) * c(2)) * (1 - c(0)) * (1 - c(1));
N(13) = 0.25 * (1 - c(2) * c(2)) * (1 + c(0)) * (1 - c(1));
N(14) = 0.25 * (1 - c(2) * c(2)) * (1 + c(0)) * (1 + c(1));
N(15) = 0.25 * (1 - c(2) * c(2)) * (1 - c(0)) * (1 + c(1));
N(16) = 0.25 * (1 - c(0) * c(0)) * (1 - c(1)) * (1 + c(2));
N(17) = 0.25 * (1 - c(1) * c(1)) * (1 + c(0)) * (1 + c(2));
N(18) = 0.25 * (1 - c(0) * c(0)) * (1 + c(1)) * (1 + c(2));
N(19) = 0.25 * (1 - c(1) * c(1)) * (1 - c(0)) * (1 + c(2));
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_serendip_hexahedron_20>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
// derivatives
// ddx
dnds(0, 0) =
0.25 * (c(0) + 0.5 * (c(1) + c(2) + 1)) * (c(1) - 1) * (c(2) - 1);
dnds(0, 1) =
0.25 * (c(0) - 0.5 * (c(1) + c(2) + 1)) * (c(1) - 1) * (c(2) - 1);
dnds(0, 2) =
-0.25 * (c(0) + 0.5 * (c(1) - c(2) - 1)) * (c(1) + 1) * (c(2) - 1);
dnds(0, 3) =
-0.25 * (c(0) - 0.5 * (c(1) - c(2) - 1)) * (c(1) + 1) * (c(2) - 1);
dnds(0, 4) =
-0.25 * (c(0) + 0.5 * (c(1) - c(2) + 1)) * (c(1) - 1) * (c(2) + 1);
dnds(0, 5) =
-0.25 * (c(0) - 0.5 * (c(1) - c(2) + 1)) * (c(1) - 1) * (c(2) + 1);
dnds(0, 6) =
0.25 * (c(0) + 0.5 * (c(1) + c(2) - 1)) * (c(1) + 1) * (c(2) + 1);
dnds(0, 7) =
0.25 * (c(0) - 0.5 * (c(1) + c(2) - 1)) * (c(1) + 1) * (c(2) + 1);
dnds(0, 8) = -0.5 * c(0) * (c(1) - 1) * (c(2) - 1);
dnds(0, 9) = 0.25 * (c(1) * c(1) - 1) * (c(2) - 1);
dnds(0, 10) = 0.5 * c(0) * (c(1) + 1) * (c(2) - 1);
dnds(0, 11) = -0.25 * (c(1) * c(1) - 1) * (c(2) - 1);
dnds(0, 12) = -0.25 * (c(2) * c(2) - 1) * (c(1) - 1);
dnds(0, 13) = 0.25 * (c(1) - 1) * (c(2) * c(2) - 1);
dnds(0, 14) = -0.25 * (c(1) + 1) * (c(2) * c(2) - 1);
dnds(0, 15) = 0.25 * (c(1) + 1) * (c(2) * c(2) - 1);
dnds(0, 16) = 0.5 * c(0) * (c(1) - 1) * (c(2) + 1);
dnds(0, 17) = -0.25 * (c(2) + 1) * (c(1) * c(1) - 1);
dnds(0, 18) = -0.5 * c(0) * (c(1) + 1) * (c(2) + 1);
dnds(0, 19) = 0.25 * (c(2) + 1) * (c(1) * c(1) - 1);
// ddy
dnds(1, 0) =
0.25 * (c(1) + 0.5 * (c(0) + c(2) + 1)) * (c(0) - 1) * (c(2) - 1);
dnds(1, 1) =
-0.25 * (c(1) - 0.5 * (c(0) - c(2) - 1)) * (c(0) + 1) * (c(2) - 1);
dnds(1, 2) =
-0.25 * (c(1) + 0.5 * (c(0) - c(2) - 1)) * (c(0) + 1) * (c(2) - 1);
dnds(1, 3) =
0.25 * (c(1) - 0.5 * (c(0) + c(2) + 1)) * (c(0) - 1) * (c(2) - 1);
dnds(1, 4) =
-0.25 * (c(1) + 0.5 * (c(0) - c(2) + 1)) * (c(0) - 1) * (c(2) + 1);
dnds(1, 5) =
0.25 * (c(1) - 0.5 * (c(0) + c(2) - 1)) * (c(0) + 1) * (c(2) + 1);
dnds(1, 6) =
0.25 * (c(1) + 0.5 * (c(0) + c(2) - 1)) * (c(0) + 1) * (c(2) + 1);
dnds(1, 7) =
-0.25 * (c(1) - 0.5 * (c(0) - c(2) + 1)) * (c(0) - 1) * (c(2) + 1);
dnds(1, 8) = -0.25 * (c(0) * c(0) - 1) * (c(2) - 1);
dnds(1, 9) = 0.5 * c(1) * (c(0) + 1) * (c(2) - 1);
dnds(1, 10) = 0.25 * (c(0) * c(0) - 1) * (c(2) - 1);
dnds(1, 11) = -0.5 * c(1) * (c(0) - 1) * (c(2) - 1);
dnds(1, 12) = -0.25 * (c(2) * c(2) - 1) * (c(0) - 1);
dnds(1, 13) = 0.25 * (c(0) + 1) * (c(2) * c(2) - 1);
dnds(1, 14) = -0.25 * (c(0) + 1) * (c(2) * c(2) - 1);
dnds(1, 15) = 0.25 * (c(0) - 1) * (c(2) * c(2) - 1);
dnds(1, 16) = 0.25 * (c(2) + 1) * (c(0) * c(0) - 1);
dnds(1, 17) = -0.5 * c(1) * (c(0) + 1) * (c(2) + 1);
dnds(1, 18) = -0.25 * (c(2) + 1) * (c(0) * c(0) - 1);
dnds(1, 19) = 0.5 * c(1) * (c(0) - 1) * (c(2) + 1);
// ddz
dnds(2, 0) =
0.25 * (c(2) + 0.5 * (c(0) + c(1) + 1)) * (c(0) - 1) * (c(1) - 1);
dnds(2, 1) =
-0.25 * (c(2) - 0.5 * (c(0) - c(1) - 1)) * (c(0) + 1) * (c(1) - 1);
dnds(2, 2) =
0.25 * (c(2) - 0.5 * (c(0) + c(1) - 1)) * (c(0) + 1) * (c(1) + 1);
dnds(2, 3) =
-0.25 * (c(2) + 0.5 * (c(0) - c(1) + 1)) * (c(0) - 1) * (c(1) + 1);
dnds(2, 4) =
0.25 * (c(2) - 0.5 * (c(0) + c(1) + 1)) * (c(0) - 1) * (c(1) - 1);
dnds(2, 5) =
-0.25 * (c(2) + 0.5 * (c(0) - c(1) - 1)) * (c(0) + 1) * (c(1) - 1);
dnds(2, 6) =
0.25 * (c(2) + 0.5 * (c(0) + c(1) - 1)) * (c(0) + 1) * (c(1) + 1);
dnds(2, 7) =
-0.25 * (c(2) - 0.5 * (c(0) - c(1) + 1)) * (c(0) - 1) * (c(1) + 1);
dnds(2, 8) = -0.25 * (c(0) * c(0) - 1) * (c(1) - 1);
dnds(2, 9) = 0.25 * (c(1) * c(1) - 1) * (c(0) + 1);
dnds(2, 10) = 0.25 * (c(0) * c(0) - 1) * (c(1) + 1);
dnds(2, 11) = -0.25 * (c(1) * c(1) - 1) * (c(0) - 1);
dnds(2, 12) = -0.5 * c(2) * (c(1) - 1) * (c(0) - 1);
dnds(2, 13) = 0.5 * c(2) * (c(0) + 1) * (c(1) - 1);
dnds(2, 14) = -0.5 * c(2) * (c(0) + 1) * (c(1) + 1);
dnds(2, 15) = 0.5 * c(2) * (c(0) - 1) * (c(1) + 1);
dnds(2, 16) = 0.25 * (c(1) - 1) * (c(0) * c(0) - 1);
dnds(2, 17) = -0.25 * (c(0) + 1) * (c(1) * c(1) - 1);
dnds(2, 18) = -0.25 * (c(1) + 1) * (c(0) * c(0) - 1);
dnds(2, 19) = 0.25 * (c(0) - 1) * (c(1) * c(1) - 1);
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_hexahedron_20>::getInradius(const Matrix<Real> & coord) {
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Vector<Real> u4 = coord(4);
Vector<Real> u5 = coord(5);
Vector<Real> u6 = coord(6);
Vector<Real> u7 = coord(7);
Vector<Real> u8 = coord(8);
Vector<Real> u9 = coord(9);
Vector<Real> u10 = coord(10);
Vector<Real> u11 = coord(11);
Vector<Real> u12 = coord(12);
Vector<Real> u13 = coord(13);
Vector<Real> u14 = coord(14);
Vector<Real> u15 = coord(15);
Vector<Real> u16 = coord(16);
Vector<Real> u17 = coord(17);
Vector<Real> u18 = coord(18);
Vector<Real> u19 = coord(19);
Real a = u0.distance(u1);
Real b = u1.distance(u2);
Real c = u2.distance(u3);
Real d = u3.distance(u0);
Real e = u0.distance(u4);
Real f = u1.distance(u5);
Real g = u2.distance(u6);
Real h = u3.distance(u7);
Real i = u4.distance(u5);
Real j = u5.distance(u6);
Real k = u6.distance(u7);
Real l = u7.distance(u4);
Real x = std::min(a, std::min(b, std::min(c, d)));
Real y = std::min(e, std::min(f, std::min(g, h)));
Real z = std::min(i, std::min(j, std::min(k, l)));
Real p = std::min(x, std::min(y, z));
return p;
}
diff --git a/src/fe_engine/element_classes/element_class_hexahedron_8_inline_impl.cc b/src/fe_engine/element_classes/element_class_hexahedron_8_inline_impl.cc
index 9fb1cc1ac..7a96249a3 100644
--- a/src/fe_engine/element_classes/element_class_hexahedron_8_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_hexahedron_8_inline_impl.cc
@@ -1,254 +1,253 @@
/**
* @file element_class_hexahedron_8_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
*
* @date creation: Mon Mar 14 2011
- * @date last modification: Sat Sep 12 2015
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _hexahedron_8
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
\zeta
^
(-1,1,1) | (1,1,1)
7---|------6
/| | /|
/ | | / |
(-1,-1,1) 4----------5 | (1,-1,1)
| | | | |
| | | | |
| | +---|-------> \xi
| | / | |
(-1,1,-1) | 3-/-----|--2 (1,1,-1)
| / / | /
|/ / |/
0-/--------1
(-1,-1,-1) / (1,-1,-1)
/
\eta
@endverbatim
*
* @subsection shapes Shape functions
* @f[
* \begin{array}{llll}
* N1 = (1 - \xi) (1 - \eta) (1 - \zeta) / 8
* & \frac{\partial N1}{\partial \xi} = - (1 - \eta) (1 - \zeta) / 8
* & \frac{\partial N1}{\partial \eta} = - (1 - \xi) (1 - \zeta) / 8
* & \frac{\partial N1}{\partial \zeta} = - (1 - \xi) (1 - \eta) / 8 \\
* N2 = (1 + \xi) (1 - \eta) (1 - \zeta) / 8
* & \frac{\partial N2}{\partial \xi} = (1 - \eta) (1 - \zeta) / 8
* & \frac{\partial N2}{\partial \eta} = - (1 + \xi) (1 - \zeta) / 8
* & \frac{\partial N2}{\partial \zeta} = - (1 + \xi) (1 - \eta) / 8 \\
* N3 = (1 + \xi) (1 + \eta) (1 - \zeta) / 8
* & \frac{\partial N3}{\partial \xi} = (1 + \eta) (1 - \zeta) / 8
* & \frac{\partial N3}{\partial \eta} = (1 + \xi) (1 - \zeta) / 8
* & \frac{\partial N3}{\partial \zeta} = - (1 + \xi) (1 + \eta) / 8 \\
* N4 = (1 - \xi) (1 + \eta) (1 - \zeta) / 8
* & \frac{\partial N4}{\partial \xi} = - (1 + \eta) (1 - \zeta) / 8
* & \frac{\partial N4}{\partial \eta} = (1 - \xi) (1 - \zeta) / 8
* & \frac{\partial N4}{\partial \zeta} = - (1 - \xi) (1 + \eta) / 8 \\
* N5 = (1 - \xi) (1 - \eta) (1 + \zeta) / 8
* & \frac{\partial N5}{\partial \xi} = - (1 - \eta) (1 + \zeta) / 8
* & \frac{\partial N5}{\partial \eta} = - (1 - \xi) (1 + \zeta) / 8
* & \frac{\partial N5}{\partial \zeta} = (1 - \xi) (1 - \eta) / 8 \\
* N6 = (1 + \xi) (1 - \eta) (1 + \zeta) / 8
* & \frac{\partial N6}{\partial \xi} = (1 - \eta) (1 + \zeta) / 8
* & \frac{\partial N6}{\partial \eta} = - (1 + \xi) (1 + \zeta) / 8
* & \frac{\partial N6}{\partial \zeta} = (1 + \xi) (1 - \eta) / 8 \\
* N7 = (1 + \xi) (1 + \eta) (1 + \zeta) / 8
* & \frac{\partial N7}{\partial \xi} = (1 + \eta) (1 + \zeta) / 8
* & \frac{\partial N7}{\partial \eta} = (1 + \xi) (1 + \zeta) / 8
* & \frac{\partial N7}{\partial \zeta} = (1 + \xi) (1 + \eta) / 8 \\
* N8 = (1 - \xi) (1 + \eta) (1 + \zeta) / 8
* & \frac{\partial N8}{\partial \xi} = - (1 + \eta) (1 + \zeta) / 8
* & \frac{\partial N8}{\partial \eta} = (1 - \xi) (1 + \zeta) / 8
* & \frac{\partial N8}{\partial \zeta} = (1 - \xi) (1 + \eta) / 8 \\
* \end{array}
* @f]
*
* @subsection quad_points Position of quadrature points
* @f{eqnarray*}{
* \xi_{q0} &=& -1/\sqrt{3} \qquad \eta_{q0} = -1/\sqrt{3} \qquad \zeta_{q0} =
-1/\sqrt{3} \\
* \xi_{q1} &=& 1/\sqrt{3} \qquad \eta_{q1} = -1/\sqrt{3} \qquad \zeta_{q1} =
-1/\sqrt{3} \\
* \xi_{q2} &=& 1/\sqrt{3} \qquad \eta_{q2} = 1/\sqrt{3} \qquad \zeta_{q2} =
-1/\sqrt{3} \\
* \xi_{q3} &=& -1/\sqrt{3} \qquad \eta_{q3} = 1/\sqrt{3} \qquad \zeta_{q3} =
-1/\sqrt{3} \\
* \xi_{q4} &=& -1/\sqrt{3} \qquad \eta_{q4} = -1/\sqrt{3} \qquad \zeta_{q4} =
1/\sqrt{3} \\
* \xi_{q5} &=& 1/\sqrt{3} \qquad \eta_{q5} = -1/\sqrt{3} \qquad \zeta_{q5} =
1/\sqrt{3} \\
* \xi_{q6} &=& 1/\sqrt{3} \qquad \eta_{q6} = 1/\sqrt{3} \qquad \zeta_{q6} =
1/\sqrt{3} \\
* \xi_{q7} &=& -1/\sqrt{3} \qquad \eta_{q7} = 1/\sqrt{3} \qquad \zeta_{q7} =
1/\sqrt{3} \\
* @f}
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_hexahedron_8, _gt_hexahedron_8,
_itp_lagrange_hexahedron_8, _ek_regular, 3,
_git_segment, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_hexahedron_8>::computeShapes(
const vector_type & c, vector_type & N) {
/// Natural coordinates
N(0) = .125 * (1 - c(0)) * (1 - c(1)) * (1 - c(2)); /// N1(q_0)
N(1) = .125 * (1 + c(0)) * (1 - c(1)) * (1 - c(2)); /// N2(q_0)
N(2) = .125 * (1 + c(0)) * (1 + c(1)) * (1 - c(2)); /// N3(q_0)
N(3) = .125 * (1 - c(0)) * (1 + c(1)) * (1 - c(2)); /// N4(q_0)
N(4) = .125 * (1 - c(0)) * (1 - c(1)) * (1 + c(2)); /// N5(q_0)
N(5) = .125 * (1 + c(0)) * (1 - c(1)) * (1 + c(2)); /// N6(q_0)
N(6) = .125 * (1 + c(0)) * (1 + c(1)) * (1 + c(2)); /// N7(q_0)
N(7) = .125 * (1 - c(0)) * (1 + c(1)) * (1 + c(2)); /// N8(q_0)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_hexahedron_8>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccccccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi}
* & \frac{\partial N3}{\partial \xi} & \frac{\partial
* N4}{\partial \xi}
* & \frac{\partial N5}{\partial \xi} & \frac{\partial
* N6}{\partial \xi}
* & \frac{\partial N7}{\partial \xi} & \frac{\partial
* N8}{\partial \xi}\\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta}
* & \frac{\partial N3}{\partial \eta} & \frac{\partial
* N4}{\partial \eta}
* & \frac{\partial N5}{\partial \eta} & \frac{\partial
* N6}{\partial \eta}
* & \frac{\partial N7}{\partial \eta} & \frac{\partial
* N8}{\partial \eta}\\
* \frac{\partial N1}{\partial \zeta} & \frac{\partial N2}{\partial
* \zeta}
* & \frac{\partial N3}{\partial \zeta} & \frac{\partial
* N4}{\partial \zeta}
* & \frac{\partial N5}{\partial \zeta} & \frac{\partial
* N6}{\partial \zeta}
* & \frac{\partial N7}{\partial \zeta} & \frac{\partial
* N8}{\partial \zeta}
* \end{array}
* \right)
* @f]
*/
dnds(0, 0) = -.125 * (1 - c(1)) * (1 - c(2));
;
dnds(0, 1) = .125 * (1 - c(1)) * (1 - c(2));
;
dnds(0, 2) = .125 * (1 + c(1)) * (1 - c(2));
;
dnds(0, 3) = -.125 * (1 + c(1)) * (1 - c(2));
;
dnds(0, 4) = -.125 * (1 - c(1)) * (1 + c(2));
;
dnds(0, 5) = .125 * (1 - c(1)) * (1 + c(2));
;
dnds(0, 6) = .125 * (1 + c(1)) * (1 + c(2));
;
dnds(0, 7) = -.125 * (1 + c(1)) * (1 + c(2));
;
dnds(1, 0) = -.125 * (1 - c(0)) * (1 - c(2));
;
dnds(1, 1) = -.125 * (1 + c(0)) * (1 - c(2));
;
dnds(1, 2) = .125 * (1 + c(0)) * (1 - c(2));
;
dnds(1, 3) = .125 * (1 - c(0)) * (1 - c(2));
;
dnds(1, 4) = -.125 * (1 - c(0)) * (1 + c(2));
;
dnds(1, 5) = -.125 * (1 + c(0)) * (1 + c(2));
;
dnds(1, 6) = .125 * (1 + c(0)) * (1 + c(2));
;
dnds(1, 7) = .125 * (1 - c(0)) * (1 + c(2));
;
dnds(2, 0) = -.125 * (1 - c(0)) * (1 - c(1));
;
dnds(2, 1) = -.125 * (1 + c(0)) * (1 - c(1));
;
dnds(2, 2) = -.125 * (1 + c(0)) * (1 + c(1));
;
dnds(2, 3) = -.125 * (1 - c(0)) * (1 + c(1));
;
dnds(2, 4) = .125 * (1 - c(0)) * (1 - c(1));
;
dnds(2, 5) = .125 * (1 + c(0)) * (1 - c(1));
;
dnds(2, 6) = .125 * (1 + c(0)) * (1 + c(1));
;
dnds(2, 7) = .125 * (1 - c(0)) * (1 + c(1));
;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_hexahedron_8>::getInradius(const Matrix<Real> & coord) {
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Vector<Real> u4 = coord(4);
Vector<Real> u5 = coord(5);
Vector<Real> u6 = coord(6);
Vector<Real> u7 = coord(7);
Real a = u0.distance(u1);
Real b = u1.distance(u2);
Real c = u2.distance(u3);
Real d = u3.distance(u0);
Real e = u0.distance(u4);
Real f = u1.distance(u5);
Real g = u2.distance(u6);
Real h = u3.distance(u7);
Real i = u4.distance(u5);
Real j = u5.distance(u6);
Real k = u6.distance(u7);
Real l = u7.distance(u4);
Real x = std::min(a, std::min(b, std::min(c, d)));
Real y = std::min(e, std::min(f, std::min(g, h)));
Real z = std::min(i, std::min(j, std::min(k, l)));
Real p = std::min(x, std::min(y, z));
return p;
}
diff --git a/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.cc b/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.cc
index b74beaa9e..1f75e71c8 100644
--- a/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.cc
@@ -1,212 +1,214 @@
/**
* @file element_class_kirchhoff_shell_inline_impl.cc
*
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 04 2014
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Feb 21 2018
*
* @brief Element class Kirchhoff Shell
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class_structural.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_CC__
#define __AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(
_itp_discrete_kirchhoff_triangle_18, _itp_lagrange_triangle_3, 6, 6, 21);
AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY(
_discrete_kirchhoff_triangle_18, _gt_triangle_3,
_itp_discrete_kirchhoff_triangle_18, _triangle_3, _ek_structural, 3,
_git_triangle, 2);
/* -------------------------------------------------------------------------- */
namespace detail {
inline void computeBasisChangeMatrix(Matrix<Real> & P,
const Matrix<Real> & X) {
Vector<Real> X1 = X(0);
Vector<Real> X2 = X(1);
Vector<Real> X3 = X(2);
Vector<Real> a1 = X2 - X1;
Vector<Real> a2 = X3 - X1;
a1.normalize();
Vector<Real> e3 = a1.crossProduct(a2);
e3.normalize();
Vector<Real> e2 = e3.crossProduct(a1);
P(0) = a1;
P(1) = e2;
P(2) = e3;
P = P.transpose();
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ElementClass<_discrete_kirchhoff_triangle_18>::computeRotationMatrix(
Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> &) {
auto dim = X.rows();
Matrix<Real> P(dim, dim);
detail::computeBasisChangeMatrix(P, X);
R.clear();
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
R(i + dim, j + dim) = R(i, j) = P(i, j);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_discrete_kirchhoff_triangle_18>::computeShapes(
const Vector<Real> & /*natural_coords*/,
const Matrix<Real> & /*real_coord*/, Matrix<Real> & /*N*/) {}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_discrete_kirchhoff_triangle_18>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coordinates,
Matrix<Real> & B) {
auto dim = real_coordinates.cols();
Matrix<Real> P(dim, dim);
detail::computeBasisChangeMatrix(P, real_coordinates);
auto X = P * real_coordinates;
Vector<Real> X1 = X(0);
Vector<Real> X2 = X(1);
Vector<Real> X3 = X(2);
std::array<Vector<Real>, 3> A = {X2 - X1, X3 - X2, X1 - X3};
std::array<Real, 3> L, C, S;
// Setting all last coordinates to 0
std::for_each(A.begin(), A.end(), [](auto & a) { a(2) = 0; });
// Computing lengths
std::transform(A.begin(), A.end(), L.begin(),
[](auto & a) { return a.template norm<L_2>(); });
// Computing cosines
std::transform(A.begin(), A.end(), L.begin(), C.begin(),
[](auto & a, auto & l) { return a(0) / l; });
// Computing sines
std::transform(A.begin(), A.end(), L.begin(), S.begin(),
[](auto & a, auto & l) { return a(1) / l; });
// Natural coordinates
Real xi = natural_coords(0);
Real eta = natural_coords(1);
// Derivative of quadratic interpolation functions
Matrix<Real> dP = {{4 * (1 - 2 * xi - eta), 4 * eta, -4 * eta},
{-4 * xi, 4 * xi, 4 * (1 - xi - 2 * eta)}};
Matrix<Real> dNx1 = {
{3. / 2 * (dP(0, 0) * C[0] / L[0] - dP(0, 2) * C[2] / L[2]),
3. / 2 * (dP(0, 1) * C[1] / L[1] - dP(0, 0) * C[0] / L[0]),
3. / 2 * (dP(0, 2) * C[2] / L[2] - dP(0, 1) * C[1] / L[1])},
{3. / 2 * (dP(1, 0) * C[0] / L[0] - dP(1, 2) * C[2] / L[2]),
3. / 2 * (dP(1, 1) * C[1] / L[1] - dP(1, 0) * C[0] / L[0]),
3. / 2 * (dP(1, 2) * C[2] / L[2] - dP(1, 1) * C[1] / L[1])}};
Matrix<Real> dNx2 = {
// clang-format off
{-1 - 3. / 4 * (dP(0, 0) * C[0] * C[0] + dP(0, 2) * C[2] * C[2]),
1 - 3. / 4 * (dP(0, 1) * C[1] * C[1] + dP(0, 0) * C[0] * C[0]),
- 3. / 4 * (dP(0, 2) * C[2] * C[2] + dP(0, 1) * C[1] * C[1])},
{-1 - 3. / 4 * (dP(1, 0) * C[0] * C[0] + dP(1, 2) * C[2] * C[2]),
- 3. / 4 * (dP(1, 1) * C[1] * C[1] + dP(1, 0) * C[0] * C[0]),
1 - 3. / 4 * (dP(1, 2) * C[2] * C[2] + dP(1, 1) * C[1] * C[1])}};
// clang-format on
Matrix<Real> dNx3 = {
{-3. / 4 * (dP(0, 0) * C[0] * S[0] + dP(0, 2) * C[2] * S[2]),
-3. / 4 * (dP(0, 1) * C[1] * S[1] + dP(0, 0) * C[0] * S[0]),
-3. / 4 * (dP(0, 2) * C[2] * S[2] + dP(0, 1) * C[1] * S[1])},
{-3. / 4 * (dP(1, 0) * C[0] * S[0] + dP(1, 2) * C[2] * S[2]),
-3. / 4 * (dP(1, 1) * C[1] * S[1] + dP(1, 0) * C[0] * S[0]),
-3. / 4 * (dP(1, 2) * C[2] * S[2] + dP(1, 1) * C[1] * S[1])}};
Matrix<Real> dNy1 = {
{3. / 2 * (dP(0, 0) * S[0] / L[0] - dP(0, 2) * S[2] / L[2]),
3. / 2 * (dP(0, 1) * S[1] / L[1] - dP(0, 0) * S[0] / L[0]),
3. / 2 * (dP(0, 2) * S[2] / L[2] - dP(0, 1) * S[1] / L[1])},
{3. / 2 * (dP(1, 0) * S[0] / L[0] - dP(1, 2) * S[2] / L[2]),
3. / 2 * (dP(1, 1) * S[1] / L[1] - dP(1, 0) * S[0] / L[0]),
3. / 2 * (dP(1, 2) * S[2] / L[2] - dP(1, 1) * S[1] / L[1])}};
Matrix<Real> dNy2 = dNx3;
Matrix<Real> dNy3 = {
// clang-format off
{-1 - 3. / 4 * (dP(0, 0) * S[0] * S[0] + dP(0, 2) * S[2] * S[2]),
1 - 3. / 4 * (dP(0, 1) * S[1] * S[1] + dP(0, 0) * S[0] * S[0]),
- 3. / 4 * (dP(0, 2) * S[2] * S[2] + dP(0, 1) * S[1] * S[1])},
{-1 - 3. / 4 * (dP(1, 0) * S[0] * S[0] + dP(1, 2) * S[2] * S[2]),
- 3. / 4 * (dP(1, 1) * S[1] * S[1] + dP(1, 0) * S[0] * S[0]),
1 - 3. / 4 * (dP(1, 2) * S[2] * S[2] + dP(1, 1) * S[1] * S[1])}};
// clang-format on
// Derivative of linear (membrane mode) functions
Matrix<Real> dNm(2, 3);
InterpolationElement<_itp_lagrange_triangle_3, _itk_lagrangian>::computeDNDS(
natural_coords, dNm);
UInt i = 0;
for (const Matrix<Real> & mat : {dNm, dNx1, dNx2, dNx3, dNy1, dNy2, dNy3}) {
B.block(mat, 0, i);
i += mat.cols();
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_discrete_kirchhoff_triangle_18,
_itk_structural>::arrangeInVoigt(const Matrix<Real> & dnds,
Matrix<Real> & B) {
Matrix<Real> dNm(2, 3), dNx1(2, 3), dNx2(2, 3), dNx3(2, 3), dNy1(2, 3),
dNy2(2, 3), dNy3(2, 3);
UInt i = 0;
for (Matrix<Real> * mat : {&dNm, &dNx1, &dNx2, &dNx3, &dNy1, &dNy2, &dNy3}) {
*mat = dnds.block(0, i, 2, 3);
i += mat->cols();
}
for (UInt i = 0; i < 3; ++i) {
// clang-format off
Matrix<Real> Bm = {{dNm(0, i), 0, 0, 0, 0, 0},
{0, dNm(1, i), 0, 0, 0, 0},
{dNm(1, i), dNm(0, i), 0, 0, 0, 0}};
Matrix<Real> Bf = {{0, 0, dNx1(0, i), -dNx3(0, i), dNx2(0, i), 0},
{0, 0, dNy1(1, i), -dNy3(1, i), dNy2(1, i), 0},
{0, 0, dNx1(1, i) + dNy1(0, i), -dNx3(1, i) - dNy3(0, i), dNx2(1, i) + dNy2(0, i), 0}};
// clang-format on
B.block(Bm, 0, i * 6);
B.block(Bf, 3, i * 6);
}
}
} // namespace akantu
#endif /* __AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_CC__ */
diff --git a/src/fe_engine/element_classes/element_class_pentahedron_15_inline_impl.cc b/src/fe_engine/element_classes/element_class_pentahedron_15_inline_impl.cc
index 55b8b9d92..74b08b40c 100644
--- a/src/fe_engine/element_classes/element_class_pentahedron_15_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_pentahedron_15_inline_impl.cc
@@ -1,173 +1,173 @@
/**
* @file element_class_pentahedron_15_inline_impl.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Sacha Laffely <sacha.laffely@epfl.ch>
* @author Damien Scantamburlo <damien.scantamburlo@epfl.ch>
*
* @date creation: Tue Mar 31 2015
- * @date last modification: Wed Sep 16 2015
+ * @date last modification: Thu Dec 28 2017
*
* @brief Specialization of the element_class class for the type
-_pentahedron_15
+ * _pentahedron_15
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+terms of the GNU Lesser General Public License as published by the Free
+Software Foundation, either version 3 of the License, or (at your option) any
+later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
z
^
|
|
| 1
| /|\
|/ | \
10 7 6
/ | \
/ | \
4 2--8--0
| \ / /
| \11 /
13 12 9---------->y
| / \ /
|/ \ /
5--14--3
/
/
/
v
x
x y z
* N0 -1 1 0
* N1 -1 0 1
* N2 -1 0 0
* N3 1 1 0
* N4 1 0 1
* N5 1 0 0
* N6 -1 0.5 0.5
* N7 -1 0 0.5
* N8 -1 0.5 0
* N9 0 1 0
* N10 0 0 1
* N11 0 0 0
* N12 1 0.5 0.5
* N13 1 0 0.5
* N14 1 0.5 0
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_pentahedron_15, _gt_pentahedron_15,
_itp_lagrange_pentahedron_15, _ek_regular,
3, _git_pentahedron, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_15>::computeShapes(
const vector_type & c, vector_type & N) {
auto & x = c(0);
auto & y = c(1);
auto & z = c(2);
// Shape Functions, Natural coordinates
N(0) = 0.5 * y * (1 - x) * (2 * y - 2 - x);
N(1) = 0.5 * z * (1 - x) * (2 * z - 2 - x);
N(2) = 0.5 * (x - 1) * (1 - y - z) * (x + 2 * y + 2 * z);
N(3) = 0.5 * y * (1 + x) * (2 * y - 2 + x);
N(4) = 0.5 * z * (1 + x) * (2 * z - 2 + x);
N(5) = 0.5 * (-x - 1) * (1 - y - z) * (-x + 2 * y + 2 * z);
N(6) = 2.0 * y * z * (1 - x);
N(7) = 2.0 * z * (1 - y - z) * (1 - x);
N(8) = 2.0 * y * (1 - x) * (1 - y - z);
N(9) = y * (1 - x * x);
N(10) = z * (1 - x * x);
N(11) = (1 - y - z) * (1 - x * x);
N(12) = 2.0 * y * z * (1 + x);
N(13) = 2.0 * z * (1 - y - z) * (1 + x);
N(14) = 2.0 * y * (1 - y - z) * (1 + x);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_15>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
auto & x = c(0);
auto & y = c(1);
auto & z = c(2);
// ddx
dnds(0, 0) = 0.5 * y * (2 * x - 2 * y + 1);
dnds(0, 1) = 0.5 * z * (2 * x - 2 * z + 1);
dnds(0, 2) = -0.5 * (2 * x + 2 * y + 2 * z - 1) * (y + z - 1);
dnds(0, 3) = 0.5 * y * (2 * x + 2 * y - 1);
dnds(0, 4) = 0.5 * z * (2 * x + 2 * z - 1);
dnds(0, 5) = -0.5 * (y + z - 1) * (2 * x - 2 * y - 2 * z + 1);
dnds(0, 6) = -2.0 * y * z;
dnds(0, 7) = 2.0 * z * (y + z - 1);
dnds(0, 8) = 2.0 * y * (y + z - 1);
dnds(0, 9) = -2.0 * x * y;
dnds(0, 10) = -2.0 * x * z;
dnds(0, 11) = 2.0 * x * (y + z - 1);
dnds(0, 12) = 2.0 * y * z;
dnds(0, 13) = -2.0 * z * (y + z - 1);
dnds(0, 14) = -2.0 * y * (y + z - 1);
// ddy
dnds(1, 0) = -0.5 * (x - 1) * (4 * y - x - 2);
dnds(1, 1) = 0.0;
dnds(1, 2) = -0.5 * (x - 1) * (4 * y + x + 2 * (2 * z - 1));
dnds(1, 3) = 0.5 * (x + 1) * (4 * y + x - 2);
dnds(1, 4) = 0.0;
dnds(1, 5) = 0.5 * (x + 1) * (4 * y - x + 2 * (2 * z - 1));
dnds(1, 6) = -2.0 * (x - 1) * z;
dnds(1, 7) = 2.0 * z * (x - 1);
dnds(1, 8) = 2.0 * (2 * y + z - 1) * (x - 1);
dnds(1, 9) = -(x * x - 1);
dnds(1, 10) = 0.0;
dnds(1, 11) = (x * x - 1);
dnds(1, 12) = 2.0 * z * (x + 1);
dnds(1, 13) = -2.0 * z * (x + 1);
dnds(1, 14) = -2.0 * (2 * y + z - 1) * (x + 1);
// ddz
dnds(2, 0) = 0.0;
dnds(2, 1) = -0.5 * (x - 1) * (4 * z - x - 2);
dnds(2, 2) = -0.5 * (x - 1) * (4 * z + x + 2 * (2 * y - 1));
dnds(2, 3) = 0.0;
dnds(2, 4) = 0.5 * (x + 1) * (4 * z + x - 2);
dnds(2, 5) = 0.5 * (x + 1) * (4 * z - x + 2 * (2 * y - 1));
dnds(2, 6) = -2.0 * (x - 1) * y;
dnds(2, 7) = 2.0 * (x - 1) * (2 * z + y - 1);
dnds(2, 8) = 2.0 * y * (x - 1);
dnds(2, 9) = 0.0;
dnds(2, 10) = -(x * x - 1);
dnds(2, 11) = (x * x - 1);
dnds(2, 12) = 2.0 * (x + 1) * y;
dnds(2, 13) = -2.0 * (x + 1) * (2 * z + y - 1);
dnds(2, 14) = -2.0 * (x + 1) * y;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real GeometricalElement<_gt_pentahedron_15>::getInradius(
const Matrix<Real> & coord) {
return GeometricalElement<_gt_pentahedron_6>::getInradius(coord);
}
diff --git a/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.cc b/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.cc
index 806c0370b..1f7de539e 100644
--- a/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.cc
@@ -1,128 +1,127 @@
/**
* @file element_class_pentahedron_6_inline_impl.cc
*
* @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
*
* @date creation: Mon Mar 14 2011
- * @date last modification: Tue Sep 01 2015
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _pentahedron_6
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+terms of the GNU Lesser General Public License as published by the Free
+Software Foundation, either version 3 of the License, or (at your option) any
+later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
/z
|
|
| 1
| /|\
|/ | \
/ | \
/ | \
/ | \
4 2-----0
| \ / /
| \/ /
| \ /----------/y
| / \ /
|/ \ /
5---.--3
/
/
/
\x
x y z
* N0 -1 1 0
* N1 -1 0 1
* N2 -1 0 0
* N3 1 1 0
* N4 1 0 1
* N5 1 0 0
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_pentahedron_6, _gt_pentahedron_6,
_itp_lagrange_pentahedron_6, _ek_regular,
3, _git_pentahedron, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_6>::computeShapes(
const vector_type & c, vector_type & N) {
/// Natural coordinates
N(0) = 0.5 * c(1) * (1 - c(0)); // N1(q)
N(1) = 0.5 * c(2) * (1 - c(0)); // N2(q)
N(2) = 0.5 * (1 - c(1) - c(2)) * (1 - c(0)); // N3(q)
N(3) = 0.5 * c(1) * (1 + c(0)); // N4(q)
N(4) = 0.5 * c(2) * (1 + c(0)); // N5(q)
N(5) = 0.5 * (1 - c(1) - c(2)) * (1 + c(0)); // N6(q)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_6>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
dnds(0, 0) = -0.5 * c(1);
dnds(0, 1) = -0.5 * c(2);
dnds(0, 2) = -0.5 * (1 - c(1) - c(2));
dnds(0, 3) = 0.5 * c(1);
dnds(0, 4) = 0.5 * c(2);
dnds(0, 5) = 0.5 * (1 - c(1) - c(2));
dnds(1, 0) = 0.5 * (1 - c(0));
dnds(1, 1) = 0.0;
dnds(1, 2) = -0.5 * (1 - c(0));
dnds(1, 3) = 0.5 * (1 + c(0));
dnds(1, 4) = 0.0;
dnds(1, 5) = -0.5 * (1 + c(0));
dnds(2, 0) = 0.0;
dnds(2, 1) = 0.5 * (1 - c(0));
dnds(2, 2) = -0.5 * (1 - c(0));
dnds(2, 3) = 0.0;
dnds(2, 4) = 0.5 * (1 + c(0));
dnds(2, 5) = -0.5 * (1 + c(0));
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_pentahedron_6>::getInradius(const Matrix<Real> & coord) {
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Real a = u0.distance(u1);
Real b = u1.distance(u2);
Real c = u2.distance(u3);
Real d = u3.distance(u0);
Real s = (a + b + c) / 2;
Real A = std::sqrt(s * (s - a) * (s - b) * (s - c));
Real ra = 2 * s / A;
Real p = std::min(ra, d);
return p;
}
diff --git a/src/fe_engine/element_classes/element_class_point_1_inline_impl.cc b/src/fe_engine/element_classes/element_class_point_1_inline_impl.cc
index ff0fbb514..838767d4f 100644
--- a/src/fe_engine/element_classes/element_class_point_1_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_point_1_inline_impl.cc
@@ -1,79 +1,78 @@
/**
* @file element_class_point_1_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _point_1
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
x
(0)
@endverbatim
*
* @subsection shapes Shape functions
* @f{eqnarray*}{
* N1 &=& 1
* @f}
*
* @subsection quad_points Position of quadrature points
* @f{eqnarray*}{
* q_0 &=& 0
* @f}
*/
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_point_1, _gt_point, _itp_lagrange_point_1,
_ek_regular, 0, _git_point, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_point_1>::computeShapes(
__attribute__((unused)) const vector_type & natural_coords,
vector_type & N) {
N(0) = 1; /// N1(q_0)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_point_1>::computeDNDS(
__attribute__((unused)) const vector_type & natural_coords,
__attribute__((unused)) matrix_type & dnds) {}
/* -------------------------------------------------------------------------- */
template <>
inline void InterpolationElement<_itp_lagrange_point_1>::computeSpecialJacobian(
__attribute__((unused)) const Matrix<Real> & J, Real & jac) {
jac = 0.;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_point>::getInradius(__attribute__((unused))
const Matrix<Real> & coord) {
return 0.;
}
diff --git a/src/fe_engine/element_classes/element_class_quadrangle_4_inline_impl.cc b/src/fe_engine/element_classes/element_class_quadrangle_4_inline_impl.cc
index f204bc660..db3a606ad 100644
--- a/src/fe_engine/element_classes/element_class_quadrangle_4_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_quadrangle_4_inline_impl.cc
@@ -1,155 +1,154 @@
/**
* @file element_class_quadrangle_4_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Mon Dec 08 2014
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _quadrangle_4
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
\eta
^
(-1,1) | (1,1)
x---------x
| | |
| | |
--|---------|-----> \xi
| | |
| | |
x---------x
(-1,-1) | (1,-1)
@endverbatim
*
* @subsection shapes Shape functions
* @f[
* \begin{array}{lll}
* N1 = (1 - \xi) (1 - \eta) / 4
* & \frac{\partial N1}{\partial \xi} = - (1 - \eta) / 4
* & \frac{\partial N1}{\partial \eta} = - (1 - \xi) / 4 \\
* N2 = (1 + \xi) (1 - \eta) / 4 \\
* & \frac{\partial N2}{\partial \xi} = (1 - \eta) / 4
* & \frac{\partial N2}{\partial \eta} = - (1 + \xi) / 4 \\
* N3 = (1 + \xi) (1 + \eta) / 4 \\
* & \frac{\partial N3}{\partial \xi} = (1 + \eta) / 4
* & \frac{\partial N3}{\partial \eta} = (1 + \xi) / 4 \\
* N4 = (1 - \xi) (1 + \eta) / 4
* & \frac{\partial N4}{\partial \xi} = - (1 + \eta) / 4
* & \frac{\partial N4}{\partial \eta} = (1 - \xi) / 4 \\
* \end{array}
* @f]
*
* @subsection quad_points Position of quadrature points
* @f{eqnarray*}{
* \xi_{q0} &=& 0 \qquad \eta_{q0} = 0
* @f}
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_quadrangle_4, _gt_quadrangle_4,
_itp_lagrange_quadrangle_4, _ek_regular, 2,
_git_segment, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_quadrangle_4>::computeShapes(
const vector_type & c, vector_type & N) {
N(0) = 1. / 4. * (1. - c(0)) * (1. - c(1)); /// N1(q_0)
N(1) = 1. / 4. * (1. + c(0)) * (1. - c(1)); /// N2(q_0)
N(2) = 1. / 4. * (1. + c(0)) * (1. + c(1)); /// N3(q_0)
N(3) = 1. / 4. * (1. - c(0)) * (1. + c(1)); /// N4(q_0)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_quadrangle_4>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi}
* & \frac{\partial N3}{\partial \xi} & \frac{\partial
* N4}{\partial \xi}\\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta}
* & \frac{\partial N3}{\partial \eta} & \frac{\partial
* N4}{\partial \eta}
* \end{array}
* \right)
* @f]
*/
dnds(0, 0) = -1. / 4. * (1. - c(1));
dnds(0, 1) = 1. / 4. * (1. - c(1));
dnds(0, 2) = 1. / 4. * (1. + c(1));
dnds(0, 3) = -1. / 4. * (1. + c(1));
dnds(1, 0) = -1. / 4. * (1. - c(0));
dnds(1, 1) = -1. / 4. * (1. + c(0));
dnds(1, 2) = 1. / 4. * (1. + c(0));
dnds(1, 3) = 1. / 4. * (1. - c(0));
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_quadrangle_4>::computeSpecialJacobian(
const Matrix<Real> & J, Real & jac) {
Vector<Real> vprod(J.cols());
Matrix<Real> Jt(J.transpose(), true);
vprod.crossProduct(Jt(0), Jt(1));
jac = vprod.norm();
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_quadrangle_4>::getInradius(const Matrix<Real> & coord) {
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Real a = u0.distance(u1);
Real b = u1.distance(u2);
Real c = u2.distance(u3);
Real d = u3.distance(u0);
// Real septimetre = (a + b + c + d) / 2.;
// Real p = Math::distance_2d(coord + 0, coord + 4);
// Real q = Math::distance_2d(coord + 2, coord + 6);
// Real area = sqrt(4*(p*p * q*q) - (a*a + b*b + c*c + d*d)*(a*a + c*c - b*b -
// d*d)) / 4.;
// Real h = sqrt(area); // to get a length
// Real h = area / septimetre; // formula of inradius for circumscritable
// quadrelateral
Real h = std::min(a, std::min(b, std::min(c, d)));
return h;
}
diff --git a/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.cc b/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.cc
index df4f635ca..632d27125 100644
--- a/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.cc
@@ -1,186 +1,185 @@
/**
* @file element_class_quadrangle_8_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed May 18 2011
- * @date last modification: Tue Apr 07 2015
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the ElementClass for the _quadrangle_8
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
\eta
^
|
(-1,1) (0,1) (1,1)
x-------x-------x
| | |
| | |
| | |
(-1,0)| | |(1,0)
----x---------------X-----> \xi
| | |
| | |
| | |
| | |
x-------x-------x
(-1,-1) (0,-1) (1,-1)
|
@endverbatim
*
* @subsection shapes Shape functions
* @f[
* \begin{array}{lll}
* N1 = (1 - \xi) (1 - \eta)(- 1 - \xi - \eta) / 4
* & \frac{\partial N1}{\partial \xi} = (1 - \eta)(2 \xi + \eta) / 4
* & \frac{\partial N1}{\partial \eta} = (1 - \xi)(\xi + 2 \eta) / 4 \\
* N2 = (1 + \xi) (1 - \eta)(- 1 + \xi - \eta) / 4 \\
* & \frac{\partial N2}{\partial \xi} = (1 - \eta)(2 \xi - \eta) / 4
* & \frac{\partial N2}{\partial \eta} = - (1 + \xi)(\xi - 2 \eta) / 4 \\
* N3 = (1 + \xi) (1 + \eta)(- 1 + \xi + \eta) / 4 \\
* & \frac{\partial N3}{\partial \xi} = (1 + \eta)(2 \xi + \eta) / 4
* & \frac{\partial N3}{\partial \eta} = (1 + \xi)(\xi + 2 \eta) / 4 \\
* N4 = (1 - \xi) (1 + \eta)(- 1 - \xi + \eta) / 4
* & \frac{\partial N4}{\partial \xi} = (1 + \eta)(2 \xi - \eta) / 4
* & \frac{\partial N4}{\partial \eta} = - (1 - \xi)(\xi - 2 \eta) / 4 \\
* N5 = (1 - \xi^2) (1 - \eta) / 2
* & \frac{\partial N1}{\partial \xi} = - \xi (1 - \eta)
* & \frac{\partial N1}{\partial \eta} = - (1 - \xi^2) / 2 \\
* N6 = (1 + \xi) (1 - \eta^2) / 2 \\
* & \frac{\partial N2}{\partial \xi} = (1 - \eta^2) / 2
* & \frac{\partial N2}{\partial \eta} = - \eta (1 + \xi) \\
* N7 = (1 - \xi^2) (1 + \eta) / 2 \\
* & \frac{\partial N3}{\partial \xi} = - \xi (1 + \eta)
* & \frac{\partial N3}{\partial \eta} = (1 - \xi^2) / 2 \\
* N8 = (1 - \xi) (1 - \eta^2) / 2
* & \frac{\partial N4}{\partial \xi} = - (1 - \eta^2) / 2
* & \frac{\partial N4}{\partial \eta} = - \eta (1 - \xi) \\
* \end{array}
* @f]
*
* @subsection quad_points Position of quadrature points
* @f{eqnarray*}{
* \xi_{q0} &=& 0 \qquad \eta_{q0} = 0
* @f}
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_quadrangle_8, _gt_quadrangle_8,
_itp_serendip_quadrangle_8, _ek_regular, 2,
_git_segment, 3);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_serendip_quadrangle_8>::computeShapes(
const vector_type & c, vector_type & N) {
/// Natural coordinates
const Real xi = c(0);
const Real eta = c(1);
N(0) = .25 * (1 - xi) * (1 - eta) * (-1 - xi - eta);
N(1) = .25 * (1 + xi) * (1 - eta) * (-1 + xi - eta);
N(2) = .25 * (1 + xi) * (1 + eta) * (-1 + xi + eta);
N(3) = .25 * (1 - xi) * (1 + eta) * (-1 - xi + eta);
N(4) = .5 * (1 - xi * xi) * (1 - eta);
N(5) = .5 * (1 + xi) * (1 - eta * eta);
N(6) = .5 * (1 - xi * xi) * (1 + eta);
N(7) = .5 * (1 - xi) * (1 - eta * eta);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_serendip_quadrangle_8>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
const Real xi = c(0);
const Real eta = c(1);
/// dN/dxi
dnds(0, 0) = .25 * (1 - eta) * (2 * xi + eta);
dnds(0, 1) = .25 * (1 - eta) * (2 * xi - eta);
dnds(0, 2) = .25 * (1 + eta) * (2 * xi + eta);
dnds(0, 3) = .25 * (1 + eta) * (2 * xi - eta);
dnds(0, 4) = -xi * (1 - eta);
dnds(0, 5) = .5 * (1 - eta * eta);
dnds(0, 6) = -xi * (1 + eta);
dnds(0, 7) = -.5 * (1 - eta * eta);
/// dN/deta
dnds(1, 0) = .25 * (1 - xi) * (2 * eta + xi);
dnds(1, 1) = .25 * (1 + xi) * (2 * eta - xi);
dnds(1, 2) = .25 * (1 + xi) * (2 * eta + xi);
dnds(1, 3) = .25 * (1 - xi) * (2 * eta - xi);
dnds(1, 4) = -.5 * (1 - xi * xi);
dnds(1, 5) = -eta * (1 + xi);
dnds(1, 6) = .5 * (1 - xi * xi);
dnds(1, 7) = -eta * (1 - xi);
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_quadrangle_8>::getInradius(const Matrix<Real> & coord) {
Real a, b, h;
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Vector<Real> u4 = coord(4);
Vector<Real> u5 = coord(5);
Vector<Real> u6 = coord(6);
Vector<Real> u7 = coord(7);
a = u0.distance(u4);
b = u4.distance(u1);
h = std::min(a, b);
a = u1.distance(u5);
b = u5.distance(u2);
h = std::min(h, std::min(a, b));
a = u2.distance(u6);
b = u6.distance(u3);
h = std::min(h, std::min(a, b));
a = u3.distance(u7);
b = u7.distance(u0);
h = std::min(h, std::min(a, b));
return h;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_serendip_quadrangle_8>::computeSpecialJacobian(
const Matrix<Real> & J, Real & jac) {
Vector<Real> vprod(J.cols());
Matrix<Real> Jt(J.transpose(), true);
vprod.crossProduct(Jt(0), Jt(1));
jac = vprod.norm();
}
diff --git a/src/fe_engine/element_classes/element_class_segment_2_inline_impl.cc b/src/fe_engine/element_classes/element_class_segment_2_inline_impl.cc
index 0ac10eca0..60a78a17c 100644
--- a/src/fe_engine/element_classes/element_class_segment_2_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_segment_2_inline_impl.cc
@@ -1,105 +1,104 @@
/**
* @file element_class_segment_2_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _segment_2
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
q
--x--------|--------x---> x
-1 0 1
@endverbatim
*
* @subsection shapes Shape functions
* @f{eqnarray*}{
* w_1(x) &=& 1/2(1 - x) \\
* w_2(x) &=& 1/2(1 + x)
* @f}
*
* @subsection quad_points Position of quadrature points
* @f{eqnarray*}{
* x_{q} &=& 0
* @f}
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_segment_2, _gt_segment_2,
_itp_lagrange_segment_2, _ek_regular, 1,
_git_segment, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_segment_2>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
/// natural coordinate
Real c = natural_coords(0);
/// shape functions
N(0) = 0.5 * (1 - c);
N(1) = 0.5 * (1 + c);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_segment_2>::computeDNDS(
__attribute__((unused)) const vector_type & natural_coords,
matrix_type & dnds) {
/// dN1/de
dnds(0, 0) = -.5;
/// dN2/de
dnds(0, 1) = .5;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_segment_2>::computeSpecialJacobian(
const Matrix<Real> & dxds, Real & jac) {
jac = dxds.norm<L_2>();
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_segment_2>::getInradius(const Matrix<Real> & coord) {
return std::abs(coord(0, 0) - coord(0, 1));
}
// /* --------------------------------------------------------------------------
// */
// template<> inline bool ElementClass<_segment_2>::contains(const Vector<Real>
// & natural_coords) {
// if (natural_coords(0) < -1.) return false;
// if (natural_coords(0) > 1.) return false;
// return true;
// }
/* -------------------------------------------------------------------------- */
diff --git a/src/fe_engine/element_classes/element_class_segment_3_inline_impl.cc b/src/fe_engine/element_classes/element_class_segment_3_inline_impl.cc
index 710de16f9..3fa470a40 100644
--- a/src/fe_engine/element_classes/element_class_segment_3_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_segment_3_inline_impl.cc
@@ -1,106 +1,105 @@
/**
* @file element_class_segment_3_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _segment_3
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
-1 0 1
-----x---------x---------x-----> x
1 3 2
@endverbatim
*
* @subsection coords Nodes coordinates
*
* @f[
* \begin{array}{lll}
* x_{1} = -1 & x_{2} = 1 & x_{3} = 0
* \end{array}
* @f]
*
* @subsection shapes Shape functions
* @f[
* \begin{array}{ll}
* w_1(x) = \frac{x}{2}(x - 1) & w'_1(x) = x - \frac{1}{2}\\
* w_2(x) = \frac{x}{2}(x + 1) & w'_2(x) = x + \frac{1}{2}\\
* w_3(x) = 1-x^2 & w'_3(x) = -2x
* \end{array}
* @f]
*
* @subsection quad_points Position of quadrature points
* @f[
* \begin{array}{ll}
* x_{q1} = -1/\sqrt{3} & x_{q2} = 1/\sqrt{3}
* \end{array}
* @f]
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_segment_3, _gt_segment_3,
_itp_lagrange_segment_3, _ek_regular, 1,
_git_segment, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_segment_3>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
Real c = natural_coords(0);
N(0) = (c - 1) * c / 2;
N(1) = (c + 1) * c / 2;
N(2) = 1 - c * c;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_segment_3>::computeDNDS(
const vector_type & natural_coords, matrix_type & dnds) {
Real c = natural_coords(0);
dnds(0, 0) = c - .5;
dnds(0, 1) = c + .5;
dnds(0, 2) = -2 * c;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_segment_3>::computeSpecialJacobian(
const Matrix<Real> & dxds, Real & jac) {
jac = Math::norm2(dxds.storage());
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_segment_3>::getInradius(const Matrix<Real> & coord) {
Real dist1 = std::abs(coord(0, 0) - coord(0, 1));
Real dist2 = std::abs(coord(0, 1) - coord(0, 2));
return std::min(dist1, dist2);
}
diff --git a/src/fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.cc b/src/fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.cc
index f5dab36fa..f1df60b6e 100644
--- a/src/fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.cc
@@ -1,278 +1,277 @@
/**
* @file element_class_tetrahedron_10_inline_impl.cc
*
* @author Peter Spijker <peter.spijker@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type
- _tetrahedron_10
+ * _tetrahedron_10
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
\zeta
^
|
(0,0,1)
x
|` .
| ` .
| ` .
| ` . (0,0.5,0.5)
| ` x.
| q4 o ` . \eta
| ` . -,
(0,0,0.5) x ` x (0.5,0,0.5) -
| ` x-(0,1,0)
| q3 o` - '
| (0,0.5,0) - ` '
| x- ` x (0.5,0.5,0)
| q1 o - o q2` '
| - ` '
| - ` '
x---------------x--------------` x-----> \xi
(0,0,0) (0.5,0,0) (1,0,0)
@endverbatim
*
* @subsection coords Nodes coordinates
*
* @f[
* \begin{array}{lll}
* \xi_{0} = 0 & \eta_{0} = 0 & \zeta_{0} = 0 \\
* \xi_{1} = 1 & \eta_{1} = 0 & \zeta_{1} = 0 \\
* \xi_{2} = 0 & \eta_{2} = 1 & \zeta_{2} = 0 \\
* \xi_{3} = 0 & \eta_{3} = 0 & \zeta_{3} = 1 \\
* \xi_{4} = 1/2 & \eta_{4} = 0 & \zeta_{4} = 0 \\
* \xi_{5} = 1/2 & \eta_{5} = 1/2 & \zeta_{5} = 0 \\
* \xi_{6} = 0 & \eta_{6} = 1/2 & \zeta_{6} = 0 \\
* \xi_{7} = 0 & \eta_{7} = 0 & \zeta_{7} = 1/2 \\
* \xi_{8} = 1/2 & \eta_{8} = 0 & \zeta_{8} = 1/2 \\
* \xi_{9} = 0 & \eta_{9} = 1/2 & \zeta_{9} = 1/2
* \end{array}
* @f]
*
* @subsection shapes Shape functions
* @f[
* \begin{array}{llll}
* N1 = (1 - \xi - \eta - \zeta) (1 - 2 \xi - 2 \eta - 2 \zeta)
* & \frac{\partial N1}{\partial \xi} = 4 \xi + 4 \eta + 4 \zeta -
3
* & \frac{\partial N1}{\partial \eta} = 4 \xi + 4 \eta + 4 \zeta -
3
* & \frac{\partial N1}{\partial \zeta} = 4 \xi + 4 \eta + 4 \zeta -
3 \\
* N2 = \xi (2 \xi - 1)
* & \frac{\partial N2}{\partial \xi} = 4 \xi - 1
* & \frac{\partial N2}{\partial \eta} = 0
* & \frac{\partial N2}{\partial \zeta} = 0 \\
* N3 = \eta (2 \eta - 1)
* & \frac{\partial N3}{\partial \xi} = 0
* & \frac{\partial N3}{\partial \eta} = 4 \eta - 1
* & \frac{\partial N3}{\partial \zeta} = 0 \\
* N4 = \zeta (2 \zeta - 1)
* & \frac{\partial N4}{\partial \xi} = 0
* & \frac{\partial N4}{\partial \eta} = 0
* & \frac{\partial N4}{\partial \zeta} = 4 \zeta - 1 \\
* N5 = 4 \xi (1 - \xi - \eta - \zeta)
* & \frac{\partial N5}{\partial \xi} = 4 - 8 \xi - 4 \eta - 4
\zeta
* & \frac{\partial N5}{\partial \eta} = -4 \xi
* & \frac{\partial N5}{\partial \zeta} = -4 \xi \\
* N6 = 4 \xi \eta
* & \frac{\partial N6}{\partial \xi} = 4 \eta
* & \frac{\partial N6}{\partial \eta} = 4 \xi
* & \frac{\partial N6}{\partial \zeta} = 0 \\
* N7 = 4 \eta (1 - \xi - \eta - \zeta)
* & \frac{\partial N7}{\partial \xi} = -4 \eta
* & \frac{\partial N7}{\partial \eta} = 4 - 4 \xi - 8 \eta - 4
\zeta
* & \frac{\partial N7}{\partial \zeta} = -4 \eta \\
* N8 = 4 \zeta (1 - \xi - \eta - \zeta)
* & \frac{\partial N8}{\partial \xi} = -4 \zeta
* & \frac{\partial N8}{\partial \eta} = -4 \zeta
* & \frac{\partial N8}{\partial \zeta} = 4 - 4 \xi - 4 \eta - 8
\zeta \\
* N9 = 4 \zeta \xi
* & \frac{\partial N9}{\partial \xi} = 4 \zeta
* & \frac{\partial N9}{\partial \eta} = 0
* & \frac{\partial N9}{\partial \zeta} = 4 \xi \\
* N10 = 4 \eta \zeta
* & \frac{\partial N10}{\partial \xi} = 0
* & \frac{\partial N10}{\partial \eta} = 4 \zeta
* & \frac{\partial N10}{\partial \zeta} = 4 \eta \\
* \end{array}
* @f]
*
* @subsection quad_points Position of quadrature points
* @f[
* a = \frac{5 - \sqrt{5}}{20}\\
* b = \frac{5 + 3 \sqrt{5}}{20}
* \begin{array}{lll}
* \xi_{q_0} = a & \eta_{q_0} = a & \zeta_{q_0} = a \\
* \xi_{q_1} = b & \eta_{q_1} = a & \zeta_{q_1} = a \\
* \xi_{q_2} = a & \eta_{q_2} = b & \zeta_{q_2} = a \\
* \xi_{q_3} = a & \eta_{q_3} = a & \zeta_{q_3} = b
* \end{array}
* @f]
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_tetrahedron_10, _gt_tetrahedron_10,
_itp_lagrange_tetrahedron_10, _ek_regular,
3, _git_tetrahedron, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_tetrahedron_10>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
/// Natural coordinates
Real xi = natural_coords(0);
Real eta = natural_coords(1);
Real zeta = natural_coords(2);
Real sum = xi + eta + zeta;
Real c0 = 1 - sum;
Real c1 = 1 - 2 * sum;
Real c2 = 2 * xi - 1;
Real c3 = 2 * eta - 1;
Real c4 = 2 * zeta - 1;
/// Shape functions
N(0) = c0 * c1;
N(1) = xi * c2;
N(2) = eta * c3;
N(3) = zeta * c4;
N(4) = 4 * xi * c0;
N(5) = 4 * xi * eta;
N(6) = 4 * eta * c0;
N(7) = 4 * zeta * c0;
N(8) = 4 * xi * zeta;
N(9) = 4 * eta * zeta;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_tetrahedron_10>::computeDNDS(
const vector_type & natural_coords, matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccccccccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi}
* & \frac{\partial N3}{\partial \xi} & \frac{\partial N4}{\partial
* \xi}
* & \frac{\partial N5}{\partial \xi} & \frac{\partial N6}{\partial
* \xi}
* & \frac{\partial N7}{\partial \xi} & \frac{\partial N8}{\partial
* \xi}
* & \frac{\partial N9}{\partial \xi} & \frac{\partial
* N10}{\partial \xi} \\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta}
* & \frac{\partial N3}{\partial \eta} & \frac{\partial N4}{\partial
* \eta}
* & \frac{\partial N5}{\partial \eta} & \frac{\partial N6}{\partial
* \eta}
* & \frac{\partial N7}{\partial \eta} & \frac{\partial N8}{\partial
* \eta}
* & \frac{\partial N9}{\partial \eta} & \frac{\partial
* N10}{\partial \eta} \\
* \frac{\partial N1}{\partial \zeta} & \frac{\partial N2}{\partial
* \zeta}
* & \frac{\partial N3}{\partial \zeta} & \frac{\partial N4}{\partial
* \zeta}
* & \frac{\partial N5}{\partial \zeta} & \frac{\partial N6}{\partial
* \zeta}
* & \frac{\partial N7}{\partial \zeta} & \frac{\partial N8}{\partial
* \zeta}
* & \frac{\partial N9}{\partial \zeta} & \frac{\partial
* N10}{\partial \zeta}
* \end{array}
* \right)
* @f]
*/
/// Natural coordinates
Real xi = natural_coords(0);
Real eta = natural_coords(1);
Real zeta = natural_coords(2);
Real sum = xi + eta + zeta;
/// \frac{\partial N_i}{\partial \xi}
dnds(0, 0) = 4 * sum - 3;
dnds(0, 1) = 4 * xi - 1;
dnds(0, 2) = 0;
dnds(0, 3) = 0;
dnds(0, 4) = 4 * (1 - sum - xi);
dnds(0, 5) = 4 * eta;
dnds(0, 6) = -4 * eta;
dnds(0, 7) = -4 * zeta;
dnds(0, 8) = 4 * zeta;
dnds(0, 9) = 0;
/// \frac{\partial N_i}{\partial \eta}
dnds(1, 0) = 4 * sum - 3;
dnds(1, 1) = 0;
dnds(1, 2) = 4 * eta - 1;
dnds(1, 3) = 0;
dnds(1, 4) = -4 * xi;
dnds(1, 5) = 4 * xi;
dnds(1, 6) = 4 * (1 - sum - eta);
dnds(1, 7) = -4 * zeta;
dnds(1, 8) = 0;
dnds(1, 9) = 4 * zeta;
/// \frac{\partial N_i}{\partial \zeta}
dnds(2, 0) = 4 * sum - 3;
dnds(2, 1) = 0;
dnds(2, 2) = 0;
dnds(2, 3) = 4 * zeta - 1;
dnds(2, 4) = -4 * xi;
dnds(2, 5) = 0;
dnds(2, 6) = -4 * eta;
dnds(2, 7) = 4 * (1 - sum - zeta);
dnds(2, 8) = 4 * xi;
dnds(2, 9) = 4 * eta;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real GeometricalElement<_gt_tetrahedron_10>::getInradius(
const Matrix<Real> & coord) {
// Only take the four corner tetrahedra
UInt tetrahedra[4][4] = {
{0, 4, 6, 7}, {4, 1, 5, 8}, {6, 5, 2, 9}, {7, 8, 9, 3}};
Real inradius = std::numeric_limits<Real>::max();
for (UInt t = 0; t < 4; t++) {
Real ir = Math::tetrahedron_inradius(
coord(tetrahedra[t][0]).storage(), coord(tetrahedra[t][1]).storage(),
coord(tetrahedra[t][2]).storage(), coord(tetrahedra[t][3]).storage());
inradius = std::min(ir, inradius);
}
return inradius;
}
diff --git a/src/fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.cc b/src/fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.cc
index 76f6d85bc..5577d6c3b 100644
--- a/src/fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.cc
@@ -1,134 +1,133 @@
/**
* @file element_class_tetrahedron_4_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _tetrahedron_4
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
\eta
^
|
x (0,0,1,0)
|`
| ` ° \xi
| ` ° -
| ` x (0,0,0,1)
| q.` - '
| -` '
| - ` '
| - ` '
x------------------x-----> \zeta
(1,0,0,0) (0,1,0,0)
@endverbatim
*
* @subsection shapes Shape functions
* @f{eqnarray*}{
* N1 &=& 1 - \xi - \eta - \zeta \\
* N2 &=& \xi \\
* N3 &=& \eta \\
* N4 &=& \zeta
* @f}
*
* @subsection quad_points Position of quadrature points
* @f[
* \xi_{q0} = 1/4 \qquad \eta_{q0} = 1/4 \qquad \zeta_{q0} = 1/4
* @f]
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_tetrahedron_4, _gt_tetrahedron_4,
_itp_lagrange_tetrahedron_4, _ek_regular,
3, _git_tetrahedron, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_tetrahedron_4>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
Real c0 = 1 - natural_coords(0) - natural_coords(1) -
natural_coords(2); /// @f$ c2 = 1 - \xi - \eta - \zeta @f$
Real c1 = natural_coords(1); /// @f$ c0 = \xi @f$
Real c2 = natural_coords(2); /// @f$ c1 = \eta @f$
Real c3 = natural_coords(0); /// @f$ c2 = \zeta @f$
N(0) = c0;
N(1) = c1;
N(2) = c2;
N(3) = c3;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_tetrahedron_4>::computeDNDS(
__attribute__((unused)) const vector_type & natural_coords,
matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi}
* & \frac{\partial N3}{\partial \xi} & \frac{\partial N4}{\partial
* \xi} \\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta}
* & \frac{\partial N3}{\partial \eta} & \frac{\partial N4}{\partial
* \eta} \\
* \frac{\partial N1}{\partial \zeta} & \frac{\partial N2}{\partial
* \zeta}
* & \frac{\partial N3}{\partial \zeta} & \frac{\partial N4}{\partial
* \zeta}
* \end{array}
* \right)
* @f]
*/
dnds(0, 0) = -1.;
dnds(0, 1) = 1.;
dnds(0, 2) = 0.;
dnds(0, 3) = 0.;
dnds(1, 0) = -1.;
dnds(1, 1) = 0.;
dnds(1, 2) = 1.;
dnds(1, 3) = 0.;
dnds(2, 0) = -1.;
dnds(2, 1) = 0.;
dnds(2, 2) = 0.;
dnds(2, 3) = 1.;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_tetrahedron_4>::getInradius(const Matrix<Real> & coord) {
return Math::tetrahedron_inradius(coord(0).storage(), coord(1).storage(),
coord(2).storage(), coord(3).storage());
}
diff --git a/src/fe_engine/element_classes/element_class_triangle_3_inline_impl.cc b/src/fe_engine/element_classes/element_class_triangle_3_inline_impl.cc
index 1b17994d1..77ff9458e 100644
--- a/src/fe_engine/element_classes/element_class_triangle_3_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_triangle_3_inline_impl.cc
@@ -1,134 +1,133 @@
/**
* @file element_class_triangle_3_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _triangle_3
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
\eta
^
|
x (0,0,1)
|`
| `
| q `
| ° `
x--------x-----> \xi
(1,0,0) (0,1,0)
@endverbatim
*
* @subsection shapes Shape functions
* @f{eqnarray*}{
* N1 &=& 1 - \xi - \eta \\
* N2 &=& \xi \\
* N3 &=& \eta
* @f}
*
* @subsection quad_points Position of quadrature points
* @f{eqnarray*}{
* \xi_{q0} &=& 1/3 \qquad \eta_{q0} = 1/3
* @f}
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_triangle_3, _gt_triangle_3,
_itp_lagrange_triangle_3, _ek_regular, 2,
_git_triangle, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_triangle_3>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
/// Natural coordinates
Real c0 =
1 - natural_coords(0) - natural_coords(1); /// @f$ c0 = 1 - \xi - \eta @f$
Real c1 = natural_coords(0); /// @f$ c1 = \xi @f$
Real c2 = natural_coords(1); /// @f$ c2 = \eta @f$
N(0) = c0; /// N1(q_0)
N(1) = c1; /// N2(q_0)
N(2) = c2; /// N3(q_0)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_triangle_3>::computeDNDS(
__attribute__((unused)) const vector_type & natural_coords,
matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi} & \frac{\partial N3}{\partial \xi} \\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta} & \frac{\partial N3}{\partial \eta}
* \end{array}
* \right)
* @f]
*/
dnds(0, 0) = -1.;
dnds(0, 1) = 1.;
dnds(0, 2) = 0.;
dnds(1, 0) = -1.;
dnds(1, 1) = 0.;
dnds(1, 2) = 1.;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_triangle_3>::computeSpecialJacobian(
const Matrix<Real> & J, Real & jac) {
Vector<Real> vprod(J.cols());
Matrix<Real> Jt(J.transpose(), true);
vprod.crossProduct(Jt(0), Jt(1));
jac = vprod.norm();
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_triangle_3>::getInradius(const Matrix<Real> & coord) {
return Math::triangle_inradius(coord(0).storage(), coord(1).storage(),
coord(2).storage());
}
/* -------------------------------------------------------------------------- */
// template<> inline bool ElementClass<_triangle_3>::contains(const Vector<Real>
// & natural_coords) {
// if (natural_coords[0] < 0.) return false;
// if (natural_coords[0] > 1.) return false;
// if (natural_coords[1] < 0.) return false;
// if (natural_coords[1] > 1.) return false;
// if (natural_coords[0]+natural_coords[1] > 1.) return false;
// return true;
// }
/* -------------------------------------------------------------------------- */
diff --git a/src/fe_engine/element_classes/element_class_triangle_6_inline_impl.cc b/src/fe_engine/element_classes/element_class_triangle_6_inline_impl.cc
index 7ccb1a5a3..aa8b3a53d 100644
--- a/src/fe_engine/element_classes/element_class_triangle_6_inline_impl.cc
+++ b/src/fe_engine/element_classes/element_class_triangle_6_inline_impl.cc
@@ -1,200 +1,199 @@
/**
* @file element_class_triangle_6_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Oct 11 2017
*
* @brief Specialization of the element_class class for the type _triangle_6
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ terms of the GNU Lesser General Public License as published by the Free
+ Software Foundation, either version 3 of the License, or (at your option) any
+ later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ details.
*
* You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* @verbatim
\eta
^
|
x 2
| `
| `
| . `
| q2 `
5 x x 4
| `
| `
| .q0 q1. `
| `
x---------x---------x-----> \xi
0 3 1
@endverbatim
*
* @subsection coords Nodes coordinates
*
* @f[
* \begin{array}{ll}
* \xi_{0} = 0 & \eta_{0} = 0 \\
* \xi_{1} = 1 & \eta_{1} = 0 \\
* \xi_{2} = 0 & \eta_{2} = 1 \\
* \xi_{3} = 1/2 & \eta_{3} = 0 \\
* \xi_{4} = 1/2 & \eta_{4} = 1/2 \\
* \xi_{5} = 0 & \eta_{5} = 1/2
* \end{array}
* @f]
*
* @subsection shapes Shape functions
* @f[
* \begin{array}{lll}
* N1 = -(1 - \xi - \eta) (1 - 2 (1 - \xi - \eta))
* & \frac{\partial N1}{\partial \xi} = 1 - 4(1 - \xi - \eta)
* & \frac{\partial N1}{\partial \eta} = 1 - 4(1 - \xi - \eta) \\
* N2 = - \xi (1 - 2 \xi)
* & \frac{\partial N2}{\partial \xi} = - 1 + 4 \xi
* & \frac{\partial N2}{\partial \eta} = 0 \\
* N3 = - \eta (1 - 2 \eta)
* & \frac{\partial N3}{\partial \xi} = 0
* & \frac{\partial N3}{\partial \eta} = - 1 + 4 \eta \\
* N4 = 4 \xi (1 - \xi - \eta)
* & \frac{\partial N4}{\partial \xi} = 4 (1 - 2 \xi - \eta)
* & \frac{\partial N4}{\partial \eta} = - 4 \xi \\
* N5 = 4 \xi \eta
* & \frac{\partial N5}{\partial \xi} = 4 \eta
* & \frac{\partial N5}{\partial \eta} = 4 \xi \\
* N6 = 4 \eta (1 - \xi - \eta)
* & \frac{\partial N6}{\partial \xi} = - 4 \eta
* & \frac{\partial N6}{\partial \eta} = 4 (1 - \xi - 2 \eta)
* \end{array}
* @f]
*
* @subsection quad_points Position of quadrature points
* @f{eqnarray*}{
* \xi_{q0} &=& 1/6 \qquad \eta_{q0} = 1/6 \\
* \xi_{q1} &=& 2/3 \qquad \eta_{q1} = 1/6 \\
* \xi_{q2} &=& 1/6 \qquad \eta_{q2} = 2/3
* @f}
*/
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_triangle_6, _gt_triangle_6,
_itp_lagrange_triangle_6, _ek_regular, 2,
_git_triangle, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_triangle_6>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
/// Natural coordinates
Real c0 =
1 - natural_coords(0) - natural_coords(1); /// @f$ c0 = 1 - \xi - \eta @f$
Real c1 = natural_coords(0); /// @f$ c1 = \xi @f$
Real c2 = natural_coords(1); /// @f$ c2 = \eta @f$
N(0) = c0 * (2 * c0 - 1.);
N(1) = c1 * (2 * c1 - 1.);
N(2) = c2 * (2 * c2 - 1.);
N(3) = 4 * c0 * c1;
N(4) = 4 * c1 * c2;
N(5) = 4 * c2 * c0;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_triangle_6>::computeDNDS(
const vector_type & natural_coords, matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccccc}
* \frac{\partial N1}{\partial \xi}
* & \frac{\partial N2}{\partial \xi}
* & \frac{\partial N3}{\partial \xi}
* & \frac{\partial N4}{\partial \xi}
* & \frac{\partial N5}{\partial \xi}
* & \frac{\partial N6}{\partial \xi} \\
*
* \frac{\partial N1}{\partial \eta}
* & \frac{\partial N2}{\partial \eta}
* & \frac{\partial N3}{\partial \eta}
* & \frac{\partial N4}{\partial \eta}
* & \frac{\partial N5}{\partial \eta}
* & \frac{\partial N6}{\partial \eta}
* \end{array}
* \right)
* @f]
*/
/// Natural coordinates
Real c0 =
1 - natural_coords(0) - natural_coords(1); /// @f$ c0 = 1 - \xi - \eta @f$
Real c1 = natural_coords(0); /// @f$ c1 = \xi @f$
Real c2 = natural_coords(1); /// @f$ c2 = \eta @f$
dnds(0, 0) = 1 - 4 * c0;
dnds(0, 1) = 4 * c1 - 1.;
dnds(0, 2) = 0.;
dnds(0, 3) = 4 * (c0 - c1);
dnds(0, 4) = 4 * c2;
dnds(0, 5) = -4 * c2;
dnds(1, 0) = 1 - 4 * c0;
dnds(1, 1) = 0.;
dnds(1, 2) = 4 * c2 - 1.;
dnds(1, 3) = -4 * c1;
dnds(1, 4) = 4 * c1;
dnds(1, 5) = 4 * (c0 - c2);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_triangle_6>::computeSpecialJacobian(
const Matrix<Real> & J, Real & jac) {
Vector<Real> vprod(J.cols());
Matrix<Real> Jt(J.transpose(), true);
vprod.crossProduct(Jt(0), Jt(1));
jac = vprod.norm();
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_triangle_6>::getInradius(const Matrix<Real> & coord) {
UInt triangles[4][3] = {{0, 3, 5}, {3, 1, 4}, {3, 4, 5}, {5, 4, 2}};
Real inradius = std::numeric_limits<Real>::max();
for (UInt t = 0; t < 4; t++) {
Real ir = Math::triangle_inradius(coord(triangles[t][0]).storage(),
coord(triangles[t][1]).storage(),
coord(triangles[t][2]).storage());
inradius = std::min(ir, inradius);
}
return inradius;
}
/* -------------------------------------------------------------------------- */
// template<> inline bool ElementClass<_triangle_6>::contains(const Vector<Real>
// & natural_coords) {
// return ElementClass<_triangle_3>::contains(natural_coords);
// }
diff --git a/src/fe_engine/element_type_conversion.hh b/src/fe_engine/element_type_conversion.hh
index bf9ac699e..124ad9c77 100644
--- a/src/fe_engine/element_type_conversion.hh
+++ b/src/fe_engine/element_type_conversion.hh
@@ -1,55 +1,57 @@
/**
* @file element_type_conversion.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Thu Jul 27 2017
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Fri Aug 11 2017
*
- * @brief conversion between different types
+ * @brief conversion between different types
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_TYPE_CONVERSION_HH__
#define __AKANTU_ELEMENT_TYPE_CONVERSION_HH__
namespace akantu {
template <class InType, class OutType> OutType convertType(const InType &) {
return OutType();
}
template <>
inline InterpolationType
convertType<ElementType, InterpolationType>(const ElementType & type) {
InterpolationType itp_type = _itp_not_defined;
#define GET_ITP(type) itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_ITP);
#undef GET_ITP
return itp_type;
}
} // namespace akantu
#endif /* __AKANTU_ELEMENT_TYPE_CONVERSION_HH__ */
diff --git a/src/fe_engine/fe_engine.cc b/src/fe_engine/fe_engine.cc
index 95a2d29a2..23bc02714 100644
--- a/src/fe_engine/fe_engine.cc
+++ b/src/fe_engine/fe_engine.cc
@@ -1,95 +1,94 @@
/**
* @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 Dec 11 2015
+ * @date last modification: Thu Feb 01 2018
*
* @brief Implementation of the FEEngine class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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 "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
FEEngine::FEEngine(Mesh & mesh, UInt element_dimension, const ID & id,
MemoryID memory_id)
: Memory(id, memory_id), mesh(mesh),
normals_on_integration_points("normals_on_quad_points", id, memory_id) {
AKANTU_DEBUG_IN();
this->element_dimension = (element_dimension != _all_dimensions)
? element_dimension
: mesh.getSpatialDimension();
this->mesh.registerEventHandler(*this, _ehp_fe_engine);
init();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FEEngine::init() {}
/* -------------------------------------------------------------------------- */
FEEngine::~FEEngine() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
typename FEEngine::ElementTypesIteratorHelper
FEEngine::elementTypes(UInt dim, GhostType ghost_type, ElementKind kind) const {
return this->getIntegratorInterface().getJacobians().elementTypes(
dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
void FEEngine::printself(std::ostream & stream, int indent) const {
std::string space;
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;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/fe_engine/fe_engine.hh b/src/fe_engine/fe_engine.hh
index 4decb1828..1c0516a8f 100644
--- a/src/fe_engine/fe_engine.hh
+++ b/src/fe_engine/fe_engine.hh
@@ -1,393 +1,393 @@
/**
* @file fe_engine.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 22 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief FEM class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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_memory.hh"
#include "element_type_map.hh"
#include "mesh_events.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_FE_ENGINE_HH__
#define __AKANTU_FE_ENGINE_HH__
namespace akantu {
class Mesh;
class Integrator;
class ShapeFunctions;
class DOFManager;
class Element;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* The generic FEEngine class derived in a FEEngineTemplate class
* containing the
* shape functions and the integration method
*/
class FEEngine : protected Memory, public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FEEngine(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "fem", MemoryID memory_id = 0);
~FEEngine() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// pre-compute all the shape functions, their derivatives and the jacobians
virtual void
initShapeFunctions(const GhostType & ghost_type = _not_ghost) = 0;
/// extract the nodal values and store them per element
template <typename T>
static void extractNodalToElementField(
const Mesh & mesh, const Array<T> & nodal_f, Array<T> & elemental_f,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter);
/// filter a field
template <typename T>
static void
filterElementalData(const Mesh & mesh, const Array<T> & quad_f,
Array<T> & filtered_f, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter);
/* ------------------------------------------------------------------------ */
/* Integration method bridges */
/* ------------------------------------------------------------------------ */
/// integrate f for all elements of type "type"
virtual void
integrate(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate a scalar value f on all elements of type "type"
virtual Real
integrate(const Array<Real> & f, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate f for all integration points of type "type" but don't sum over
/// all integration points
virtual void integrateOnIntegrationPoints(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate one element scalar value on all elements of type "type"
virtual Real integrate(const Vector<Real> & f, const ElementType & type,
UInt index,
const GhostType & ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* compatibility with old FEEngine fashion */
/* ------------------------------------------------------------------------ */
#ifndef SWIG
/// get the number of integration points
virtual UInt
getNbIntegrationPoints(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const = 0;
/// get the precomputed shapes
const virtual Array<Real> &
getShapes(const ElementType & type, const GhostType & ghost_type = _not_ghost,
UInt id = 0) const = 0;
/// get the derivatives of shapes
const virtual Array<Real> &
getShapesDerivatives(const ElementType & type,
const GhostType & ghost_type = _not_ghost,
UInt id = 0) const = 0;
/// get integration points
const virtual Matrix<Real> &
getIntegrationPoints(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const = 0;
#endif
/* ------------------------------------------------------------------------ */
/* Shape method bridges */
/* ------------------------------------------------------------------------ */
/// Compute the gradient nablauq on the integration points of an element type
/// from nodal values u
virtual void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq,
const UInt nb_degree_of_freedom, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Interpolate a nodal field u at the integration points of an element type
/// -> uq
virtual void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Interpolate a nodal field u at the integration points of many element
/// types -> uq
virtual void interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements = nullptr) const = 0;
/// pre multiplies a tensor by the shapes derivaties
virtual void
computeBtD(const Array<Real> & Ds, Array<Real> & BtDs,
const ElementType & type, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// left and right multiplies a tensor by the shapes derivaties
virtual void
computeBtDB(const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
const ElementType & type, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Compute the interpolation point position in the global coordinates for
/// many element types
virtual void computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & integration_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements = nullptr) const = 0;
/// Compute the interpolation point position in the global coordinates for an
/// element type
virtual void computeIntegrationPointsCoordinates(
Array<Real> & integration_points_coordinates, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
virtual void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & integration_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// interpolate field at given position (interpolation_points) from given
/// values of this field at integration points (field)
virtual void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
virtual void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> &
integration_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// interpolate on a phyiscal point inside an element
virtual void interpolate(const Vector<Real> & real_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const Element & element) const = 0;
/// compute the shape on a provided point
virtual void
computeShapes(const Vector<Real> & real_coords, UInt elem,
const ElementType & type, Vector<Real> & shapes,
const GhostType & ghost_type = _not_ghost) const = 0;
/// compute the shape derivatives on a provided point
virtual void
computeShapeDerivatives(const Vector<Real> & real__coords, UInt element,
const ElementType & type,
Matrix<Real> & shape_derivatives,
const GhostType & ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* Other methods */
/* ------------------------------------------------------------------------ */
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
const GhostType & ghost_type = _not_ghost) = 0;
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
__attribute__((unused)) const Array<Real> & field,
__attribute__((unused)) const GhostType & ghost_type = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
__attribute__((unused)) const Array<Real> & field,
__attribute__((unused)) Array<Real> & normal,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) const GhostType & ghost_type = _not_ghost) const {
AKANTU_TO_IMPLEMENT();
}
#ifdef AKANTU_STRUCTURAL_MECHANICS
/// assemble a field as a matrix for structural elements (ex. rho to mass
/// matrix)
virtual void assembleFieldMatrix(
__attribute__((unused)) const Array<Real> & field_1,
__attribute__((unused)) UInt nb_degree_of_freedom,
__attribute__((unused)) SparseMatrix & M,
__attribute__((unused)) Array<Real> * n,
__attribute__((unused)) ElementTypeMapArray<Real> & rotation_mat,
__attribute__((unused)) ElementType type,
__attribute__((unused)) const GhostType & ghost_type) const {
AKANTU_TO_IMPLEMENT();
}
/// compute shapes function in a matrix for structural elements
virtual void computeShapesMatrix(
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) UInt nb_degree_of_freedom,
__attribute__((unused)) UInt nb_nodes_per_element,
__attribute__((unused)) Array<Real> * n, __attribute__((unused)) UInt id,
__attribute__((unused)) UInt degree_to_interpolate,
__attribute__((unused)) UInt degree_interpolated,
__attribute__((unused)) const bool sign,
__attribute__((unused)) const GhostType & ghost_type) const {
AKANTU_TO_IMPLEMENT();
}
#endif
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
private:
/// initialise the class
void init();
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler interface */
/* ------------------------------------------------------------------------ */
public:
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) final {}
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) final {}
void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) override{};
void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) override {}
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override {}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
using ElementTypesIteratorHelper =
ElementTypeMapArray<Real, ElementType>::ElementTypesIteratorHelper;
ElementTypesIteratorHelper elementTypes(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
/// get the dimension of the element handeled by this fe_engine object
AKANTU_GET_MACRO(ElementDimension, element_dimension, UInt);
/// get the mesh contained in the fem object
AKANTU_GET_MACRO(Mesh, mesh, const Mesh &);
/// get the mesh contained in the fem object
AKANTU_GET_MACRO_NOT_CONST(Mesh, mesh, Mesh &);
/// get the in-radius of an element
static inline Real getElementInradius(const Matrix<Real> & coord,
const ElementType & type);
/// get the normals on integration points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(NormalsOnIntegrationPoints,
normals_on_integration_points, Real);
/// get cohesive element type for a given facet type
static inline ElementType
getCohesiveElementType(const ElementType & type_facet);
/// get igfem element type for a given regular type
static inline Vector<ElementType>
getIGFEMElementTypes(const ElementType & type);
/// get the interpolation element associated to an element type
static inline InterpolationType
getInterpolationType(const ElementType & el_type);
/// get the shape function class (probably useless: see getShapeFunction in
/// fe_engine_template.hh)
virtual const ShapeFunctions & getShapeFunctionsInterface() const = 0;
/// get the integrator class (probably useless: see getIntegrator in
/// fe_engine_template.hh)
virtual const Integrator & getIntegratorInterface() const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// spatial dimension of the problem
UInt element_dimension;
/// the mesh on which all computation are made
Mesh & mesh;
/// normals at integration points
ElementTypeMapArray<Real> normals_on_integration_points;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const FEEngine & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "fe_engine_inline_impl.cc"
#include "fe_engine_template.hh"
#endif /* __AKANTU_FE_ENGINE_HH__ */
diff --git a/src/fe_engine/fe_engine_inline_impl.cc b/src/fe_engine/fe_engine_inline_impl.cc
index 48940bdb0..a04ec296e 100644
--- a/src/fe_engine/fe_engine_inline_impl.cc
+++ b/src/fe_engine/fe_engine_inline_impl.cc
@@ -1,199 +1,199 @@
/**
* @file fe_engine_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 20 2010
- * @date last modification: Sat Sep 05 2015
+ * @date last modification: Sun Aug 13 2017
*
* @brief Implementation of the inline functions of the FEEngine Class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include "element_type_conversion.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_FE_ENGINE_INLINE_IMPL_CC__
#define __AKANTU_FE_ENGINE_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline Real FEEngine::getElementInradius(const Matrix<Real> & coord,
const ElementType & type) {
AKANTU_DEBUG_IN();
Real inradius = 0;
#define GET_INRADIUS(type) inradius = ElementClass<type>::getInradius(coord);
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_INRADIUS);
#undef GET_INRADIUS
AKANTU_DEBUG_OUT();
return inradius;
}
/* -------------------------------------------------------------------------- */
inline InterpolationType
FEEngine::getInterpolationType(const ElementType & type) {
return convertType<ElementType, InterpolationType>(type);
}
/* -------------------------------------------------------------------------- */
/// @todo rewrite this function in order to get the cohesive element
/// type directly from the facet
#if defined(AKANTU_COHESIVE_ELEMENT)
inline ElementType FEEngine::getCohesiveElementType(const ElementType & type) {
AKANTU_DEBUG_IN();
ElementType ctype;
#define GET_COHESIVE_TYPE(type) \
ctype = CohesiveFacetProperty<type>::cohesive_type;
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_COHESIVE_TYPE);
#undef GET_COHESIVE_TYPE
AKANTU_DEBUG_OUT();
return ctype;
}
#else
inline ElementType
FEEngine::getCohesiveElementType(__attribute__((unused))
const ElementType & type_facet) {
return _not_defined;
}
#endif
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IGFEM)
} // akantu
#include "igfem_helper.hh"
namespace akantu {
inline Vector<ElementType>
FEEngine::getIGFEMElementTypes(const ElementType & type) {
#define GET_IGFEM_ELEMENT_TYPES(type) \
return IGFEMHelper::getIGFEMElementTypes<type>();
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(GET_IGFEM_ELEMENT_TYPES);
#undef GET_IGFEM_ELEMENT_TYPES
}
#endif
/* -------------------------------------------------------------------------- */
template <typename T>
void FEEngine::extractNodalToElementField(const Mesh & mesh,
const Array<T> & nodal_f,
Array<T> & elemental_f,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = nodal_f.getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
elemental_f.resize(nb_element);
T * nodal_f_val = nodal_f.storage();
T * f_val = elemental_f.storage();
UInt * el_conn;
for (UInt el = 0; el < nb_element; ++el) {
if (filter_elements != empty_filter)
el_conn = conn_val + filter_elements(el) * nb_nodes_per_element;
else
el_conn = conn_val + el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = *(el_conn + n);
std::copy(nodal_f_val + node * nb_degree_of_freedom,
nodal_f_val + (node + 1) * nb_degree_of_freedom, f_val);
f_val += nb_degree_of_freedom;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void FEEngine::filterElementalData(const Mesh & mesh, const Array<T> & elem_f,
Array<T> & filtered_f,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0) {
filtered_f.resize(0);
return;
}
UInt nb_degree_of_freedom = elem_f.getNbComponent();
UInt nb_data_per_element = elem_f.size() / nb_element;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
filtered_f.resize(nb_element * nb_data_per_element);
T * elem_f_val = elem_f.storage();
T * f_val = filtered_f.storage();
UInt el_offset;
for (UInt el = 0; el < nb_element; ++el) {
if (filter_elements != empty_filter)
el_offset = filter_elements(el);
else
el_offset = el;
std::copy(elem_f_val +
el_offset * nb_data_per_element * nb_degree_of_freedom,
elem_f_val +
(el_offset + 1) * nb_data_per_element * nb_degree_of_freedom,
f_val);
f_val += nb_degree_of_freedom * nb_data_per_element;
}
AKANTU_DEBUG_OUT();
}
} // akantu
#endif /* __AKANTU_FE_ENGINE_INLINE_IMPL_CC__ */
diff --git a/src/fe_engine/fe_engine_template.hh b/src/fe_engine/fe_engine_template.hh
index 14e5793b6..4325dbce6 100644
--- a/src/fe_engine/fe_engine_template.hh
+++ b/src/fe_engine/fe_engine_template.hh
@@ -1,407 +1,407 @@
/**
* @file fe_engine_template.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Mon Jan 29 2018
*
* @brief templated class that calls integration and shape objects
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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_FE_ENGINE_TEMPLATE_HH__
#define __AKANTU_FE_ENGINE_TEMPLATE_HH__
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "integrator.hh"
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManager;
namespace fe_engine {
namespace details {
template <ElementKind> struct AssembleLumpedTemplateHelper;
template <ElementKind> struct AssembleFieldMatrixHelper;
} // namespace details
} // namespace fe_engine
template <ElementKind, typename> struct AssembleFieldMatrixStructHelper;
struct DefaultIntegrationOrderFunctor {
template <ElementType type> static inline constexpr int getOrder() {
return ElementClassProperty<type>::polynomial_degree;
}
};
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind = _ek_regular,
class IntegrationOrderFunctor = DefaultIntegrationOrderFunctor>
class FEEngineTemplate : public FEEngine {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using Integ = I<kind, IntegrationOrderFunctor>;
using Shape = S<kind>;
FEEngineTemplate(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
ID id = "fem", MemoryID memory_id = 0);
~FEEngineTemplate() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// pre-compute all the shape functions, their derivatives and the jacobians
void initShapeFunctions(const GhostType & ghost_type = _not_ghost) override;
void initShapeFunctions(const Array<Real> & nodes,
const GhostType & ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Integration method bridges */
/* ------------------------------------------------------------------------ */
/// integrate f for all elements of type "type"
void
integrate(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// integrate a scalar value on all elements of type "type"
Real
integrate(const Array<Real> & f, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// integrate one element scalar value on all elements of type "type"
Real integrate(const Vector<Real> & f, const ElementType & type, UInt index,
const GhostType & ghost_type = _not_ghost) const override;
/// integrate partially around an integration point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
void integrateOnIntegrationPoints(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate on a phyiscal point inside an element
void interpolate(const Vector<Real> & real_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const Element & element) const override;
/// get the number of integration points
UInt getNbIntegrationPoints(
const ElementType & type,
const GhostType & ghost_type = _not_ghost) const override;
/// get shapes precomputed
const Array<Real> & getShapes(const ElementType & type,
const GhostType & ghost_type = _not_ghost,
UInt id = 0) const override;
/// get the derivatives of shapes
const Array<Real> &
getShapesDerivatives(const ElementType & type,
const GhostType & ghost_type = _not_ghost,
UInt id = 0) const override;
/// get integration points
const inline Matrix<Real> & getIntegrationPoints(
const ElementType & type,
const GhostType & ghost_type = _not_ghost) const override;
/* ------------------------------------------------------------------------ */
/* Shape method bridges */
/* ------------------------------------------------------------------------ */
/// compute the gradient of a nodal field on the integration points
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq,
const UInt nb_degree_of_freedom, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate a nodal field on the integration points
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate a nodal field on the integration points given a
/// by_element_type
void interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements =
nullptr) const override;
/// pre multiplies a tensor by the shapes derivaties
void
computeBtD(const Array<Real> & Ds, Array<Real> & BtDs,
const ElementType & type, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const override;
/// left and right multiplies a tensor by the shapes derivaties
void computeBtDB(
const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
const ElementType & type, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const override;
/// compute the position of integration points given by an element_type_map
/// from nodes position
inline void computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements =
nullptr) const override;
/// compute the position of integration points from nodes position
inline void computeIntegrationPointsCoordinates(
Array<Real> & quadrature_points_coordinates, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate field at given position (interpolation_points) from given
/// values of this field at integration points (field)
inline void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const override;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
inline void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const override;
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
inline void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter =
nullptr) const override;
/// find natural coords from real coords provided an element
void inverseMap(const Vector<Real> & real_coords, UInt element,
const ElementType & type, Vector<Real> & natural_coords,
const GhostType & ghost_type = _not_ghost) const;
/// return true if the coordinates provided are inside the element, false
/// otherwise
inline bool contains(const Vector<Real> & real_coords, UInt element,
const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// compute the shape on a provided point
inline void
computeShapes(const Vector<Real> & real_coords, UInt element,
const ElementType & type, Vector<Real> & shapes,
const GhostType & ghost_type = _not_ghost) const override;
/// compute the shape derivatives on a provided point
inline void computeShapeDerivatives(
const Vector<Real> & real__coords, UInt element, const ElementType & type,
Matrix<Real> & shape_derivatives,
const GhostType & ghost_type = _not_ghost) const override;
/* ------------------------------------------------------------------------ */
/* Other methods */
/* ------------------------------------------------------------------------ */
/// pre-compute normals on integration points
void computeNormalsOnIntegrationPoints(
const GhostType & ghost_type = _not_ghost) override;
void computeNormalsOnIntegrationPoints(
const Array<Real> & field,
const GhostType & ghost_type = _not_ghost) override;
void computeNormalsOnIntegrationPoints(
const Array<Real> & field, Array<Real> & normal, const ElementType & type,
const GhostType & ghost_type = _not_ghost) const override;
template <ElementType type>
void computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
const GhostType & ghost_type) const;
private:
// To avoid a weird full specialization of a method in a non specalized class
void
computeNormalsOnIntegrationPointsPoint1(const Array<Real> &,
Array<Real> & normal,
const GhostType & ghost_type) const;
public:
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// assemble a field as a lumped matrix (ex. rho in lumped mass)
template <class Functor>
void assembleFieldLumped(const Functor & field_funct, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
ElementType type,
const GhostType & ghost_type) const;
/// assemble a field as a matrix (ex. rho to mass matrix)
template <class Functor>
void assembleFieldMatrix(const Functor & field_funct, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
ElementType type,
const GhostType & ghost_type) const;
#ifdef AKANTU_STRUCTURAL_MECHANICS
/// assemble a field as a matrix (ex. rho to mass matrix)
void assembleFieldMatrix(const Array<Real> & field_1,
UInt nb_degree_of_freedom, SparseMatrix & M,
Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat,
const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// compute shapes function in a matrix for structural elements
void
computeShapesMatrix(const ElementType & type, UInt nb_degree_of_freedom,
UInt nb_nodes_per_element, Array<Real> * n, UInt id,
UInt degree_to_interpolate, UInt degree_interpolated,
const bool sign,
const GhostType & ghost_type = _not_ghost) const override;
#endif
private:
friend struct fe_engine::details::AssembleLumpedTemplateHelper<kind>;
friend struct fe_engine::details::AssembleFieldMatrixHelper<kind>;
friend struct AssembleFieldMatrixStructHelper<kind, void>;
/// templated function to compute the scaling to assemble a lumped matrix
template <class Functor, ElementType type>
void assembleFieldLumped(const Functor & field_funct, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const;
/// @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j
/// dV = \int \rho \varphi_i dV @f$
template <ElementType type>
void assembleLumpedRowSum(const Array<Real> & field, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const;
/// @f$ \tilde{M}_{i} = c * M_{ii} = \int_{V_e} \rho dV @f$
template <ElementType type>
void assembleLumpedDiagonalScaling(const Array<Real> & field,
const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager,
const GhostType & ghost_type) const;
/// assemble a field as a matrix (ex. rho to mass matrix)
template <class Functor, ElementType type>
void assembleFieldMatrix(const Functor & field_funct, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const;
#ifdef AKANTU_STRUCTURAL_MECHANICS
/// assemble a field as a matrix for structural elements (ex. rho to mass
/// matrix)
template <ElementType type>
void assembleFieldMatrix(const Array<Real> & field_1,
UInt nb_degree_of_freedom, SparseMatrix & M,
Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat,
__attribute__((unused))
const GhostType & ghost_type) const;
#endif
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler interface */
/* ------------------------------------------------------------------------ */
public:
void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) override;
void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) override;
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the shape class (probably useless: see getShapeFunction)
const ShapeFunctions & getShapeFunctionsInterface() const override {
return shape_functions;
};
/// get the shape class
const Shape & getShapeFunctions() const { return shape_functions; };
/// get the integrator class (probably useless: see getIntegrator)
const Integrator & getIntegratorInterface() const override {
return integrator;
};
/// get the integrator class
const Integ & getIntegrator() const { return integrator; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
Integ integrator;
Shape shape_functions;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "fe_engine_template_tmpl.hh"
#include "fe_engine_template_tmpl_field.hh"
/* -------------------------------------------------------------------------- */
/* Shape Linked specialization */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "fe_engine_template_tmpl_struct.hh"
#endif
/* -------------------------------------------------------------------------- */
/* Shape IGFEM specialization */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IGFEM)
#include "fe_engine_template_tmpl_igfem.hh"
#endif
#endif /* __AKANTU_FE_ENGINE_TEMPLATE_HH__ */
diff --git a/src/fe_engine/fe_engine_template_cohesive.cc b/src/fe_engine/fe_engine_template_cohesive.cc
index d93f779f0..447463fc4 100644
--- a/src/fe_engine/fe_engine_template_cohesive.cc
+++ b/src/fe_engine/fe_engine_template_cohesive.cc
@@ -1,133 +1,132 @@
/**
* @file fe_engine_template_cohesive.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Oct 31 2012
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Specialization of the FEEngineTemplate for cohesive element
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine_template.hh"
#include "integrator_gauss.hh"
#include "shape_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* compatibility functions */
/* -------------------------------------------------------------------------- */
template <>
Real FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
integrate(const Array<Real> & f, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == 1,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
#endif
Real integral = 0.;
#define INTEGRATE(type) \
integral = integrator.integrate<type>(f, ghost_type, filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INTEGRATE);
#undef INTEGRATE
AKANTU_DEBUG_OUT();
return integral;
}
/* -------------------------------------------------------------------------- */
template <>
void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
integrate(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
#ifndef AKANTU_NDEBUG
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements == filter_elements)
nb_element = filter_elements.size();
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.size() == nb_element,
"The vector intf(" << intf.getID()
<< ") has not the good size.");
#endif
#define INTEGRATE(type) \
integrator.integrate<type>(f, intf, nb_degree_of_freedom, ghost_type, \
filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INTEGRATE);
#undef INTEGRATE
}
/* -------------------------------------------------------------------------- */
template <>
void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
gradientOnIntegrationPoints(const Array<Real> &, Array<Real> &, const UInt,
const ElementType &, const GhostType &,
const Array<UInt> &) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/fe_engine/fe_engine_template_tmpl.hh b/src/fe_engine/fe_engine_template_tmpl.hh
index 1d5c54b00..bace4d338 100644
--- a/src/fe_engine/fe_engine_template_tmpl.hh
+++ b/src/fe_engine/fe_engine_template_tmpl.hh
@@ -1,1374 +1,1373 @@
/**
* @file fe_engine_template_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Thu Nov 19 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Template implementation of FEEngineTemplate
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dof_manager.hh"
#include "fe_engine_template.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::FEEngineTemplate(
Mesh & mesh, UInt spatial_dimension, ID id, MemoryID memory_id)
: FEEngine(mesh, spatial_dimension, id, memory_id),
integrator(mesh, id, memory_id), shape_functions(mesh, id, memory_id) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::~FEEngineTemplate() =
default;
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GradientOnIntegrationPointsHelper {
template <class S>
static void call(const S &, Mesh &, const Array<Real> &, Array<Real> &,
const UInt, const ElementType &, const GhostType &,
const Array<UInt> &) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_GRADIENT(type) \
if (element_dimension == ElementClass<type>::getSpatialDimension()) \
shape_functions.template gradientOnIntegrationPoints<type>( \
u, nablauq, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GradientOnIntegrationPointsHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, Mesh & mesh, \
const Array<Real> & u, Array<Real> & nablauq, \
const UInt nb_degree_of_freedom, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
UInt element_dimension = mesh.getSpatialDimension(type); \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_GRADIENT, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER,
AKANTU_FE_ENGINE_LIST_GRADIENT_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER
#undef COMPUTE_GRADIENT
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
gradientOnIntegrationPoints(const Array<Real> & u, Array<Real> & nablauq,
const UInt nb_degree_of_freedom,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
UInt nb_points =
shape_functions.getIntegrationPoints(type, ghost_type).cols();
#ifndef AKANTU_NDEBUG
UInt element_dimension = mesh.getSpatialDimension(type);
AKANTU_DEBUG_ASSERT(u.size() == mesh.getNbNodes(),
"The vector u(" << u.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(u.getNbComponent() == nb_degree_of_freedom,
"The vector u("
<< u.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(
nablauq.getNbComponent() == nb_degree_of_freedom * element_dimension,
"The vector nablauq(" << nablauq.getID()
<< ") has not the good number of component.");
// AKANTU_DEBUG_ASSERT(nablauq.size() == nb_element * nb_points,
// "The vector nablauq(" << nablauq.getID()
// << ") has not the good size.");
#endif
nablauq.resize(nb_element * nb_points);
fe_engine::details::GradientOnIntegrationPointsHelper<kind>::call(
shape_functions, mesh, u, nablauq, nb_degree_of_freedom, type, ghost_type,
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::initShapeFunctions(
const GhostType & ghost_type) {
initShapeFunctions(mesh.getNodes(), ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::initShapeFunctions(
const Array<Real> & nodes, const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
integrator.initIntegrator(nodes, type, ghost_type);
const auto & control_points = getIntegrationPoints(type, ghost_type);
shape_functions.initShapeFunctions(nodes, control_points, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateHelper {};
#define INTEGRATE(type) \
integrator.template integrate<type>(f, intf, nb_degree_of_freedom, \
ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_HELPER(kind) \
template <> struct IntegrateHelper<kind> { \
template <class I> \
static void call(const I & integrator, const Array<Real> & f, \
Array<Real> & intf, UInt nb_degree_of_freedom, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_INTEGRATE_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
#ifndef AKANTU_NDEBUG
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
#endif
intf.resize(nb_element);
fe_engine::details::IntegrateHelper<kind>::call(integrator, f, intf,
nb_degree_of_freedom, type,
ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateScalarHelper {};
#define INTEGRATE(type) \
integral = \
integrator.template integrate<type>(f, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER(kind) \
template <> struct IntegrateScalarHelper<kind> { \
template <class I> \
static Real call(const I & integrator, const Array<Real> & f, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
Real integral = 0.; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
return integral; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
Real FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & f, const ElementType & type,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
// std::stringstream sstr; sstr << ghost_type;
// AKANTU_DEBUG_ASSERT(sstr.str() == nablauq.getTag(),
// "The vector " << nablauq.getID() << " is not taged " <<
// ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
UInt nb_quadrature_points = getNbIntegrationPoints(type, ghost_type);
AKANTU_DEBUG_ASSERT(
f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << ") has not the good size. (" << f.size()
<< "!=" << nb_quadrature_points * nb_element << ")");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == 1,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
#endif
Real integral = fe_engine::details::IntegrateScalarHelper<kind>::call(
integrator, f, type, ghost_type, filter_elements);
AKANTU_DEBUG_OUT();
return integral;
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateScalarOnOneElementHelper {};
#define INTEGRATE(type) \
res = integrator.template integrate<type>(f, index, ghost_type);
#define AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER(kind) \
template <> struct IntegrateScalarOnOneElementHelper<kind> { \
template <class I> \
static Real call(const I & integrator, const Vector<Real> & f, \
const ElementType & type, UInt index, \
const GhostType & ghost_type) { \
Real res = 0.; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
return res; \
} \
};
AKANTU_BOOST_ALL_KIND(
AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
Real FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Vector<Real> & f, const ElementType & type, UInt index,
const GhostType & ghost_type) const {
Real res = fe_engine::details::IntegrateScalarOnOneElementHelper<kind>::call(
integrator, f, type, index, ghost_type);
return res;
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateOnIntegrationPointsHelper {};
#define INTEGRATE(type) \
integrator.template integrateOnIntegrationPoints<type>( \
f, intf, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct IntegrateOnIntegrationPointsHelper<kind> { \
template <class I> \
static void call(const I & integrator, const Array<Real> & f, \
Array<Real> & intf, UInt nb_degree_of_freedom, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(
AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
UInt nb_quadrature_points = getNbIntegrationPoints(type);
#ifndef AKANTU_NDEBUG
// std::stringstream sstr; sstr << ghost_type;
// AKANTU_DEBUG_ASSERT(sstr.str() == nablauq.getTag(),
// "The vector " << nablauq.getID() << " is not taged " <<
// ghost_type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
#endif
intf.resize(nb_element * nb_quadrature_points);
fe_engine::details::IntegrateOnIntegrationPointsHelper<kind>::call(
integrator, f, intf, nb_degree_of_freedom, type, ghost_type,
filter_elements);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct InterpolateOnIntegrationPointsHelper {
template <class S>
static void call(const S &, const Array<Real> &, Array<Real> &,
const UInt, const ElementType &, const GhostType &,
const Array<UInt> &) {
AKANTU_TO_IMPLEMENT();
}
};
#define INTERPOLATE(type) \
shape_functions.template interpolateOnIntegrationPoints<type>( \
u, uq, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct InterpolateOnIntegrationPointsHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & u, \
Array<Real> & uq, const UInt nb_degree_of_freedom, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTERPOLATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER,
AKANTU_FE_ENGINE_LIST_INTERPOLATE_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER
#undef INTERPOLATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateOnIntegrationPoints(const Array<Real> & u, Array<Real> & uq,
const UInt nb_degree_of_freedom,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_points =
shape_functions.getIntegrationPoints(type, ghost_type).cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
#ifndef AKANTU_NDEBUG
AKANTU_DEBUG_ASSERT(u.size() == mesh.getNbNodes(),
"The vector u(" << u.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(u.getNbComponent() == nb_degree_of_freedom,
"The vector u("
<< u.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(uq.getNbComponent() == nb_degree_of_freedom,
"The vector uq("
<< uq.getID()
<< ") has not the good number of component.");
#endif
uq.resize(nb_element * nb_points);
fe_engine::details::InterpolateOnIntegrationPointsHelper<kind>::call(
shape_functions, u, uq, nb_degree_of_freedom, type, ghost_type,
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements) const {
AKANTU_DEBUG_IN();
const Array<UInt> * filter = nullptr;
for (auto ghost_type : ghost_types) {
for (auto & type : uq.elementTypes(_all_dimensions, ghost_type, kind)) {
UInt nb_quad_per_element = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = 0;
if (filter_elements) {
filter = &((*filter_elements)(type, ghost_type));
nb_element = filter->size();
} else {
filter = &empty_filter;
nb_element = mesh.getNbElement(type, ghost_type);
}
UInt nb_tot_quad = nb_quad_per_element * nb_element;
Array<Real> & quad = uq(type, ghost_type);
quad.resize(nb_tot_quad);
interpolateOnIntegrationPoints(u, quad, quad.getNbComponent(), type,
ghost_type, *filter);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeBtDHelper {};
#define COMPUTE_BTD(type) \
shape_functions.template computeBtD<type>(Ds, BtDs, ghost_type, \
filter_elements);
#define AKANTU_SPECIALIZE_COMPUTE_BtD_HELPER(kind) \
template <> struct ComputeBtDHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & Ds, \
Array<Real> & BtDs, const ElementType & type, \
const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_BTD, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_COMPUTE_BtD_HELPER)
#undef AKANTU_SPECIALIZE_COMPUTE_BtD_HELPER
#undef COMPUTE_BTD
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeBtD(
const Array<Real> & Ds, Array<Real> & BtDs, const ElementType & type,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
fe_engine::details::ComputeBtDHelper<kind>::call(
shape_functions, Ds, BtDs, type, ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeBtDBHelper {};
#define COMPUTE_BTDB(type) \
shape_functions.template computeBtDB<type>(Ds, BtDBs, order_d, ghost_type, \
filter_elements);
#define AKANTU_SPECIALIZE_COMPUTE_BtDB_HELPER(kind) \
template <> struct ComputeBtDBHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & Ds, \
Array<Real> & BtDBs, UInt order_d, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_BTDB, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_COMPUTE_BtDB_HELPER)
#undef AKANTU_SPECIALIZE_COMPUTE_BtDB_HELPER
#undef COMPUTE_BTDB
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeBtDB(
const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
const ElementType & type, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
fe_engine::details::ComputeBtDBHelper<kind>::call(
shape_functions, Ds, BtDBs, order_d, type, ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
interpolateOnIntegrationPoints(
nodes_coordinates, quadrature_points_coordinates, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
Array<Real> & quadrature_points_coordinates, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
interpolateOnIntegrationPoints(
nodes_coordinates, quadrature_points_coordinates, spatial_dimension, type,
ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_for_interpolation", getID(),
getMemoryID());
quadrature_points_coordinates.initialize(*this,
_nb_component = spatial_dimension);
computeIntegrationPointsCoordinates(quadrature_points_coordinates,
element_filter);
shape_functions.initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates,
interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, quadrature_points_coordinates,
element_filter);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
ElementTypeMapArray<Real> interpolation_points_coordinates_matrices(
"interpolation_points_coordinates_matrices", id, memory_id);
ElementTypeMapArray<Real> quad_points_coordinates_inv_matrices(
"quad_points_coordinates_inv_matrices", id, memory_id);
initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates,
interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, element_filter);
interpolateElementalFieldFromIntegrationPoints(
field, interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, result, ghost_type, element_filter);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
shape_functions.interpolateElementalFieldFromIntegrationPoints(
field, interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, result, ghost_type, element_filter);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct InterpolateHelper {
template <class S>
static void call(const S &, const Vector<Real> &, UInt,
const Matrix<Real> &, Vector<Real> &,
const ElementType &, const GhostType &) {
AKANTU_TO_IMPLEMENT();
}
};
#define INTERPOLATE(type) \
shape_functions.template interpolate<type>( \
real_coords, element, nodal_values, interpolated, ghost_type);
#define AKANTU_SPECIALIZE_INTERPOLATE_HELPER(kind) \
template <> struct InterpolateHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const Matrix<Real> & nodal_values, \
Vector<Real> & interpolated, const ElementType & type, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTERPOLATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_INTERPOLATE_HELPER,
AKANTU_FE_ENGINE_LIST_INTERPOLATE)
#undef AKANTU_SPECIALIZE_INTERPOLATE_HELPER
#undef INTERPOLATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::interpolate(
const Vector<Real> & real_coords, const Matrix<Real> & nodal_values,
Vector<Real> & interpolated, const Element & element) const {
AKANTU_DEBUG_IN();
fe_engine::details::InterpolateHelper<kind>::call(
shape_functions, real_coords, element.element, nodal_values, interpolated,
element.type, element.ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
computeNormalsOnIntegrationPoints(mesh.getNodes(), ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
// Real * coord = mesh.getNodes().storage();
UInt spatial_dimension = mesh.getSpatialDimension();
// allocate the normal arrays
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
UInt size = mesh.getNbElement(type, ghost_type);
if (normals_on_integration_points.exists(type, ghost_type)) {
normals_on_integration_points(type, ghost_type).resize(size);
} else {
normals_on_integration_points.alloc(size, spatial_dimension, type,
ghost_type);
}
}
// loop over the type to build the normals
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
Array<Real> & normals_on_quad =
normals_on_integration_points(type, ghost_type);
computeNormalsOnIntegrationPoints(field, normals_on_quad, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeNormalsOnIntegrationPoints {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
static void call(const FEEngineTemplate<I, S, k, IOF> &,
const Array<Real> &, Array<Real> &, const ElementType &,
const GhostType &) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_NORMALS_ON_INTEGRATION_POINTS(type) \
fem.template computeNormalsOnIntegrationPoints<type>(field, normal, \
ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS(kind) \
template <> struct ComputeNormalsOnIntegrationPoints<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF> \
static void call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const Array<Real> & field, Array<Real> & normal, \
const ElementType & type, const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_NORMALS_ON_INTEGRATION_POINTS, \
kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS,
AKANTU_FE_ENGINE_LIST_COMPUTE_NORMALS_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS
#undef COMPUTE_NORMALS_ON_INTEGRATION_POINTS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
const ElementType & type,
const GhostType & ghost_type) const {
fe_engine::details::ComputeNormalsOnIntegrationPoints<kind>::call(
*this, field, normal, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
if (type == _point_1) {
computeNormalsOnIntegrationPointsPoint1(field, normal, ghost_type);
return;
}
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_points = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
normal.resize(nb_element * nb_points);
Array<Real>::matrix_iterator normals_on_quad =
normal.begin_reinterpret(spatial_dimension, nb_points, nb_element);
Array<Real> f_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, field, f_el, type, ghost_type);
const Matrix<Real> & quads =
integrator.template getIntegrationPoints<type>(ghost_type);
Array<Real>::matrix_iterator f_it =
f_el.begin(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem) {
ElementClass<type>::computeNormalsOnNaturalCoordinates(quads, *f_it,
*normals_on_quad);
++normals_on_quad;
++f_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
template <ElementKind kind> struct InverseMapHelper {
template <class S>
static void
call(const S & /*shape_functions*/, const Vector<Real> & /*real_coords*/,
UInt /*element*/, const ElementType & /*type*/,
Vector<Real> & /*natural_coords*/, const GhostType & /*ghost_type*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define INVERSE_MAP(type) \
shape_functions.template inverseMap<type>(real_coords, element, \
natural_coords, ghost_type);
#define AKANTU_SPECIALIZE_INVERSE_MAP_HELPER(kind) \
template <> struct InverseMapHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType & type, Vector<Real> & natural_coords, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INVERSE_MAP, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_INVERSE_MAP_HELPER,
AKANTU_FE_ENGINE_LIST_INVERSE_MAP)
#undef AKANTU_SPECIALIZE_INVERSE_MAP_HELPER
#undef INVERSE_MAP
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::inverseMap(
const Vector<Real> & real_coords, UInt element, const ElementType & type,
Vector<Real> & natural_coords, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
InverseMapHelper<kind>::call(shape_functions, real_coords, element, type,
natural_coords, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ContainsHelper {
template <class S>
static void call(const S &, const Vector<Real> &, UInt,
const ElementType &, const GhostType &) {
AKANTU_TO_IMPLEMENT();
}
};
#define CONTAINS(type) \
contain = shape_functions.template contains<type>(real_coords, element, \
ghost_type);
#define AKANTU_SPECIALIZE_CONTAINS_HELPER(kind) \
template <> struct ContainsHelper<kind> { \
template <template <ElementKind> class S, ElementKind k> \
static bool call(const S<k> & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType & type, const GhostType & ghost_type) { \
bool contain = false; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(CONTAINS, kind); \
return contain; \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_CONTAINS_HELPER,
AKANTU_FE_ENGINE_LIST_CONTAINS)
#undef AKANTU_SPECIALIZE_CONTAINS_HELPER
#undef CONTAINS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline bool FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::contains(
const Vector<Real> & real_coords, UInt element, const ElementType & type,
const GhostType & ghost_type) const {
return fe_engine::details::ContainsHelper<kind>::call(
shape_functions, real_coords, element, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeShapesHelper {
template <class S>
static void call(const S &, const Vector<Real> &, UInt, const ElementType,
Vector<Real> &, const GhostType &) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_SHAPES(type) \
shape_functions.template computeShapes<type>(real_coords, element, shapes, \
ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER(kind) \
template <> struct ComputeShapesHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType type, Vector<Real> & shapes, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_SHAPES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER,
AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES)
#undef AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER
#undef COMPUTE_SHAPES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapes(
const Vector<Real> & real_coords, UInt element, const ElementType & type,
Vector<Real> & shapes, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::ComputeShapesHelper<kind>::call(
shape_functions, real_coords, element, type, shapes, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeShapeDerivativesHelper {
template <class S>
static void call(__attribute__((unused)) const S & shape_functions,
__attribute__((unused)) const Vector<Real> & real_coords,
__attribute__((unused)) UInt element,
__attribute__((unused)) const ElementType type,
__attribute__((unused)) Matrix<Real> & shape_derivatives,
__attribute__((unused)) const GhostType & ghost_type) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_SHAPE_DERIVATIVES(type) \
Matrix<Real> coords_mat(real_coords.storage(), shape_derivatives.rows(), 1); \
Tensor3<Real> shapesd_tensor(shape_derivatives.storage(), \
shape_derivatives.rows(), \
shape_derivatives.cols(), 1); \
shape_functions.template computeShapeDerivatives<type>( \
coords_mat, element, shapesd_tensor, ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER(kind) \
template <> struct ComputeShapeDerivativesHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType type, Matrix<Real> & shape_derivatives, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_SHAPE_DERIVATIVES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER,
AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES_DERIVATIVES)
#undef AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER
#undef COMPUTE_SHAPE_DERIVATIVES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapeDerivatives(
const Vector<Real> & real_coords, UInt element, const ElementType & type,
Matrix<Real> & shape_derivatives, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::ComputeShapeDerivativesHelper<kind>::call(
shape_functions, real_coords, element, type, shape_derivatives,
ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetNbIntegrationPointsHelper {};
#define GET_NB_INTEGRATION_POINTS(type) \
nb_quad_points = integrator.template getNbIntegrationPoints<type>(ghost_type);
#define AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GetNbIntegrationPointsHelper<kind> { \
template <template <ElementKind, class> class I, ElementKind k, class IOF> \
static UInt call(const I<k, IOF> & integrator, const ElementType type, \
const GhostType & ghost_type) { \
UInt nb_quad_points = 0; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_NB_INTEGRATION_POINTS, kind); \
return nb_quad_points; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER
#undef GET_NB_INTEGRATION
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline UInt
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getNbIntegrationPoints(
const ElementType & type, const GhostType & ghost_type) const {
return fe_engine::details::GetNbIntegrationPointsHelper<kind>::call(
integrator, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetShapesHelper {};
#define GET_SHAPES(type) ret = &(shape_functions.getShapes(type, ghost_type));
#define AKANTU_SPECIALIZE_GET_SHAPES_HELPER(kind) \
template <> struct GetShapesHelper<kind> { \
template <class S> \
static const Array<Real> & call(const S & shape_functions, \
const ElementType type, \
const GhostType & ghost_type) { \
const Array<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_SHAPES, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_SHAPES_HELPER)
#undef AKANTU_SPECIALIZE_GET_SHAPES_HELPER
#undef GET_SHAPES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Array<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getShapes(
const ElementType & type, const GhostType & ghost_type,
__attribute__((unused)) UInt id) const {
return fe_engine::details::GetShapesHelper<kind>::call(shape_functions, type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetShapesDerivativesHelper {
template <template <ElementKind> class S, ElementKind k>
static const Array<Real> & call(const S<k> &, const ElementType &,
const GhostType &, UInt) {
AKANTU_TO_IMPLEMENT();
}
};
#define GET_SHAPES_DERIVATIVES(type) \
ret = &(shape_functions.getShapesDerivatives(type, ghost_type));
#define AKANTU_SPECIALIZE_GET_SHAPES_DERIVATIVES_HELPER(kind) \
template <> struct GetShapesDerivativesHelper<kind> { \
template <template <ElementKind> class S, ElementKind k> \
static const Array<Real> & \
call(const S<k> & shape_functions, const ElementType type, \
const GhostType & ghost_type, __attribute__((unused)) UInt id) { \
const Array<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_SHAPES_DERIVATIVES, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_GET_SHAPES_DERIVATIVES_HELPER,
AKANTU_FE_ENGINE_LIST_GET_SHAPES_DERIVATIVES)
#undef AKANTU_SPECIALIZE_GET_SHAPE_DERIVATIVES_HELPER
#undef GET_SHAPES_DERIVATIVES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Array<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getShapesDerivatives(
const ElementType & type, const GhostType & ghost_type,
__attribute__((unused)) UInt id) const {
return fe_engine::details::GetShapesDerivativesHelper<kind>::call(
shape_functions, type, ghost_type, id);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetIntegrationPointsHelper {};
#define GET_INTEGRATION_POINTS(type) \
ret = &(integrator.template getIntegrationPoints<type>(ghost_type));
#define AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GetIntegrationPointsHelper<kind> { \
template <template <ElementKind, class> class I, ElementKind k, class IOF> \
static const Matrix<Real> & call(const I<k, IOF> & integrator, \
const ElementType type, \
const GhostType & ghost_type) { \
const Matrix<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_INTEGRATION_POINTS, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER
#undef GET_INTEGRATION_POINTS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Matrix<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getIntegrationPoints(
const ElementType & type, const GhostType & ghost_type) const {
return fe_engine::details::GetIntegrationPointsHelper<kind>::call(
integrator, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::printself(
std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "FEEngineTemplate [" << std::endl;
stream << space << " + parent [" << std::endl;
FEEngine::printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << " + shape functions [" << std::endl;
shape_functions.printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << " + integrator [" << std::endl;
integrator.printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsAdded(
const Array<Element> & new_elements, const NewElementsEvent &) {
integrator.onElementsAdded(new_elements);
shape_functions.onElementsAdded(new_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsRemoved(
const Array<Element> &, const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsChanged(
const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &, const ChangedElementsEvent &) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPointsPoint1(
const Array<Real> &, Array<Real> & normal,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(mesh.getSpatialDimension() == 1,
"Mesh dimension must be 1 to compute normals on points!");
const ElementType type = _point_1;
UInt spatial_dimension = mesh.getSpatialDimension();
// UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_points = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
normal.resize(nb_element * nb_points);
Array<Real>::matrix_iterator normals_on_quad =
normal.begin_reinterpret(spatial_dimension, nb_points, nb_element);
const Array<std::vector<Element>> & segments =
mesh.getElementToSubelement(type, ghost_type);
const Array<Real> & coords = mesh.getNodes();
const Mesh * mesh_segment;
if (mesh.isMeshFacets())
mesh_segment = &(mesh.getMeshParent());
else
mesh_segment = &mesh;
for (UInt elem = 0; elem < nb_element; ++elem) {
UInt nb_segment = segments(elem).size();
AKANTU_DEBUG_ASSERT(
nb_segment > 0,
"Impossible to compute a normal on a point connected to 0 segments");
Real normal_value = 1;
if (nb_segment == 1) {
const Element & segment = segments(elem)[0];
const Array<UInt> & segment_connectivity =
mesh_segment->getConnectivity(segment.type, segment.ghost_type);
// const Vector<UInt> & segment_points =
// segment_connectivity.begin(Mesh::getNbNodesPerElement(segment.type))[segment.element];
Real difference;
if (segment_connectivity(0) == elem) {
difference = coords(elem) - coords(segment_connectivity(1));
} else {
difference = coords(elem) - coords(segment_connectivity(0));
}
normal_value = difference / std::abs(difference);
}
for (UInt n(0); n < nb_points; ++n) {
(*normals_on_quad)(0, n) = normal_value;
}
++normals_on_quad;
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/fe_engine/fe_engine_template_tmpl_field.hh b/src/fe_engine/fe_engine_template_tmpl_field.hh
index 205071102..1cc83c4ae 100644
--- a/src/fe_engine/fe_engine_template_tmpl_field.hh
+++ b/src/fe_engine/fe_engine_template_tmpl_field.hh
@@ -1,426 +1,428 @@
/**
* @file fe_engine_template_tmpl_field.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jul 25 2017
+ * @date creation: Wed Aug 09 2017
+ * @date last modification: Thu Dec 07 2017
*
- * @brief implementation of the assemble field s functions
+ * @brief implementation of the assemble field s functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "fe_engine_template.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH__
#define __AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Matrix lumping functions */
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
namespace {
template <class Functor>
void fillField(const Functor & field_funct, Array<Real> & field,
UInt nb_element, UInt nb_integration_points,
const ElementType & type, const GhostType & ghost_type) {
UInt nb_degree_of_freedom = field.getNbComponent();
field.resize(nb_integration_points * nb_element);
auto field_it = field.begin_reinterpret(
nb_degree_of_freedom, nb_integration_points, nb_element);
Element el{type, 0, ghost_type};
for (; el.element < nb_element; ++el.element, ++field_it) {
field_funct(*field_it, el);
}
}
} // namespace
} // namespace details
} // namespace fe_engine
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct AssembleLumpedTemplateHelper {};
#define ASSEMBLE_LUMPED(type) \
fem.template assembleFieldLumped<Functor, type>(field_funct, lumped, dof_id, \
dof_manager, ghost_type)
#define AKANTU_SPECIALIZE_ASSEMBLE_HELPER(kind) \
template <> struct AssembleLumpedTemplateHelper<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF, \
class Functor> \
static void call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const Functor & field_funct, const ID & lumped, \
const ID & dof_id, DOFManager & dof_manager, \
ElementType type, const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_LUMPED, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_ASSEMBLE_HELPER)
#undef AKANTU_SPECIALIZE_ASSEMBLE_HELPER
#undef ASSEMBLE_LUMPED
} // namespace details
} // namespace fe_engine
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IOF>
template <class Functor>
void FEEngineTemplate<I, S, kind, IOF>::assembleFieldLumped(
const Functor & field_funct, const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager, ElementType type,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::AssembleLumpedTemplateHelper<kind>::call(
*this, field_funct, matrix_id, dof_id, dof_manager, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <class Functor, ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldLumped(
const Functor & field_funct, const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_degree_of_freedom = dof_manager.getDOFs(dof_id).getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_integration_points = this->getNbIntegrationPoints(type);
Array<Real> field(0, nb_degree_of_freedom);
fe_engine::details::fillField(field_funct, field, nb_element,
nb_integration_points, type, ghost_type);
switch (type) {
case _triangle_6:
case _quadrangle_8:
case _tetrahedron_10:
case _hexahedron_20:
case _pentahedron_15:
this->template assembleLumpedDiagonalScaling<type>(field, matrix_id, dof_id,
dof_manager, ghost_type);
break;
default:
this->template assembleLumpedRowSum<type>(field, matrix_id, dof_id,
dof_manager, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j dV =
* \int \rho \varphi_i dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
assembleLumpedRowSum(const Array<Real> & field, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt shapes_size = ElementClass<type>::getShapeSize();
UInt nb_degree_of_freedom = field.getNbComponent();
Array<Real> * field_times_shapes =
new Array<Real>(0, shapes_size * nb_degree_of_freedom);
shape_functions.template fieldTimesShapes<type>(field, *field_times_shapes,
ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<Real> * int_field_times_shapes = new Array<Real>(
nb_element, shapes_size * nb_degree_of_freedom, "inte_rho_x_shapes");
integrator.template integrate<type>(
*field_times_shapes, *int_field_times_shapes,
nb_degree_of_freedom * shapes_size, ghost_type, empty_filter);
delete field_times_shapes;
dof_manager.assembleElementalArrayToLumpedMatrix(
dof_id, *int_field_times_shapes, matrix_id, type, ghost_type);
delete int_field_times_shapes;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = c * M_{ii} = \int_{V_e} \rho dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
assembleLumpedDiagonalScaling(const Array<Real> & field,
const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
const ElementType & type_p1 = ElementClass<type>::getP1ElementType();
UInt nb_nodes_per_element_p1 = Mesh::getNbNodesPerElement(type_p1);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = field.getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
Vector<Real> nodal_factor(nb_nodes_per_element);
#define ASSIGN_WEIGHT_TO_NODES(corner, mid) \
{ \
for (UInt n = 0; n < nb_nodes_per_element_p1; n++) \
nodal_factor(n) = corner; \
for (UInt n = nb_nodes_per_element_p1; n < nb_nodes_per_element; n++) \
nodal_factor(n) = mid; \
}
if (type == _triangle_6)
ASSIGN_WEIGHT_TO_NODES(1. / 12., 1. / 4.);
if (type == _tetrahedron_10)
ASSIGN_WEIGHT_TO_NODES(1. / 32., 7. / 48.);
if (type == _quadrangle_8)
ASSIGN_WEIGHT_TO_NODES(
3. / 76.,
16. / 76.); /** coeff. derived by scaling
* the diagonal terms of the corresponding
* consistent mass computed with 3x3 gauss points;
* coeff. are (1./36., 8./36.) for 2x2 gauss points */
if (type == _hexahedron_20)
ASSIGN_WEIGHT_TO_NODES(
7. / 248.,
16. / 248.); /** coeff. derived by scaling
* the diagonal terms of the corresponding
* consistent mass computed with 3x3x3 gauss points;
* coeff. are (1./40.,
* 1./15.) for 2x2x2 gauss points */
if (type == _pentahedron_15) {
// coefficients derived by scaling the diagonal terms of the corresponding
// consistent mass computed with 8 gauss points;
for (UInt n = 0; n < nb_nodes_per_element_p1; n++)
nodal_factor(n) = 51. / 2358.;
Real mid_triangle = 192. / 2358.;
Real mid_quadrangle = 300. / 2358.;
nodal_factor(6) = mid_triangle;
nodal_factor(7) = mid_triangle;
nodal_factor(8) = mid_triangle;
nodal_factor(9) = mid_quadrangle;
nodal_factor(10) = mid_quadrangle;
nodal_factor(11) = mid_quadrangle;
nodal_factor(12) = mid_triangle;
nodal_factor(13) = mid_triangle;
nodal_factor(14) = mid_triangle;
}
if (nb_element == 0) {
AKANTU_DEBUG_OUT();
return;
}
#undef ASSIGN_WEIGHT_TO_NODES
/// compute @f$ \int \rho dV = \rho V @f$ for each element
auto int_field = std::make_unique<Array<Real>>(
field.size(), nb_degree_of_freedom, "inte_rho_x");
integrator.template integrate<type>(field, *int_field, nb_degree_of_freedom,
ghost_type, empty_filter);
/// distribute the mass of the element to the nodes
auto lumped_per_node = std::make_unique<Array<Real>>(
nb_element, nb_degree_of_freedom * nb_nodes_per_element, "mass_per_node");
auto int_field_it = int_field->begin(nb_degree_of_freedom);
auto lumped_per_node_it =
lumped_per_node->begin(nb_degree_of_freedom, nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Vector<Real> l = (*lumped_per_node_it)(n);
l = *int_field_it;
l *= nodal_factor(n);
}
++int_field_it;
++lumped_per_node_it;
}
dof_manager.assembleElementalArrayToLumpedMatrix(dof_id, *lumped_per_node,
matrix_id, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct AssembleFieldMatrixHelper {};
#define ASSEMBLE_MATRIX(type) \
fem.template assembleFieldMatrix<Functor, type>( \
field_funct, matrix_id, dof_id, dof_manager, ghost_type)
#define AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER(kind) \
template <> struct AssembleFieldMatrixHelper<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF, \
class Functor> \
static void call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const Functor & field_funct, const ID & matrix_id, \
const ID & dof_id, DOFManager & dof_manager, \
ElementType type, const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_MATRIX, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER)
#undef AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER
#undef ASSEMBLE_MATRIX
} // namespace details
} // namespace fe_engine
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IOF>
template <class Functor>
void FEEngineTemplate<I, S, kind, IOF>::assembleFieldMatrix(
const Functor & field_funct, const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager, ElementType type,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::AssembleFieldMatrixHelper<kind>::template call(
*this, field_funct, matrix_id, dof_id, dof_manager, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j dV =
* \int \rho \varphi_i dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <class Functor, ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
const Functor & field_funct, const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt shapes_size = ElementClass<type>::getShapeSize();
UInt nb_degree_of_freedom = dof_manager.getDOFs(dof_id).getNbComponent();
UInt lmat_size = nb_degree_of_freedom * shapes_size;
UInt nb_element = mesh.getNbElement(type, ghost_type);
// \int N * N so degree 2 * degree of N
const UInt polynomial_degree =
2 * ElementClassProperty<type>::polynomial_degree;
// getting the integration points
Matrix<Real> integration_points =
integrator.template getIntegrationPoints<type, polynomial_degree>();
UInt nb_integration_points = integration_points.cols();
UInt vect_size = nb_integration_points * nb_element;
// getting the shapes on the integration points
Array<Real> shapes(0, shapes_size);
shape_functions.template computeShapesOnIntegrationPoints<type>(
mesh.getNodes(), integration_points, shapes, ghost_type);
// Extending the shape functions
/// \TODO move this in the shape functions as Voigt format shapes to have the
/// code in common with the structural elements
Array<Real> modified_shapes(vect_size, lmat_size * nb_degree_of_freedom, 0.);
Array<Real> local_mat(vect_size, lmat_size * lmat_size);
auto mshapes_it = modified_shapes.begin(nb_degree_of_freedom, lmat_size);
auto shapes_it = shapes.begin(shapes_size);
for (UInt q = 0; q < vect_size; ++q, ++mshapes_it, ++shapes_it) {
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
for (UInt s = 0; s < shapes_size; ++s) {
(*mshapes_it)(d, s * nb_degree_of_freedom + d) = (*shapes_it)(s);
}
}
}
// getting the value to assemble on the integration points
Array<Real> field(vect_size, nb_degree_of_freedom);
fe_engine::details::fillField(field_funct, field, nb_element,
nb_integration_points, type, ghost_type);
// computing \rho * N
mshapes_it = modified_shapes.begin(nb_degree_of_freedom, lmat_size);
auto lmat = local_mat.begin(lmat_size, lmat_size);
auto field_it = field.begin_reinterpret(nb_degree_of_freedom, field.size());
for (UInt q = 0; q < vect_size; ++q, ++lmat, ++mshapes_it, ++field_it) {
const auto & rho = *field_it;
const auto & N = *mshapes_it;
auto & mat = *lmat;
Matrix<Real> Nt = N.transpose();
for (UInt d = 0; d < Nt.cols(); ++d) {
Nt(d) *= rho(d);
}
mat.template mul<false, false>(Nt, N);
}
// integrate the elemental values
Array<Real> int_field_times_shapes(nb_element, lmat_size * lmat_size,
"inte_rho_x_shapes");
this->integrator.template integrate<type, polynomial_degree>(
local_mat, int_field_times_shapes, lmat_size * lmat_size, ghost_type);
// assemble the elemental values to the matrix
dof_manager.assembleElementalMatricesToMatrix(
matrix_id, dof_id, int_field_times_shapes, type, ghost_type);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* __AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH__ */
diff --git a/src/fe_engine/fe_engine_template_tmpl_struct.hh b/src/fe_engine/fe_engine_template_tmpl_struct.hh
index 410af8f66..e6318d1e5 100644
--- a/src/fe_engine/fe_engine_template_tmpl_struct.hh
+++ b/src/fe_engine/fe_engine_template_tmpl_struct.hh
@@ -1,99 +1,99 @@
/**
* @file fe_engine_template_tmpl_struct.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 07 2014
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Template implementation of FEEngineTemplate for Structural Element
* Kinds
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_structural.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementKind kind, typename = void>
struct AssembleFieldMatrixStructHelper {};
template <ElementKind kind>
struct AssembleFieldMatrixStructHelper<
kind, typename std::enable_if<kind == _ek_structural>::type> {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
static void call(const FEEngineTemplate<I, S, k, IOF> & fem,
const Array<Real> & field_1, UInt nb_degree_of_freedom,
SparseMatrix & M, Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat,
const ElementType & type, const GhostType & ghost_type) {
#define ASSEMBLE_MATRIX(type) \
fem.template assembleFieldMatrix<type>(field_1, nb_degree_of_freedom, M, n, \
rotation_mat, ghost_type)
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_MATRIX, _ek_structural);
#undef ASSEMBLE_MATRIX
}
};
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
const Array<Real> & field_1, UInt nb_degree_of_freedom, SparseMatrix & M,
Array<Real> * n, ElementTypeMapArray<Real> & rotation_mat,
const ElementType & type, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
AssembleFieldMatrixStructHelper<kind>::template call(
*this, field_1, nb_degree_of_freedom, M, n, rotation_mat, type,
ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapesMatrix(
const ElementType &, UInt, UInt, Array<Real> *, UInt, UInt, UInt,
const bool, const GhostType &) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
const Array<Real> &, UInt, SparseMatrix &, Array<Real> *,
ElementTypeMapArray<Real> &, const GhostType &) const {
AKANTU_TO_IMPLEMENT();
}
} // akantu
diff --git a/src/fe_engine/gauss_integration.cc b/src/fe_engine/gauss_integration.cc
index d4f4d8caf..ec718269d 100644
--- a/src/fe_engine/gauss_integration.cc
+++ b/src/fe_engine/gauss_integration.cc
@@ -1,238 +1,238 @@
/**
- * @file integration_element.cc
+ * @file gauss_integration.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Thu Nov 05 2015
+ * @date last modification: Mon Jun 19 2017
*
- * @brief Definition of the integration constants, some of the value are taken
+ * @brief Definition of the integration constants, some of the value are taken
* from r3.01.01 doc from Code Aster
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_class.hh"
using std::sqrt;
namespace akantu {
/* clang-format off */
/* -------------------------------------------------------------------------- */
/* Points */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_point, 1>::quad_positions[] = {0};
template<> Real GaussIntegrationTypeData<_git_point, 1>::quad_weights[] = {1.};
/* -------------------------------------------------------------------------- */
/* Segments */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 1>::quad_positions[] = {0.};
template<> Real GaussIntegrationTypeData<_git_segment, 1>::quad_weights[] = {2.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 2>::quad_positions[] = {-1./sqrt(3.), 1./sqrt(3.)};
template<> Real GaussIntegrationTypeData<_git_segment, 2>::quad_weights[] = {1., 1.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 3>::quad_positions[] = {-sqrt(3./5.), 0., sqrt(3./5.)};
template<> Real GaussIntegrationTypeData<_git_segment, 3>::quad_weights[] = {5./9., 8./9., 5./9.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 4>::quad_positions[] = {-sqrt((3. + 2.*sqrt(6./5.))/7.),
-sqrt((3. - 2.*sqrt(6./5.))/7.),
sqrt((3. - 2.*sqrt(6./5.))/7.),
sqrt((3. + 2.*sqrt(6./5.))/7.)};
template<> Real GaussIntegrationTypeData<_git_segment, 4>::quad_weights[] = {(18. - sqrt(30.))/36.,
(18. + sqrt(30.))/36.,
(18. + sqrt(30.))/36.,
(18. - sqrt(30.))/36.};
/* -------------------------------------------------------------------------- */
/* Triangles */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_triangle, 1>::quad_positions[] = {1./3., 1./3.};
template<> Real GaussIntegrationTypeData<_git_triangle, 1>::quad_weights[] = {1./2.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_triangle, 3>::quad_positions[] = {1./6., 1./6.,
2./3., 1./6.,
1./6., 2./3.};
template<> Real GaussIntegrationTypeData<_git_triangle, 3>::quad_weights[] = {1./6., 1./6., 1./6.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_triangle, 4>::quad_positions[] = {1./5., 1./5.,
3./5., 1./5.,
1./5., 3./5.,
1./3., 1./3.};
template<> Real GaussIntegrationTypeData<_git_triangle, 4>::quad_weights[] = {25./(24.*4.), 25./(24.*4.), 25./(24.*4.), -27/(24.*4.)};
/* -------------------------------------------------------------------------- */
/// Found those one in the TrigGaussRuleInfo from mathematica and matched them to the code aster values
/// http://www.colorado.edu/engineering/CAS/courses.d/AFEM.d/AFEM.AppI.d/AFEM.AppI.pdf
static const Real tri_6_a = (8. - std::sqrt(10.) + std::sqrt(38.-44.*std::sqrt(2./5.)))/18.;
static const Real tri_6_b = (8. - std::sqrt(10.) - std::sqrt(38.-44.*std::sqrt(2./5.)))/18.;
static const Real tri_6_w1 = (620. - std::sqrt(213125. - 53320.*std::sqrt(10.)))/7440.;
static const Real tri_6_w2 = (620. + std::sqrt(213125. - 53320.*std::sqrt(10.)))/7440.;
template<> Real GaussIntegrationTypeData<_git_triangle, 6>::quad_positions[] = {tri_6_b, tri_6_b,
1. - 2. * tri_6_b, tri_6_b,
tri_6_b, 1. - 2. * tri_6_b,
tri_6_a, 1. - 2. * tri_6_a,
tri_6_a, tri_6_a,
1. - 2. * tri_6_a, tri_6_a};
template<> Real GaussIntegrationTypeData<_git_triangle, 6>::quad_weights[] = {tri_6_w1, tri_6_w1, tri_6_w1,
tri_6_w2, tri_6_w2, tri_6_w2};
/* -------------------------------------------------------------------------- */
static const Real tri_7_a = (6. + std::sqrt(15.)) / 21.;
static const Real tri_7_b = (6. - std::sqrt(15.)) / 21.;
static const Real tri_7_w1 = (155. + std::sqrt(15.))/2400.;
static const Real tri_7_w2 = (155. - std::sqrt(15.))/2400.;
template<> Real GaussIntegrationTypeData<_git_triangle, 7>::quad_positions[] = { 1./3., 1./3.,
tri_7_a, tri_7_a,
1. - 2.*tri_7_a, tri_7_a,
tri_7_a, 1. - 2.*tri_7_a,
tri_7_b, tri_7_b,
1. - 2.*tri_7_b, tri_7_b,
tri_7_b, 1. - 2.*tri_7_b};
template<> Real GaussIntegrationTypeData<_git_triangle, 7>::quad_weights[] = {9./80.,
tri_7_w1, tri_7_w1, tri_7_w1,
tri_7_w2, tri_7_w2, tri_7_w2};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* Tetrahedrons */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 1>::quad_positions[] = {1./4., 1./4., 1./4.};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 1>::quad_weights[] = {1./6.};
/* -------------------------------------------------------------------------- */
static const Real tet_4_a = (5. - std::sqrt(5.))/20.;
static const Real tet_4_b = (5. + 3.*std::sqrt(5.))/20.;
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 4>::quad_positions[] = {tet_4_a, tet_4_a, tet_4_a,
tet_4_b, tet_4_a, tet_4_a,
tet_4_a, tet_4_b, tet_4_a,
tet_4_a, tet_4_a, tet_4_b};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 4>::quad_weights[] = {1./24., 1./24., 1./24., 1./24.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 5>::quad_positions[] = {1./4., 1./4., 1./4.,
1./6., 1./6., 1./6.,
1./6., 1./6., 1./2.,
1./6., 1./2., 1./6.,
1./2., 1./6., 1./6.,};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 5>::quad_weights[] = {-2./15., 3./40.,
3./40., 3./40.,
3./40.};
/* -------------------------------------------------------------------------- */
static const Real tet_15_a = (7. + std::sqrt(15.))/34.;
static const Real tet_15_b = (13. - 3. * std::sqrt(15.))/34.;
static const Real tet_15_c = (7. - std::sqrt(15.))/34.;
static const Real tet_15_d = (13. + 3. * std::sqrt(15.))/34.;
static const Real tet_15_e = (5. - std::sqrt(15.))/20.;
static const Real tet_15_f = (5. + std::sqrt(15.))/20.;
static const Real tet_15_w1 = (2665. - 14. * std::sqrt(15.))/226800.;
static const Real tet_15_w2 = (2665. + 14. * std::sqrt(15.))/226800.;
static const Real tet_15_w3 = 5./567.;
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 15>::quad_positions[] = {1./4., 1./4., 1./4.,
tet_15_a, tet_15_a, tet_15_a,
tet_15_a, tet_15_a, tet_15_b,
tet_15_a, tet_15_b, tet_15_a,
tet_15_b, tet_15_a, tet_15_a,
tet_15_c, tet_15_c, tet_15_c,
tet_15_c, tet_15_c, tet_15_d,
tet_15_c, tet_15_d, tet_15_c,
tet_15_d, tet_15_c, tet_15_c,
tet_15_e, tet_15_e, tet_15_f,
tet_15_e, tet_15_f, tet_15_e,
tet_15_f, tet_15_e, tet_15_e,
tet_15_e, tet_15_f, tet_15_f,
tet_15_f, tet_15_e, tet_15_f,
tet_15_f, tet_15_f, tet_15_e};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 15>::quad_weights[] = {8./405.,
tet_15_w1, tet_15_w1, tet_15_w1, tet_15_w1,
tet_15_w2, tet_15_w2, tet_15_w2, tet_15_w2,
tet_15_w3, tet_15_w3, tet_15_w3, tet_15_w3, tet_15_w3, tet_15_w3};
/* -------------------------------------------------------------------------- */
/* Pentahedrons */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_pentahedron, 6>::quad_positions[] = {-1./sqrt(3.), 0.5, 0.5,
-1./sqrt(3.), 0. , 0.5,
-1./sqrt(3.), 0.5, 0.,
1./sqrt(3.), 0.5, 0.5,
1./sqrt(3.), 0. , 0.5,
1./sqrt(3.), 0.5 ,0.};
template<> Real GaussIntegrationTypeData<_git_pentahedron, 6>::quad_weights[] = {1./6., 1./6., 1./6.,
1./6., 1./6., 1./6.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_pentahedron, 8>::quad_positions[] = {-sqrt(3.)/3., 1./3., 1./3.,
-sqrt(3.)/3., 0.6, 0.2,
-sqrt(3.)/3., 0.2, 0.6,
-sqrt(3.)/3., 0.2, 0.2,
sqrt(3.)/3., 1./3., 1./3.,
sqrt(3.)/3., 0.6, 0.2,
sqrt(3.)/3., 0.2, 0.6,
sqrt(3.)/3., 0.2, 0.2};
template<> Real GaussIntegrationTypeData<_git_pentahedron, 8>::quad_weights[] = {-27./96., 25./96., 25./96., 25./96.,
-27./96., 25./96., 25./96., 25./96.};
/* -------------------------------------------------------------------------- */
static const Real pent_21_x = std::sqrt(3./5.);
static const Real pent_21_a = (6. + std::sqrt(15.)) / 21.;
static const Real pent_21_b = (6. - std::sqrt(15.)) / 21.;
static const Real pent_21_w1_1 = 5./9.;
static const Real pent_21_w2_1 = 8./9.;
static const Real pent_21_w1_2 = (155. + std::sqrt(15.))/2400.;
static const Real pent_21_w2_2 = (155. - std::sqrt(15.))/2400.;
template<> Real GaussIntegrationTypeData<_git_pentahedron, 21>::quad_positions[] = {- pent_21_x, 1./3., 1./3.,
- pent_21_x, pent_21_a, pent_21_a,
- pent_21_x, 1. - 2.*pent_21_a, pent_21_a,
- pent_21_x, pent_21_a, 1. - 2.*pent_21_a,
- pent_21_x, pent_21_b, pent_21_b,
- pent_21_x, 1. - 2.*pent_21_b, pent_21_b,
- pent_21_x, pent_21_b, 1. - 2.*pent_21_b,
0., 1./3., 1./3.,
0., pent_21_a, pent_21_a,
0., 1. - 2.*pent_21_a, pent_21_a,
0., pent_21_a, 1. - 2.*pent_21_a,
0., pent_21_b, pent_21_b,
0., 1. - 2.*pent_21_b, pent_21_b,
0., pent_21_b, 1. - 2.*pent_21_b,
pent_21_x, 1./3., 1./3.,
pent_21_x, pent_21_a, pent_21_a,
pent_21_x, 1. - 2.*pent_21_a, pent_21_a,
pent_21_x, pent_21_a, 1. - 2.*pent_21_a,
pent_21_x, pent_21_b, pent_21_b,
pent_21_x, 1. - 2.*pent_21_b, pent_21_b,
pent_21_x, pent_21_b, 1. - 2.*pent_21_b};
template<> Real GaussIntegrationTypeData<_git_pentahedron, 21>::quad_weights[] = {pent_21_w1_1 * 9. / 80.,
pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2,
pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2,
pent_21_w2_1 * 9. / 80.,
pent_21_w1_2*pent_21_w1_2, pent_21_w1_2*pent_21_w1_2, pent_21_w1_2*pent_21_w1_2,
pent_21_w1_2*pent_21_w2_2, pent_21_w1_2*pent_21_w2_2, pent_21_w1_2*pent_21_w2_2,
pent_21_w1_1 * 9. / 80.,
pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2,
pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2};
} // akantu
diff --git a/src/fe_engine/gauss_integration_tmpl.hh b/src/fe_engine/gauss_integration_tmpl.hh
index 6ddb1e673..7e9a17e10 100644
--- a/src/fe_engine/gauss_integration_tmpl.hh
+++ b/src/fe_engine/gauss_integration_tmpl.hh
@@ -1,272 +1,273 @@
/**
* @file gauss_integration_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue May 10 10:48:21 2016
+ * @date creation: Tue May 10 2016
+ * @date last modification: Wed Nov 29 2017
*
* @brief implementation of the gauss integration helpers
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GAUSS_INTEGRATION_TMPL_HH__
#define __AKANTU_GAUSS_INTEGRATION_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* GaussIntegrationElement */
/* -------------------------------------------------------------------------- */
namespace _aka_gauss_helpers {
template <GaussIntegrationType type, UInt n>
struct GaussIntegrationNbPoints {};
template <UInt n> struct GaussIntegrationNbPoints<_git_not_defined, n> {
static const UInt nb_points = 0;
};
template <UInt n> struct GaussIntegrationNbPoints<_git_point, n> {
static const UInt nb_points = 1;
};
template <UInt n> struct GaussIntegrationNbPoints<_git_segment, n> {
static const UInt nb_points = (n + 1) / 2 + ((n + 1) % 2 ? 1 : 0);
};
#define DECLARE_GAUSS_NB_POINTS(type, order, points) \
template <> struct GaussIntegrationNbPoints<type, order> { \
static const UInt nb_points = points; \
}
#define DECLARE_GAUSS_NB_POINTS_PENT(type, order, xo, yo) \
template <> struct GaussIntegrationNbPoints<type, order> { \
static const UInt x_order = xo; \
static const UInt yz_order = yo; \
static const UInt nb_points = 1; \
}
DECLARE_GAUSS_NB_POINTS(_git_triangle, 1, 1);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 2, 3);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 3, 4);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 4, 6);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 5, 7);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 1, 1);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 2, 4);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 3, 5);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 4, 15);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 5, 15);
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 1, 3,
2); // order 3 in x, order 2 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 2, 3,
2); // order 3 in x, order 2 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 3, 3,
3); // order 3 in x, order 3 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 4, 5,
5); // order 5 in x, order 5 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 5, 5,
5); // order 5 in x, order 5 in y and z
template <GaussIntegrationType type, UInt n, UInt on = n,
bool end_recurse = false>
struct GaussIntegrationNbPointsHelper {
static const UInt pnp = GaussIntegrationNbPoints<type, n>::nb_points;
static const UInt order = n;
static const UInt nb_points = pnp;
};
template <GaussIntegrationType type, UInt n, UInt on>
struct GaussIntegrationNbPointsHelper<type, n, on, true> {
static const UInt nb_points = 0;
};
/* ------------------------------------------------------------------------ */
/* Generic helper */
/* ------------------------------------------------------------------------ */
template <GaussIntegrationType type, UInt dimension, UInt n>
struct GaussIntegrationTypeDataHelper {
using git_np = GaussIntegrationNbPoints<type, n>;
using git_data = GaussIntegrationTypeData<type, git_np::nb_points>;
static UInt getNbQuadraturePoints() { return git_np::nb_points; }
static const Matrix<Real> getQuadraturePoints() {
return Matrix<Real>(git_data::quad_positions, dimension,
git_np::nb_points);
}
static const Vector<Real> getWeights() {
return Vector<Real>(git_data::quad_weights, git_np::nb_points);
}
};
/* ------------------------------------------------------------------------ */
/* helper for _segment _quadrangle _hexahedron */
/* ------------------------------------------------------------------------ */
template <UInt dimension, UInt dp>
struct GaussIntegrationTypeDataHelper<_git_segment, dimension, dp> {
using git_np = GaussIntegrationNbPoints<_git_segment, dp>;
using git_data = GaussIntegrationTypeData<_git_segment, git_np::nb_points>;
static UInt getNbQuadraturePoints() {
return Math::pow<dimension>(git_np::nb_points);
}
static const Matrix<Real> getQuadraturePoints() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad = git_np::nb_points;
Matrix<Real> quads(dimension, tot_nquad);
Vector<Real> pos(git_data::quad_positions, nquad);
UInt offset = 1;
for (UInt d = 0; d < dimension; ++d) {
for (UInt n = 0, q = 0; n < tot_nquad; ++n, q += offset) {
UInt rq = q % tot_nquad + q / tot_nquad;
quads(d, rq) = pos(n % nquad);
}
offset *= nquad;
}
return quads;
}
static const Vector<Real> getWeights() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad = git_np::nb_points;
Vector<Real> quads_weights(tot_nquad, 1.);
Vector<Real> weights(git_data::quad_weights, nquad);
UInt offset = 1;
for (UInt d = 0; d < dimension; ++d) {
for (UInt n = 0, q = 0; n < tot_nquad; ++n, q += offset) {
UInt rq = q % tot_nquad + q / tot_nquad;
quads_weights(rq) *= weights(n % nquad);
}
offset *= nquad;
}
return quads_weights;
}
};
/* ------------------------------------------------------------------------ */
/* helper for _pentahedron */
/* ------------------------------------------------------------------------ */
template <UInt dimension, UInt dp>
struct GaussIntegrationTypeDataHelper<_git_pentahedron, dimension, dp> {
using git_info = GaussIntegrationNbPoints<_git_pentahedron, dp>;
using git_np_seg =
GaussIntegrationNbPoints<_git_segment, git_info::x_order>;
using git_np_tri =
GaussIntegrationNbPoints<_git_triangle, git_info::yz_order>;
using git_data_seg =
GaussIntegrationTypeData<_git_segment, git_np_seg::nb_points>;
using git_data_tri =
GaussIntegrationTypeData<_git_triangle, git_np_tri::nb_points>;
static UInt getNbQuadraturePoints() {
return git_np_seg::nb_points * git_np_tri::nb_points;
}
static const Matrix<Real> getQuadraturePoints() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad_seg = git_np_seg::nb_points;
UInt nquad_tri = git_np_tri::nb_points;
Matrix<Real> quads(dimension, tot_nquad);
Matrix<Real> pos_seg_w(git_data_seg::quad_positions, 1, nquad_seg);
Matrix<Real> pos_tri_w(git_data_tri::quad_positions, 2, nquad_tri);
for (UInt ns = 0, q = 0; ns < nquad_seg; ++ns) {
Vector<Real> pos_seg = pos_seg_w(ns);
for (UInt nt = 0; nt < nquad_tri; ++nt, ++q) {
Vector<Real> pos_tri = pos_tri_w(nt);
Vector<Real> quad = quads(q);
quad(_x) = pos_seg(_x);
quad(_y) = pos_tri(_x);
quad(_z) = pos_tri(_y);
}
}
return quads;
}
static const Vector<Real> getWeights() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad_seg = git_np_seg::nb_points;
UInt nquad_tri = git_np_tri::nb_points;
Vector<Real> quads_weights(tot_nquad);
Vector<Real> weight_seg(git_data_seg::quad_weights, nquad_seg);
Vector<Real> weight_tri(git_data_tri::quad_weights, nquad_tri);
for (UInt ns = 0, q = 0; ns < nquad_seg; ++ns) {
for (UInt nt = 0; nt < nquad_tri; ++nt, ++q) {
quads_weights(q) = weight_seg(ns) * weight_tri(nt);
}
}
return quads_weights;
}
};
}
template <ElementType element_type, UInt n>
const Matrix<Real>
GaussIntegrationElement<element_type, n>::getQuadraturePoints() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
using interpolation_property = InterpolationProperty<itp_type>;
using data_helper = _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n>;
Matrix<Real> tmp(data_helper::getQuadraturePoints());
return tmp;
}
/* -------------------------------------------------------------------------- */
template <ElementType element_type, UInt n>
const Vector<Real> GaussIntegrationElement<element_type, n>::getWeights() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
using interpolation_property = InterpolationProperty<itp_type>;
using data_helper = _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n>;
Vector<Real> tmp(data_helper::getWeights());
return tmp;
}
/* -------------------------------------------------------------------------- */
template <ElementType element_type, UInt n>
UInt GaussIntegrationElement<element_type, n>::getNbQuadraturePoints() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
using interpolation_property = InterpolationProperty<itp_type>;
using data_helper = _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n>;
return data_helper::getNbQuadraturePoints();
}
} // akantu
#endif /* __AKANTU_GAUSS_INTEGRATION_TMPL_HH__ */
diff --git a/src/fe_engine/geometrical_element_property.cc b/src/fe_engine/geometrical_element_property.cc
index c7086bbed..60e7f11f8 100644
--- a/src/fe_engine/geometrical_element_property.cc
+++ b/src/fe_engine/geometrical_element_property.cc
@@ -1,60 +1,62 @@
/**
* @file geometrical_element_property.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Wed Nov 29 2017
+ * @date creation: Wed Nov 29 2017
+ * @date last modification: Thu Nov 30 2017
*
- * @brief A Documented file.
+ * @brief A Documented file.
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
/* -------------------------------------------------------------------------- */
namespace akantu {
#define AKANTU_INSTANTIATE_TYPES(r, data, type) \
constexpr std::array<UInt, ElementClass<type>::getNbFacetTypes()> \
GeometricalElementProperty< \
ElementClassProperty<type>::geometrical_type>::nb_facets; \
constexpr std::array<UInt, ElementClass<type>::getNbFacetTypes()> \
GeometricalElementProperty< \
ElementClassProperty<type>::geometrical_type>::nb_nodes_per_facet; \
constexpr std::array< \
UInt, detail::sizeFacetConnectivity<GeometricalElementProperty< \
ElementClassProperty<type>::geometrical_type>>()> \
GeometricalElementProperty<ElementClassProperty< \
type>::geometrical_type>::facet_connectivity_vect; \
constexpr std::array<ElementType, ElementClass<type>::getNbFacetTypes()> \
ElementClassExtraGeometryProperties<type>::facet_type;
BOOST_PP_SEQ_FOR_EACH(AKANTU_INSTANTIATE_TYPES, _,
(_not_defined)AKANTU_ek_regular_ELEMENT_TYPE)
#if defined(AKANTU_COHESIVE_ELEMENT)
BOOST_PP_SEQ_FOR_EACH(AKANTU_INSTANTIATE_TYPES, _,
AKANTU_ek_cohesive_ELEMENT_TYPE)
#endif
} // akantu
diff --git a/src/fe_engine/geometrical_element_property.hh b/src/fe_engine/geometrical_element_property.hh
index e6f42d94e..d3a70224b 100644
--- a/src/fe_engine/geometrical_element_property.hh
+++ b/src/fe_engine/geometrical_element_property.hh
@@ -1,489 +1,488 @@
/**
- * @file geometrical_element.cc
+ * @file geometrical_element_property.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Feb 21 2013
- * @date last modification: Thu Jan 21 2016
+ * @date creation: Wed Nov 29 2017
*
* @brief Specialization of the geometrical types
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#include <array>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GEOMETRICAL_ELEMENT_PROPERTY_HH__
#define __AKANTU_GEOMETRICAL_ELEMENT_PROPERTY_HH__
namespace akantu {
namespace detail {
template <typename properties> constexpr size_t sizeFacetConnectivity() {
size_t s = 0;
for (size_t n = 0; n < properties::nb_facet_types; ++n) {
s += properties::nb_facets[n] * properties::nb_nodes_per_facet[n];
}
return s == 0 ? 1 : s;
}
}
template <> struct GeometricalElementProperty<_gt_not_defined> {
static constexpr UInt spatial_dimension{0};
static constexpr UInt nb_nodes_per_element{0};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{0}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{0}};
static constexpr std::array<UInt, 1> facet_connectivity_vect{{0}};
};
template <> struct GeometricalElementProperty<_gt_point> {
static constexpr UInt spatial_dimension{0};
static constexpr UInt nb_nodes_per_element{1};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{1}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{1}};
static constexpr std::array<UInt, 1> facet_connectivity_vect{{0}};
};
template <> struct GeometricalElementProperty<_gt_segment_2> {
static constexpr UInt spatial_dimension{1};
static constexpr UInt nb_nodes_per_element{2};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{1}};
static constexpr std::array<UInt, 2> facet_connectivity_vect{{0, 1}};
};
template <> struct GeometricalElementProperty<_gt_segment_3> {
static constexpr UInt spatial_dimension{1};
static constexpr UInt nb_nodes_per_element{3};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{1}};
// clang-format off
static constexpr std::array<UInt, 2> facet_connectivity_vect{{0, 1}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_triangle_3> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{3};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{3}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{2}};
// clang-format off
static constexpr std::array<UInt, 6> facet_connectivity_vect{{
0, 1, 2,
1, 2, 0}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_triangle_6> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{6};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{3}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 9> facet_connectivity_vect{{
0, 1, 2,
1, 2, 0,
3, 4, 5}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_tetrahedron_4> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{4};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{4}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 12> facet_connectivity_vect{{
0, 1, 2, 0,
2, 2, 0, 1,
1, 3, 3, 3}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_tetrahedron_10> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{10};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{4}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{6}};
// clang-format off
static constexpr std::array<UInt, 6*4> facet_connectivity_vect{{
0, 1, 2, 0,
2, 2, 0, 1,
1, 3, 3, 3,
6, 5, 6, 4,
5, 9, 7, 8,
4, 8, 9, 7}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_quadrangle_4> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{4};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{4}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{2}};
// clang-format off
static constexpr std::array<UInt, 2*4> facet_connectivity_vect{{
0, 1, 2, 3,
1, 2, 3, 0}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_quadrangle_8> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{8};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{4}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 4*3> facet_connectivity_vect{{
0, 1, 2, 3,
1, 2, 3, 0,
4, 5, 6, 7}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_hexahedron_8> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{8};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{6}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{4}};
// clang-format off
static constexpr std::array<UInt, 4*6> facet_connectivity_vect{{
0, 0, 1, 2, 3, 4,
3, 1, 2, 3, 0, 5,
2, 5, 6, 7, 4, 6,
1, 4, 5, 6, 7, 7}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_hexahedron_20> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{20};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{6}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{8}};
// clang-format off
static constexpr std::array<UInt, 8*6> facet_connectivity_vect{{
0, 1, 2, 3, 0, 4,
1, 2, 3, 0, 3, 5,
5, 6, 7, 4, 2, 6,
4, 5, 6, 7, 1, 7,
8, 9, 10, 11, 11, 16,
13, 14, 15, 12, 10, 17,
16, 17, 18, 19, 9, 18,
12, 13, 14, 15, 8, 19}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_pentahedron_6> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{6};
static constexpr UInt nb_facet_types{2};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2, 3}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3, 4}};
// clang-format off
static constexpr std::array<UInt, 3*2 + 4*3> facet_connectivity_vect{{
// first type
0, 3,
2, 4,
1, 5,
// second type
0, 0, 1,
1, 3, 2,
4, 5, 5,
3, 2, 4}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_pentahedron_15> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{15};
static constexpr UInt nb_facet_types{2};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2, 3}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{6, 8}};
// clang-format off
static constexpr std::array<UInt, 6*2 + 8*3> facet_connectivity_vect{{
// first type
0, 3,
2, 4,
1, 5,
8, 12,
7, 13,
6, 14,
// second type
0, 0, 1,
1, 3, 2,
4, 5, 5,
3, 2, 4,
6, 9, 7,
10, 14, 11,
12, 11, 13,
9, 8, 10}};
// clang-format on
};
#if defined(AKANTU_COHESIVE_ELEMENT)
/* --------------------------------------------------------------------------
*/
template <> struct GeometricalElementProperty<_gt_cohesive_2d_4> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{4};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{2}};
// clang-format off
static constexpr std::array<UInt, 2 * 2> facet_connectivity_vect{{
0, 2,
1, 3}};
// clang-format on
};
/* --------------------------------------------------------------------------
*/
template <> struct GeometricalElementProperty<_gt_cohesive_2d_6> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{6};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 3*2> facet_connectivity_vect{{
0, 3,
1, 4,
2, 5}};
// clang-format on
};
/* --------------------------------------------------------------------------
*/
template <> struct GeometricalElementProperty<_gt_cohesive_1d_2> {
static constexpr UInt spatial_dimension{1};
static constexpr UInt nb_nodes_per_element{2};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{1}};
// clang-format off
static constexpr std::array<UInt, 2> facet_connectivity_vect{{0, 1}};
// clang-format on
};
/* --------------------------------------------------------------------------
*/
template <> struct GeometricalElementProperty<_gt_cohesive_3d_6> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{6};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 3*2> facet_connectivity_vect{{
0, 3,
1, 4,
2, 5}};
// clang-format on
};
/* --------------------------------------------------------------------------
*/
template <> struct GeometricalElementProperty<_gt_cohesive_3d_12> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{12};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{6}};
// clang-format off
static constexpr std::array<UInt, 6*2> facet_connectivity_vect{{
0, 6,
1, 7,
2, 8,
3, 9,
4, 10,
5, 11}};
// clang-format on
};
/* --------------------------------------------------------------------------
*/
template <> struct GeometricalElementProperty<_gt_cohesive_3d_8> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{8};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{4}};
// clang-format off
static constexpr std::array<UInt, 4*2> facet_connectivity_vect{{
0, 4,
1, 5,
2, 6,
3, 7}};
// clang-format on
};
/* --------------------------------------------------------------------------
*/
template <> struct GeometricalElementProperty<_gt_cohesive_3d_16> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{16};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{8}};
// clang-format off
static constexpr std::array<UInt, 8*2> facet_connectivity_vect{{
0, 8,
1, 9,
2, 10,
3, 11,
4, 12,
5, 13,
6, 14,
7, 15}};
// clang-format on
};
#endif // AKANTU_COHESIVE_ELEMENT
/* ------------------------------------------------------------------------ */
template <> struct ElementClassExtraGeometryProperties<_not_defined> {
static constexpr ElementType p1_type{_not_defined};
static constexpr std::array<ElementType, 1> facet_type{{_not_defined}};
};
template <> struct ElementClassExtraGeometryProperties<_point_1> {
static constexpr ElementType p1_type{_point_1};
static constexpr std::array<ElementType, 1> facet_type{{_point_1}};
};
template <> struct ElementClassExtraGeometryProperties<_segment_2> {
static constexpr ElementType p1_type{_segment_2};
static constexpr std::array<ElementType, 1> facet_type{{_point_1}};
};
template <> struct ElementClassExtraGeometryProperties<_segment_3> {
static constexpr ElementType p1_type{_segment_2};
static constexpr std::array<ElementType, 1> facet_type{{_point_1}};
};
template <> struct ElementClassExtraGeometryProperties<_triangle_3> {
static constexpr ElementType p1_type{_triangle_3};
static constexpr std::array<ElementType, 1> facet_type{{_segment_2}};
};
template <> struct ElementClassExtraGeometryProperties<_triangle_6> {
static constexpr ElementType p1_type{_triangle_3};
static constexpr std::array<ElementType, 1> facet_type{{_segment_3}};
};
template <> struct ElementClassExtraGeometryProperties<_tetrahedron_4> {
static constexpr ElementType p1_type{_tetrahedron_4};
static constexpr std::array<ElementType, 1> facet_type{{_triangle_3}};
};
template <> struct ElementClassExtraGeometryProperties<_tetrahedron_10> {
static constexpr ElementType p1_type{_tetrahedron_4};
static constexpr std::array<ElementType, 1> facet_type{{_triangle_6}};
};
template <> struct ElementClassExtraGeometryProperties<_quadrangle_4> {
static constexpr ElementType p1_type{_quadrangle_4};
static constexpr std::array<ElementType, 1> facet_type{{_segment_2}};
};
template <> struct ElementClassExtraGeometryProperties<_quadrangle_8> {
static constexpr ElementType p1_type{_quadrangle_4};
static constexpr std::array<ElementType, 1> facet_type{{_segment_3}};
};
template <> struct ElementClassExtraGeometryProperties<_hexahedron_8> {
static constexpr ElementType p1_type{_hexahedron_8};
static constexpr std::array<ElementType, 1> facet_type{{_quadrangle_4}};
};
template <> struct ElementClassExtraGeometryProperties<_hexahedron_20> {
static constexpr ElementType p1_type{_hexahedron_8};
static constexpr std::array<ElementType, 1> facet_type{{_quadrangle_8}};
};
template <> struct ElementClassExtraGeometryProperties<_pentahedron_6> {
static constexpr ElementType p1_type{_pentahedron_6};
static constexpr std::array<ElementType, 2> facet_type{
{_triangle_3, _quadrangle_4}};
};
template <> struct ElementClassExtraGeometryProperties<_pentahedron_15> {
static constexpr ElementType p1_type{_pentahedron_6};
static constexpr std::array<ElementType, 2> facet_type{
{_triangle_6, _quadrangle_8}};
};
#if defined(AKANTU_COHESIVE_ELEMENT)
template <> struct ElementClassExtraGeometryProperties<_cohesive_2d_4> {
static constexpr ElementType p1_type{_cohesive_2d_4};
static constexpr std::array<ElementType, 1> facet_type{{_segment_2}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_2d_6> {
static constexpr ElementType p1_type{_cohesive_2d_4};
static constexpr std::array<ElementType, 1> facet_type{{_segment_3}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_1d_2> {
static constexpr ElementType p1_type{_cohesive_1d_2};
static constexpr std::array<ElementType, 1> facet_type{{_point_1}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_3d_6> {
static constexpr ElementType p1_type{_cohesive_3d_6};
static constexpr std::array<ElementType, 1> facet_type{{_triangle_3}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_3d_12> {
static constexpr ElementType p1_type{_cohesive_3d_6};
static constexpr std::array<ElementType, 1> facet_type{{_triangle_6}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_3d_8> {
static constexpr ElementType p1_type{_cohesive_3d_8};
static constexpr std::array<ElementType, 1> facet_type{{_quadrangle_4}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_3d_16> {
static constexpr ElementType p1_type{_cohesive_3d_8};
static constexpr std::array<ElementType, 1> facet_type{{_quadrangle_8}};
};
#endif // AKANTU_COHESIVE_ELEMENT
} // namespace akantu
#endif /* __AKANTU_GEOMETRICAL_ELEMENT_PROPERTY_HH__ */
diff --git a/src/fe_engine/integration_point.hh b/src/fe_engine/integration_point.hh
index 9c8eb8056..0e09a5b89 100644
--- a/src/fe_engine/integration_point.hh
+++ b/src/fe_engine/integration_point.hh
@@ -1,169 +1,170 @@
/**
* @file integration_point.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Jun 17 2015
- * @date last modification: Sun Nov 15 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief definition of the class IntegrationPoint
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_types.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_QUADRATURE_POINT_H
#define AKANTU_QUADRATURE_POINT_H
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
class IntegrationPoint;
extern const IntegrationPoint IntegrationPointNull;
/* -------------------------------------------------------------------------- */
class IntegrationPoint : public Element {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using position_type = Vector<Real>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationPoint(const Element & element, UInt num_point = 0,
UInt nb_quad_per_element = 0)
: Element(element), num_point(num_point),
global_num(element.element * nb_quad_per_element + num_point),
position(nullptr, 0){};
IntegrationPoint(ElementType type = _not_defined, UInt element = 0,
UInt num_point = 0, GhostType ghost_type = _not_ghost)
: Element{type, element, ghost_type}, num_point(num_point),
position(nullptr, 0){};
IntegrationPoint(UInt element, UInt num_point, UInt global_num,
const position_type & position, ElementType type,
GhostType ghost_type = _not_ghost)
: Element{type, element, ghost_type}, num_point(num_point),
global_num(global_num), position(nullptr, 0) {
this->position.shallowCopy(position);
};
IntegrationPoint(const IntegrationPoint & quad)
: Element(quad), num_point(quad.num_point), global_num(quad.global_num),
position(nullptr, 0) {
position.shallowCopy(quad.position);
};
virtual ~IntegrationPoint() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
inline bool operator==(const IntegrationPoint & quad) const {
return Element::operator==(quad) && this->num_point == quad.num_point;
}
inline bool operator!=(const IntegrationPoint & quad) const {
return Element::operator!=(quad) || (num_point != quad.num_point) ||
(global_num != quad.global_num);
}
bool operator<(const IntegrationPoint & rhs) const {
bool res = Element::operator<(rhs) ||
(Element::operator==(rhs) && this->num_point < rhs.num_point);
return res;
}
inline IntegrationPoint & operator=(const IntegrationPoint & q) {
if (this != &q) {
element = q.element;
type = q.type;
ghost_type = q.ghost_type;
num_point = q.num_point;
global_num = q.global_num;
position.shallowCopy(q.position);
}
return *this;
}
/// get the position of the integration point
AKANTU_GET_MACRO(Position, position, const position_type &);
/// set the position of the integration point
void setPosition(const position_type & position) {
this->position.shallowCopy(position);
}
/// deep copy of the position of the integration point
void copyPosition(const position_type & position) {
this->position.deepCopy(position);
}
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "IntegrationPoint [";
stream << *static_cast<const Element *>(this);
stream << ", " << num_point << "(" << global_num << ")"
<< "]";
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
/// number of quadrature point in the element
UInt num_point;
/// global number of the quadrature point
UInt global_num{0};
// TODO might be temporary: however this class should be tought maybe...
std::string material_id;
private:
/// position of the quadrature point
position_type position;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const IntegrationPoint & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#endif /* AKANTU_QUADRATURE_POINT_H */
diff --git a/src/fe_engine/integrator.hh b/src/fe_engine/integrator.hh
index a9071ffe0..c751cfff4 100644
--- a/src/fe_engine/integrator.hh
+++ b/src/fe_engine/integrator.hh
@@ -1,136 +1,135 @@
/**
* @file integrator.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 22 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief interface for integrator classes
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_INTEGRATOR_HH__
#define __AKANTU_INTEGRATOR_HH__
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Integrator : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Integrator(const Mesh & mesh, const ID & id = "integrator",
const MemoryID & memory_id = 0)
: Memory(id, memory_id), mesh(mesh),
jacobians("jacobians", id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
~Integrator() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// empty method
template <ElementType type>
inline void precomputeJacobiansOnQuadraturePoints(__attribute__((unused))
GhostType ghost_type) {}
/// empty method
void integrateOnElement(const Array<Real> & /*f*/, Real * /*intf*/,
UInt /*nb_degree_of_freedom*/,
const Element & /*elem*/,
GhostType /*ghost_type*/) const {};
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Integrator [" << std::endl;
jacobians.printself(stream, indent + 1);
stream << space << "]" << std::endl;
};
/* ------------------------------------------------------------------------ */
public:
virtual void onElementsAdded(const Array<Element> &) {}
virtual void
onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> & new_numbering) {
jacobians.onElementsRemoved(new_numbering);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// access to the jacobians
Array<Real> & getJacobians(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return jacobians(type, ghost_type);
};
/// access to the jacobians const
const Array<Real> &
getJacobians(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
return jacobians(type, ghost_type);
};
AKANTU_GET_MACRO(Jacobians, jacobians, const ElementTypeMapArray<Real> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// mesh associated to the integrator
const Mesh & mesh;
/// jacobians for all elements
ElementTypeMapArray<Real> jacobians;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "integrator_inline_impl.cc"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Integrator & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* __AKANTU_INTEGRATOR_HH__ */
diff --git a/src/fe_engine/integrator_gauss.hh b/src/fe_engine/integrator_gauss.hh
index 4b76a5962..469f19832 100644
--- a/src/fe_engine/integrator_gauss.hh
+++ b/src/fe_engine/integrator_gauss.hh
@@ -1,199 +1,199 @@
/**
* @file integrator_gauss.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 22 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Gauss integration facilities
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "integrator.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTEGRATOR_GAUSS_HH__
#define __AKANTU_INTEGRATOR_GAUSS_HH__
namespace akantu {
namespace integrator {
namespace details {
template <ElementKind> struct GaussIntegratorComputeJacobiansHelper;
} // namespace details
} // namespace fe_engine
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss : public Integrator {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegratorGauss(const Mesh & mesh, const ID & id = "integrator_gauss",
const MemoryID & memory_id = 0);
~IntegratorGauss() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initIntegrator(const Array<Real> & nodes, const ElementType & type,
const GhostType & ghost_type);
template <ElementType type>
inline void initIntegrator(const Array<Real> & nodes,
const GhostType & ghost_type);
/// integrate f on the element "elem" of type "type"
template <ElementType type>
inline void integrateOnElement(const Array<Real> & f, Real * intf,
UInt nb_degree_of_freedom, const UInt elem,
const GhostType & ghost_type) const;
/// integrate f for all elements of type "type"
template <ElementType type>
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate scalar field in_f
template <ElementType type, UInt polynomial_degree>
Real integrate(const Array<Real> & in_f,
const GhostType & ghost_type = _not_ghost) const;
/// integrate partially around a quadrature point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
template <ElementType type>
Real integrate(const Vector<Real> & in_f, UInt index,
const GhostType & ghost_type) const;
/// integrate scalar field in_f
template <ElementType type>
Real integrate(const Array<Real> & in_f, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate a field without using the pre-computed values
template <ElementType type, UInt polynomial_degree>
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, const GhostType & ghost_type) const;
/// integrate partially around a quadrature point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
template <ElementType type>
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const;
/// return a matrix with quadrature points natural coordinates
template <ElementType type>
const Matrix<Real> & getIntegrationPoints(const GhostType & ghost_type) const;
/// return number of quadrature points
template <ElementType type>
UInt getNbIntegrationPoints(const GhostType & ghost_type) const;
template <ElementType type, UInt n> Matrix<Real> getIntegrationPoints() const;
template <ElementType type, UInt n>
Vector<Real> getIntegrationWeights() const;
protected:
friend struct integrator::details::GaussIntegratorComputeJacobiansHelper<
kind>;
template <ElementType type>
void computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// precompute jacobians on elements of type "type"
template <ElementType type>
void precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
const GhostType & ghost_type);
// multiply the jacobians by the integration weights and stores the results in
// jacobians
template <ElementType type, UInt polynomial_degree>
void multiplyJacobiansByWeights(Array<Real> & jacobians) const;
/// compute the vector of quadrature points natural coordinates
template <ElementType type>
void computeQuadraturePoints(const GhostType & ghost_type);
/// check that the jacobians are not negative
template <ElementType type>
void checkJacobians(const GhostType & ghost_type) const;
/// internal integrate partially around a quadrature point (@f$ intf_q = f_q *
/// J_q *
/// w_q @f$)
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
const Array<Real> & jacobians,
UInt nb_element) const;
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, const Array<Real> & jacobians,
UInt nb_element) const;
public:
/// compute the jacobians on quad points for a given element
template <ElementType type>
void
computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & integration_points,
Vector<Real> & jacobians) const;
public:
void onElementsAdded(const Array<Element> & elements) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// integrate the field f with the jacobian jac -> inte
inline void integrate(Real * f, Real * jac, Real * inte,
UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const;
private:
/// ElementTypeMap of the quadrature points
ElementTypeMap<Matrix<Real>> quadrature_points;
};
} // namespace akantu
#include "integrator_gauss_inline_impl.cc"
#endif /* __AKANTU_INTEGRATOR_GAUSS_HH__ */
diff --git a/src/fe_engine/integrator_gauss_inline_impl.cc b/src/fe_engine/integrator_gauss_inline_impl.cc
index 681123e63..56fe0c8e3 100644
--- a/src/fe_engine/integrator_gauss_inline_impl.cc
+++ b/src/fe_engine/integrator_gauss_inline_impl.cc
@@ -1,709 +1,709 @@
/**
* @file integrator_gauss_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Thu Nov 19 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief inline function of gauss integrator
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "mesh_iterators.hh"
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace debug {
struct IntegratorGaussException : public Exception {};
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::integrateOnElement(
const Array<Real> & f, Real * intf, UInt nb_degree_of_freedom,
const UInt elem, const GhostType & ghost_type) const {
Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points = ElementClass<type>::getNbQuadraturePoints();
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f do not have the good number of component.");
Real * f_val = f.storage() + elem * f.getNbComponent();
Real * jac_val = jac_loc.storage() + elem * nb_quadrature_points;
integrate(f_val, jac_val, intf, nb_degree_of_freedom, nb_quadrature_points);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Vector<Real> & in_f, UInt index, const GhostType & ghost_type) const {
const Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points =
GaussIntegrationElement<type>::getNbQuadraturePoints();
AKANTU_DEBUG_ASSERT(in_f.size() == nb_quadrature_points,
"The vector f do not have nb_quadrature_points entries.");
Real * jac_val = jac_loc.storage() + index * nb_quadrature_points;
Real intf;
integrate(in_f.storage(), jac_val, &intf, 1, nb_quadrature_points);
return intf;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
Real * f, Real * jac, Real * inte, UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const {
memset(inte, 0, nb_degree_of_freedom * sizeof(Real));
Real * cjac = jac;
for (UInt q = 0; q < nb_quadrature_points; ++q) {
for (UInt dof = 0; dof < nb_degree_of_freedom; ++dof) {
inte[dof] += *f * *cjac;
++f;
}
++cjac;
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline const Matrix<Real> &
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationPoints(
const GhostType & ghost_type) const {
AKANTU_DEBUG_ASSERT(
quadrature_points.exists(type, ghost_type),
"Quadrature points for type "
<< quadrature_points.printType(type, ghost_type)
<< " have not been initialized."
<< " Did you use 'computeQuadraturePoints' function ?");
return quadrature_points(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline UInt
IntegratorGauss<kind, IntegrationOrderFunctor>::getNbIntegrationPoints(
const GhostType & ghost_type) const {
AKANTU_DEBUG_ASSERT(
quadrature_points.exists(type, ghost_type),
"Quadrature points for type "
<< quadrature_points.printType(type, ghost_type)
<< " have not been initialized."
<< " Did you use 'computeQuadraturePoints' function ?");
return quadrature_points(type, ghost_type).cols();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
inline Matrix<Real>
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationPoints() const {
return GaussIntegrationElement<type,
polynomial_degree>::getQuadraturePoints();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
inline Vector<Real>
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationWeights() const {
return GaussIntegrationElement<type, polynomial_degree>::getWeights();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
IntegratorGauss<kind, IntegrationOrderFunctor>::computeQuadraturePoints(
const GhostType & ghost_type) {
Matrix<Real> & quads = quadrature_points(type, ghost_type);
const UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
quads =
GaussIntegrationElement<type, polynomial_degree>::getQuadraturePoints();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & quad,
Vector<Real> & jacobians) const {
// jacobian
ElementClass<type>::computeJacobian(quad, node_coords, jacobians);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
IntegratorGauss<kind, IntegrationOrderFunctor>::IntegratorGauss(
const Mesh & mesh, const ID & id, const MemoryID & memory_id)
: Integrator(mesh, id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::checkJacobians(
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->quadrature_points(type, ghost_type).cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
Real * jacobians_val = jacobians(type, ghost_type).storage();
for (UInt i = 0; i < nb_element * nb_quadrature_points;
++i, ++jacobians_val) {
if (*jacobians_val < 0)
AKANTU_CUSTOM_EXCEPTION_INFO(debug::IntegratorGaussException{},
"Negative jacobian computed,"
<< " possible problem in the element "
"node ordering (Quadrature Point "
<< i % nb_quadrature_points << ":"
<< i / nb_quadrature_points << ":"
<< type << ":" << ghost_type << ")");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = quad_points.cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
auto jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
auto jacobians_begin = jacobians_it;
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
auto x_it = x_el.begin(spatial_dimension, nb_nodes_per_element);
nb_element = x_el.size();
// Matrix<Real> local_coord(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
const Matrix<Real> & x = *x_it;
Vector<Real> & J = *jacobians_it;
computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
if (filter_elements == empty_filter) {
++jacobians_it;
} else {
jacobians_it = jacobians_begin + filter_elements(elem);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
template <>
template <ElementType type>
void IntegratorGauss<_ek_structural, DefaultIntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
const UInt spatial_dimension = mesh.getSpatialDimension();
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const UInt nb_quadrature_points = quad_points.cols();
const UInt nb_dofs = ElementClass<type>::getNbDegreeOfFreedom();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
auto jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
auto jacobians_begin = jacobians_it;
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
auto x_it = x_el.begin(spatial_dimension, nb_nodes_per_element);
nb_element = x_el.size();
const bool has_extra_normal =
mesh.hasData<Real>("extra_normal", type, ghost_type);
Array<Real>::const_vector_iterator extra_normal, extra_normal_begin;
if (has_extra_normal) {
extra_normal = mesh.getData<Real>("extra_normal", type, ghost_type)
.begin(spatial_dimension);
extra_normal_begin = extra_normal;
}
// Matrix<Real> local_coord(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
const Matrix<Real> & X = *x_it;
Vector<Real> & J = *jacobians_it;
Matrix<Real> R(nb_dofs, nb_dofs);
if (has_extra_normal)
ElementClass<type>::computeRotationMatrix(R, X, *extra_normal);
else
ElementClass<type>::computeRotationMatrix(R, X, Vector<Real>(X.rows()));
// Extracting relevant lines
auto x = (R.block(0, 0, spatial_dimension, spatial_dimension) * X)
.block(0, 0, ElementClass<type>::getNaturalSpaceDimension(),
ElementClass<type>::getNbNodesPerElement());
computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
if (filter_elements == empty_filter) {
++jacobians_it;
++extra_normal;
} else {
jacobians_it = jacobians_begin + filter_elements(elem);
extra_normal = extra_normal_begin + filter_elements(elem);
}
}
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
template <>
template <ElementType type>
void IntegratorGauss<_ek_cohesive, DefaultIntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = quad_points.cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
auto jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
auto jacobians_begin = jacobians_it;
Vector<Real> weights = GaussIntegrationElement<type>::getWeights();
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
auto x_it = x_el.begin(spatial_dimension, nb_nodes_per_element);
UInt nb_nodes_per_subelement = nb_nodes_per_element / 2;
Matrix<Real> x(spatial_dimension, nb_nodes_per_subelement);
nb_element = x_el.size();
auto compute = [&](const auto & el) {
Vector<Real> J(jacobians_begin[el]);
for (UInt s = 0; s < spatial_dimension; ++s)
for (UInt n = 0; n < nb_nodes_per_subelement; ++n)
x(s, n) =
((*x_it)(s, n) + (*x_it)(s, n + nb_nodes_per_subelement)) * .5;
if (type == _cohesive_1d_2)
J(0) = 1;
else
this->computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
};
for_each_element(nb_element, filter_elements, compute);
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & jacobians_tmp = jacobians.alloc(0, 1, type, ghost_type);
this->computeJacobiansOnIntegrationPoints<type>(
nodes, quadrature_points(type, ghost_type), jacobians_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
void IntegratorGauss<kind, IntegrationOrderFunctor>::multiplyJacobiansByWeights(
Array<Real> & jacobians) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points =
GaussIntegrationElement<type, polynomial_degree>::getNbQuadraturePoints();
UInt nb_element = jacobians.size() / nb_quadrature_points;
Vector<Real> weights =
GaussIntegrationElement<type, polynomial_degree>::getWeights();
auto jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
auto jacobians_end =
jacobians.end_reinterpret(nb_quadrature_points, nb_element);
for (; jacobians_it != jacobians_end; ++jacobians_it) {
Vector<Real> & J = *jacobians_it;
J *= weights;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
const Array<Real> & jacobians, UInt nb_element) const {
AKANTU_DEBUG_IN();
intf.resize(nb_element);
if (nb_element == 0)
return;
UInt nb_points = jacobians.size() / nb_element;
Array<Real>::const_matrix_iterator J_it;
Array<Real>::matrix_iterator inte_it;
Array<Real>::const_matrix_iterator f_it;
f_it = in_f.begin_reinterpret(nb_degree_of_freedom, nb_points, nb_element);
inte_it = intf.begin_reinterpret(nb_degree_of_freedom, 1, nb_element);
J_it = jacobians.begin_reinterpret(nb_points, 1, nb_element);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Matrix<Real> & f = *f_it;
const Matrix<Real> & J = *J_it;
Matrix<Real> & inte_f = *inte_it;
inte_f.mul<false, false>(f, J);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
const Array<Real> & jac_loc = jacobians(type, ghost_type);
if (filter_elements != empty_filter) {
UInt nb_element = filter_elements.size();
Array<Real> * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
this->integrate(in_f, intf, nb_degree_of_freedom, *filtered_J, nb_element);
delete filtered_J;
} else {
UInt nb_element = mesh.getNbElement(type, ghost_type);
this->integrate(in_f, intf, nb_degree_of_freedom, jac_loc, nb_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
Matrix<Real> quads = this->getIntegrationPoints<type, polynomial_degree>();
Array<Real> jacobians;
this->computeJacobiansOnIntegrationPoints<type>(mesh.getNodes(), quads,
jacobians, ghost_type);
this->multiplyJacobiansByWeights<type, polynomial_degree>(jacobians);
this->integrate(in_f, intf, nb_degree_of_freedom, jacobians,
mesh.getNbElement(type, ghost_type));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
Array<Real> intfv(0, 1);
integrate<type, polynomial_degree>(in_f, intfv, 1, ghost_type);
Real res = Math::reduce(intfv);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
Array<Real> intfv(0, 1);
integrate<type>(in_f, intfv, 1, ghost_type, filter_elements);
Real res = Math::reduce(intfv);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom,
const Array<Real> & jacobians,
UInt nb_element) const {
AKANTU_DEBUG_IN();
UInt nb_points = jacobians.size() / nb_element;
intf.resize(nb_element * nb_points);
auto J_it = jacobians.begin();
auto f_it = in_f.begin(nb_degree_of_freedom);
auto inte_it = intf.begin(nb_degree_of_freedom);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Real & J = *J_it;
const Vector<Real> & f = *f_it;
Vector<Real> & inte_f = *inte_it;
inte_f = f;
inte_f *= J;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
const Array<Real> & jac_loc = this->jacobians(type, ghost_type);
if (filter_elements != empty_filter) {
UInt nb_element = filter_elements.size();
Array<Real> * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
this->integrateOnIntegrationPoints(in_f, intf, nb_degree_of_freedom,
*filtered_J, nb_element);
} else {
UInt nb_element = mesh.getNbElement(type, ghost_type);
this->integrateOnIntegrationPoints(in_f, intf, nb_degree_of_freedom,
jac_loc, nb_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::onElementsAdded(
const Array<Element> & new_elements) {
const auto & nodes = mesh.getNodes();
for (auto elements_range : MeshElementsByTypes(new_elements)) {
auto type = elements_range.getType();
auto ghost_type = elements_range.getGhostType();
if (mesh.getKind(type) != kind)
continue;
auto & elements = elements_range.getElements();
if (not jacobians.exists(type, ghost_type))
jacobians.alloc(0, 1, type, ghost_type);
this->computeJacobiansOnIntegrationPoints(
nodes, quadrature_points(type, ghost_type), jacobians(type, ghost_type),
type, ghost_type, elements);
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::initIntegrator(
const Array<Real> & nodes, const GhostType & ghost_type) {
computeQuadraturePoints<type>(ghost_type);
precomputeJacobiansOnQuadraturePoints<type>(nodes, ghost_type);
checkJacobians<type>(ghost_type);
constexpr UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
multiplyJacobiansByWeights<type, polynomial_degree>(
this->jacobians(type, ghost_type));
}
namespace integrator {
namespace details {
template <ElementKind kind> struct GaussIntegratorInitHelper {};
#define INIT_INTEGRATOR(type) \
_int.template initIntegrator<type>(nodes, ghost_type)
#define AKANTU_GAUSS_INTERGRATOR_INIT_HELPER(kind) \
template <> struct GaussIntegratorInitHelper<kind> { \
template <ElementKind k, class IOF> \
static void call(IntegratorGauss<k, IOF> & _int, \
const Array<Real> & nodes, const ElementType & type, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INIT_INTEGRATOR, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_GAUSS_INTERGRATOR_INIT_HELPER)
#undef AKANTU_GAUSS_INTERGRATOR_INIT_HELPER
#undef INIT_INTEGRATOR
} // namespace details
} // namespace integrator
template <ElementKind kind, class IntegrationOrderFunctor>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::initIntegrator(
const Array<Real> & nodes, const ElementType & type,
const GhostType & ghost_type) {
integrator::details::GaussIntegratorInitHelper<kind>::call(*this, nodes, type,
ghost_type);
}
namespace integrator {
namespace details {
template <ElementKind kind> struct GaussIntegratorComputeJacobiansHelper {};
#define AKANTU_COMPUTE_JACOBIANS(type) \
_int.template computeJacobiansOnIntegrationPoints<type>( \
nodes, quad_points, jacobians, ghost_type, filter_elements);
#define AKANTU_GAUSS_INTERGRATOR_COMPUTE_JACOBIANS(kind) \
template <> struct GaussIntegratorComputeJacobiansHelper<kind> { \
template <ElementKind k, class IOF> \
static void \
call(const IntegratorGauss<k, IOF> & _int, const Array<Real> & nodes, \
const Matrix<Real> & quad_points, Array<Real> & jacobians, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(AKANTU_COMPUTE_JACOBIANS, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_GAUSS_INTERGRATOR_COMPUTE_JACOBIANS)
#undef AKANTU_GAUSS_INTERGRATOR_COMPUTE_JACOBIANS
#undef AKANTU_COMPUTE_JACOBIANS
} // namespace details
} // namespace integrator
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
integrator::details::GaussIntegratorComputeJacobiansHelper<kind>::call(
*this, nodes, quad_points, jacobians, type, ghost_type, filter_elements);
}
} // namespace akantu
diff --git a/src/fe_engine/interpolation_element_tmpl.hh b/src/fe_engine/interpolation_element_tmpl.hh
index 9507deb58..febbb6ddd 100644
--- a/src/fe_engine/interpolation_element_tmpl.hh
+++ b/src/fe_engine/interpolation_element_tmpl.hh
@@ -1,73 +1,73 @@
/**
* @file interpolation_element_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 06 2013
- * @date last modification: Tue Apr 07 2015
+ * @date last modification: Wed Nov 29 2017
*
* @brief interpolation property description
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTERPOLATION_ELEMENT_TMPL_HH__
#define __AKANTU_INTERPOLATION_ELEMENT_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Regular Elements */
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_not_defined, _itk_not_defined, 0,
0);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_point_1,
_itk_lagrangian, 1, 0);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_segment_2,
_itk_lagrangian, 2, 1);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_segment_3,
_itk_lagrangian, 3, 1);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_triangle_3,
_itk_lagrangian, 3, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_triangle_6,
_itk_lagrangian, 6, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_tetrahedron_4,
_itk_lagrangian, 4, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_tetrahedron_10,
_itk_lagrangian, 10, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_quadrangle_4,
_itk_lagrangian, 4, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_serendip_quadrangle_8,
_itk_lagrangian, 8, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_hexahedron_8,
_itk_lagrangian, 8, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_serendip_hexahedron_20,
_itk_lagrangian, 20, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_pentahedron_6,
_itk_lagrangian, 6, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_pentahedron_15,
_itk_lagrangian, 15, 3);
} // akantu
#endif /* __AKANTU_INTERPOLATION_ELEMENT_TMPL_HH__ */
diff --git a/src/fe_engine/shape_cohesive.hh b/src/fe_engine/shape_cohesive.hh
index 96e0867e9..45c4bfd40 100644
--- a/src/fe_engine/shape_cohesive.hh
+++ b/src/fe_engine/shape_cohesive.hh
@@ -1,183 +1,182 @@
/**
* @file shape_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Thu Oct 22 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief shape functions for cohesive elements description
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_COHESIVE_HH__
#define __AKANTU_SHAPE_COHESIVE_HH__
namespace akantu {
struct CohesiveReduceFunctionMean {
inline Real operator()(Real u_plus, Real u_minus) {
return .5 * (u_plus + u_minus);
}
};
struct CohesiveReduceFunctionOpening {
inline Real operator()(Real u_plus, Real u_minus) {
return (u_plus - u_minus);
}
};
template <> class ShapeLagrange<_ek_cohesive> : public ShapeLagrangeBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, const ID & id = "shape_cohesive",
const MemoryID & memory_id = 0);
~ShapeLagrange() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
const ElementType & type,
const GhostType & ghost_type);
/// extract the nodal values and store them per element
template <ElementType type, class ReduceFunction>
void extractNodalToElementField(
const Array<Real> & nodal_f, Array<Real> & elemental_f,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// computes the shape functions derivatives for given interpolation points
template <ElementType type>
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const override;
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// pre compute all shape derivatives on the element integration points from
/// natural coordinates
template <ElementType type>
void precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type, class ReduceFunction>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
const GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
const GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const {
interpolateOnIntegrationPoints<type, CohesiveReduceFunctionMean>(
u, uq, nb_degree_of_freedom, ghost_type, filter_elements);
}
/// compute the gradient of u on the integration points in the natural
/// coordinates
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const {
variationOnIntegrationPoints<type, CohesiveReduceFunctionMean>(
u, nablauq, nb_degree_of_freedom, ghost_type, filter_elements);
}
template <ElementType type>
void computeBtD(const Array<Real> & /*Ds*/, Array<Real> & /*BtDs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
template <ElementType type>
void computeBtDB(const Array<Real> & /*Ds*/, Array<Real> & /*BtDBs*/,
UInt /*order_d*/, GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the gradient of u on the integration points
template <ElementType type, class ReduceFunction>
void variationOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// compute the normals to the field u on integration points
template <ElementType type, class ReduceFunction>
void computeNormalsOnIntegrationPoints(
const Array<Real> & u, Array<Real> & normals_u,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// multiply a field by shape functions
template <ElementType type>
void fieldTimesShapes(__attribute__((unused)) const Array<Real> & field,
__attribute__((unused))
Array<Real> & fiedl_times_shapes,
__attribute__((unused)) GhostType ghost_type) const {
AKANTU_TO_IMPLEMENT();
}
};
/// standard output stream operator
template <class ShapeFunction>
inline std::ostream & operator<<(std::ostream & stream,
const ShapeCohesive<ShapeFunction> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "shape_cohesive_inline_impl.cc"
#endif /* __AKANTU_SHAPE_COHESIVE_HH__ */
diff --git a/src/fe_engine/shape_cohesive_inline_impl.cc b/src/fe_engine/shape_cohesive_inline_impl.cc
index df81e9a8f..ad02dbffc 100644
--- a/src/fe_engine/shape_cohesive_inline_impl.cc
+++ b/src/fe_engine/shape_cohesive_inline_impl.cc
@@ -1,328 +1,328 @@
/**
* @file shape_cohesive_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 03 2012
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Mon Feb 19 2018
*
* @brief ShapeCohesive inline implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "shape_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_COHESIVE_INLINE_IMPL_CC__
#define __AKANTU_SHAPE_COHESIVE_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline ShapeLagrange<_ek_cohesive>::ShapeLagrange(const Mesh & mesh,
const ID & id,
const MemoryID & memory_id)
: ShapeLagrangeBase(mesh, _ek_cohesive, id, memory_id) {}
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
/* -------------------------------------------------------------------------- */
inline void ShapeLagrange<_ek_cohesive>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
const ElementType & type, const GhostType & ghost_type) {
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_cohesive>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> &, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
UInt spatial_dimension = ElementClass<type>::getNaturalSpaceDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
AKANTU_DEBUG_ASSERT(shape_derivatives.getNbComponent() == size_of_shapesd,
"The shapes_derivatives array does not have the correct "
<< "number of component");
shape_derivatives.resize(nb_element * nb_points);
Real * shapesd_val = shape_derivatives.storage();
auto compute = [&](const auto & el) {
auto ptr = shapesd_val + el * nb_points * size_of_shapesd;
Tensor3<Real> B(ptr, spatial_dimension, nb_nodes_per_element, nb_points);
ElementClass<type>::computeDNDS(integration_points, B);
};
for_each_element(nb_element, filter_elements, compute);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void
ShapeLagrange<_ek_cohesive>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const ElementType & type,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
#define AKANTU_COMPUTE_SHAPES(type) \
computeShapeDerivativesOnIntegrationPoints<type>( \
nodes, integration_points, shape_derivatives, ghost_type, \
filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(AKANTU_COMPUTE_SHAPES);
#undef AKANTU_COMPUTE_SHAPES
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_cohesive>::precomputeShapesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapes = ElementClass<type>::getShapeSize();
Array<Real> & shapes_tmp =
shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
this->computeShapesOnIntegrationPoints<type>(nodes, natural_coords,
shapes_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_cohesive>::precomputeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
Array<Real> & shapes_derivatives_tmp =
shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
this->computeShapeDerivativesOnIntegrationPoints<type>(
nodes, natural_coords, shapes_derivatives_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::extractNodalToElementField(
const Array<Real> & nodal_f, Array<Real> & elemental_f,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_itp_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_degree_of_freedom = nodal_f.getNbComponent();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
const auto & conn_array = this->mesh.getConnectivity(type, ghost_type);
auto conn = conn_array.begin(conn_array.getNbComponent() / 2, 2);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
elemental_f.resize(nb_element);
Array<Real>::matrix_iterator u_it =
elemental_f.begin(nb_degree_of_freedom, nb_nodes_per_itp_element);
ReduceFunction reduce_function;
auto compute = [&](const auto & el) {
Matrix<Real> & u = *u_it;
Matrix<UInt> el_conn(conn[el]);
// compute the average/difference of the nodal field loaded from cohesive
// element
for (UInt n = 0; n < el_conn.rows(); ++n) {
UInt node_plus = el_conn(n, 0);
UInt node_minus = el_conn(n, 1);
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
Real u_plus = nodal_f(node_plus, d);
Real u_minus = nodal_f(node_minus, d);
u(d, n) = reduce_function(u_plus, u_minus);
}
}
++u_it;
};
for_each_element(nb_element, filter_elements, compute);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(this->shapes.exists(itp_type, ghost_type),
"No shapes for the type "
<< this->shapes.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
this->extractNodalToElementField<type, ReduceFunction>(in_u, u_el, ghost_type,
filter_elements);
this->template interpolateElementalFieldOnIntegrationPoints<type>(
u_el, out_uq, ghost_type, shapes(itp_type, ghost_type), filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::variationOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(
this->shapes_derivatives.exists(itp_type, ghost_type),
"No shapes for the type "
<< this->shapes_derivatives.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
this->extractNodalToElementField<type, ReduceFunction>(in_u, u_el, ghost_type,
filter_elements);
this->template gradientElementalFieldOnIntegrationPoints<type>(
u_el, nablauq, ghost_type, shapes_derivatives(itp_type, ghost_type),
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::computeNormalsOnIntegrationPoints(
const Array<Real> & u, Array<Real> & normals_u, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
UInt nb_points = this->integration_points(type, ghost_type).cols();
UInt spatial_dimension = this->mesh.getSpatialDimension();
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
normals_u.resize(nb_points * nb_element);
Array<Real> tangents_u(0, (spatial_dimension * (spatial_dimension - 1)));
if (spatial_dimension > 1) {
tangents_u.resize(nb_element * nb_points);
this->template variationOnIntegrationPoints<type, ReduceFunction>(
u, tangents_u, spatial_dimension, ghost_type, filter_elements);
}
Real * tangent = tangents_u.storage();
if (spatial_dimension == 3) {
for (auto & normal : make_view(normals_u, spatial_dimension)) {
Math::vectorProduct3(tangent, tangent + spatial_dimension,
normal.storage());
normal /= normal.norm();
tangent += spatial_dimension * 2;
}
} else if (spatial_dimension == 2) {
for (auto & normal : make_view(normals_u, spatial_dimension)) {
Vector<Real> a1(tangent, spatial_dimension);
normal(0) = -a1(1);
normal(1) = a1(0);
normal.normalize();
tangent += spatial_dimension;
}
} else if (spatial_dimension == 1) {
const auto facet_type = Mesh::getFacetType(type);
const auto & mesh_facets = mesh.getMeshFacets();
const auto & facets = mesh_facets.getSubelementToElement(type, ghost_type);
const auto & segments =
mesh_facets.getElementToSubelement(facet_type, ghost_type);
Real values[2];
for (auto el : arange(nb_element)) {
if (filter_elements != empty_filter)
el = filter_elements(el);
for (UInt p = 0; p < 2; ++p) {
Element facet = facets(el, p);
Element segment = segments(facet.element)[0];
Vector<Real> barycenter(values + p, 1);
mesh.getBarycenter(segment, barycenter);
}
Real difference = values[0] - values[1];
AKANTU_DEBUG_ASSERT(difference != 0.,
"Error in normal computation for cohesive elements");
normals_u(el) = difference / std::abs(difference);
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* __AKANTU_SHAPE_COHESIVE_INLINE_IMPL_CC__ */
diff --git a/src/fe_engine/shape_functions.cc b/src/fe_engine/shape_functions.cc
index 15d67f780..b45c222a9 100644
--- a/src/fe_engine/shape_functions.cc
+++ b/src/fe_engine/shape_functions.cc
@@ -1,243 +1,245 @@
/**
* @file shape_functions.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Thu Jul 27 2017
+ * @date creation: Wed Aug 09 2017
+ * @date last modification: Wed Oct 11 2017
*
- * @brief implementation of th shape functions interface
+ * @brief implementation of th shape functions interface
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ShapeFunctions::ShapeFunctions(const Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: Memory(id, memory_id), shapes("shapes_generic", id, memory_id),
shapes_derivatives("shapes_derivatives_generic", id, memory_id),
mesh(mesh) {}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void
ShapeFunctions::initElementalFieldInterpolationFromIntegrationPoints(
const Array<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const Array<Real> & quadrature_points_coordinates,
const GhostType & ghost_type, const Array<UInt> & element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
UInt nb_element_filter;
if (element_filter == empty_filter)
nb_element_filter = nb_element;
else
nb_element_filter = element_filter.size();
UInt nb_quad_per_element =
GaussIntegrationElement<type>::getNbQuadraturePoints();
UInt nb_interpolation_points_per_elem =
interpolation_points_coordinates.size() / nb_element;
AKANTU_DEBUG_ASSERT(interpolation_points_coordinates.size() % nb_element == 0,
"Number of interpolation points should be a multiple of "
"total number of elements");
if (!quad_points_coordinates_inv_matrices.exists(type, ghost_type))
quad_points_coordinates_inv_matrices.alloc(
nb_element_filter, nb_quad_per_element * nb_quad_per_element, type,
ghost_type);
else
quad_points_coordinates_inv_matrices(type, ghost_type)
.resize(nb_element_filter);
if (!interpolation_points_coordinates_matrices.exists(type, ghost_type))
interpolation_points_coordinates_matrices.alloc(
nb_element_filter,
nb_interpolation_points_per_elem * nb_quad_per_element, type,
ghost_type);
else
interpolation_points_coordinates_matrices(type, ghost_type)
.resize(nb_element_filter);
Array<Real> & quad_inv_mat =
quad_points_coordinates_inv_matrices(type, ghost_type);
Array<Real> & interp_points_mat =
interpolation_points_coordinates_matrices(type, ghost_type);
Matrix<Real> quad_coord_matrix(nb_quad_per_element, nb_quad_per_element);
Array<Real>::const_matrix_iterator quad_coords_it =
quadrature_points_coordinates.begin_reinterpret(
spatial_dimension, nb_quad_per_element, nb_element_filter);
Array<Real>::const_matrix_iterator points_coords_begin =
interpolation_points_coordinates.begin_reinterpret(
spatial_dimension, nb_interpolation_points_per_elem, nb_element);
Array<Real>::matrix_iterator inv_quad_coord_it =
quad_inv_mat.begin(nb_quad_per_element, nb_quad_per_element);
Array<Real>::matrix_iterator int_points_mat_it = interp_points_mat.begin(
nb_interpolation_points_per_elem, nb_quad_per_element);
/// loop over the elements of the current material and element type
for (UInt el = 0; el < nb_element_filter;
++el, ++inv_quad_coord_it, ++int_points_mat_it, ++quad_coords_it) {
/// matrix containing the quadrature points coordinates
const Matrix<Real> & quad_coords = *quad_coords_it;
/// matrix to store the matrix inversion result
Matrix<Real> & inv_quad_coord_matrix = *inv_quad_coord_it;
/// insert the quad coordinates in a matrix compatible with the
/// interpolation
buildElementalFieldInterpolationMatrix<type>(quad_coords,
quad_coord_matrix);
/// invert the interpolation matrix
inv_quad_coord_matrix.inverse(quad_coord_matrix);
/// matrix containing the interpolation points coordinates
const Matrix<Real> & points_coords =
points_coords_begin[element_filter(el)];
/// matrix to store the interpolation points coordinates
/// compatible with these functions
Matrix<Real> & inv_points_coord_matrix = *int_points_mat_it;
/// insert the quad coordinates in a matrix compatible with the
/// interpolation
buildElementalFieldInterpolationMatrix<type>(points_coords,
inv_points_coord_matrix);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ShapeFunctions::initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
for (auto ghost_type : ghost_types) {
Mesh::type_iterator it, last;
if (element_filter) {
it = element_filter->firstType(spatial_dimension, ghost_type);
last = element_filter->lastType(spatial_dimension, ghost_type);
} else {
it = mesh.firstType(spatial_dimension, ghost_type);
last = mesh.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<UInt> * elem_filter;
if (element_filter)
elem_filter = &((*element_filter)(type, ghost_type));
else
elem_filter = &(empty_filter);
#define AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS(type) \
this->initElementalFieldInterpolationFromIntegrationPoints<type>( \
interpolation_points_coordinates(type, ghost_type), \
interpolation_points_coordinates_matrices, \
quad_points_coordinates_inv_matrices, \
quadrature_points_coordinates(type, ghost_type), ghost_type, \
*elem_filter)
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(
AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS);
#undef AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ShapeFunctions::interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
Mesh::type_iterator it, last;
if (element_filter) {
it = element_filter->firstType(spatial_dimension, ghost_type);
last = element_filter->lastType(spatial_dimension, ghost_type);
} else {
it = mesh.firstType(spatial_dimension, ghost_type);
last = mesh.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<UInt> * elem_filter;
if (element_filter)
elem_filter = &((*element_filter)(type, ghost_type));
else
elem_filter = &(empty_filter);
#define AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS(type) \
interpolateElementalFieldFromIntegrationPoints<type>( \
field(type, ghost_type), \
interpolation_points_coordinates_matrices(type, ghost_type), \
quad_points_coordinates_inv_matrices(type, ghost_type), result, \
ghost_type, *elem_filter)
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(
AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS);
#undef AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/fe_engine/shape_functions.hh b/src/fe_engine/shape_functions.hh
index 8d2626a4a..1780f87b8 100644
--- a/src/fe_engine/shape_functions.hh
+++ b/src/fe_engine/shape_functions.hh
@@ -1,215 +1,214 @@
/**
* @file shape_functions.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 22 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief shape function class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_FUNCTIONS_HH__
#define __AKANTU_SHAPE_FUNCTIONS_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
class ShapeFunctions : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeFunctions(const Mesh & mesh, const ID & id = "shape",
const MemoryID & memory_id = 0);
~ShapeFunctions() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Shapes [" << std::endl;
integration_points.printself(stream, indent + 1);
// shapes.printself(stream, indent + 1);
// shapes_derivatives.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/// set the integration points for a given element
template <ElementType type>
void setIntegrationPointsByType(const Matrix<Real> & integration_points,
const GhostType & ghost_type);
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * element_filter) const;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const;
protected:
/// interpolate nodal values stored by element on the integration points
template <ElementType type>
void interpolateElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & uq, const GhostType & ghost_type,
const Array<Real> & shapes,
const Array<UInt> & filter_elements = empty_filter) const;
/// gradient of nodal values stored by element on the control points
template <ElementType type>
void gradientElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & out_nablauq,
const GhostType & ghost_type, const Array<Real> & shapes_derivatives,
const Array<UInt> & filter_elements) const;
protected:
/// By element versions of non-templated eponym methods
template <ElementType type>
inline void interpolateElementalFieldFromIntegrationPoints(
const Array<Real> & field,
const Array<Real> & interpolation_points_coordinates_matrices,
const Array<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
const Array<UInt> & element_filter) const;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
template <ElementType type>
inline void initElementalFieldInterpolationFromIntegrationPoints(
const Array<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const Array<Real> & quadrature_points_coordinates,
const GhostType & ghost_type, const Array<UInt> & element_filter) const;
/// build matrix for the interpolation of field form integration points
template <ElementType type>
inline void buildElementalFieldInterpolationMatrix(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order =
ElementClassProperty<type>::polynomial_degree) const;
/// build the so called interpolation matrix (first collumn is 1, then the
/// other collumns are the traansposed coordinates)
inline void buildInterpolationMatrix(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix,
UInt integration_order) const;
public:
virtual void onElementsAdded(const Array<Element> &) {
AKANTU_TO_IMPLEMENT();
}
virtual void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &) {
AKANTU_TO_IMPLEMENT();
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the size of the shapes returned by the element class
static inline UInt getShapeSize(const ElementType & type);
/// get the size of the shapes derivatives returned by the element class
static inline UInt getShapeDerivativesSize(const ElementType & type);
inline const Matrix<Real> &
getIntegrationPoints(const ElementType & type,
const GhostType & ghost_type) const {
return integration_points(type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get a the shapes vector
inline const Array<Real> &
getShapes(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get a the shapes derivatives vector
inline const Array<Real> &
getShapesDerivatives(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// shape functions for all elements
ElementTypeMapArray<Real, InterpolationType> shapes;
/// shape functions derivatives for all elements
ElementTypeMapArray<Real, InterpolationType> shapes_derivatives;
/// associated mesh
const Mesh & mesh;
/// shape functions for all elements
ElementTypeMap<Matrix<Real>> integration_points;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ShapeFunctions & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "shape_functions_inline_impl.cc"
#endif /* __AKANTU_SHAPE_FUNCTIONS_HH__ */
diff --git a/src/fe_engine/shape_functions_inline_impl.cc b/src/fe_engine/shape_functions_inline_impl.cc
index f7d05f8c4..84814402b 100644
--- a/src/fe_engine/shape_functions_inline_impl.cc
+++ b/src/fe_engine/shape_functions_inline_impl.cc
@@ -1,402 +1,401 @@
/**
* @file shape_functions_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Oct 27 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief ShapeFunctions inline implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_CC__
#define __AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline const Array<Real> &
ShapeFunctions::getShapes(const ElementType & el_type,
const GhostType & ghost_type) const {
return shapes(FEEngine::getInterpolationType(el_type), ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const Array<Real> &
ShapeFunctions::getShapesDerivatives(const ElementType & el_type,
const GhostType & ghost_type) const {
return shapes_derivatives(FEEngine::getInterpolationType(el_type),
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline UInt ShapeFunctions::getShapeSize(const ElementType & type) {
AKANTU_DEBUG_IN();
UInt shape_size = 0;
#define GET_SHAPE_SIZE(type) shape_size = ElementClass<type>::getShapeSize()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SHAPE_SIZE); // ,
#undef GET_SHAPE_SIZE
AKANTU_DEBUG_OUT();
return shape_size;
}
/* -------------------------------------------------------------------------- */
inline UInt ShapeFunctions::getShapeDerivativesSize(const ElementType & type) {
AKANTU_DEBUG_IN();
UInt shape_derivatives_size = 0;
#define GET_SHAPE_DERIVATIVES_SIZE(type) \
shape_derivatives_size = ElementClass<type>::getShapeDerivativesSize()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SHAPE_DERIVATIVES_SIZE); // ,
#undef GET_SHAPE_DERIVATIVES_SIZE
AKANTU_DEBUG_OUT();
return shape_derivatives_size;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeFunctions::setIntegrationPointsByType(const Matrix<Real> & points,
const GhostType & ghost_type) {
if (not this->integration_points.exists(type, ghost_type))
this->integration_points(type, ghost_type).shallowCopy(points);
}
/* -------------------------------------------------------------------------- */
inline void
ShapeFunctions::buildInterpolationMatrix(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix,
UInt integration_order) const {
switch (integration_order) {
case 1: {
for (UInt i = 0; i < coordinates.cols(); ++i)
coordMatrix(i, 0) = 1;
break;
}
case 2: {
UInt nb_quadrature_points = coordMatrix.cols();
for (UInt i = 0; i < coordinates.cols(); ++i) {
coordMatrix(i, 0) = 1;
for (UInt j = 1; j < nb_quadrature_points; ++j)
coordMatrix(i, j) = coordinates(j - 1, i);
}
break;
}
default: {
AKANTU_TO_IMPLEMENT();
break;
}
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix(
const Matrix<Real> &, Matrix<Real> &, UInt) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_segment_2>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_segment_3>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_triangle_3>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_triangle_6>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_tetrahedron_4>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_tetrahedron_10>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/**
* @todo Write a more efficient interpolation for quadrangles by
* dropping unnecessary quadrature points
*
*/
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_quadrangle_4>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
if (integration_order !=
ElementClassProperty<_quadrangle_4>::polynomial_degree) {
AKANTU_TO_IMPLEMENT();
} else {
for (UInt i = 0; i < coordinates.cols(); ++i) {
Real x = coordinates(0, i);
Real y = coordinates(1, i);
coordMatrix(i, 0) = 1;
coordMatrix(i, 1) = x;
coordMatrix(i, 2) = y;
coordMatrix(i, 3) = x * y;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_quadrangle_8>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
if (integration_order !=
ElementClassProperty<_quadrangle_8>::polynomial_degree) {
AKANTU_TO_IMPLEMENT();
} else {
for (UInt i = 0; i < coordinates.cols(); ++i) {
// UInt j = 0;
Real x = coordinates(0, i);
Real y = coordinates(1, i);
coordMatrix(i, 0) = 1;
coordMatrix(i, 1) = x;
coordMatrix(i, 2) = y;
coordMatrix(i, 3) = x * y;
// for (UInt e = 0; e <= 2; ++e) {
// for (UInt n = 0; n <= 2; ++n) {
// coordMatrix(i, j) = std::pow(x, e) * std::pow(y, n);
// ++j;
// }
// }
}
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::interpolateElementalFieldFromIntegrationPoints(
const Array<Real> & field,
const Array<Real> & interpolation_points_coordinates_matrices,
const Array<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
const Array<UInt> & element_filter) const {
AKANTU_DEBUG_IN();
auto nb_element = this->mesh.getNbElement(type, ghost_type);
auto nb_quad_per_element =
GaussIntegrationElement<type>::getNbQuadraturePoints();
auto nb_interpolation_points_per_elem =
interpolation_points_coordinates_matrices.getNbComponent() /
nb_quad_per_element;
if (!result.exists(type, ghost_type))
result.alloc(nb_element * nb_interpolation_points_per_elem,
field.getNbComponent(), type, ghost_type);
if (element_filter != empty_filter)
nb_element = element_filter.size();
Matrix<Real> coefficients(nb_quad_per_element, field.getNbComponent());
auto & result_vec = result(type, ghost_type);
auto field_it = field.begin_reinterpret(field.getNbComponent(),
nb_quad_per_element, nb_element);
auto interpolation_points_coordinates_it =
interpolation_points_coordinates_matrices.begin(
nb_interpolation_points_per_elem, nb_quad_per_element);
auto result_begin = result_vec.begin_reinterpret(
field.getNbComponent(), nb_interpolation_points_per_elem,
result_vec.size() / nb_interpolation_points_per_elem);
auto inv_quad_coord_it = quad_points_coordinates_inv_matrices.begin(
nb_quad_per_element, nb_quad_per_element);
/// loop over the elements of the current filter and element type
for (UInt el = 0; el < nb_element; ++el, ++field_it, ++inv_quad_coord_it,
++interpolation_points_coordinates_it) {
/**
* matrix containing the inversion of the quadrature points'
* coordinates
*/
const auto & inv_quad_coord_matrix = *inv_quad_coord_it;
/**
* multiply it by the field values over quadrature points to get
* the interpolation coefficients
*/
coefficients.mul<false, true>(inv_quad_coord_matrix, *field_it);
/// matrix containing the points' coordinates
const auto & coord = *interpolation_points_coordinates_it;
/// multiply the coordinates matrix by the coefficients matrix and store the
/// result
Matrix<Real> res(result_begin[element_filter(el)]);
res.mul<true, true>(coefficients, coord);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::interpolateElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & uq, const GhostType & ghost_type,
const Array<Real> & shapes, const Array<UInt> & filter_elements) const {
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_nodes_per_element = ElementClass<type>::getShapeSize();
auto nb_points = shapes.size() / mesh.getNbElement(type, ghost_type);
auto nb_degree_of_freedom = u_el.getNbComponent() / nb_nodes_per_element;
Array<Real>::const_matrix_iterator N_it;
Array<Real> * filtered_N = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filtered_N = new Array<Real>(0, shapes.getNbComponent());
FEEngine::filterElementalData(mesh, shapes, *filtered_N, type, ghost_type,
filter_elements);
N_it = filtered_N->begin_reinterpret(nb_nodes_per_element, nb_points,
nb_element);
} else {
N_it =
shapes.begin_reinterpret(nb_nodes_per_element, nb_points, nb_element);
}
uq.resize(nb_element * nb_points);
auto u_it = u_el.begin(nb_degree_of_freedom, nb_nodes_per_element);
auto inter_u_it =
uq.begin_reinterpret(nb_degree_of_freedom, nb_points, nb_element);
for (UInt el = 0; el < nb_element; ++el, ++N_it, ++u_it, ++inter_u_it) {
const auto & u = *u_it;
const auto & N = *N_it;
auto & inter_u = *inter_u_it;
inter_u.template mul<false, false>(u, N);
}
delete filtered_N;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeFunctions::gradientElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & out_nablauq,
const GhostType & ghost_type, const Array<Real> & shapes_derivatives,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
auto nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
auto nb_points = integration_points(type, ghost_type).cols();
auto element_dimension = ElementClass<type>::getNaturalSpaceDimension();
auto nb_degree_of_freedom = u_el.getNbComponent() / nb_nodes_per_element;
auto nb_element = mesh.getNbElement(type, ghost_type);
Array<Real>::const_matrix_iterator B_it;
Array<Real> * filtered_B = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filtered_B = new Array<Real>(0, shapes_derivatives.getNbComponent());
FEEngine::filterElementalData(mesh, shapes_derivatives, *filtered_B, type,
ghost_type, filter_elements);
B_it = filtered_B->begin(element_dimension, nb_nodes_per_element);
} else {
B_it = shapes_derivatives.begin(element_dimension, nb_nodes_per_element);
}
out_nablauq.resize(nb_element * nb_points);
auto u_it = u_el.begin(nb_degree_of_freedom, nb_nodes_per_element);
auto nabla_u_it = out_nablauq.begin(nb_degree_of_freedom, element_dimension);
for (UInt el = 0; el < nb_element; ++el, ++u_it) {
const auto & u = *u_it;
for (UInt q = 0; q < nb_points; ++q, ++B_it, ++nabla_u_it) {
const auto & B = *B_it;
auto & nabla_u = *nabla_u_it;
nabla_u.template mul<false, true>(u, B);
}
}
delete filtered_B;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_CC__ */
diff --git a/src/fe_engine/shape_lagrange.hh b/src/fe_engine/shape_lagrange.hh
index 36a3c321f..d3ff031d1 100644
--- a/src/fe_engine/shape_lagrange.hh
+++ b/src/fe_engine/shape_lagrange.hh
@@ -1,172 +1,172 @@
/**
* @file shape_lagrange.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Thu Nov 05 2015
+ * @date last modification: Mon Jan 29 2018
*
* @brief lagrangian shape functions class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_base.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_LAGRANGE_HH__
#define __AKANTU_SHAPE_LAGRANGE_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Shape> class ShapeCohesive;
class ShapeIGFEM;
template <ElementKind kind> class ShapeLagrange : public ShapeLagrangeBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, const ID & id = "shape_lagrange",
const MemoryID & memory_id = 0);
~ShapeLagrange() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialization function for structural elements not yet implemented
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
const ElementType & type,
const GhostType & ghost_type);
/// computes the shape functions derivatives for given interpolation points
template <ElementType type>
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const override;
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
const GhostType & ghost_type);
/// pre compute all shape derivatives on the element integration points from
/// natural coordinates
template <ElementType type>
void
precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
const GhostType & ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
const Array<Real> & shapes, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// interpolate on physical point
template <ElementType type>
void interpolate(const Vector<Real> & real_coords, UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const GhostType & ghost_type) const;
/// compute the gradient of u on the integration points
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void computeBtD(const Array<Real> & Ds, Array<Real> & BtDs,
GhostType ghost_type,
const Array<UInt> & filter_elements) const;
template <ElementType type>
void computeBtDB(const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// multiply a field by shape functions @f$ fts_{ij} = f_i * \varphi_j @f$
template <ElementType type>
void fieldTimesShapes(const Array<Real> & field,
Array<Real> & field_times_shapes,
GhostType ghost_type) const;
/// find natural coords from real coords provided an element
template <ElementType type>
void inverseMap(const Vector<Real> & real_coords, UInt element,
Vector<Real> & natural_coords,
const GhostType & ghost_type = _not_ghost) const;
/// return true if the coordinates provided are inside the element, false
/// otherwise
template <ElementType type>
bool contains(const Vector<Real> & real_coords, UInt elem,
const GhostType & ghost_type) const;
/// compute the shape on a provided point
template <ElementType type>
void computeShapes(const Vector<Real> & real_coords, UInt elem,
Vector<Real> & shapes, const GhostType & ghost_type) const;
/// compute the shape derivatives on a provided point
template <ElementType type>
void computeShapeDerivatives(const Matrix<Real> & real_coords, UInt elem,
Tensor3<Real> & shapes,
const GhostType & ghost_type) const;
protected:
/// compute the shape derivatives on integration points for a given element
template <ElementType type>
inline void
computeShapeDerivativesOnCPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_inline_impl.cc"
#endif /* __AKANTU_SHAPE_LAGRANGE_HH__ */
diff --git a/src/fe_engine/shape_lagrange_base.cc b/src/fe_engine/shape_lagrange_base.cc
index 30fa00208..f2ef2f88a 100644
--- a/src/fe_engine/shape_lagrange_base.cc
+++ b/src/fe_engine/shape_lagrange_base.cc
@@ -1,158 +1,162 @@
/**
* @file shape_lagrange_base.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Thu Jul 27 2017
+ * @date creation: Wed Aug 09 2017
+ * @date last modification: Tue Feb 20 2018
+ *
+ * @brief common par for the shape lagrange
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_base.hh"
#include "mesh_iterators.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
ShapeLagrangeBase::ShapeLagrangeBase(const Mesh & mesh,
const ElementKind & kind, const ID & id,
const MemoryID & memory_id)
: ShapeFunctions(mesh, id, memory_id), _kind(kind) {}
/* -------------------------------------------------------------------------- */
ShapeLagrangeBase::~ShapeLagrangeBase() = default;
/* -------------------------------------------------------------------------- */
#define AKANTU_COMPUTE_SHAPES(type) \
_this.template computeShapesOnIntegrationPoints<type>( \
nodes, integration_points, shapes, ghost_type, filter_elements)
namespace shape_lagrange {
namespace details {
template <ElementKind kind> struct Helper {
template <class S>
static void call(const S &, const Array<Real> &, const Matrix<Real> &,
Array<Real> &, const ElementType &, const GhostType &,
const Array<UInt> &) {
AKANTU_TO_IMPLEMENT();
}
};
#define AKANTU_COMPUTE_SHAPES_KIND(kind) \
template <> struct Helper<kind> { \
template <class S> \
static void call(const S & _this, const Array<Real> & nodes, \
const Matrix<Real> & integration_points, \
Array<Real> & shapes, const ElementType & type, \
const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(AKANTU_COMPUTE_SHAPES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_COMPUTE_SHAPES_KIND,
AKANTU_FE_ENGINE_LIST_LAGRANGE_BASE)
} // namespace details
} // namespace shape_lagrange
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, const ElementType & type,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
auto kind = Mesh::getKind(type);
#define AKANTU_COMPUTE_SHAPES_KIND_SWITCH(kind) \
shape_lagrange::details::Helper<kind>::call( \
*this, nodes, integration_points, shapes, type, ghost_type, \
filter_elements);
AKANTU_BOOST_LIST_SWITCH(
AKANTU_COMPUTE_SHAPES_KIND_SWITCH,
BOOST_PP_LIST_TO_SEQ(AKANTU_FE_ENGINE_LIST_LAGRANGE_BASE), kind);
#undef AKANTU_COMPUTE_SHAPES
#undef AKANTU_COMPUTE_SHAPES_KIND
#undef AKANTU_COMPUTE_SHAPES_KIND_SWITCH
}
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::onElementsAdded(const Array<Element> & new_elements) {
AKANTU_DEBUG_IN();
const auto & nodes = mesh.getNodes();
for (auto elements_range : MeshElementsByTypes(new_elements)) {
auto type = elements_range.getType();
auto ghost_type = elements_range.getGhostType();
if (mesh.getKind(type) != _kind)
continue;
auto & elements = elements_range.getElements();
auto itp_type = FEEngine::getInterpolationType(type);
if (not this->shapes_derivatives.exists(itp_type, ghost_type)) {
auto size_of_shapesd = this->getShapeDerivativesSize(type);
this->shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
}
if (not shapes.exists(itp_type, ghost_type)) {
auto size_of_shapes = this->getShapeSize(type);
this->shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
}
const auto & natural_coords = integration_points(type, ghost_type);
computeShapesOnIntegrationPoints(nodes, natural_coords,
shapes(itp_type, ghost_type), type,
ghost_type, elements);
computeShapeDerivativesOnIntegrationPoints(
nodes, natural_coords, shapes_derivatives(itp_type, ghost_type), type,
ghost_type, elements);
}
#undef INIT_SHAPE_FUNCTIONS
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::onElementsRemoved(
const Array<Element> &, const ElementTypeMapArray<UInt> & new_numbering) {
this->shapes.onElementsRemoved(new_numbering);
this->shapes_derivatives.onElementsRemoved(new_numbering);
}
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Shapes Lagrange [" << std::endl;
ShapeFunctions::printself(stream, indent + 1);
shapes.printself(stream, indent + 1);
shapes_derivatives.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/fe_engine/shape_lagrange_base.hh b/src/fe_engine/shape_lagrange_base.hh
index 08d915f7d..c50b27689 100644
--- a/src/fe_engine/shape_lagrange_base.hh
+++ b/src/fe_engine/shape_lagrange_base.hh
@@ -1,91 +1,92 @@
-
/**
* @file shape_lagrange_base.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Thu Jul 27 2017
+ * @date creation: Wed Aug 09 2017
+ * @date last modification: Wed Nov 08 2017
*
- * @brief Base class for the shape lagrange
+ * @brief Base class for the shape lagrange
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_LAGRANGE_BASE_HH__
#define __AKANTU_SHAPE_LAGRANGE_BASE_HH__
namespace akantu {
class ShapeLagrangeBase : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrangeBase(const Mesh & mesh, const ElementKind & kind,
const ID & id = "shape_lagrange",
const MemoryID & memory_id = 0);
~ShapeLagrangeBase() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// computes the shape functions for given interpolation points
virtual void computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// computes the shape functions derivatives for given interpolation points
virtual void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
template <ElementType type>
void computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
public:
void onElementsAdded(const Array<Element> & elements) override;
void
onElementsRemoved(const Array<Element> & elements,
const ElementTypeMapArray<UInt> & new_numbering) override;
protected:
/// The kind to consider
ElementKind _kind;
};
} // namespace akantu
#include "shape_lagrange_base_inline_impl.cc"
#endif /* __AKANTU_SHAPE_LAGRANGE_BASE_HH__ */
diff --git a/src/fe_engine/shape_lagrange_base_inline_impl.cc b/src/fe_engine/shape_lagrange_base_inline_impl.cc
index 4b9ebbf08..448d3b36a 100644
--- a/src/fe_engine/shape_lagrange_base_inline_impl.cc
+++ b/src/fe_engine/shape_lagrange_base_inline_impl.cc
@@ -1,82 +1,84 @@
/**
* @file shape_lagrange_base_inline_impl.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Thu Jul 27 2017
+ * @date creation: Wed Aug 09 2017
+ * @date last modification: Wed Oct 11 2017
*
- * @brief A Documented file.
+ * @brief A Documented file.
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_base.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_CC__
#define __AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrangeBase::computeShapesOnIntegrationPoints(
const Array<Real> &, const Matrix<Real> & integration_points,
Array<Real> & shapes, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
shapes.resize(nb_element * nb_points);
#if !defined(AKANTU_NDEBUG)
UInt size_of_shapes = ElementClass<type>::getShapeSize();
AKANTU_DEBUG_ASSERT(shapes.getNbComponent() == size_of_shapes,
"The shapes array does not have the correct "
<< "number of component");
#endif
auto shapes_it = shapes.begin_reinterpret(
ElementClass<type>::getNbNodesPerInterpolationElement(), nb_points,
nb_element);
auto shapes_begin = shapes_it;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
for (UInt elem = 0; elem < nb_element; ++elem) {
if (filter_elements != empty_filter)
shapes_it = shapes_begin + filter_elements(elem);
Matrix<Real> & N = *shapes_it;
ElementClass<type>::computeShapes(integration_points, N);
if (filter_elements == empty_filter)
++shapes_it;
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* __AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_CC__ */
diff --git a/src/fe_engine/shape_lagrange_inline_impl.cc b/src/fe_engine/shape_lagrange_inline_impl.cc
index e8b8aaba0..7a86db51f 100644
--- a/src/fe_engine/shape_lagrange_inline_impl.cc
+++ b/src/fe_engine/shape_lagrange_inline_impl.cc
@@ -1,526 +1,526 @@
/**
* @file shape_lagrange_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 27 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief ShapeLagrange inline implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "aka_voigthelper.hh"
#include "fe_engine.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_CC__
#define __AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
if (ElementClass<type>::getNaturalSpaceDimension() == \
mesh.getSpatialDimension() || \
kind != _ek_regular) \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
template <ElementKind kind>
inline void ShapeLagrange<kind>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
const ElementType & type, const GhostType & ghost_type) {
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
#undef INIT_SHAPE_FUNCTIONS
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
inline void ShapeLagrange<kind>::computeShapeDerivativesOnCPointsByElement(
const Matrix<Real> & node_coords, const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const {
AKANTU_DEBUG_IN();
// compute dnds
Tensor3<Real> dnds(node_coords.rows(), node_coords.cols(),
natural_coords.cols());
ElementClass<type>::computeDNDS(natural_coords, dnds);
// compute jacobian
Tensor3<Real> J(node_coords.rows(), natural_coords.rows(),
natural_coords.cols());
ElementClass<type>::computeJMat(dnds, node_coords, J);
// compute dndx
ElementClass<type>::computeShapeDerivatives(J, dnds, shapesd);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::inverseMap(const Vector<Real> & real_coords,
UInt elem, Vector<Real> & natural_coords,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
ElementClass<type>::inverseMap(real_coords, nodes_coord, natural_coords);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
bool ShapeLagrange<kind>::contains(const Vector<Real> & real_coords, UInt elem,
const GhostType & ghost_type) const {
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> natural_coords(spatial_dimension);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
return ElementClass<type>::contains(natural_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolate(const Vector<Real> & real_coords,
UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const GhostType & ghost_type) const {
UInt nb_shapes = ElementClass<type>::getShapeSize();
Vector<Real> shapes(nb_shapes);
computeShapes<type>(real_coords, elem, shapes, ghost_type);
ElementClass<type>::interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapes(const Vector<Real> & real_coords,
UInt elem, Vector<Real> & shapes,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> natural_coords(spatial_dimension);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
ElementClass<type>::computeShapes(natural_coords, shapes);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapeDerivatives(
const Matrix<Real> & real_coords, UInt elem, Tensor3<Real> & shapesd,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_points = real_coords.cols();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
AKANTU_DEBUG_ASSERT(mesh.getSpatialDimension() == shapesd.size(0) &&
nb_nodes_per_element == shapesd.size(1),
"Shape size doesn't match");
AKANTU_DEBUG_ASSERT(nb_points == shapesd.size(2),
"Number of points doesn't match shapes size");
Matrix<Real> natural_coords(spatial_dimension, nb_points);
// Creates the matrix of natural coordinates
for (UInt i = 0; i < nb_points; i++) {
Vector<Real> real_point = real_coords(i);
Vector<Real> natural_point = natural_coords(i);
inverseMap<type>(real_point, elem, natural_point, ghost_type);
}
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
computeShapeDerivativesOnCPointsByElement<type>(nodes_coord, natural_coords,
shapesd);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
ShapeLagrange<kind>::ShapeLagrange(const Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: ShapeLagrangeBase(mesh, kind, id, memory_id) {}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
AKANTU_DEBUG_ASSERT(shape_derivatives.getNbComponent() == size_of_shapesd,
"The shapes_derivatives array does not have the correct "
<< "number of component");
shape_derivatives.resize(nb_element * nb_points);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
Real * shapesd_val = shape_derivatives.storage();
Array<Real>::matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
if (filter_elements != empty_filter)
shapesd_val = shape_derivatives.storage() +
filter_elements(elem) * size_of_shapesd * nb_points;
Matrix<Real> & X = *x_it;
Tensor3<Real> B(shapesd_val, spatial_dimension, nb_nodes_per_element,
nb_points);
computeShapeDerivativesOnCPointsByElement<type>(X, integration_points, B);
if (filter_elements == empty_filter)
shapesd_val += size_of_shapesd * nb_points;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
void ShapeLagrange<kind>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const ElementType & type,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
#define AKANTU_COMPUTE_SHAPES(type) \
computeShapeDerivativesOnIntegrationPoints<type>( \
nodes, integration_points, shape_derivatives, ghost_type, \
filter_elements);
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(AKANTU_COMPUTE_SHAPES);
#undef AKANTU_COMPUTE_SHAPES
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::precomputeShapesOnIntegrationPoints(
const Array<Real> & nodes, const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapes = ElementClass<type>::getShapeSize();
Array<Real> & shapes_tmp =
shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
this->computeShapesOnIntegrationPoints<type>(nodes, natural_coords,
shapes_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::precomputeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
Array<Real> & shapes_derivatives_tmp =
shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
this->computeShapeDerivativesOnIntegrationPoints<type>(
nodes, natural_coords, shapes_derivatives_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
const Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->interpolateElementalFieldOnIntegrationPoints<type>(
u_el, out_uq, ghost_type, shapes, filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(shapes.exists(itp_type, ghost_type),
"No shapes for the type "
<< shapes.printType(itp_type, ghost_type));
this->interpolateOnIntegrationPoints<type>(in_u, out_uq, nb_degree_of_freedom,
shapes(itp_type, ghost_type),
ghost_type, filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::gradientOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_nablauq,
UInt nb_degree_of_freedom, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(
shapes_derivatives.exists(itp_type, ghost_type),
"No shapes derivatives for the type "
<< shapes_derivatives.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->gradientElementalFieldOnIntegrationPoints<type>(
u_el, out_nablauq, ghost_type, shapes_derivatives(itp_type, ghost_type),
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeBtD(
const Array<Real> & Ds, Array<Real> & BtDs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
const auto & shapes_derivatives =
this->shapes_derivatives(itp_type, ghost_type);
auto spatial_dimension = mesh.getSpatialDimension();
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> shapes_derivatives_filtered(0,
shapes_derivatives.getNbComponent());
auto && view =
make_view(shapes_derivatives, spatial_dimension, nb_nodes_per_element);
auto B_it = view.begin();
auto B_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes_derivatives,
shapes_derivatives_filtered, type, ghost_type,
filter_elements);
auto && view = make_view(shapes_derivatives_filtered, spatial_dimension,
nb_nodes_per_element);
B_it = view.begin();
B_end = view.end();
}
for (auto && values :
zip(range(B_it, B_end),
make_view(Ds, Ds.getNbComponent() / spatial_dimension,
spatial_dimension),
make_view(BtDs, BtDs.getNbComponent() / nb_nodes_per_element,
nb_nodes_per_element))) {
const auto & B = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D = std::get<2>(values);
// transposed due to the storage layout of B
Bt_D.template mul<false, false>(D, B);
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeBtDB(
const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
const auto & shapes_derivatives =
this->shapes_derivatives(itp_type, ghost_type);
constexpr auto dim = ElementClass<type>::getSpatialDimension();
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> shapes_derivatives_filtered(0,
shapes_derivatives.getNbComponent());
auto && view = make_view(shapes_derivatives, dim, nb_nodes_per_element);
auto B_it = view.begin();
auto B_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes_derivatives,
shapes_derivatives_filtered, type, ghost_type,
filter_elements);
auto && view =
make_view(shapes_derivatives_filtered, dim, nb_nodes_per_element);
B_it = view.begin();
B_end = view.end();
}
if (order_d == 4) {
UInt tangent_size = VoigtHelper<dim>::size;
Matrix<Real> B(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> Bt_D(dim * nb_nodes_per_element, tangent_size);
for (auto && values :
zip(range(B_it, B_end), make_view(Ds, tangent_size, tangent_size),
make_view(BtDBs, dim * nb_nodes_per_element,
dim * nb_nodes_per_element))) {
const auto & Bfull = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D_B = std::get<2>(values);
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(Bfull, B,
nb_nodes_per_element);
Bt_D.template mul<true, false>(B, D);
Bt_D_B.template mul<false, false>(Bt_D, B);
}
} else if (order_d == 2) {
Matrix<Real> Bt_D(nb_nodes_per_element, dim);
for (auto && values :
zip(range(B_it, B_end), make_view(Ds, dim, dim),
make_view(BtDBs, nb_nodes_per_element, nb_nodes_per_element))) {
const auto & B = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D_B = std::get<2>(values);
Bt_D.template mul<true, false>(B, D);
Bt_D_B.template mul<false, false>(Bt_D, B);
}
}
}
template <>
template <>
inline void ShapeLagrange<_ek_regular>::computeBtDB<_point_1>(
const Array<Real> & /*Ds*/, Array<Real> & /*BtDBs*/, UInt /*order_d*/,
GhostType /*ghost_type*/, const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::fieldTimesShapes(const Array<Real> & field,
Array<Real> & field_times_shapes,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
field_times_shapes.resize(field.size());
UInt size_of_shapes = ElementClass<type>::getShapeSize();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
UInt nb_degree_of_freedom = field.getNbComponent();
const auto & shape = shapes(itp_type, ghost_type);
auto field_it = field.begin(nb_degree_of_freedom, 1);
auto shapes_it = shape.begin(1, size_of_shapes);
auto it = field_times_shapes.begin(nb_degree_of_freedom, size_of_shapes);
auto end = field_times_shapes.end(nb_degree_of_freedom, size_of_shapes);
for (; it != end; ++it, ++field_it, ++shapes_it) {
it->template mul<false, false>(*field_it, *shapes_it);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* __AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_CC__ */
diff --git a/src/fe_engine/shape_structural.cc b/src/fe_engine/shape_structural.cc
index cf7315dd2..ef9b443c0 100644
--- a/src/fe_engine/shape_structural.cc
+++ b/src/fe_engine/shape_structural.cc
@@ -1,53 +1,53 @@
/**
* @file shape_structural.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jul 15 2011
- * @date last modification: Sun Oct 19 2014
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Thu Dec 21 2017
*
* @brief ShapeStructural implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_structural.hh"
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
ShapeStructural<_ek_structural>::ShapeStructural(Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: ShapeFunctions(mesh, id, memory_id),
rotation_matrices("rotation_matrices", id, memory_id) {}
/* -------------------------------------------------------------------------- */
template <> ShapeStructural<_ek_structural>::~ShapeStructural() = default;
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/fe_engine/shape_structural.hh b/src/fe_engine/shape_structural.hh
index bd888aa0e..cefe2841f 100644
--- a/src/fe_engine/shape_structural.hh
+++ b/src/fe_engine/shape_structural.hh
@@ -1,177 +1,176 @@
/**
* @file shape_structural.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Thu Oct 22 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief shape class for element with different set of shapes functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_STRUCTURAL_HH__
#define __AKANTU_SHAPE_STRUCTURAL_HH__
namespace akantu {
template <ElementKind kind> class ShapeStructural : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
// Ctors/Dtors should be explicitely implemented for _ek_structural
public:
ShapeStructural(Mesh & mesh, const ID & id = "shape_structural",
const MemoryID & memory_id = 0);
~ShapeStructural() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "ShapesStructural [" << std::endl;
rotation_matrices.printself(stream, indent + 1);
ShapeFunctions::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/// compute shape functions on given integration points
template <ElementType type>
void computeShapesOnIntegrationPoints(
const Array<Real> &, const Matrix<Real> & integration_points,
Array<Real> & shapes, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// initialization function for structural elements
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
const ElementType & type,
const GhostType & ghost_type);
/// precompute the rotation matrices for the elements dofs
template <ElementType type>
void precomputeRotationMatrices(const Array<Real> & nodes,
const GhostType & ghost_type);
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
const GhostType & ghost_type);
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void
precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
const GhostType & ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// compute the gradient of u on the integration points
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// interpolate on physical point
template <ElementType type>
void interpolate(const Vector<Real> & /*real_coords*/, UInt /*elem*/,
const Matrix<Real> & /*nodal_values*/,
Vector<Real> & /*interpolated*/,
const GhostType & /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the shapes on a provided point
template <ElementType type>
void computeShapes(const Vector<Real> & /*real_coords*/, UInt /*elem*/,
Vector<Real> & /*shapes*/,
const GhostType & /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the shape derivatives on a provided point
template <ElementType type>
void computeShapeDerivatives(const Matrix<Real> & /*real_coords*/,
UInt /*elem*/, Tensor3<Real> & /*shapes*/,
const GhostType & /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
}
/// multiply a field by shape functions
template <ElementType type>
void
fieldTimesShapes(__attribute__((unused)) const Array<Real> & field,
__attribute__((unused)) Array<Real> & field_times_shapes,
__attribute__((unused)) const GhostType & ghost_type) const {
AKANTU_TO_IMPLEMENT();
}
/// get the rotations vector
inline const Array<Real> &
getRotations(const ElementType & el_type,
__attribute__((unused))
const GhostType & ghost_type = _not_ghost) const {
return rotation_matrices(el_type);
}
template <ElementType type>
void computeBtD(const Array<Real> & /*Ds*/, Array<Real> & /*BtDs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
template <ElementType type>
void computeBtDB(const Array<Real> & /*Ds*/, Array<Real> & /*BtDBs*/,
UInt /*order_d*/, GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
protected:
ElementTypeMapArray<Real> rotation_matrices;
};
} // namespace akantu
#include "shape_structural_inline_impl.cc"
#endif /* __AKANTU_SHAPE_STRUCTURAL_HH__ */
diff --git a/src/fe_engine/shape_structural_inline_impl.cc b/src/fe_engine/shape_structural_inline_impl.cc
index 1919521a3..b13bc8b4d 100644
--- a/src/fe_engine/shape_structural_inline_impl.cc
+++ b/src/fe_engine/shape_structural_inline_impl.cc
@@ -1,430 +1,431 @@
/**
* @file shape_structural_inline_impl.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Dec 13 2010
- * @date last modification: Thu Oct 15 2015
+ * @date creation: Wed Oct 11 2017
+ * @date last modification: Wed Feb 21 2018
*
* @brief ShapeStructural inline implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh_iterators.hh"
#include "shape_structural.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_CC__
#define __AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_CC__
namespace akantu {
namespace {
/// Extract nodal coordinates per elements
template <ElementType type>
std::unique_ptr<Array<Real>>
getNodesPerElement(const Mesh & mesh, const Array<Real> & nodes,
const GhostType & ghost_type) {
const auto dim = ElementClass<type>::getSpatialDimension();
const auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nodes_per_element =
std::make_unique<Array<Real>>(0, dim * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, *nodes_per_element, type,
ghost_type);
return nodes_per_element;
}
}
template <ElementKind kind>
inline void ShapeStructural<kind>::initShapeFunctions(
const Array<Real> & /* unused */, const Matrix<Real> & /* unused */,
const ElementType & /* unused */, const GhostType & /* unused */) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeRotationMatrices<type>(nodes, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
template <>
inline void ShapeStructural<_ek_structural>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
const ElementType & type, const GhostType & ghost_type) {
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
#undef INIT_SHAPE_FUNCTIONS
/* -------------------------------------------------------------------------- */
template <>
template <ElementType type>
void ShapeStructural<_ek_structural>::computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
shapes.resize(nb_element * nb_points);
UInt ndof = ElementClass<type>::getNbDegreeOfFreedom();
#if !defined(AKANTU_NDEBUG)
UInt size_of_shapes = ElementClass<type>::getShapeSize();
AKANTU_DEBUG_ASSERT(shapes.getNbComponent() == size_of_shapes,
"The shapes array does not have the correct "
<< "number of component");
#endif
auto shapes_it = shapes.begin_reinterpret(
ElementClass<type>::getNbNodesPerInterpolationElement(), ndof, nb_points,
nb_element);
auto shapes_begin = shapes_it;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
auto nodes_per_element = getNodesPerElement<type>(mesh, nodes, ghost_type);
auto nodes_it = nodes_per_element->begin(mesh.getSpatialDimension(),
Mesh::getNbNodesPerElement(type));
auto nodes_begin = nodes_it;
for (UInt elem = 0; elem < nb_element; ++elem) {
if (filter_elements != empty_filter) {
shapes_it = shapes_begin + filter_elements(elem);
nodes_it = nodes_begin + filter_elements(elem);
}
Tensor3<Real> & N = *shapes_it;
auto & real_coord = *nodes_it;
ElementClass<type>::computeShapes(integration_points, real_coord, N);
if (filter_elements == empty_filter)
++shapes_it;
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::precomputeRotationMatrices(
const Array<Real> & nodes, const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
const auto spatial_dimension = mesh.getSpatialDimension();
const auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto nb_element = mesh.getNbElement(type, ghost_type);
const auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
if (not this->rotation_matrices.exists(type, ghost_type)) {
this->rotation_matrices.alloc(0, nb_dof * nb_dof, type, ghost_type);
}
auto & rot_matrices = this->rotation_matrices(type, ghost_type);
rot_matrices.resize(nb_element);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
bool has_extra_normal = mesh.hasData<Real>("extra_normal", type, ghost_type);
Array<Real>::const_vector_iterator extra_normal;
if (has_extra_normal)
extra_normal = mesh.getData<Real>("extra_normal", type, ghost_type)
.begin(spatial_dimension);
for (auto && tuple :
zip(make_view(x_el, spatial_dimension, nb_nodes_per_element),
make_view(rot_matrices, nb_dof, nb_dof))) {
// compute shape derivatives
auto & X = std::get<0>(tuple);
auto & R = std::get<1>(tuple);
if (has_extra_normal) {
ElementClass<type>::computeRotationMatrix(R, X, *extra_normal);
++extra_normal;
} else {
ElementClass<type>::computeRotationMatrix(
R, X, Vector<Real>(spatial_dimension));
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::precomputeShapesOnIntegrationPoints(
const Array<Real> & nodes, const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
const auto & natural_coords = integration_points(type, ghost_type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_points = integration_points(type, ghost_type).cols();
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
const auto dim = ElementClass<type>::getSpatialDimension();
auto itp_type = FEEngine::getInterpolationType(type);
if (not shapes.exists(itp_type, ghost_type)) {
auto size_of_shapes = this->getShapeSize(type);
this->shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
}
auto & shapes_ = this->shapes(itp_type, ghost_type);
shapes_.resize(nb_element * nb_points);
auto nodes_per_element = getNodesPerElement<type>(mesh, nodes, ghost_type);
for (auto && tuple :
zip(make_view(shapes_, nb_dof, nb_dof * nb_nodes_per_element, nb_points),
make_view(*nodes_per_element, dim, nb_nodes_per_element))) {
auto & N = std::get<0>(tuple);
auto & real_coord = std::get<1>(tuple);
ElementClass<type>::computeShapes(natural_coords, real_coord, N);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::precomputeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
const auto & natural_coords = integration_points(type, ghost_type);
const auto spatial_dimension = mesh.getSpatialDimension();
const auto natural_spatial_dimension =
ElementClass<type>::getNaturalSpaceDimension();
const auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto nb_points = natural_coords.cols();
const auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
const auto nb_element = mesh.getNbElement(type, ghost_type);
const auto nb_stress_components = ElementClass<type>::getNbStressComponents();
auto itp_type = FEEngine::getInterpolationType(type);
if (not this->shapes_derivatives.exists(itp_type, ghost_type)) {
auto size_of_shapesd = this->getShapeDerivativesSize(type);
this->shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
}
auto & rot_matrices = this->rotation_matrices(type, ghost_type);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
auto & shapesd = this->shapes_derivatives(itp_type, ghost_type);
shapesd.resize(nb_element * nb_points);
for (auto && tuple :
zip(make_view(x_el, spatial_dimension, nb_nodes_per_element),
make_view(shapesd, nb_stress_components,
nb_nodes_per_element * nb_dof, nb_points),
make_view(rot_matrices, nb_dof, nb_dof))) {
// compute shape derivatives
auto & X = std::get<0>(tuple);
auto & B = std::get<1>(tuple);
auto & RDOFs = std::get<2>(tuple);
Tensor3<Real> dnds(natural_spatial_dimension,
ElementClass<type>::interpolation_property::dnds_columns,
B.size(2));
ElementClass<type>::computeDNDS(natural_coords, X, dnds);
Tensor3<Real> J(natural_spatial_dimension, natural_spatial_dimension,
natural_coords.cols());
// Computing the coordinates of the element in the natural space
auto R = RDOFs.block(0, 0, spatial_dimension, spatial_dimension);
Matrix<Real> T(B.size(1), B.size(1), 0);
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
T.block(RDOFs, i * RDOFs.rows(), i * RDOFs.rows());
}
// Rotate to local basis
auto x =
(R * X).block(0, 0, natural_spatial_dimension, nb_nodes_per_element);
ElementClass<type>::computeJMat(natural_coords, x, J);
ElementClass<type>::computeShapeDerivatives(J, dnds, T, B);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_dof,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(out_uq.getNbComponent() == nb_dof,
"The output array shape is not correct");
auto itp_type = FEEngine::getInterpolationType(type);
const auto & shapes_ = shapes(itp_type, ghost_type);
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement();
auto nb_quad_points_per_element = integration_points(type, ghost_type).cols();
Array<Real> u_el(0, nb_nodes_per_element * nb_dof);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
auto nb_quad_points = nb_quad_points_per_element * u_el.size();
out_uq.resize(nb_quad_points);
auto out_it = out_uq.begin_reinterpret(nb_dof, 1, nb_quad_points_per_element,
u_el.size());
auto shapes_it =
shapes_.begin_reinterpret(nb_dof, nb_dof * nb_nodes_per_element,
nb_quad_points_per_element, nb_element);
auto u_it = u_el.begin_reinterpret(nb_dof * nb_nodes_per_element, 1,
nb_quad_points_per_element, u_el.size());
for_each_element(nb_element, filter_elements, [&](auto && el) {
auto & uq = *out_it;
const auto & u = *u_it;
auto N = Tensor3<Real>(shapes_it[el]);
for (auto && q : arange(uq.size(2))) {
auto uq_q = Matrix<Real>(uq(q));
auto u_q = Matrix<Real>(u(q));
auto N_q = Matrix<Real>(N(q));
uq_q.mul<false, false>(N_q, u_q);
}
++out_it;
++u_it;
});
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::gradientOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_nablauq, UInt nb_dof,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
auto itp_type = FEEngine::getInterpolationType(type);
const auto & shapesd = shapes_derivatives(itp_type, ghost_type);
auto nb_element = mesh.getNbElement(type, ghost_type);
auto element_dimension = ElementClass<type>::getSpatialDimension();
auto nb_quad_points_per_element = integration_points(type, ghost_type).cols();
auto nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement();
Array<Real> u_el(0, nb_nodes_per_element * nb_dof);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
auto nb_quad_points = nb_quad_points_per_element * u_el.size();
out_nablauq.resize(nb_quad_points);
auto out_it = out_nablauq.begin_reinterpret(
element_dimension, 1, nb_quad_points_per_element, u_el.size());
auto shapesd_it = shapesd.begin_reinterpret(
element_dimension, nb_dof * nb_nodes_per_element,
nb_quad_points_per_element, nb_element);
auto u_it = u_el.begin_reinterpret(nb_dof * nb_nodes_per_element, 1,
nb_quad_points_per_element, u_el.size());
for_each_element(nb_element, filter_elements, [&](auto && el) {
auto & nablau = *out_it;
const auto & u = *u_it;
auto B = Tensor3<Real>(shapesd_it[el]);
for (auto && q : arange(nablau.size(2))) {
auto nablau_q = Matrix<Real>(nablau(q));
auto u_q = Matrix<Real>(u(q));
auto B_q = Matrix<Real>(B(q));
nablau_q.mul<false, false>(B_q, u_q);
}
++out_it;
++u_it;
});
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
template <ElementType type>
void ShapeStructural<_ek_structural>::computeBtD(
const Array<Real> & Ds, Array<Real> & BtDs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
auto nb_stress = ElementClass<type>::getNbStressComponents();
auto nb_dof_per_element = ElementClass<type>::getNbDegreeOfFreedom() *
mesh.getNbNodesPerElement(type);
const auto & shapes_derivatives =
this->shapes_derivatives(itp_type, ghost_type);
Array<Real> shapes_derivatives_filtered(0,
shapes_derivatives.getNbComponent());
auto && view = make_view(shapes_derivatives, nb_stress, nb_dof_per_element);
auto B_it = view.begin();
auto B_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes_derivatives,
shapes_derivatives_filtered, type, ghost_type,
filter_elements);
auto && view =
make_view(shapes_derivatives_filtered, nb_stress, nb_dof_per_element);
B_it = view.begin();
B_end = view.end();
}
for (auto && values : zip(range(B_it, B_end), make_view(Ds, nb_stress),
make_view(BtDs, BtDs.getNbComponent()))) {
const auto & B = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D = std::get<2>(values);
Bt_D.template mul<true>(B, D);
}
}
} // namespace akantu
#endif /* __AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_CC__ */
diff --git a/src/geometry/aabb_primitives/aabb_primitive.cc b/src/geometry/aabb_primitives/aabb_primitive.cc
index 56b56a7bd..93c51c16b 100644
--- a/src/geometry/aabb_primitives/aabb_primitive.cc
+++ b/src/geometry/aabb_primitives/aabb_primitive.cc
@@ -1,49 +1,49 @@
/**
* @file aabb_primitive.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Jan 31 2018
*
* @brief Macro classe (primitive) for AABB CGAL algos
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aabb_primitive.hh"
namespace akantu {
Triangle_primitive::Point Triangle_primitive::reference_point() const {
return primitive.vertex(0);
}
Line_arc_primitive::Point Line_arc_primitive::reference_point() const {
Real x = to_double(primitive.source().x());
Real y = to_double(primitive.source().y());
Real z = to_double(primitive.source().z());
return cgal::Spherical::Point_3(x, y, z);
}
} // akantu
diff --git a/src/geometry/aabb_primitives/aabb_primitive.hh b/src/geometry/aabb_primitives/aabb_primitive.hh
index af9ac05f4..9bae09a10 100644
--- a/src/geometry/aabb_primitives/aabb_primitive.hh
+++ b/src/geometry/aabb_primitives/aabb_primitive.hh
@@ -1,89 +1,89 @@
/**
* @file aabb_primitive.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Mar 13 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Jan 31 2018
*
* @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)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AABB_PRIMITIVE_HH__
#define __AKANTU_AABB_PRIMITIVE_HH__
#include "aka_common.hh"
#include "line_arc.hh"
#include "tetrahedron.hh"
#include "triangle.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/**
* This macro defines a class that is used in the CGAL AABB tree algorithm.
* All the `typedef`s and methods are required by the AABB module.
*
* The member variables are
* - the id of the element associated to the primitive
* - the geometric primitive of the element
*
* @param name the name of the primitive type
* @param kernel the name of the kernel used
*/
#define AKANTU_AABB_CLASS(name, kernel) \
class name##_primitive { \
typedef std::list<name<kernel>>::iterator Iterator; \
\
public: \
typedef UInt Id; \
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; } \
Point reference_point() const; \
const Id & id() const { return meshId; } \
\
protected: \
Id meshId; \
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, cgal::Cartesian);
AKANTU_AABB_CLASS(Line_arc, cgal::Spherical);
#undef AKANTU_AABB_CLASS
} // akantu
#endif // __AKANTU_AABB_PRIMITIVE_HH__
diff --git a/src/geometry/aabb_primitives/line_arc.hh b/src/geometry/aabb_primitives/line_arc.hh
index 603525067..611649790 100644
--- a/src/geometry/aabb_primitives/line_arc.hh
+++ b/src/geometry/aabb_primitives/line_arc.hh
@@ -1,77 +1,77 @@
/**
* @file line_arc.hh
*
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Jun 19 2017
*
* @brief Segment classe (geometry) for AABB CGAL algos
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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_LINE_ARC_HH__
#define __AKANTU_LINE_ARC_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Triangle_3 primitive
template <typename K> class Line_arc : public CGAL::Line_arc_3<K> {
public:
/// Default constructor
Line_arc() : CGAL::Line_arc_3<K>(), mesh_id(0), seg_id(0) {}
/// Copy constructor
Line_arc(const Line_arc & other)
: CGAL::Line_arc_3<K>(other), mesh_id(other.mesh_id),
seg_id(other.seg_id) {}
/// Construct from 3 points
// "CGAL-4.5/doc_html/Circular_kernel_3/classCGAL_1_1Line__arc__3.html"
Line_arc(const CGAL::Line_3<K> & l, const CGAL::Circular_arc_point_3<K> & a,
const CGAL::Circular_arc_point_3<K> & b)
: CGAL::Line_arc_3<K>(l, a, b), mesh_id(0), seg_id(0) {}
public:
UInt id() const { return mesh_id; }
UInt segId() const { return seg_id; }
void setId(UInt newId) { mesh_id = newId; }
void setSegId(UInt newId) { seg_id = newId; }
protected:
/// Id of the element represented by the primitive
UInt mesh_id;
/// Id of the segment represented by the primitive
UInt seg_id;
};
} // akantu
#endif // __AKANTU_LINE_ARC_HH__
diff --git a/src/geometry/aabb_primitives/tetrahedron.hh b/src/geometry/aabb_primitives/tetrahedron.hh
index c6d31b3de..64e7855a7 100644
--- a/src/geometry/aabb_primitives/tetrahedron.hh
+++ b/src/geometry/aabb_primitives/tetrahedron.hh
@@ -1,70 +1,70 @@
/**
* @file tetrahedron.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Feb 27 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Jun 19 2017
*
* @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)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TETRAHEDRON_HH__
#define __AKANTU_TETRAHEDRON_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Tetrahedron_3 primitive
template <typename K> class Tetrahedron : public CGAL::Tetrahedron_3<K> {
public:
/// Default constructor
Tetrahedron() : CGAL::Tetrahedron_3<K>(), meshId(0) {}
/// Copy constructor
Tetrahedron(const Tetrahedron & other)
: CGAL::Tetrahedron_3<K>(other), meshId(other.meshId) {}
/// Construct from 4 points
Tetrahedron(const CGAL::Point_3<K> & a, const CGAL::Point_3<K> & b,
const CGAL::Point_3<K> & c, const CGAL::Point_3<K> & d)
: CGAL::Tetrahedron_3<K>(a, b, c, d), meshId(0) {}
public:
UInt id() const { return meshId; }
void setId(UInt newId) { meshId = newId; }
protected:
/// Id of the element represented by the primitive
UInt meshId;
};
} // akantu
#endif
diff --git a/src/geometry/aabb_primitives/triangle.hh b/src/geometry/aabb_primitives/triangle.hh
index 90a36b4bd..17d7b194a 100644
--- a/src/geometry/aabb_primitives/triangle.hh
+++ b/src/geometry/aabb_primitives/triangle.hh
@@ -1,70 +1,70 @@
/**
* @file triangle.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Jun 19 2017
*
* @brief Triangle classe (geometry) for AABB CGAL algos
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TRIANGLE_HH__
#define __AKANTU_TRIANGLE_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Triangle_3 primitive
template <typename K> class Triangle : public CGAL::Triangle_3<K> {
public:
/// Default constructor
Triangle() : CGAL::Triangle_3<K>(), meshId(0) {}
/// Copy constructor
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)
: CGAL::Triangle_3<K>(a, b, c), meshId(0) {}
public:
UInt id() const { return meshId; }
void setId(UInt newId) { meshId = newId; }
protected:
/// Id of the element represented by the primitive
UInt meshId;
};
} // akantu
#endif // __AKANTU_TRIANGLE_HH__
diff --git a/src/geometry/geom_helper_functions.hh b/src/geometry/geom_helper_functions.hh
index 0d68d20e2..f3cc29d22 100644
--- a/src/geometry/geom_helper_functions.hh
+++ b/src/geometry/geom_helper_functions.hh
@@ -1,112 +1,112 @@
/**
* @file geom_helper_functions.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Jan 31 2018
*
* @brief Helper functions for the computational geometry algorithms
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef _AKANTU_GEOM_HELPER_FUNCTIONS_HH__
#define _AKANTU_GEOM_HELPER_FUNCTIONS_HH__
#include "aka_common.hh"
#include "aka_math.hh"
#include "tree_type_helper.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/// Fuzzy compare of two points
template <class Point>
inline bool comparePoints(const Point & a, const Point & b) {
return Math::are_float_equal(a.x(), b.x()) &&
Math::are_float_equal(a.y(), b.y()) &&
Math::are_float_equal(a.z(), b.z());
}
template <>
inline bool comparePoints(const cgal::Spherical::Circular_arc_point_3 & a,
const cgal::Spherical::Circular_arc_point_3 & b) {
return Math::are_float_equal(CGAL::to_double(a.x()),
CGAL::to_double(b.x())) &&
Math::are_float_equal(CGAL::to_double(a.y()),
CGAL::to_double(b.y())) &&
Math::are_float_equal(CGAL::to_double(a.z()), CGAL::to_double(b.z()));
}
/// Fuzzy compare of two segments
template <class K>
inline bool compareSegments(const CGAL::Segment_3<K> & a,
const CGAL::Segment_3<K> & b) {
return (comparePoints(a.source(), b.source()) &&
comparePoints(a.target(), b.target())) ||
(comparePoints(a.source(), b.target()) &&
comparePoints(a.target(), b.source()));
}
/// Compare segment pairs
inline bool
compareSegmentPairs(const std::pair<cgal::Cartesian::Segment_3, UInt> & a,
const std::pair<cgal::Cartesian::Segment_3, UInt> & b) {
return compareSegments(a.first, b.first);
}
/// Pair ordering operator based on first member
struct segmentPairsLess {
inline bool
operator()(const std::pair<cgal::Cartesian::Segment_3, UInt> & a,
const std::pair<cgal::Cartesian::Segment_3, UInt> & b) {
return CGAL::compare_lexicographically(a.first.min(), b.first.min()) ||
CGAL::compare_lexicographically(a.first.max(), b.first.max());
}
};
/* -------------------------------------------------------------------------- */
/* Predicates */
/* -------------------------------------------------------------------------- */
/// Predicate used to determine if two segments are equal
class IsSameSegment {
public:
IsSameSegment(const cgal::Cartesian::Segment_3 & segment)
: segment(segment) {}
bool
operator()(const std::pair<cgal::Cartesian::Segment_3, UInt> & test_pair) {
return compareSegments(segment, test_pair.first);
}
protected:
const cgal::Cartesian::Segment_3 segment;
};
} // akantu
#endif // _AKANTU_GEOM_HELPER_FUNCTIONS_HH__
diff --git a/src/geometry/mesh_abstract_intersector.hh b/src/geometry/mesh_abstract_intersector.hh
index 5467a673b..2bf1c1b29 100644
--- a/src/geometry/mesh_abstract_intersector.hh
+++ b/src/geometry/mesh_abstract_intersector.hh
@@ -1,121 +1,121 @@
/**
* @file mesh_abstract_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Jun 19 2017
*
* @brief Abstract class for intersection computations
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_ABSTRACT_INTERSECTOR_HH__
#define __AKANTU_MESH_ABSTRACT_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_geom_abstract.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Class used to perform intersections on a mesh and construct output
* data
*/
template <class Query> class MeshAbstractIntersector : public MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshAbstractIntersector(Mesh & mesh);
/// Destructor
virtual ~MeshAbstractIntersector();
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the new_node_per_elem array
AKANTU_GET_MACRO(NewNodePerElem, *new_node_per_elem, const Array<UInt> &);
/// get the intersection_points array
AKANTU_GET_MACRO(IntersectionPoints, intersection_points,
const Array<Real> *);
/// get the nb_seg_by_el UInt
AKANTU_GET_MACRO(NbSegByEl, nb_seg_by_el, UInt);
/**
* @brief Compute the intersection with a query object
*
* This function needs to be implemented for every subclass. It computes the
* intersections
* with the tree of primitives and creates the data for the user.
*
* @param query the CGAL primitive of the query object
*/
virtual void computeIntersectionQuery(const Query & query) = 0;
/// Compute intersection points between the mesh primitives (segments) and a
/// query (surface in 3D or a curve in 2D), double intersection points for the
/// same primitives are not considered. A maximum intersection node per
/// element is set : 2 in 2D and 4 in 3D
virtual void computeMeshQueryIntersectionPoint(const Query & query,
UInt nb_old_nodes) = 0;
/// Compute intersection between the mesh and a list of queries
virtual void
computeIntersectionQueryList(const std::list<Query> & query_list);
/// Compute intersection points between the mesh and a list of queries
virtual void
computeMeshQueryListIntersectionPoint(const std::list<Query> & query_list,
UInt nb_old_nodes);
/// Compute whatever result is needed from the user (should be move to the
/// appropriate specific classe for genericity)
virtual void
buildResultFromQueryList(const std::list<Query> & query_list) = 0;
protected:
/// new node per element (column 0: number of new nodes, then odd is the
/// intersection node number and even the ID of the intersected segment)
Array<UInt> * new_node_per_elem;
/// intersection output: new intersection points
/// (computeMeshQueryListIntersectionPoint)
Array<Real> * intersection_points;
/// number of segment in a considered element of the templated type of element
/// specialized intersector
const UInt nb_seg_by_el;
};
} // akantu
#include "mesh_abstract_intersector_tmpl.hh"
#endif // __AKANTU_MESH_ABSTRACT_INTERSECTOR_HH__
diff --git a/src/geometry/mesh_abstract_intersector_tmpl.hh b/src/geometry/mesh_abstract_intersector_tmpl.hh
index 8ed2a1da4..ccd833882 100644
--- a/src/geometry/mesh_abstract_intersector_tmpl.hh
+++ b/src/geometry/mesh_abstract_intersector_tmpl.hh
@@ -1,83 +1,83 @@
/**
* @file mesh_abstract_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Jun 19 2017
*
* @brief General class for intersection computations
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH__
#define __AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH__
#include "aka_common.hh"
#include "mesh_abstract_intersector.hh"
namespace akantu {
template <class Query>
MeshAbstractIntersector<Query>::MeshAbstractIntersector(Mesh & mesh)
: MeshGeomAbstract(mesh), new_node_per_elem(NULL),
intersection_points(NULL), nb_seg_by_el(0) {}
template <class Query>
MeshAbstractIntersector<Query>::~MeshAbstractIntersector() {}
template <class Query>
void MeshAbstractIntersector<Query>::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();
}
template <class Query>
void MeshAbstractIntersector<Query>::computeMeshQueryListIntersectionPoint(
const std::list<Query> & query_list, UInt nb_old_nodes) {
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) {
computeMeshQueryIntersectionPoint(*query_it, nb_old_nodes);
}
AKANTU_DEBUG_OUT();
}
} // akantu
#endif // __AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH__
diff --git a/src/geometry/mesh_geom_abstract.hh b/src/geometry/mesh_geom_abstract.hh
index 8805f7050..530924b48 100644
--- a/src/geometry/mesh_geom_abstract.hh
+++ b/src/geometry/mesh_geom_abstract.hh
@@ -1,65 +1,65 @@
/**
* @file mesh_geom_abstract.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Jun 19 2017
*
* @brief Class for constructing the CGAL primitives of a mesh
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_GEOM_ABSTRACT_HH__
#define __AKANTU_MESH_GEOM_ABSTRACT_HH__
#include "aka_common.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/// Abstract class for mesh geometry operations
class MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshGeomAbstract(Mesh & mesh) : mesh(mesh){};
/// Destructor
virtual ~MeshGeomAbstract(){};
public:
/// Construct geometric data for computational geometry algorithms
virtual void constructData(GhostType ghost_type = _not_ghost) = 0;
protected:
/// Mesh used to construct the primitives
Mesh & mesh;
};
} // akantu
#endif // __AKANTU_MESH_GEOM_ABSTRACT_HH__
diff --git a/src/geometry/mesh_geom_common.hh b/src/geometry/mesh_geom_common.hh
index ccc6f8d8b..528e965a8 100644
--- a/src/geometry/mesh_geom_common.hh
+++ b/src/geometry/mesh_geom_common.hh
@@ -1,57 +1,57 @@
/**
* @file mesh_geom_common.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Jan 31 2018
*
* @brief Common file for MeshGeom module
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_MESH_GEOM_COMMON_HH__
#define __AKANTU_MESH_GEOM_COMMON_HH__
#include "aka_common.hh"
#include <CGAL/MP_Float.h>
#include <CGAL/Quotient.h>
#include <CGAL/Algebraic_kernel_for_spheres_2_3.h>
#include <CGAL/Cartesian.h>
#include <CGAL/Simple_cartesian.h>
#include <CGAL/Spherical_kernel_3.h>
namespace akantu {
namespace cgal {
using Cartesian = CGAL::Simple_cartesian<Real>;
using Spherical = CGAL::Spherical_kernel_3<
CGAL::Simple_cartesian<CGAL::Quotient<CGAL::MP_Float>>,
CGAL::Algebraic_kernel_for_spheres_2_3<CGAL::Quotient<CGAL::MP_Float>>>;
} // cgal
} // akantu
#endif // __AKANTU_MESH_GEOM_COMMON_HH__
diff --git a/src/geometry/mesh_geom_factory.hh b/src/geometry/mesh_geom_factory.hh
index 68f1b927b..1b31ea553 100644
--- a/src/geometry/mesh_geom_factory.hh
+++ b/src/geometry/mesh_geom_factory.hh
@@ -1,107 +1,107 @@
/**
* @file mesh_geom_factory.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 27 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Jun 19 2017
*
* @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)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 "geom_helper_functions.hh"
#include "mesh.hh"
#include "mesh_geom_abstract.hh"
#include "tree_type_helper.hh"
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Class used to construct AABB tree for intersection computations
*
* This class constructs a CGAL AABB tree of one type of element in a mesh
* for fast intersection computations.
*/
template <UInt dim, ElementType el_type, class Primitive, class Kernel>
class MeshGeomFactory : public MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshGeomFactory(Mesh & mesh);
/// Desctructor
virtual ~MeshGeomFactory();
public:
/// Construct AABB tree for fast intersection computing
virtual void constructData(GhostType ghost_type = _not_ghost);
/**
* @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:
/// AABB data tree
typename TreeTypeHelper<Primitive, Kernel>::tree * data_tree;
/// Primitive list
typename TreeTypeHelper<Primitive, Kernel>::container_type primitive_list;
};
} // 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 5caf3048b..a7028a652 100644
--- a/src/geometry/mesh_geom_factory_tmpl.hh
+++ b/src/geometry/mesh_geom_factory_tmpl.hh
@@ -1,271 +1,271 @@
/**
* @file mesh_geom_factory_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 27 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Jan 31 2018
*
* @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)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "mesh_geom_factory.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type, class Primitive, class Kernel>
MeshGeomFactory<dim, type, Primitive, Kernel>::MeshGeomFactory(Mesh & mesh)
: MeshGeomAbstract(mesh), data_tree(NULL), primitive_list() {}
template <UInt dim, ElementType type, class Primitive, class Kernel>
MeshGeomFactory<dim, type, Primitive, Kernel>::~MeshGeomFactory() {
delete data_tree;
}
/**
* This function loops over the elements of `type` in the mesh and creates the
* AABB tree of geometrical primitves (`data_tree`).
*/
template <UInt dim, ElementType type, class Primitive, class Kernel>
void MeshGeomFactory<dim, type, Primitive, Kernel>::constructData(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
primitive_list.clear();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
const Array<Real> & nodes = mesh.getNodes();
UInt el_index = 0;
Array<UInt>::const_vector_iterator it =
connectivity.begin(nb_nodes_per_element);
Array<UInt>::const_vector_iterator end =
connectivity.end(nb_nodes_per_element);
Matrix<Real> node_coordinates(dim, nb_nodes_per_element);
// This loop builds the list of primitives
for (; it != end; ++it, ++el_index) {
const Vector<UInt> & el_connectivity = *it;
for (UInt i = 0; i < nb_nodes_per_element; i++)
for (UInt j = 0; j < dim; j++)
node_coordinates(j, i) = nodes(el_connectivity(i), j);
// the unique elemental id assigned to the primitive is the
// linearized element index over ghost type
addPrimitive(node_coordinates, el_index);
}
delete data_tree;
// This condition allows the use of the mesh geom module
// even if types are not compatible with AABB tree algorithm
if (TreeTypeHelper<Primitive, Kernel>::is_valid)
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, _triangle_3) decomposed into Triangle<cgal::Cartesian>
template <>
inline void
MeshGeomFactory<2, _triangle_3, Triangle<cgal::Cartesian>, cgal::Cartesian>::
addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
TreeTypeHelper<Triangle<cgal::Cartesian>,
cgal::Cartesian>::container_type & list) {
TreeTypeHelper<Triangle<cgal::Cartesian>, cgal::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<cgal::Cartesian> t(a, b, c);
t.setId(id);
list.push_back(t);
}
// (2D, _triangle_6) decomposed into Triangle<cgal::Cartesian>
template <>
inline void
MeshGeomFactory<2, _triangle_6, Triangle<cgal::Cartesian>, cgal::Cartesian>::
addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
TreeTypeHelper<Triangle<cgal::Cartesian>,
cgal::Cartesian>::container_type & list) {
TreeTypeHelper<Triangle<cgal::Cartesian>, cgal::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<cgal::Cartesian> t(a, b, c);
t.setId(id);
list.push_back(t);
}
// (2D, _triangle_3) decomposed into Line_arc<cgal::Spherical>
template <>
inline void
MeshGeomFactory<2, _triangle_3, Line_arc<cgal::Spherical>, cgal::Spherical>::
addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
TreeTypeHelper<Line_arc<cgal::Spherical>,
cgal::Spherical>::container_type & list) {
TreeTypeHelper<Line_arc<cgal::Spherical>, cgal::Spherical>::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.);
/*std::cout << "elem " << id << " node 1 : x_node=" << node_coordinates(0, 0)
<< ", x_arc_node=" << a.x() << ", y_node=" << node_coordinates(1, 0)
<< ", y_arc_node=" << a.y() << std::endl ;
std::cout << "elem " << id << " node 2 : x_node=" << node_coordinates(0, 1)
<< ", x_arc_node=" << b.x() << ", y_node=" << node_coordinates(1, 1)
<< ", y_arc_node=" << b.y() << std::endl ;
std::cout << "elem " << id << " node 2 : x_node=" << node_coordinates(0, 2)
<< ", x_arc_node=" << c.x() << ", y_node=" << node_coordinates(1, 2)
<< ", y_arc_node=" << c.y() << std::endl ;*/
CGAL::Line_3<cgal::Spherical> l1(a, b), l2(b, c), l3(c, a);
Line_arc<cgal::Spherical> s1(l1, a, b), s2(l2, b, c), s3(l3, c, a);
s1.setId(id);
s1.setSegId(0);
s2.setId(id);
s2.setSegId(1);
s3.setId(id);
s3.setSegId(2);
list.push_back(s1);
list.push_back(s2);
list.push_back(s3);
}
#if defined(AKANTU_IGFEM)
// (2D, _igfem_triangle_4) decomposed into Line_arc<cgal::Spherical>
template <>
inline void MeshGeomFactory<2, _igfem_triangle_4, Line_arc<cgal::Spherical>,
cgal::Spherical>::
addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
TreeTypeHelper<Line_arc<cgal::Spherical>,
cgal::Spherical>::container_type & list) {
TreeTypeHelper<Line_arc<cgal::Spherical>, cgal::Spherical>::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.);
CGAL::Line_3<cgal::Spherical> l1(a, b), l2(b, c), l3(c, a);
Line_arc<cgal::Spherical> s1(l1, a, b), s2(l2, b, c), s3(l3, c, a);
s1.setId(id);
s1.setSegId(0);
s2.setId(id);
s2.setSegId(1);
s3.setId(id);
s3.setSegId(2);
list.push_back(s1);
list.push_back(s2);
list.push_back(s3);
}
// (2D, _igfem_triangle_4) decomposed into Line_arc<cgal::Spherical>
template <>
inline void MeshGeomFactory<2, _igfem_triangle_5, Line_arc<cgal::Spherical>,
cgal::Spherical>::
addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
TreeTypeHelper<Line_arc<cgal::Spherical>,
cgal::Spherical>::container_type & list) {
TreeTypeHelper<Line_arc<cgal::Spherical>, cgal::Spherical>::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.);
CGAL::Line_3<cgal::Spherical> l1(a, b), l2(b, c), l3(c, a);
Line_arc<cgal::Spherical> s1(l1, a, b), s2(l2, b, c), s3(l3, c, a);
s1.setId(id);
s1.setSegId(0);
s2.setId(id);
s2.setSegId(1);
s3.setId(id);
s3.setSegId(2);
list.push_back(s1);
list.push_back(s2);
list.push_back(s3);
}
#endif
// (3D, _tetrahedron_4) decomposed into Triangle<cgal::Cartesian>
template <>
inline void
MeshGeomFactory<3, _tetrahedron_4, Triangle<cgal::Cartesian>, cgal::Cartesian>::
addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
TreeTypeHelper<Triangle<cgal::Cartesian>,
cgal::Cartesian>::container_type & list) {
TreeTypeHelper<Triangle<cgal::Cartesian>, cgal::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<cgal::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);
list.push_back(t1);
list.push_back(t2);
list.push_back(t3);
list.push_back(t4);
}
} // akantu
#endif // __AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
diff --git a/src/geometry/mesh_geom_intersector.hh b/src/geometry/mesh_geom_intersector.hh
index d8552c6f3..a0082b077 100644
--- a/src/geometry/mesh_geom_intersector.hh
+++ b/src/geometry/mesh_geom_intersector.hh
@@ -1,74 +1,74 @@
/**
* @file mesh_geom_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Jun 19 2017
*
* @brief General class for intersection computations
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_GEOM_INTERSECTOR_HH__
#define __AKANTU_MESH_GEOM_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_abstract_intersector.hh"
#include "mesh_geom_factory.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Class used to perform intersections on a mesh and construct output
* data
*/
template <UInt dim, ElementType type, class Primitive, class Query,
class Kernel>
class MeshGeomIntersector : public MeshAbstractIntersector<Query> {
public:
/// Construct from mesh
explicit MeshGeomIntersector(Mesh & mesh);
/// Destructor
virtual ~MeshGeomIntersector();
public:
/// Construct the primitive tree object
virtual void constructData(GhostType ghost_type = _not_ghost);
protected:
/// Factory object containing the primitive tree
MeshGeomFactory<dim, type, Primitive, Kernel> factory;
};
} // akantu
#include "mesh_geom_intersector_tmpl.hh"
#endif // __AKANTU_MESH_GEOM_INTERSECTOR_HH__
diff --git a/src/geometry/mesh_geom_intersector_tmpl.hh b/src/geometry/mesh_geom_intersector_tmpl.hh
index 0e2ab5bb9..7bedae20d 100644
--- a/src/geometry/mesh_geom_intersector_tmpl.hh
+++ b/src/geometry/mesh_geom_intersector_tmpl.hh
@@ -1,64 +1,64 @@
/**
* @file mesh_geom_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Jun 19 2017
*
* @brief General class for intersection computations
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
#define __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type, class Primitive, class Query,
class Kernel>
MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::MeshGeomIntersector(
Mesh & mesh)
: MeshAbstractIntersector<Query>(mesh), factory(mesh) {}
template <UInt dim, ElementType type, class Primitive, class Query,
class Kernel>
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(
GhostType ghost_type) {
this->intersection_points->resize(0);
factory.constructData(ghost_type);
}
} // akantu
#endif // __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
diff --git a/src/geometry/mesh_segment_intersector.hh b/src/geometry/mesh_segment_intersector.hh
index 6e7c38e2d..b6691c10b 100644
--- a/src/geometry/mesh_segment_intersector.hh
+++ b/src/geometry/mesh_segment_intersector.hh
@@ -1,109 +1,109 @@
/**
* @file mesh_segment_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Jan 31 2018
*
* @brief Computation of mesh intersection with segments
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
#define __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type>
class MeshSegmentIntersector
: public MeshGeomIntersector<dim, type, Triangle<cgal::Cartesian>,
cgal::Cartesian::Segment_3, cgal::Cartesian> {
using K = cgal::Cartesian;
/// Parent class type
typedef MeshGeomIntersector<dim, type, Triangle<K>, K::Segment_3, K>
parent_type;
/// Result of intersection function type
typedef typename IntersectionTypeHelper<TreeTypeHelper<Triangle<K>, K>,
K::Segment_3>::intersection_type
result_type;
/// Pair of segments and element id
typedef std::pair<K::Segment_3, UInt> pair_type;
public:
/// Construct from mesh
explicit MeshSegmentIntersector(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 intersection points between the mesh and a query
virtual void computeMeshQueryIntersectionPoint(const K::Segment_3 & query,
UInt nb_old_nodes);
/// Compute the embedded mesh
virtual void
buildResultFromQueryList(const std::list<K::Segment_3> & query_list);
void setPhysicalName(const std::string & other) {
current_physical_name = other;
}
protected:
/// Compute segments from intersection list
void computeSegments(const std::list<result_type> & intersections,
std::set<pair_type, segmentPairsLess> & segments,
const K::Segment_3 & query);
protected:
/// Result mesh
Mesh & result_mesh;
/// Physical name of the current batch of queries
std::string current_physical_name;
};
} // akantu
#include "mesh_segment_intersector_tmpl.hh"
#endif // __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
diff --git a/src/geometry/mesh_segment_intersector_tmpl.hh b/src/geometry/mesh_segment_intersector_tmpl.hh
index 92538a104..80f75640f 100644
--- a/src/geometry/mesh_segment_intersector_tmpl.hh
+++ b/src/geometry/mesh_segment_intersector_tmpl.hh
@@ -1,283 +1,283 @@
/**
* @file mesh_segment_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Computation of mesh intersection with segments
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
#define __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "tree_type_helper.hh"
namespace akantu {
template <UInt dim, ElementType type>
MeshSegmentIntersector<dim, type>::MeshSegmentIntersector(Mesh & mesh,
Mesh & result_mesh)
: parent_type(mesh), result_mesh(result_mesh), current_physical_name() {
this->intersection_points = new Array<Real>(0, dim);
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::set<std::pair<K::Segment_3, UInt>, segmentPairsLess> segment_set;
this->factory.getTree().all_intersections(query,
std::back_inserter(result_list));
this->computeSegments(result_list, segment_set, query);
// Arrays for storing nodes and connectivity
Array<Real> & nodes = result_mesh.getNodes();
Array<UInt> & connectivity = result_mesh.getConnectivity(_segment_2);
// Arrays for storing associated element and physical name
bool valid_elemental_data = true;
Array<Element> * associated_element = 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::set<pair_type, segmentPairsLess>::iterator it = segment_set.begin(),
end = segment_set.end();
// Loop over the segment pairs
for (; it != end; ++it) {
if (!it->first.is_degenerate()) {
Vector<UInt> segment_connectivity(2);
segment_connectivity(0) = result_mesh.getNbNodes();
segment_connectivity(1) = result_mesh.getNbNodes() + 1;
connectivity.push_back(segment_connectivity);
// Copy nodes
Vector<Real> source(dim), target(dim);
for (UInt j = 0; j < dim; j++) {
source(j) = it->first.source()[j];
target(j) = it->first.target()[j];
}
nodes.push_back(source);
nodes.push_back(target);
// Copy associated element info
if (valid_elemental_data) {
associated_element->push_back(Element{type, it->second, _not_ghost});
associated_physical_name->push_back(current_physical_name);
}
}
}
AKANTU_DEBUG_OUT();
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeMeshQueryIntersectionPoint(
const K::Segment_3 & /*query*/, UInt /*nb_old_nodes*/) {
AKANTU_ERROR("The method: computeMeshQueryIntersectionPoint has not "
"been implemented in class MeshSegmentIntersector!");
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::buildResultFromQueryList(
const std::list<K::Segment_3> & query_list) {
AKANTU_DEBUG_IN();
this->computeIntersectionQueryList(query_list);
AKANTU_DEBUG_OUT();
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeSegments(
const std::list<result_type> & intersections,
std::set<pair_type, segmentPairsLess> & segments,
const K::Segment_3 & query) {
AKANTU_DEBUG_IN();
/*
* Number of intersections = 0 means
*
* - query is completely outside mesh
* - query is completely inside primitive
*
* We try to determine the case and still construct the segment list
*/
if (intersections.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::set<UInt> ray1_results, ray2_results;
this->factory.getTree().all_intersected_primitives(
ray1, std::inserter(ray1_results, ray1_results.begin()));
this->factory.getTree().all_intersected_primitives(
ray2, std::inserter(ray2_results, ray2_results.begin()));
bool inside_primitive = false;
UInt primitive_id = 0;
std::set<UInt>::iterator ray2_it = ray2_results.begin(),
ray2_end = ray2_results.end();
// Test if first list contains an element of second list
for (; ray2_it != ray2_end && !inside_primitive; ++ray2_it) {
if (ray1_results.find(*ray2_it) != ray1_results.end()) {
inside_primitive = true;
primitive_id = *ray2_it;
}
}
if (inside_primitive) {
segments.insert(std::make_pair(query, primitive_id));
}
}
else {
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
segments.insert(std::make_pair(*segment, el));
}
// Result of intersection is a point
else if (const K::Point_3 * point =
boost::get<K::Point_3>(&((*it)->first))) {
// We only want to treat points differently if we're in 3D with Tetra4
// elements This should be optimized by compilator
if (dim == 3 && type == _tetrahedron_4) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
TreeTypeHelper<Triangle<K>, K>::container_type facets;
const Array<Real> & nodes = this->mesh.getNodes();
Array<UInt>::const_vector_iterator connectivity_vec =
this->mesh.getConnectivity(type).begin(nb_nodes_per_element);
const Vector<UInt> & el_connectivity = connectivity_vec[el];
Matrix<Real> node_coordinates(dim, nb_nodes_per_element);
for (UInt i = 0; i < nb_nodes_per_element; i++)
for (UInt j = 0; j < dim; j++)
node_coordinates(j, i) = nodes(el_connectivity(i), j);
this->factory.addPrimitive(node_coordinates, el, facets);
// Local tree
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));
bool out_point_found = false;
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);
segments.insert(std::make_pair(seg, el));
out_point_found = true;
}
}
}
if (!out_point_found) {
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);
const K::Point_3 * inside_point = NULL;
if (tetra.has_on_bounded_side(query.source()) &&
!tetra.has_on_boundary(query.source()))
inside_point = &query.source();
else if (tetra.has_on_bounded_side(query.target()) &&
!tetra.has_on_boundary(query.target()))
inside_point = &query.target();
if (inside_point) {
K::Segment_3 seg(*inside_point, *point);
segments.insert(std::make_pair(seg, el));
}
}
delete local_tree;
}
}
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif // __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
diff --git a/src/geometry/mesh_sphere_intersector.hh b/src/geometry/mesh_sphere_intersector.hh
index 46c5e9f69..4066d67c4 100644
--- a/src/geometry/mesh_sphere_intersector.hh
+++ b/src/geometry/mesh_sphere_intersector.hh
@@ -1,119 +1,119 @@
/**
* @file mesh_sphere_intersector.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jun 23 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Computation of mesh intersection with sphere(s)
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_SPHERE_INTERSECTOR_HH__
#define __AKANTU_MESH_SPHERE_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type>
class MeshSphereIntersector
: public MeshGeomIntersector<dim, type, Line_arc<cgal::Spherical>,
cgal::Spherical::Sphere_3, cgal::Spherical> {
using SK = cgal::Spherical;
using K = cgal::Cartesian;
/// Parent class type
typedef MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK>
parent_type;
/// Result of intersection function type
typedef typename IntersectionTypeHelper<TreeTypeHelper<Triangle<K>, K>,
K::Segment_3>::intersection_type
result_type;
/// Pair of intersection points and element id
typedef std::pair<SK::Circular_arc_point_3, UInt> pair_type;
public:
/// Construct from mesh
explicit MeshSphereIntersector(Mesh & mesh);
/// Destructor
virtual ~MeshSphereIntersector();
public:
/// Construct the primitive tree object
virtual void constructData(GhostType ghost_type = _not_ghost);
/**
* @brief Computes the intersection of the mesh with a sphere
*
* @param query (sphere) to compute the intersections with the mesh
*/
virtual void computeIntersectionQuery(const SK::Sphere_3 & /*query*/) {
AKANTU_ERROR("This function is not implemented for spheres (It was "
"to generic and has been replaced by "
"computeMeshQueryIntersectionPoint");
}
/// Compute intersection points between the mesh primitives (segments) and a
/// query (surface in 3D or a curve in 2D), double intersection points for the
/// same primitives are not considered. A maximum is set to the number of
/// intersection nodes per element: 2 in 2D and 4 in 3D
virtual void computeMeshQueryIntersectionPoint(const SK::Sphere_3 & query,
UInt nb_old_nodes);
/// Build the IGFEM mesh
virtual void
buildResultFromQueryList(const std::list<SK::Sphere_3> & /*query*/) {
AKANTU_ERROR("This function is no longer implemented to split "
"geometrical operations and dedicated result "
"construction");
}
/// Set the tolerance
void setToleranceIntersectionOnNode(UInt tol) {
this->tol_intersection_on_node = tol;
}
protected:
/// tolerance for which the intersection is considered on the mesh node
/// (relative to the segment lenght)
Real tol_intersection_on_node;
};
} // akantu
#include "mesh_sphere_intersector_tmpl.hh"
#endif // __AKANTU_MESH_SPHERE_INTERSECTOR_HH__
diff --git a/src/geometry/mesh_sphere_intersector_tmpl.hh b/src/geometry/mesh_sphere_intersector_tmpl.hh
index 818132a63..d47d652ef 100644
--- a/src/geometry/mesh_sphere_intersector_tmpl.hh
+++ b/src/geometry/mesh_sphere_intersector_tmpl.hh
@@ -1,215 +1,215 @@
/**
* @file mesh_sphere_intersector_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jun 23 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Computation of mesh intersection with spheres
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__
#define __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "mesh_sphere_intersector.hh"
#include "tree_type_helper.hh"
namespace akantu {
template <UInt dim, ElementType type>
MeshSphereIntersector<dim, type>::MeshSphereIntersector(Mesh & mesh)
: parent_type(mesh), tol_intersection_on_node(1e-10) {
#if defined(AKANTU_IGFEM)
if ((type == _triangle_3) || (type == _igfem_triangle_4) ||
(type == _igfem_triangle_5)) {
const_cast<UInt &>(this->nb_seg_by_el) = 3;
} else {
AKANTU_ERROR("Not ready for mesh type " << type);
}
#else
if ((type != _triangle_3))
AKANTU_ERROR("Not ready for mesh type " << type);
#endif
// initialize the intersection pointsss array with the spatial dimension
this->intersection_points = new Array<Real>(0, dim);
// A maximum is set to the number of intersection nodes per element to limit
// the size of new_node_per_elem: 2 in 2D and 4 in 3D
this->new_node_per_elem = new Array<UInt>(0, 1 + 4 * (dim - 1));
}
template <UInt dim, ElementType type>
MeshSphereIntersector<dim, type>::~MeshSphereIntersector() {
delete this->new_node_per_elem;
delete this->intersection_points;
}
template <UInt dim, ElementType type>
void MeshSphereIntersector<dim, type>::constructData(GhostType ghost_type) {
this->new_node_per_elem->resize(this->mesh.getNbElement(type, ghost_type));
this->new_node_per_elem->clear();
MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK>::constructData(
ghost_type);
}
template <UInt dim, ElementType type>
void MeshSphereIntersector<dim, type>::computeMeshQueryIntersectionPoint(
const SK::Sphere_3 & query, UInt nb_old_nodes) {
/// function to replace computeIntersectionQuery in a more generic geometry
/// module version
// The newNodeEvent is not send from this method who only compute the
// intersection points
AKANTU_DEBUG_IN();
Array<Real> & nodes = this->mesh.getNodes();
UInt nb_node = nodes.size() + this->intersection_points->size();
// Tolerance for proximity checks should be defined by user
Real global_tolerance = Math::getTolerance();
Math::setTolerance(tol_intersection_on_node);
typedef boost::variant<pair_type> sk_inter_res;
TreeTypeHelper<Line_arc<cgal::Spherical>, cgal::Spherical>::const_iterator
it = this->factory.getPrimitiveList().begin(),
end = this->factory.getPrimitiveList().end();
for (; it != end; ++it) { // loop on the primitives (segments)
std::list<sk_inter_res> s_results;
CGAL::intersection(*it, query, std::back_inserter(s_results));
if (s_results.size() == 1) { // just one point
if (pair_type * pair = boost::get<pair_type>(&s_results.front())) {
if (pair->second == 1) { // not a point tangent to the sphere
// the intersection point written as a vector
Vector<Real> new_node(dim, 0.0);
cgal::Cartesian::Point_3 point(CGAL::to_double(pair->first.x()),
CGAL::to_double(pair->first.y()),
CGAL::to_double(pair->first.z()));
for (UInt i = 0; i < dim; i++) {
new_node(i) = point[i];
}
/// boolean to decide wheter intersection point is on a standard node
/// of the mesh or not
bool is_on_mesh = false;
/// boolean to decide if this intersection point has been already
/// computed for a neighbor element
bool is_new = true;
/// check if intersection point has already been computed
UInt n = nb_old_nodes;
// check if we already compute this intersection and add it as a node
// for a neighboor element of another type
auto existing_node = nodes.begin(dim);
for (; n < nodes.size(); ++n) { // loop on the nodes from nb_old_nodes
if (Math::are_vector_equal(dim, new_node.storage(),
existing_node[n].storage())) {
is_new = false;
break;
}
}
if (is_new) {
auto intersection_points_it = this->intersection_points->begin(dim);
auto intersection_points_end = this->intersection_points->end(dim);
for (; intersection_points_it != intersection_points_end;
++intersection_points_it, ++n) {
if (Math::are_vector_equal(dim, new_node.storage(),
intersection_points_it->storage())) {
is_new = false;
break;
}
}
}
// get the initial and final points of the primitive (segment) and
// write them as vectors
cgal::Cartesian::Point_3 source_cgal(
CGAL::to_double(it->source().x()),
CGAL::to_double(it->source().y()),
CGAL::to_double(it->source().z()));
cgal::Cartesian::Point_3 target_cgal(
CGAL::to_double(it->target().x()),
CGAL::to_double(it->target().y()),
CGAL::to_double(it->target().z()));
Vector<Real> source(dim), target(dim);
for (UInt i = 0; i < dim; i++) {
source(i) = source_cgal[i];
target(i) = target_cgal[i];
}
// Check if we are close from a node of the primitive (segment)
if (Math::are_vector_equal(dim, source.storage(),
new_node.storage()) ||
Math::are_vector_equal(dim, target.storage(),
new_node.storage())) {
is_on_mesh = true;
is_new = false;
}
if (is_new) { // if the intersection point is a new one add it to the
// list
this->intersection_points->push_back(new_node);
nb_node++;
}
// deduce the element id
UInt element_id = it->id();
// fill the new_node_per_elem array
if (!is_on_mesh) { // if the node is not on a mesh node
UInt & nb_new_nodes_per_el =
(*this->new_node_per_elem)(element_id, 0);
nb_new_nodes_per_el += 1;
AKANTU_DEBUG_ASSERT(
2 * nb_new_nodes_per_el <
this->new_node_per_elem->getNbComponent(),
"You might have to interface crossing the same material");
(*this->new_node_per_elem)(element_id,
(2 * nb_new_nodes_per_el) - 1) = n;
(*this->new_node_per_elem)(element_id, 2 * nb_new_nodes_per_el) =
it->segId();
}
}
}
}
}
Math::setTolerance(global_tolerance);
AKANTU_DEBUG_OUT();
}
} // akantu
#endif // __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__
diff --git a/src/geometry/tree_type_helper.hh b/src/geometry/tree_type_helper.hh
index d43bdf549..f0cf08c21 100644
--- a/src/geometry/tree_type_helper.hh
+++ b/src/geometry/tree_type_helper.hh
@@ -1,109 +1,109 @@
/**
* @file tree_type_helper.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Thu Feb 01 2018
*
* @brief Converts element types of a mesh to CGAL primitive types
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TREE_TYPE_HELPER_HH__
#define __AKANTU_TREE_TYPE_HELPER_HH__
#include "aka_common.hh"
#include "line_arc.hh"
#include "tetrahedron.hh"
#include "triangle.hh"
#include "aabb_primitive.hh"
#include "mesh_geom_common.hh"
#include <CGAL/AABB_traits.h>
#include <CGAL/AABB_tree.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Replacement class for algorithm that can't use the AABB tree types
template <typename iterator> struct VoidTree {
VoidTree(const iterator & /*begin*/, const iterator & /*end*/) {}
};
/// Helper class used to ease the use of CGAL AABB tree algorithm
template <class Primitive, class Kernel> struct TreeTypeHelper {
static const bool is_valid = false;
typedef Primitive primitive_type;
typedef typename std::list<primitive_type> container_type;
typedef typename container_type::iterator iterator;
typedef typename container_type::const_iterator const_iterator;
typedef typename CGAL::Point_3<Kernel> point_type;
typedef VoidTree<iterator> 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> { \
static const bool is_valid = true; \
typedef my_primitive<my_kernel> primitive_type; \
typedef my_primitive##_primitive aabb_primitive_type; \
typedef CGAL::Point_3<my_kernel> point_type; \
\
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(Triangle, cgal::Cartesian::Segment_3, cgal::Cartesian);
// TREE_TYPE_HELPER_MACRO(Line_arc, cgal::Spherical::Sphere_3, cgal::Spherical);
#undef TREE_TYPE_HELPER_MACRO
} // akantu
#endif // __AKANTU_TREE_TYPE_HELPER_HH__
diff --git a/src/io/dumper/dumpable.cc b/src/io/dumper/dumpable.cc
index 04997c49c..e35791864 100644
--- a/src/io/dumper/dumpable.cc
+++ b/src/io/dumper/dumpable.cc
@@ -1,285 +1,285 @@
/**
* @file dumpable.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the dumpable interface
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumpable.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include <io_helper.hh>
namespace akantu {
/* -------------------------------------------------------------------------- */
Dumpable::Dumpable() : default_dumper("") {}
/* -------------------------------------------------------------------------- */
Dumpable::~Dumpable() {
auto it = dumpers.begin();
auto end = dumpers.end();
for (; it != end; ++it) {
delete it->second;
}
}
/* -------------------------------------------------------------------------- */
void Dumpable::registerExternalDumper(DumperIOHelper & dumper,
const std::string & dumper_name,
const bool is_default) {
this->dumpers[dumper_name] = &dumper;
if (is_default)
this->default_dumper = dumper_name;
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpMesh(const Mesh & mesh, UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & element_kind) {
this->addDumpMeshToDumper(this->default_dumper, mesh, spatial_dimension,
ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpMeshToDumper(const std::string & dumper_name,
const Mesh & mesh, UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & element_kind) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerMesh(mesh, spatial_dimension, ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
const GhostType & ghost_type, const ElementKind & element_kind) {
this->addDumpFilteredMeshToDumper(this->default_dumper, mesh, elements_filter,
nodes_filter, spatial_dimension, ghost_type,
element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
const GhostType & ghost_type, const ElementKind & element_kind) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerFilteredMesh(mesh, elements_filter, nodes_filter,
spatial_dimension, ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpField(const std::string & field_id) {
this->addDumpFieldToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldExternal(const std::string & field_id,
dumper::Field * field) {
this->addDumpFieldExternalToDumper(this->default_dumper, field_id, field);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field);
}
/* -------------------------------------------------------------------------- */
void Dumpable::removeDumpField(const std::string & field_id) {
this->removeDumpFieldFromDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.unRegisterField(field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldVector(const std::string & field_id) {
this->addDumpFieldVectorToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldVectorToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldTensor(const std::string & field_id) {
this->addDumpFieldTensorToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldTensorToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::setDirectory(const std::string & directory) {
this->setDirectoryToDumper(this->default_dumper, directory);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setBaseName(const std::string & basename) {
this->setBaseNameToDumper(this->default_dumper, basename);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setBaseName(basename);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTimeStepToDumper(Real time_step) {
this->setTimeStepToDumper(this->default_dumper, time_step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTimeStepToDumper(const std::string & dumper_name,
Real time_step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTextModeToDumper(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.getDumper().setMode(iohelper::TEXT);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTextModeToDumper() {
DumperIOHelper & dumper = this->getDumper(this->default_dumper);
dumper.getDumper().setMode(iohelper::TEXT);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump();
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump() { this->dump(this->default_dumper); }
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name, UInt step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump(step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(UInt step) { this->dump(this->default_dumper, step); }
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name, Real time, UInt step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump(time, step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(Real time, UInt step) {
this->dump(this->default_dumper, time, step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field);
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Dumpable::getDumper() {
return this->getDumper(this->default_dumper);
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Dumpable::getDumper(const std::string & dumper_name) {
auto it = this->dumpers.find(dumper_name);
auto end = this->dumpers.end();
if (it == end)
AKANTU_EXCEPTION("Dumper " << dumper_name
<< "has not been registered, yet.");
return *(it->second);
}
/* -------------------------------------------------------------------------- */
std::string Dumpable::getDefaultDumperName() const {
return this->default_dumper;
}
} // akantu
#endif
diff --git a/src/io/dumper/dumpable.hh b/src/io/dumper/dumpable.hh
index 985e3b9f7..3ef6f269e 100644
--- a/src/io/dumper/dumpable.hh
+++ b/src/io/dumper/dumpable.hh
@@ -1,48 +1,47 @@
/**
* @file dumpable.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Tue Jan 06 2015
+ * @date last modification: Wed Feb 03 2016
*
* @brief Interface for object who wants to dump themselves
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPABLE_HH__
#define __AKANTU_DUMPABLE_HH__
#ifdef AKANTU_USE_IOHELPER
#include "dumpable_iohelper.hh"
#else
#include "dumpable_dummy.hh"
#endif // AKANTU_USE_IOHELPER
#endif /* __AKANTU_DUMPABLE_HH__ */
diff --git a/src/io/dumper/dumpable_dummy.hh b/src/io/dumper/dumpable_dummy.hh
index 0b9fb4694..eb9420dfd 100644
--- a/src/io/dumper/dumpable_dummy.hh
+++ b/src/io/dumper/dumpable_dummy.hh
@@ -1,265 +1,264 @@
/**
* @file dumpable_dummy.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Fri Aug 21 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Interface for object who wants to dump themselves
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPABLE_DUMMY_HH__
#define __AKANTU_DUMPABLE_DUMMY_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wunused"
namespace dumper {
class Field;
}
class DumperIOHelper;
class Mesh;
/* -------------------------------------------------------------------------- */
class Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Dumpable(){};
virtual ~Dumpable(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <class T>
inline void registerDumper(const std::string & dumper_name,
const std::string & file_name = "",
const bool is_default = false) {}
void registerExternalDumper(DumperIOHelper * dumper,
const std::string & dumper_name,
const bool is_default = false) {}
void addDumpMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {}
void addDumpMeshToDumper(const std::string & dumper_name, const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
}
void addDumpFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
}
void addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {}
virtual void addDumpField(const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
virtual void addDumpFieldExternal(const std::string & field_id,
dumper::Field * field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
virtual void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void addDumpFieldExternal(const std::string & field_id,
const Array<T> & field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void
addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void removeDumpField(const std::string & field_id) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setDirecory(const std::string & directory) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setBaseName(const std::string & basename) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setTextModeToDumper(const std::string & dumper_name) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setTextModeToDumper() {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump() {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name, UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(Real current_time, UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name, Real current_time, UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
protected:
void internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
protected:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper & getDumper() {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
DumperIOHelper & getDumper(const std::string & dumper_name) {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <class T> T & getDumper(const std::string & dumper_name) {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
std::string getDefaultDumperName() {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
#pragma GCC diagnostic pop
} // akantu
#endif /* __AKANTU_DUMPABLE_DUMMY_HH__ */
diff --git a/src/io/dumper/dumpable_inline_impl.hh b/src/io/dumper/dumpable_inline_impl.hh
index 638462db5..012b570b4 100644
--- a/src/io/dumper/dumpable_inline_impl.hh
+++ b/src/io/dumper/dumpable_inline_impl.hh
@@ -1,134 +1,134 @@
/**
* @file dumpable_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the Dumpable class
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPABLE_INLINE_IMPL_HH__
#define __AKANTU_DUMPABLE_INLINE_IMPL_HH__
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_elemental_field.hh"
#include "dumper_nodal_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class T>
inline void Dumpable::registerDumper(const std::string & dumper_name,
const std::string & file_name,
const bool is_default) {
if (this->dumpers.find(dumper_name) != this->dumpers.end()) {
AKANTU_DEBUG_INFO("Dumper " + dumper_name + "is already registered.");
}
std::string name = file_name;
if (name == "")
name = dumper_name;
this->dumpers[dumper_name] = new T(name);
if (is_default)
this->default_dumper = dumper_name;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternal(const std::string & field_id,
const Array<T> & field) {
this->addDumpFieldExternalToDumper<T>(this->default_dumper, field_id, field);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void
Dumpable::addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field) {
dumper::Field * field_cont = new dumper::NodalField<T>(field);
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field_cont);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & element_kind) {
this->addDumpFieldExternalToDumper(this->default_dumper, field_id, field,
spatial_dimension, ghost_type,
element_kind);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field, UInt spatial_dimension,
const GhostType & ghost_type, const ElementKind & element_kind) {
dumper::Field * field_cont;
#if defined(AKANTU_IGFEM)
if (element_kind == _ek_igfem) {
field_cont = new dumper::IGFEMElementalField<T>(field, spatial_dimension,
ghost_type, element_kind);
} else
#endif
field_cont = new dumper::ElementalField<T>(field, spatial_dimension,
ghost_type, element_kind);
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field_cont);
}
/* -------------------------------------------------------------------------- */
template <class T>
inline T & Dumpable::getDumper(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
try {
auto & templated_dumper = dynamic_cast<T &>(dumper);
return templated_dumper;
} catch (std::bad_cast &) {
AKANTU_EXCEPTION("Dumper " << dumper_name << " is not of type: "
<< debug::demangle(typeid(T).name()));
}
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif
#endif /* __AKANTU_DUMPABLE_INLINE_IMPL_HH__ */
diff --git a/src/io/dumper/dumpable_iohelper.hh b/src/io/dumper/dumpable_iohelper.hh
index e9252526f..02bacd64f 100644
--- a/src/io/dumper/dumpable_iohelper.hh
+++ b/src/io/dumper/dumpable_iohelper.hh
@@ -1,192 +1,192 @@
/**
* @file dumpable_iohelper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 06 2015
- * @date last modification: Thu Nov 19 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Interface for object who wants to dump themselves
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPABLE_IOHELPER_HH__
#define __AKANTU_DUMPABLE_IOHELPER_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Dumpable();
virtual ~Dumpable();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create a new dumper (of templated type T) and register it under
/// dumper_name. file_name is used for construction of T. is default states if
/// this dumper is the default dumper.
template <class T>
inline void registerDumper(const std::string & dumper_name,
const std::string & file_name = "",
const bool is_default = false);
/// register an externally created dumper
void registerExternalDumper(DumperIOHelper & dumper,
const std::string & dumper_name,
const bool is_default = false);
/// register a mesh to the default dumper
void addDumpMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a mesh to the default identified by its name
void addDumpMeshToDumper(const std::string & dumper_name, const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a filtered mesh as the default dumper
void addDumpFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a filtered mesh and provides a name
void addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// to implement
virtual void addDumpField(const std::string & field_id);
/// to implement
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/// add a field
virtual void addDumpFieldExternal(const std::string & field_id,
dumper::Field * field);
virtual void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field);
template <typename T>
inline void addDumpFieldExternal(const std::string & field_id,
const Array<T> & field);
template <typename T>
inline void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field);
template <typename T>
inline void
addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
template <typename T>
inline void addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
void removeDumpField(const std::string & field_id);
void removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldVector(const std::string & field_id);
virtual void addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensor(const std::string & field_id);
virtual void addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id);
void setDirectory(const std::string & directory);
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory);
void setBaseName(const std::string & basename);
void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename);
void setTimeStepToDumper(Real time_step);
void setTimeStepToDumper(const std::string & dumper_name, Real time_step);
void setTextModeToDumper(const std::string & dumper_name);
void setTextModeToDumper();
virtual void dump();
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
virtual void dump(const std::string & dumper_name);
virtual void dump(const std::string & dumper_name, UInt step);
virtual void dump(const std::string & dumper_name, Real time, UInt step);
public:
void internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper & getDumper();
DumperIOHelper & getDumper(const std::string & dumper_name);
template <class T> T & getDumper(const std::string & dumper_name);
std::string getDefaultDumperName() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using DumperMap = std::map<std::string, DumperIOHelper *>;
using DumperSet = std::set<std::string>;
DumperMap dumpers;
std::string default_dumper;
};
} // akantu
#endif /* __AKANTU_DUMPABLE_IOHELPER_HH__ */
diff --git a/src/io/dumper/dumper_compute.hh b/src/io/dumper/dumper_compute.hh
index 7af59b85c..0989f62b2 100644
--- a/src/io/dumper/dumper_compute.hh
+++ b/src/io/dumper/dumper_compute.hh
@@ -1,274 +1,274 @@
/**
* @file dumper_compute.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Sun Dec 03 2017
*
* @brief Field that map a function to another field
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_COMPUTE_HH__
#define __AKANTU_DUMPER_COMPUTE_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dumper_field.hh"
#include "dumper_iohelper.hh"
#include "dumper_type_traits.hh"
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
class ComputeFunctorInterface {
public:
virtual ~ComputeFunctorInterface() = default;
virtual UInt getDim() = 0;
virtual UInt getNbComponent(UInt old_nb_comp) = 0;
};
/* -------------------------------------------------------------------------- */
template <typename return_type>
class ComputeFunctorOutput : public ComputeFunctorInterface {
public:
ComputeFunctorOutput() = default;
~ComputeFunctorOutput() override = default;
};
/* -------------------------------------------------------------------------- */
template <typename input_type, typename return_type>
class ComputeFunctor : public ComputeFunctorOutput<return_type> {
public:
ComputeFunctor() = default;
~ComputeFunctor() override = default;
virtual return_type func(const input_type & d, Element global_index) = 0;
};
/* -------------------------------------------------------------------------- */
template <typename SubFieldCompute, typename _return_type>
class FieldCompute : public Field {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using sub_iterator = typename SubFieldCompute::iterator;
using sub_types = typename SubFieldCompute::types;
using sub_return_type = typename sub_types::return_type;
using return_type = _return_type;
using data_type = typename sub_types::data_type;
using types =
TypeTraits<data_type, return_type, ElementTypeMapArray<data_type>>;
class iterator {
public:
iterator(const sub_iterator & it,
ComputeFunctor<sub_return_type, return_type> & func)
: it(it), func(func) {}
bool operator!=(const iterator & it) const { return it.it != this->it; }
iterator operator++() {
++this->it;
return *this;
}
UInt currentGlobalIndex() { return this->it.currentGlobalIndex(); }
return_type operator*() { return func.func(*it, it.getCurrentElement()); }
Element getCurrentElement() { return this->it.getCurrentElement(); }
UInt element_type() { return this->it.element_type(); }
protected:
sub_iterator it;
ComputeFunctor<sub_return_type, return_type> & func;
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FieldCompute(SubFieldCompute & cont, ComputeFunctorInterface & func)
: sub_field(cont),
func(dynamic_cast<ComputeFunctor<sub_return_type, return_type> &>(
func)) {
this->checkHomogeneity();
};
~FieldCompute() override {
delete &(this->sub_field);
delete &(this->func);
}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addElemDataField(id, *this);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
iterator begin() { return iterator(sub_field.begin(), func); }
iterator end() { return iterator(sub_field.end(), func); }
UInt getDim() { return func.getDim(); }
UInt size() {
throw;
// return Functor::size();
return 0;
}
void checkHomogeneity() override { this->homogeneous = true; };
iohelper::DataType getDataType() {
return iohelper::getDataType<data_type>();
}
/// get the number of components of the hosted field
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) override {
ElementTypeMap<UInt> nb_components;
const ElementTypeMap<UInt> & old_nb_components =
this->sub_field.getNbComponents(dim, ghost_type, kind);
ElementTypeMap<UInt>::type_iterator tit =
old_nb_components.firstType(dim, ghost_type, kind);
ElementTypeMap<UInt>::type_iterator end =
old_nb_components.lastType(dim, ghost_type, kind);
while (tit != end) {
UInt nb_comp = old_nb_components(*tit, ghost_type);
nb_components(*tit, ghost_type) = func.getNbComponent(nb_comp);
++tit;
}
return nb_components;
};
/// for connection to a FieldCompute
inline Field * connect(FieldComputeProxy & proxy) override;
/// for connection to a FieldCompute
ComputeFunctorInterface * connect(HomogenizerProxy & proxy) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
SubFieldCompute & sub_field;
ComputeFunctor<sub_return_type, return_type> & func;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class FieldComputeProxy {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FieldComputeProxy(ComputeFunctorInterface & func) : func(func){};
inline static Field * createFieldCompute(Field * field,
ComputeFunctorInterface & func) {
/// that looks fishy an object passed as a ref and destroyed at their end of
/// the function
FieldComputeProxy compute_proxy(func);
return field->connect(compute_proxy);
}
template <typename T> Field * connectToField(T * ptr) {
if (dynamic_cast<ComputeFunctorOutput<Vector<Real>> *>(&func)) {
return this->connectToFunctor<Vector<Real>>(ptr);
} else if (dynamic_cast<ComputeFunctorOutput<Vector<UInt>> *>(&func)) {
return this->connectToFunctor<Vector<UInt>>(ptr);
}
else if (dynamic_cast<ComputeFunctorOutput<Matrix<UInt>> *>(&func)) {
return this->connectToFunctor<Matrix<UInt>>(ptr);
}
else if (dynamic_cast<ComputeFunctorOutput<Matrix<Real>> *>(&func)) {
return this->connectToFunctor<Matrix<Real>>(ptr);
}
else
throw;
}
template <typename output, typename T> Field * connectToFunctor(T * ptr) {
auto * functor_ptr = new FieldCompute<T, output>(*ptr, func);
return functor_ptr;
}
template <typename output, typename SubFieldCompute, typename return_type1,
typename return_type2>
Field *
connectToFunctor(__attribute__((unused))
FieldCompute<FieldCompute<SubFieldCompute, return_type1>,
return_type2> * ptr) {
throw; // return new FieldCompute<T,output>(*ptr,func);
return nullptr;
}
template <typename output, typename SubFieldCompute, typename return_type1,
typename return_type2, typename return_type3, typename return_type4>
Field * connectToFunctor(
__attribute__((unused)) FieldCompute<
FieldCompute<FieldCompute<FieldCompute<SubFieldCompute, return_type1>,
return_type2>,
return_type3>,
return_type4> * ptr) {
throw; // return new FieldCompute<T,output>(*ptr,func);
return nullptr;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
ComputeFunctorInterface & func;
};
/* -------------------------------------------------------------------------- */
/// for connection to a FieldCompute
template <typename SubFieldCompute, typename return_type>
inline Field *
FieldCompute<SubFieldCompute, return_type>::connect(FieldComputeProxy & proxy) {
return proxy.connectToField(this);
}
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
#endif /* __AKANTU_DUMPER_COMPUTE_HH__ */
diff --git a/src/io/dumper/dumper_element_iterator.hh b/src/io/dumper/dumper_element_iterator.hh
index 24319d083..9710b7d7c 100644
--- a/src/io/dumper/dumper_element_iterator.hh
+++ b/src/io/dumper/dumper_element_iterator.hh
@@ -1,178 +1,178 @@
/**
* @file dumper_element_iterator.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Fri May 15 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Iterators for elemental fields
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_ELEMENT_ITERATOR_HH__
#define __AKANTU_DUMPER_ELEMENT_ITERATOR_HH__
/* -------------------------------------------------------------------------- */
#include "element.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <class types, template <class> class final_iterator>
class element_iterator {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using it_type = typename types::it_type;
using field_type = typename types::field_type;
using array_type = typename types::array_type;
using array_iterator = typename types::array_iterator;
using iterator = final_iterator<types>;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
element_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: field(field), tit(t_it), tit_end(t_it_end), array_it(array_it),
array_it_end(array_it_end), ghost_type(ghost_type) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
bool operator!=(const iterator & it) const {
return (ghost_type != it.ghost_type) ||
(tit != it.tit || (array_it != it.array_it));
}
iterator & operator++() {
++array_it;
while (array_it == array_it_end && tit != tit_end) {
++tit;
if (tit != tit_end) {
const array_type & vect = field(*tit, ghost_type);
UInt _nb_data_per_elem = getNbDataPerElem(*tit);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.size() * nb_component) / _nb_data_per_elem;
array_it = vect.begin_reinterpret(_nb_data_per_elem, size);
array_it_end = vect.end_reinterpret(_nb_data_per_elem, size);
}
}
return *(static_cast<iterator *>(this));
};
ElementType getType() { return *tit; }
UInt element_type() { return getIOHelperType(*tit); }
Element getCurrentElement() {
return Element{*tit, array_it.getCurrentIndex(), _not_ghost};
}
UInt getNbDataPerElem(const ElementType & type) const {
if (!nb_data_per_elem.exists(type, ghost_type))
return field(type, ghost_type).getNbComponent();
return nb_data_per_elem(type, ghost_type);
}
void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data) {
this->nb_data_per_elem = nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the field to iterate on
const field_type & field;
/// field iterator
typename field_type::type_iterator tit;
/// field iterator end
typename field_type::type_iterator tit_end;
/// array iterator
array_iterator array_it;
/// internal iterator end
array_iterator array_it_end;
/// ghost type identification
const GhostType ghost_type;
/// number of data per element
ElementTypeMap<UInt> nb_data_per_elem;
};
/* -------------------------------------------------------------------------- */
template <typename types>
class elemental_field_iterator
: public element_iterator<types, elemental_field_iterator> {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
using parent =
element_iterator<types, ::akantu::dumper::elemental_field_iterator>;
using it_type = typename types::it_type;
using return_type = typename types::return_type;
using field_type = typename types::field_type;
using array_iterator = typename types::array_iterator;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
elemental_field_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
return_type operator*() { return *this->array_it; }
private:
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_DUMPER_ELEMENT_ITERATOR_HH__ */
diff --git a/src/io/dumper/dumper_element_partition.hh b/src/io/dumper/dumper_element_partition.hh
index 3718e35e2..4885ebe09 100644
--- a/src/io/dumper/dumper_element_partition.hh
+++ b/src/io/dumper/dumper_element_partition.hh
@@ -1,118 +1,118 @@
/**
* @file dumper_element_partition.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Tue Jul 14 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief ElementPartition field
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
#ifdef AKANTU_IGFEM
#include "dumper_igfem_element_partition.hh"
#endif
/* -------------------------------------------------------------------------- */
template <class types>
class element_partition_field_iterator
: public element_iterator<types, element_partition_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using parent =
element_iterator<types, dumper::element_partition_field_iterator>;
using return_type =
typename SingleType<unsigned int, Vector, true>::return_type;
using array_iterator = typename types::array_iterator;
using field_type = typename types::field_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
element_partition_field_iterator(
const field_type & field, const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it, const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {
prank = Communicator::getStaticCommunicator().whoAmI();
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
return_type operator*() { return return_type(1, prank); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
UInt prank;
};
/* -------------------------------------------------------------------------- */
template <bool filtered = false>
class ElementPartitionField
: public GenericElementalField<SingleType<UInt, Vector, filtered>,
element_partition_field_iterator> {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
using types = SingleType<UInt, Vector, filtered>;
using iterator = element_partition_field_iterator<types>;
using parent = GenericElementalField<types, element_partition_field_iterator>;
using field_type = typename types::field_type;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
ElementPartitionField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: parent(field, spatial_dimension, ghost_type, element_kind) {
this->homogeneous = true;
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
UInt getDim() override { return 1; }
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
diff --git a/src/io/dumper/dumper_elemental_field.hh b/src/io/dumper/dumper_elemental_field.hh
index c62bf7b6c..3caf94b40 100644
--- a/src/io/dumper/dumper_elemental_field.hh
+++ b/src/io/dumper/dumper_elemental_field.hh
@@ -1,77 +1,76 @@
/**
* @file dumper_elemental_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Aug 17 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief description of elemental fields
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_ELEMENTAL_FIELD_HH__
#define __AKANTU_DUMPER_ELEMENTAL_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "dumper_field.hh"
#include "dumper_generic_elemental_field.hh"
#ifdef AKANTU_IGFEM
#include "dumper_igfem_elemental_field.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <typename T, template <class> class ret = Vector,
bool filtered = false>
class ElementalField
: public GenericElementalField<SingleType<T, ret, filtered>,
elemental_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using types = SingleType<T, ret, filtered>;
using field_type = typename types::field_type;
using iterator = elemental_field_iterator<types>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: GenericElementalField<types, elemental_field_iterator>(
field, spatial_dimension, ghost_type, element_kind) {}
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
#endif /* __AKANTU_DUMPER_ELEMENTAL_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_field.hh b/src/io/dumper/dumper_field.hh
index 66544d73e..ebe765ce8 100644
--- a/src/io/dumper/dumper_field.hh
+++ b/src/io/dumper/dumper_field.hh
@@ -1,137 +1,137 @@
/**
* @file dumper_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Common interface for fields
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_FIELD_HH__
#define __AKANTU_DUMPER_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
class FieldComputeProxy;
class FieldComputeBaseInterface;
class ComputeFunctorInterface;
class HomogenizerProxy;
/* -------------------------------------------------------------------------- */
/// Field interface
class Field {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Field() = default;
virtual ~Field() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
#ifdef AKANTU_USE_IOHELPER
/// register this to the provided dumper
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) = 0;
#endif
/// set the number of data per item (used for elements fields at the moment)
virtual void setNbData(__attribute__((unused)) UInt nb_data) {
AKANTU_TO_IMPLEMENT();
};
/// set the number of data per elem (used for elements fields at the moment)
virtual void setNbDataPerElem(__attribute__((unused))
const ElementTypeMap<UInt> & nb_data) {
AKANTU_TO_IMPLEMENT();
};
/// set the number of data per elem (used for elements fields at the moment)
virtual void setNbDataPerElem(__attribute__((unused)) UInt nb_data) {
AKANTU_TO_IMPLEMENT();
};
/// get the number of components of the hosted field
virtual ElementTypeMap<UInt>
getNbComponents(__attribute__((unused)) UInt dim = _all_dimensions,
__attribute__((unused)) GhostType ghost_type = _not_ghost,
__attribute__((unused)) ElementKind kind = _ek_not_defined) {
throw;
};
/// for connection to a FieldCompute
inline virtual Field * connect(__attribute__((unused))
FieldComputeProxy & proxy) {
throw;
};
/// for connection to a FieldCompute
inline virtual ComputeFunctorInterface * connect(__attribute__((unused))
HomogenizerProxy & proxy) {
throw;
};
/// check if the same quantity of data for all element types
virtual void checkHomogeneity() = 0;
/// return the dumper name
std::string getGroupName() { return group_name; };
/// return the id of the field
std::string getID() { return field_id; };
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the flag to know if the field is homogeneous/contiguous
virtual bool isHomogeneous() { return homogeneous; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the flag to know if it is homogeneous
bool homogeneous{false};
/// the name of the group it was associated to
std::string group_name;
/// the name of the dumper it was associated to
std::string field_id;
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
#endif /* __AKANTU_DUMPER_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_filtered_connectivity.hh b/src/io/dumper/dumper_filtered_connectivity.hh
index 1dfe20e0d..bfda0e792 100644
--- a/src/io/dumper/dumper_filtered_connectivity.hh
+++ b/src/io/dumper/dumper_filtered_connectivity.hh
@@ -1,152 +1,152 @@
/**
* @file dumper_filtered_connectivity.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Mon Aug 17 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief FilteredConnectivities field
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "dumper_generic_elemental_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <class types>
class filtered_connectivity_field_iterator
: public element_iterator<types, filtered_connectivity_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef element_iterator<types, dumper::filtered_connectivity_field_iterator>
parent;
using return_type = typename types::return_type;
using field_type = typename types::field_type;
using array_iterator = typename types::array_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
filtered_connectivity_field_iterator(
const field_type & field, const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it, const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
return_type operator*() {
const Vector<UInt> & old_connect = *this->array_it;
Vector<UInt> new_connect(old_connect.size());
Array<UInt>::const_iterator<UInt> nodes_begin = nodal_filter->begin();
Array<UInt>::const_iterator<UInt> nodes_end = nodal_filter->end();
for (UInt i(0); i < old_connect.size(); ++i) {
Array<UInt>::const_iterator<UInt> new_id =
std::find(nodes_begin, nodes_end, old_connect(i));
if (new_id == nodes_end)
AKANTU_EXCEPTION("Node not found in the filter!");
new_connect(i) = new_id - nodes_begin;
}
return new_connect;
}
void setNodalFilter(const Array<UInt> & new_nodal_filter) {
nodal_filter = &new_nodal_filter;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Array<UInt> * nodal_filter;
};
/* -------------------------------------------------------------------------- */
class FilteredConnectivityField
: public GenericElementalField<SingleType<UInt, Vector, true>,
filtered_connectivity_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef SingleType<UInt, Vector, true> types;
using iterator = filtered_connectivity_field_iterator<types>;
using field_type = types::field_type;
typedef GenericElementalField<types, filtered_connectivity_field_iterator>
parent;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FilteredConnectivityField(const field_type & field,
const Array<UInt> & nodal_filter,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: parent(field, spatial_dimension, ghost_type, element_kind),
nodal_filter(nodal_filter) {}
~FilteredConnectivityField() override {
// since the field is created in registerFilteredMesh it is destroyed here
delete const_cast<field_type *>(&this->field);
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
iterator begin() override {
iterator it = parent::begin();
it.setNodalFilter(nodal_filter);
return it;
}
iterator end() override {
iterator it = parent::end();
it.setNodalFilter(nodal_filter);
return it;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Array<UInt> & nodal_filter;
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
/* -------------------------------------------------------------------------- */
diff --git a/src/io/dumper/dumper_generic_elemental_field.hh b/src/io/dumper/dumper_generic_elemental_field.hh
index bf532fb86..f616aa8b7 100644
--- a/src/io/dumper/dumper_generic_elemental_field.hh
+++ b/src/io/dumper/dumper_generic_elemental_field.hh
@@ -1,225 +1,225 @@
/**
* @file dumper_generic_elemental_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Wed Nov 08 2017
*
* @brief Generic interface for elemental fields
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH__
#define __AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_element_iterator.hh"
#include "dumper_field.hh"
#include "dumper_homogenizing_field.hh"
#include "element_type_map_filter.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <class _types, template <class> class iterator_type>
class GenericElementalField : public Field {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
// check dumper_type_traits.hh for additional information over these types
using types = _types;
using data_type = typename types::data_type;
using it_type = typename types::it_type;
using field_type = typename types::field_type;
using array_type = typename types::array_type;
using array_iterator = typename types::array_iterator;
using field_type_iterator = typename field_type::type_iterator;
using iterator = iterator_type<types>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GenericElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: field(field), spatial_dimension(spatial_dimension),
ghost_type(ghost_type), element_kind(element_kind) {
this->checkHomogeneity();
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the number of components of the hosted field
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) override {
return this->field.getNbComponents(dim, ghost_type, kind);
};
/// return the size of the contained data: i.e. the number of elements ?
virtual UInt size() {
checkHomogeneity();
return this->nb_total_element;
}
/// return the iohelper datatype to be dumped
iohelper::DataType getDataType() {
return iohelper::getDataType<data_type>();
}
protected:
/// return the number of entries per element
UInt getNbDataPerElem(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
if (!nb_data_per_elem.exists(type, ghost_type))
return field(type, ghost_type).getNbComponent();
return nb_data_per_elem(type, this->ghost_type);
}
/// check if the same quantity of data for all element types
void checkHomogeneity() override;
public:
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addElemDataField(id, *this);
};
/// for connection to a FieldCompute
inline Field * connect(FieldComputeProxy & proxy) override {
return proxy.connectToField(this);
}
/// for connection to a Homogenizer
inline ComputeFunctorInterface * connect(HomogenizerProxy & proxy) override {
return proxy.connectToField(this);
};
virtual iterator begin() {
field_type_iterator tit;
field_type_iterator end;
/// type iterators on the elemental field
tit = this->field.firstType(this->spatial_dimension, this->ghost_type,
this->element_kind);
end = this->field.lastType(this->spatial_dimension, this->ghost_type,
this->element_kind);
/// skip all types without data
ElementType type = *tit;
for (; tit != end && this->field(*tit, this->ghost_type).size() == 0;
++tit) {
}
type = *tit;
if (tit == end)
return this->end();
/// getting information for the field of the given type
const array_type & vect = this->field(type, this->ghost_type);
UInt nb_data_per_elem = this->getNbDataPerElem(type);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.size() * nb_component) / nb_data_per_elem;
/// define element-wise iterator
array_iterator it = vect.begin_reinterpret(nb_data_per_elem, size);
array_iterator it_end = vect.end_reinterpret(nb_data_per_elem, size);
/// define data iterator
iterator rit =
iterator(this->field, tit, end, it, it_end, this->ghost_type);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
virtual iterator end() {
field_type_iterator tit;
field_type_iterator end;
tit = this->field.firstType(this->spatial_dimension, this->ghost_type,
this->element_kind);
end = this->field.lastType(this->spatial_dimension, this->ghost_type,
this->element_kind);
ElementType type = *tit;
for (; tit != end; ++tit)
type = *tit;
const array_type & vect = this->field(type, this->ghost_type);
UInt nb_data = this->getNbDataPerElem(type);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.size() * nb_component) / nb_data;
array_iterator it = vect.end_reinterpret(nb_data, size);
iterator rit = iterator(this->field, end, end, it, it, this->ghost_type);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
virtual UInt getDim() {
if (this->homogeneous) {
field_type_iterator tit = this->field.firstType(
this->spatial_dimension, this->ghost_type, this->element_kind);
return this->getNbDataPerElem(*tit);
}
throw;
return 0;
}
void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data) override {
nb_data_per_elem = nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the ElementTypeMapArray embedded in the field
const field_type & field;
/// total number of elements
UInt nb_total_element;
/// the spatial dimension of the problem
UInt spatial_dimension;
/// whether this is a ghost field or not (for type selection)
GhostType ghost_type;
/// The element kind to operate on
ElementKind element_kind;
/// The number of data per element type
ElementTypeMap<UInt> nb_data_per_elem;
};
/* -------------------------------------------------------------------------- */
#include "dumper_generic_elemental_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
#endif /* __AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_generic_elemental_field_tmpl.hh b/src/io/dumper/dumper_generic_elemental_field_tmpl.hh
index 80b6a524a..f22b9be0f 100644
--- a/src/io/dumper/dumper_generic_elemental_field_tmpl.hh
+++ b/src/io/dumper/dumper_generic_elemental_field_tmpl.hh
@@ -1,69 +1,69 @@
/**
* @file dumper_generic_elemental_field_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the template functions of the ElementalField
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 <class types, template <class> class iterator>
void GenericElementalField<types, iterator>::checkHomogeneity() {
using field_type_iterator = typename field_type::type_iterator;
using array_type = typename field_type::array_type;
field_type_iterator tit;
field_type_iterator end;
tit = field.firstType(spatial_dimension, ghost_type, element_kind);
end = field.lastType(spatial_dimension, ghost_type, element_kind);
this->nb_total_element = 0;
UInt nb_comp = 0;
bool homogen = true;
if (tit != end) {
nb_comp = this->field(*tit, ghost_type).getNbComponent();
for (; tit != end; ++tit) {
const array_type & vect = this->field(*tit, ghost_type);
UInt nb_element = vect.size();
UInt nb_comp_cur = vect.getNbComponent();
if (homogen && nb_comp != nb_comp_cur)
homogen = false;
this->nb_total_element += nb_element;
// this->nb_data_per_elem(*tit,this->ghost_type) = nb_comp_cur;
}
if (!homogen)
nb_comp = 0;
}
this->homogeneous = homogen;
}
/* -------------------------------------------------------------------------- */
diff --git a/src/io/dumper/dumper_homogenizing_field.hh b/src/io/dumper/dumper_homogenizing_field.hh
index ba39b1986..c95bf75bb 100644
--- a/src/io/dumper/dumper_homogenizing_field.hh
+++ b/src/io/dumper/dumper_homogenizing_field.hh
@@ -1,216 +1,216 @@
/**
* @file dumper_homogenizing_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Tue Jul 14 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief description of field homogenizing field
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__
#define __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_compute.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <typename type>
inline type typeConverter(const type & input,
__attribute__((unused))
Vector<typename type::value_type> & res,
__attribute__((unused)) UInt nb_data) {
throw;
return input;
}
/* -------------------------------------------------------------------------- */
template <typename type>
inline Matrix<type> typeConverter(const Matrix<type> & input,
Vector<type> & res, UInt nb_data) {
Matrix<type> tmp(res.storage(), input.rows(), nb_data / input.rows());
Matrix<type> tmp2(tmp, true);
return tmp2;
}
/* -------------------------------------------------------------------------- */
template <typename type>
inline Vector<type> typeConverter(__attribute__((unused))
const Vector<type> & input,
__attribute__((unused)) Vector<type> & res,
__attribute__((unused)) UInt nb_data) {
return res;
}
/* -------------------------------------------------------------------------- */
template <typename type>
class AvgHomogenizingFunctor : public ComputeFunctor<type, type> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
using value_type = typename type::value_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
AvgHomogenizingFunctor(ElementTypeMap<UInt> & nb_datas) {
ElementTypeMap<UInt>::type_iterator tit = nb_datas.firstType();
ElementTypeMap<UInt>::type_iterator end = nb_datas.lastType();
nb_data = nb_datas(*tit);
for (; tit != end; ++tit)
if (nb_data != nb_datas(*tit))
throw;
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
type func(const type & d, Element /*global_index*/) override {
Vector<value_type> res(this->nb_data);
if (d.size() % this->nb_data)
throw;
UInt nb_to_average = d.size() / this->nb_data;
value_type * ptr = d.storage();
for (UInt i = 0; i < nb_to_average; ++i) {
Vector<value_type> tmp(ptr, this->nb_data);
res += tmp;
ptr += this->nb_data;
}
res /= nb_to_average;
return typeConverter(d, res, this->nb_data);
};
UInt getDim() override { return nb_data; };
UInt getNbComponent(UInt /*old_nb_comp*/) override { throw; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// The size of data: i.e. the size of the vector to be returned
UInt nb_data;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class HomogenizerProxy {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
HomogenizerProxy() = default;
public:
inline static ComputeFunctorInterface * createHomogenizer(Field & field);
template <typename T>
inline ComputeFunctorInterface * connectToField(T * field) {
ElementTypeMap<UInt> nb_components = field->getNbComponents();
using ret_type = typename T::types::return_type;
return this->instantiateHomogenizer<ret_type>(nb_components);
}
template <typename ret_type>
inline ComputeFunctorInterface *
instantiateHomogenizer(ElementTypeMap<UInt> & nb_components);
};
/* -------------------------------------------------------------------------- */
template <typename ret_type>
inline ComputeFunctorInterface *
HomogenizerProxy::instantiateHomogenizer(ElementTypeMap<UInt> & nb_components) {
using Homogenizer = dumper::AvgHomogenizingFunctor<ret_type>;
auto * foo = new Homogenizer(nb_components);
return foo;
}
template <>
inline ComputeFunctorInterface *
HomogenizerProxy::instantiateHomogenizer<Vector<iohelper::ElemType>>(
__attribute__((unused)) ElementTypeMap<UInt> & nb_components) {
throw;
return nullptr;
}
/* -------------------------------------------------------------------------- */
/// for connection to a FieldCompute
template <typename SubFieldCompute, typename return_type>
inline ComputeFunctorInterface *
FieldCompute<SubFieldCompute, return_type>::connect(HomogenizerProxy & proxy) {
return proxy.connectToField(this);
}
/* -------------------------------------------------------------------------- */
inline ComputeFunctorInterface *
HomogenizerProxy::createHomogenizer(Field & field) {
HomogenizerProxy homogenizer_proxy;
return field.connect(homogenizer_proxy);
}
/* -------------------------------------------------------------------------- */
// inline ComputeFunctorInterface & createHomogenizer(Field & field){
// HomogenizerProxy::createHomogenizer(field);
// throw;
// ComputeFunctorInterface * ptr = NULL;
// return *ptr;
// }
// /* --------------------------------------------------------------------------
// */
__END_AKANTU_DUMPER__
} // namespace akantu
#endif /* __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_internal_material_field.hh b/src/io/dumper/dumper_internal_material_field.hh
index 26924dda3..c9410ace0 100644
--- a/src/io/dumper/dumper_internal_material_field.hh
+++ b/src/io/dumper/dumper_internal_material_field.hh
@@ -1,73 +1,72 @@
/**
* @file dumper_internal_material_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Sep 17 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief description of material internal field
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH__
#define __AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_quadrature_point_iterator.hh"
#ifdef AKANTU_IGFEM
#include "dumper_igfem_material_internal_field.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <typename T, bool filtered = false>
class InternalMaterialField
: public GenericElementalField<SingleType<T, Vector, filtered>,
quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using types = SingleType<T, Vector, filtered>;
using parent = GenericElementalField<types, quadrature_point_iterator>;
using field_type = typename types::field_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
InternalMaterialField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: parent(field, spatial_dimension, ghost_type, element_kind) {}
};
__END_AKANTU_DUMPER__
} // akantu
#endif /* __AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_iohelper.cc b/src/io/dumper/dumper_iohelper.cc
index ce23d1089..d4c9443c0 100644
--- a/src/io/dumper/dumper_iohelper.cc
+++ b/src/io/dumper/dumper_iohelper.cc
@@ -1,318 +1,317 @@
/**
* @file dumper_iohelper.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Thu Sep 17 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief implementation of DumperIOHelper
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <io_helper.hh>
#include "dumper_elemental_field.hh"
#include "dumper_filtered_connectivity.hh"
#include "dumper_iohelper.hh"
#include "dumper_nodal_field.hh"
#include "dumper_variable.hh"
#include "mesh.hh"
#if defined(AKANTU_IGFEM)
#include "dumper_igfem_connectivity.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DumperIOHelper::DumperIOHelper() = default;
/* -------------------------------------------------------------------------- */
DumperIOHelper::~DumperIOHelper() {
for (auto it = fields.begin(); it != fields.end(); ++it) {
delete it->second;
}
delete dumper;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setParallelContext(bool is_parallel) {
UInt whoami = Communicator::getStaticCommunicator().whoAmI();
UInt nb_proc = Communicator::getStaticCommunicator().getNbProc();
if (is_parallel)
dumper->setParallelContext(whoami, nb_proc);
else
dumper->setParallelContext(0, 1);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setDirectory(const std::string & directory) {
this->directory = directory;
dumper->setPrefix(directory);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setBaseName(const std::string & basename) {
filename = basename;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setTimeStep(Real time_step) {
if (!time_activated)
this->dumper->activateTimeDescFiles(time_step);
else
this->dumper->setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump() {
try {
dumper->dump(filename, count);
} catch (iohelper::IOHelperException & e) {
AKANTU_ERROR(
"I was not able to dump your data with a Dumper: " << e.what());
}
++count;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump(UInt step) {
this->count = step;
this->dump();
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump(Real current_time, UInt step) {
this->dumper->setCurrentTime(current_time);
this->dump(step);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerMesh(const Mesh & mesh, UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & element_kind) {
#if defined(AKANTU_IGFEM)
if (element_kind == _ek_igfem) {
registerField("connectivities",
new dumper::IGFEMConnectivityField(
mesh.getConnectivities(), spatial_dimension, ghost_type));
} else
#endif
registerField("connectivities",
new dumper::ElementalField<UInt>(mesh.getConnectivities(),
spatial_dimension,
ghost_type, element_kind));
registerField("positions", new dumper::NodalField<Real>(mesh.getNodes()));
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
const GhostType & ghost_type, const ElementKind & element_kind) {
auto * f_connectivities = new ElementTypeMapArrayFilter<UInt>(
mesh.getConnectivities(), elements_filter);
this->registerField("connectivities",
new dumper::FilteredConnectivityField(
*f_connectivities, nodes_filter, spatial_dimension,
ghost_type, element_kind));
this->registerField("positions", new dumper::NodalField<Real, true>(
mesh.getNodes(), 0, 0, &nodes_filter));
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerField(const std::string & field_id,
dumper::Field * field) {
auto it = fields.find(field_id);
if (it != fields.end()) {
AKANTU_DEBUG_WARNING(
"The field "
<< field_id << " is already registered in this Dumper. Field ignored.");
return;
}
fields[field_id] = field;
field->registerToDumper(field_id, *dumper);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::unRegisterField(const std::string & field_id) {
auto it = fields.find(field_id);
if (it == fields.end()) {
AKANTU_DEBUG_WARNING(
"The field " << field_id
<< " is not registered in this Dumper. Nothing to do.");
return;
}
delete it->second;
fields.erase(it);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerVariable(const std::string & variable_id,
dumper::VariableBase * variable) {
auto it = variables.find(variable_id);
if (it != variables.end()) {
AKANTU_DEBUG_WARNING(
"The Variable "
<< variable_id
<< " is already registered in this Dumper. Variable ignored.");
return;
}
variables[variable_id] = variable;
variable->registerToDumper(variable_id, *dumper);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::unRegisterVariable(const std::string & variable_id) {
auto it = variables.find(variable_id);
if (it == variables.end()) {
AKANTU_DEBUG_WARNING(
"The variable " << variable_id
<< " is not registered in this Dumper. Nothing to do.");
return;
}
delete it->second;
variables.erase(it);
}
/* -------------------------------------------------------------------------- */
template <ElementType type> iohelper::ElemType getIOHelperType() {
AKANTU_TO_IMPLEMENT();
return iohelper::MAX_ELEM_TYPE;
}
template <> iohelper::ElemType getIOHelperType<_point_1>() {
return iohelper::POINT_SET;
}
template <> iohelper::ElemType getIOHelperType<_segment_2>() {
return iohelper::LINE1;
}
template <> iohelper::ElemType getIOHelperType<_segment_3>() {
return iohelper::LINE2;
}
template <> iohelper::ElemType getIOHelperType<_triangle_3>() {
return iohelper::TRIANGLE1;
}
template <> iohelper::ElemType getIOHelperType<_triangle_6>() {
return iohelper::TRIANGLE2;
}
template <> iohelper::ElemType getIOHelperType<_quadrangle_4>() {
return iohelper::QUAD1;
}
template <> iohelper::ElemType getIOHelperType<_quadrangle_8>() {
return iohelper::QUAD2;
}
template <> iohelper::ElemType getIOHelperType<_tetrahedron_4>() {
return iohelper::TETRA1;
}
template <> iohelper::ElemType getIOHelperType<_tetrahedron_10>() {
return iohelper::TETRA2;
}
template <> iohelper::ElemType getIOHelperType<_hexahedron_8>() {
return iohelper::HEX1;
}
template <> iohelper::ElemType getIOHelperType<_hexahedron_20>() {
return iohelper::HEX2;
}
template <> iohelper::ElemType getIOHelperType<_pentahedron_6>() {
return iohelper::PRISM1;
}
template <> iohelper::ElemType getIOHelperType<_pentahedron_15>() {
return iohelper::PRISM2;
}
#if defined(AKANTU_COHESIVE_ELEMENT)
template <> iohelper::ElemType getIOHelperType<_cohesive_1d_2>() {
return iohelper::COH1D2;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_2d_4>() {
return iohelper::COH2D4;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_2d_6>() {
return iohelper::COH2D6;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_3d_6>() {
return iohelper::COH3D6;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_3d_12>() {
return iohelper::COH3D12;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_3d_8>() {
return iohelper::COH3D8;
}
// template <>
// iohelper::ElemType getIOHelperType<_cohesive_3d_16>() { return
// iohelper::COH3D16; }
#endif
#if defined(AKANTU_STRUCTURAL_MECHANICS)
template <> iohelper::ElemType getIOHelperType<_bernoulli_beam_2>() {
return iohelper::BEAM2;
}
template <> iohelper::ElemType getIOHelperType<_bernoulli_beam_3>() {
return iohelper::BEAM3;
}
#endif
/* -------------------------------------------------------------------------- */
UInt getIOHelperType(ElementType type) {
UInt ioh_type = iohelper::MAX_ELEM_TYPE;
#define GET_IOHELPER_TYPE(type) ioh_type = getIOHelperType<type>();
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_IOHELPER_TYPE);
#undef GET_IOHELPER_TYPE
return ioh_type;
}
/* -------------------------------------------------------------------------- */
} // akantu
namespace iohelper {
template <> DataType getDataType<akantu::NodeType>() { return _int; }
}
diff --git a/src/io/dumper/dumper_iohelper.hh b/src/io/dumper/dumper_iohelper.hh
index 862e79e98..f824215bd 100644
--- a/src/io/dumper/dumper_iohelper.hh
+++ b/src/io/dumper/dumper_iohelper.hh
@@ -1,159 +1,158 @@
/**
* @file dumper_iohelper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Sun Dec 03 2017
*
* @brief Define the akantu dumper interface for IOhelper dumpers
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_types.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPER_IOHELPER_HH__
#define __AKANTU_DUMPER_IOHELPER_HH__
/* -------------------------------------------------------------------------- */
namespace iohelper {
class Dumper;
}
namespace akantu {
UInt getIOHelperType(ElementType type);
namespace dumper {
class Field;
class VariableBase;
}
class Mesh;
class DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper();
virtual ~DumperIOHelper();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register a given Mesh for the current dumper
virtual void registerMesh(const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a filtered Mesh (provided filter lists) for the current dumper
virtual void
registerFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a Field object identified by name and provided by pointer
void registerField(const std::string & field_id, dumper::Field * field);
/// remove the Field identified by name from managed fields
void unRegisterField(const std::string & field_id);
/// register a VariableBase object identified by name and provided by pointer
void registerVariable(const std::string & variable_id,
dumper::VariableBase * variable);
/// remove a VariableBase identified by name from managed fields
void unRegisterVariable(const std::string & variable_id);
/// request dump: this calls IOHelper dump routine
virtual void dump();
/// request dump: this first set the current step and then calls IOHelper dump
/// routine
virtual void dump(UInt step);
/// request dump: this first set the current step and current time and then
/// calls IOHelper dump routine
virtual void dump(Real current_time, UInt step);
/// set the parallel context for IOHeper
virtual void setParallelContext(bool is_parallel);
/// set the directory where to generate the dumped files
virtual void setDirectory(const std::string & directory);
/// set the base name (needed by most IOHelper dumpers)
virtual void setBaseName(const std::string & basename);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// direct access to the iohelper::Dumper object
AKANTU_GET_MACRO(Dumper, *dumper, iohelper::Dumper &)
/// set the timestep of the iohelper::Dumper
void setTimeStep(Real time_step);
public:
/* ------------------------------------------------------------------------ */
/* Variable wrapper */
template <typename T, bool is_scal = std::is_arithmetic<T>::value>
class Variable;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// internal iohelper::Dumper
iohelper::Dumper * dumper;
using Fields = std::map<std::string, dumper::Field *>;
using Variables = std::map<std::string, dumper::VariableBase *>;
/// list of registered fields to dump
Fields fields;
Variables variables;
/// dump counter
UInt count{0};
/// directory name
std::string directory;
/// filename prefix
std::string filename;
/// is time tracking activated in the dumper
bool time_activated{false};
};
} // akantu
#endif /* __AKANTU_DUMPER_IOHELPER_HH__ */
diff --git a/src/io/dumper/dumper_iohelper_paraview.cc b/src/io/dumper/dumper_iohelper_paraview.cc
index 4527586fa..fb8531321 100644
--- a/src/io/dumper/dumper_iohelper_paraview.cc
+++ b/src/io/dumper/dumper_iohelper_paraview.cc
@@ -1,67 +1,66 @@
/**
- * @file dumper_paraview.cc
+ * @file dumper_iohelper_paraview.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Mon Jan 22 2018
*
* @brief implementations of DumperParaview
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper_paraview.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
DumperParaview::DumperParaview(const std::string & filename,
const std::string & directory, bool parallel)
: DumperIOHelper() {
iohelper::DumperParaview * dumper_para = new iohelper::DumperParaview();
dumper = dumper_para;
setBaseName(filename);
this->setParallelContext(parallel);
dumper_para->setMode(iohelper::BASE64);
dumper_para->setPrefix(directory);
dumper_para->init();
}
/* -------------------------------------------------------------------------- */
DumperParaview::~DumperParaview() = default;
/* -------------------------------------------------------------------------- */
void DumperParaview::setBaseName(const std::string & basename) {
DumperIOHelper::setBaseName(basename);
static_cast<iohelper::DumperParaview *>(dumper)->setVTUSubDirectory(filename +
"-VTU");
}
} // namespace akantu
diff --git a/src/io/dumper/dumper_iohelper_paraview.hh b/src/io/dumper/dumper_iohelper_paraview.hh
index eac1bf120..312045070 100644
--- a/src/io/dumper/dumper_iohelper_paraview.hh
+++ b/src/io/dumper/dumper_iohelper_paraview.hh
@@ -1,72 +1,71 @@
/**
- * @file dumper_paraview.hh
+ * @file dumper_iohelper_paraview.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Mon Jan 22 2018
*
* @brief Dumper Paraview using IOHelper
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPER_PARAVIEW_HH__
#define __AKANTU_DUMPER_PARAVIEW_HH__
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class DumperParaview : public DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperParaview(const std::string & filename,
const std::string & directory = "./paraview",
bool parallel = true);
~DumperParaview() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
// void dump();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
void setBaseName(const std::string & basename) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // akantu
#endif /* __AKANTU_DUMPER_PARAVIEW_HH__ */
diff --git a/src/io/dumper/dumper_material_padders.hh b/src/io/dumper/dumper_material_padders.hh
index df66fb2cf..5c5501f53 100644
--- a/src/io/dumper/dumper_material_padders.hh
+++ b/src/io/dumper/dumper_material_padders.hh
@@ -1,289 +1,289 @@
/**
* @file dumper_material_padders.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Fri Mar 27 2015
+ * @date last modification: Wed Nov 29 2017
*
* @brief Material padders for plane stress/ plane strain
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_MATERIAL_PADDERS_HH__
#define __AKANTU_DUMPER_MATERIAL_PADDERS_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_padding_helper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
class MaterialFunctor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialFunctor(const SolidMechanicsModel & model)
: model(model), material_index(model.getMaterialByElement()),
nb_data_per_element("nb_data_per_element", model.getID(),
model.getMemoryID()),
spatial_dimension(model.getSpatialDimension()) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
/// return the material from the global element index
const Material & getMaterialFromGlobalIndex(Element global_index) {
UInt index = global_index.element;
UInt material_id = material_index(global_index.type)(index);
const Material & material = model.getMaterial(material_id);
return material;
}
/// return the type of the element from global index
ElementType getElementTypeFromGlobalIndex(Element global_index) {
return global_index.type;
}
protected:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// all material padders probably need access to solid mechanics model
const SolidMechanicsModel & model;
/// they also need an access to the map from global ids to material id and
/// local ids
const ElementTypeMapArray<UInt> & material_index;
/// the number of data per element
const ElementTypeMapArray<UInt> nb_data_per_element;
UInt spatial_dimension;
};
/* -------------------------------------------------------------------------- */
template <class T, class R>
class MaterialPadder : public MaterialFunctor,
public PadderGeneric<Vector<T>, R> {
public:
MaterialPadder(const SolidMechanicsModel & model) : MaterialFunctor(model) {}
};
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
class StressPadder : public MaterialPadder<Real, Matrix<Real>> {
public:
StressPadder(const SolidMechanicsModel & model)
: MaterialPadder<Real, Matrix<Real>>(model) {
this->setPadding(3, 3);
}
inline Matrix<Real> func(const Vector<Real> & in,
Element global_element_id) override {
UInt nrows = spatial_dimension;
UInt ncols = in.size() / nrows;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> stress = this->pad(in, nrows, ncols, nb_data);
const Material & material =
this->getMaterialFromGlobalIndex(global_element_id);
bool plane_strain = true;
if (spatial_dimension == 2)
plane_strain = !((bool)material.getParam("Plane_Stress"));
if (plane_strain) {
Real nu = material.getParam("nu");
for (UInt d = 0; d < nb_data; ++d) {
stress(2, 2 + 3 * d) =
nu * (stress(0, 0 + 3 * d) + stress(1, 1 + 3 * d));
}
}
return stress;
}
UInt getDim() override { return 9; };
UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
};
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
class StrainPadder : public MaterialFunctor,
public PadderGeneric<Matrix<Real>, Matrix<Real>> {
public:
StrainPadder(const SolidMechanicsModel & model) : MaterialFunctor(model) {
this->setPadding(3, 3);
}
inline Matrix<Real> func(const Matrix<Real> & in,
Element global_element_id) override {
UInt nrows = spatial_dimension;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> strain = this->pad(in, nb_data);
const Material & material =
this->getMaterialFromGlobalIndex(global_element_id);
bool plane_stress = material.getParam("Plane_Stress");
if (plane_stress) {
Real nu = material.getParam("nu");
for (UInt d = 0; d < nb_data; ++d) {
strain(2, 2 + 3 * d) =
nu / (nu - 1) * (strain(0, 0 + 3 * d) + strain(1, 1 + 3 * d));
}
}
return strain;
}
UInt getDim() override { return 9; };
UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
};
/* -------------------------------------------------------------------------- */
template <bool green_strain>
class ComputeStrain : public MaterialFunctor,
public ComputeFunctor<Vector<Real>, Matrix<Real>> {
public:
ComputeStrain(const SolidMechanicsModel & model) : MaterialFunctor(model) {}
inline Matrix<Real> func(const Vector<Real> & in,
Element /*global_element_id*/) override {
UInt nrows = spatial_dimension;
UInt ncols = in.size() / nrows;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> ret_all_strain(nrows, ncols);
Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
Tensor3<Real> all_strain(ret_all_strain.storage(), nrows, nrows, nb_data);
for (UInt d = 0; d < nb_data; ++d) {
Matrix<Real> grad_u = all_grad_u(d);
Matrix<Real> strain = all_strain(d);
if (spatial_dimension == 2) {
if (green_strain)
Material::gradUToGreenStrain<2>(grad_u, strain);
else
Material::gradUToEpsilon<2>(grad_u, strain);
} else if (spatial_dimension == 3) {
if (green_strain)
Material::gradUToGreenStrain<3>(grad_u, strain);
else
Material::gradUToEpsilon<3>(grad_u, strain);
}
}
return ret_all_strain;
}
UInt getDim() override { return spatial_dimension * spatial_dimension; };
UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
};
/* -------------------------------------------------------------------------- */
template <bool green_strain>
class ComputePrincipalStrain
: public MaterialFunctor,
public ComputeFunctor<Vector<Real>, Matrix<Real>> {
public:
ComputePrincipalStrain(const SolidMechanicsModel & model)
: MaterialFunctor(model) {}
inline Matrix<Real> func(const Vector<Real> & in,
Element /*global_element_id*/) override {
UInt nrows = spatial_dimension;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> ret_all_strain(nrows, nb_data);
Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
Matrix<Real> strain(nrows, nrows);
for (UInt d = 0; d < nb_data; ++d) {
Matrix<Real> grad_u = all_grad_u(d);
if (spatial_dimension == 2) {
if (green_strain)
Material::gradUToGreenStrain<2>(grad_u, strain);
else
Material::gradUToEpsilon<2>(grad_u, strain);
} else if (spatial_dimension == 3) {
if (green_strain)
Material::gradUToGreenStrain<3>(grad_u, strain);
else
Material::gradUToEpsilon<3>(grad_u, strain);
}
Vector<Real> principal_strain(ret_all_strain(d));
strain.eig(principal_strain);
}
return ret_all_strain;
}
UInt getDim() override { return spatial_dimension; };
UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
};
/* -------------------------------------------------------------------------- */
class ComputeVonMisesStress
: public MaterialFunctor,
public ComputeFunctor<Vector<Real>, Vector<Real>> {
public:
ComputeVonMisesStress(const SolidMechanicsModel & model)
: MaterialFunctor(model) {}
inline Vector<Real> func(const Vector<Real> & in,
Element /*global_element_id*/) override {
UInt nrows = spatial_dimension;
UInt nb_data = in.size() / (nrows * nrows);
Vector<Real> von_mises_stress(nb_data);
Matrix<Real> deviatoric_stress(3, 3);
for (UInt d = 0; d < nb_data; ++d) {
Matrix<Real> cauchy_stress(in.storage() + d * nrows * nrows, nrows,
nrows);
von_mises_stress(d) = Material::stressToVonMises(cauchy_stress);
}
return von_mises_stress;
}
UInt getDim() override { return 1; };
UInt getNbComponent(UInt /*old_nb_comp*/) override { return this->getDim(); };
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
#endif /* __AKANTU_DUMPER_MATERIAL_PADDERS_HH__ */
diff --git a/src/io/dumper/dumper_nodal_field.hh b/src/io/dumper/dumper_nodal_field.hh
index bda109fb0..1b3430204 100644
--- a/src/io/dumper/dumper_nodal_field.hh
+++ b/src/io/dumper/dumper_nodal_field.hh
@@ -1,249 +1,248 @@
/**
* @file dumper_nodal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Tue Jan 06 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Description of nodal fields
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_NODAL_FIELD_HH__
#define __AKANTU_DUMPER_NODAL_FIELD_HH__
#include "dumper_field.hh"
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
// This represents a iohelper compatible field
template <typename T, bool filtered = false, class Container = Array<T>,
class Filter = Array<UInt>>
class NodalField;
/* -------------------------------------------------------------------------- */
template <typename T, class Container, class Filter>
class NodalField<T, false, Container, Filter> : public dumper::Field {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
/// associated iterator with any nodal field (non filetered)
class iterator : public iohelper::iterator<T, iterator, Vector<T>> {
public:
iterator(T * vect, UInt offset, UInt n, UInt stride,
__attribute__((unused)) const UInt * filter = nullptr)
:
internal_it(vect),
offset(offset), n(n), stride(stride) {}
bool operator!=(const iterator & it) const override {
return internal_it != it.internal_it;
}
iterator & operator++() override {
internal_it += offset;
return *this;
};
Vector<T> operator*() override {
return Vector<T>(internal_it + stride, n);
};
private:
T * internal_it;
UInt offset, n, stride;
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
NodalField(const Container & field, UInt n = 0, UInt stride = 0,
__attribute__((unused)) const Filter * filter = nullptr)
:
field(field),
n(n), stride(stride), padding(0) {
AKANTU_DEBUG_ASSERT(filter == nullptr,
"Filter passed to unfiltered NodalField!");
if (n == 0) {
this->n = field.getNbComponent() - stride;
}
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addNodeDataField(id, *this);
}
inline iterator begin() {
return iterator(field.storage(), field.getNbComponent(), n, stride);
}
inline iterator end() {
return iterator(field.storage() + field.getNbComponent() * field.size(),
field.getNbComponent(), n, stride);
}
bool isHomogeneous() override { return true; }
void checkHomogeneity() override { this->homogeneous = true; }
virtual UInt getDim() {
if (this->padding)
return this->padding;
else
return n;
}
void setPadding(UInt padding) { this->padding = padding; }
UInt size() { return field.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Container & field;
UInt n, stride;
UInt padding;
};
/* -------------------------------------------------------------------------- */
template <typename T, class Container, class Filter>
class NodalField<T, true, Container, Filter> : public dumper::Field {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
class iterator : public iohelper::iterator<T, iterator, Vector<T>> {
public:
iterator(T * const vect, UInt _offset, UInt _n, UInt _stride,
const UInt * filter)
:
internal_it(vect),
offset(_offset), n(_n), stride(_stride), filter(filter) {}
bool operator!=(const iterator & it) const override {
return filter != it.filter;
}
iterator & operator++() override {
++filter;
return *this;
}
Vector<T> operator*() override {
return Vector<T>(internal_it + *(filter)*offset + stride, n);
}
private:
T * const internal_it;
UInt offset, n, stride;
const UInt * filter;
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
NodalField(const Container & _field, UInt _n = 0, UInt _stride = 0,
const Filter * filter = NULL)
: field(_field), n(_n), stride(_stride), filter(filter), padding(0) {
AKANTU_DEBUG_ASSERT(this->filter != nullptr,
"No filter passed to filtered NodalField!");
AKANTU_DEBUG_ASSERT(this->filter->getNbComponent() == 1,
"Multi-component filter given to NodalField ("
<< this->filter->getNbComponent()
<< " components detected, sould be 1");
if (n == 0) {
this->n = field.getNbComponent() - stride;
}
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addNodeDataField(id, *this);
}
inline iterator begin() {
return iterator(field.storage(), field.getNbComponent(), n, stride,
filter->storage());
}
inline iterator end() {
return iterator(field.storage(), field.getNbComponent(), n, stride,
filter->storage() + filter->size());
}
bool isHomogeneous() override { return true; }
void checkHomogeneity() override { this->homogeneous = true; }
virtual UInt getDim() {
if (this->padding)
return this->padding;
else
return n;
}
void setPadding(UInt padding) { this->padding = padding; }
UInt size() { return filter->size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Container & field;
UInt n, stride;
const Filter * filter;
UInt padding;
};
__END_AKANTU_DUMPER__
} // akantu
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_DUMPER_NODAL_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_padding_helper.hh b/src/io/dumper/dumper_padding_helper.hh
index 5a9f75fc4..5875ebe35 100644
--- a/src/io/dumper/dumper_padding_helper.hh
+++ b/src/io/dumper/dumper_padding_helper.hh
@@ -1,132 +1,132 @@
/**
* @file dumper_padding_helper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Mon Jun 19 2017
*
* @brief Padding helper for field iterators
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_PADDING_HELPER_HH__
#define __AKANTU_DUMPER_PADDING_HELPER_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_compute.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
class PadderInterface {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PadderInterface() {
padding_m = 0;
padding_n = 0;
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void setPadding(UInt m, UInt n = 0) {
padding_m = m;
padding_n = n;
}
virtual UInt getPaddedDim(UInt nb_data) { return nb_data; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
/// padding informations
UInt padding_n, padding_m;
};
/* -------------------------------------------------------------------------- */
template <class input_type, class output_type>
class PadderGeneric : public ComputeFunctor<input_type, output_type>,
public PadderInterface {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PadderGeneric() : PadderInterface() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline output_type pad(const input_type & in,
__attribute__((unused)) UInt nb_data) {
return in; // trick due to the fact that IOHelper padds the vectors (avoid a
// copy of data)
}
};
/* -------------------------------------------------------------------------- */
template <class T>
class PadderGeneric<Vector<T>, Matrix<T>>
: public ComputeFunctor<Vector<T>, Matrix<T>>, public PadderInterface {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
inline Matrix<T> pad(const Vector<T> & _in, UInt nrows, UInt ncols,
UInt nb_data) {
Matrix<T> in(_in.storage(), nrows, ncols);
if (padding_m <= nrows && padding_n * nb_data <= ncols)
return in;
else {
Matrix<T> ret(padding_m, padding_n * nb_data);
UInt nb_cols_per_data = in.cols() / nb_data;
for (UInt d = 0; d < nb_data; ++d)
for (UInt i = 0; i < in.rows(); ++i)
for (UInt j = 0; j < nb_cols_per_data; ++j)
ret(i, j + d * padding_n) = in(i, j + d * nb_cols_per_data);
return ret;
}
}
};
/* -------------------------------------------------------------------------- */
} // akantu
__END_AKANTU_DUMPER__
#endif /* __AKANTU_DUMPER_PADDING_HELPER_HH__ */
diff --git a/src/io/dumper/dumper_quadrature_point_iterator.hh b/src/io/dumper/dumper_quadrature_point_iterator.hh
index 52156376f..dc970f2e2 100644
--- a/src/io/dumper/dumper_quadrature_point_iterator.hh
+++ b/src/io/dumper/dumper_quadrature_point_iterator.hh
@@ -1,74 +1,74 @@
/**
* @file dumper_quadrature_point_iterator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Tue Sep 02 2014
- * @date last modification: Thu Sep 17 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Nov 08 2017
*
* @brief Description of quadrature point iterator
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH__
#define __AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_elemental_field.hh"
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <typename types>
class quadrature_point_iterator
: public element_iterator<types, quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using parent = element_iterator<types, dumper::quadrature_point_iterator>;
using data_type = typename types::data_type;
using return_type = typename types::return_type;
using field_type = typename types::field_type;
using array_iterator = typename types::array_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
quadrature_point_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
return_type operator*() { return *this->array_it; }
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // namespace akantu
#endif /* __AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH__ */
diff --git a/src/io/dumper/dumper_text.cc b/src/io/dumper/dumper_text.cc
index ece87f179..acd6603e4 100644
--- a/src/io/dumper/dumper_text.cc
+++ b/src/io/dumper/dumper_text.cc
@@ -1,113 +1,112 @@
/**
* @file dumper_text.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Tue Nov 07 2017
*
* @brief implementation of text dumper
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_text.hh"
#include "communicator.hh"
#include "dumper_nodal_field.hh"
#include "mesh.hh"
#include <io_helper.hh>
namespace akantu {
/* -------------------------------------------------------------------------- */
DumperText::DumperText(const std::string & basename,
iohelper::TextDumpMode mode, bool parallel)
: DumperIOHelper() {
AKANTU_DEBUG_IN();
iohelper::DumperText * dumper_text = new iohelper::DumperText(mode);
this->dumper = dumper_text;
this->setBaseName(basename);
this->setParallelContext(parallel);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DumperText::registerMesh(const Mesh & mesh,
__attribute__((unused)) UInt spatial_dimension,
__attribute__((unused))
const GhostType & ghost_type,
__attribute__((unused))
const ElementKind & element_kind) {
registerField("position", new dumper::NodalField<Real>(mesh.getNodes()));
// in parallel we need node type
UInt nb_proc = mesh.getCommunicator().getNbProc();
if (nb_proc > 1) {
registerField("nodes_type",
new dumper::NodalField<NodeType>(mesh.getNodesType()));
}
}
/* -------------------------------------------------------------------------- */
void DumperText::registerFilteredMesh(
const Mesh & mesh,
__attribute__((unused)) const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
__attribute__((unused)) UInt spatial_dimension,
__attribute__((unused)) const GhostType & ghost_type,
__attribute__((unused)) const ElementKind & element_kind) {
registerField("position", new dumper::NodalField<Real, true>(
mesh.getNodes(), 0, 0, &nodes_filter));
// in parallel we need node type
UInt nb_proc = mesh.getCommunicator().getNbProc();
if (nb_proc > 1) {
registerField("nodes_type", new dumper::NodalField<NodeType, true>(
mesh.getNodesType(), 0, 0, &nodes_filter));
}
}
/* -------------------------------------------------------------------------- */
void DumperText::setBaseName(const std::string & basename) {
AKANTU_DEBUG_IN();
DumperIOHelper::setBaseName(basename);
static_cast<iohelper::DumperText *>(this->dumper)
->setDataSubDirectory(this->filename + "-DataFiles");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DumperText::setPrecision(UInt prec) {
AKANTU_DEBUG_IN();
static_cast<iohelper::DumperText *>(this->dumper)->setPrecision(prec);
AKANTU_DEBUG_OUT();
}
} // akantu
diff --git a/src/io/dumper/dumper_text.hh b/src/io/dumper/dumper_text.hh
index d8e253b31..e7d1ce990 100644
--- a/src/io/dumper/dumper_text.hh
+++ b/src/io/dumper/dumper_text.hh
@@ -1,88 +1,87 @@
/**
* @file dumper_text.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief to dump into a text file
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPER_TEXT_HH__
#define __AKANTU_DUMPER_TEXT_HH__
/* -------------------------------------------------------------------------- */
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DumperText : public DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperText(const std::string & basename = "dumper_text",
iohelper::TextDumpMode mode = iohelper::_tdm_space,
bool parallel = true);
~DumperText() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void
registerMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) override;
void registerFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) override;
void setBaseName(const std::string & basename) override;
private:
void registerNodeTypeField();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
void setPrecision(UInt prec);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // akantu
#endif /* __AKANTU_DUMPER_TEXT_HH__ */
diff --git a/src/io/dumper/dumper_type_traits.hh b/src/io/dumper/dumper_type_traits.hh
index e2f8edf3c..c7f688a8a 100644
--- a/src/io/dumper/dumper_type_traits.hh
+++ b/src/io/dumper/dumper_type_traits.hh
@@ -1,90 +1,90 @@
/**
* @file dumper_type_traits.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Mon Sep 21 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Type traits for field properties
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_DUMPER_TYPE_TRAITS_HH__
#define __AKANTU_DUMPER_TYPE_TRAITS_HH__
/* -------------------------------------------------------------------------- */
#include "element_type_map.hh"
#include "element_type_map_filter.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <class data, class ret, class field> struct TypeTraits {
//! the stored data (real, int, uint, ...)
using data_type = data;
//! the type returned by the operator *
using return_type = ret;
//! the field type (ElementTypeMap or ElementTypeMapFilter)
using field_type = field;
//! the type over which we iterate
using it_type = typename field_type::type;
//! the type of array (Array<T> or ArrayFilter<T>)
using array_type = typename field_type::array_type;
//! the iterator over the array
using array_iterator = typename array_type::const_vector_iterator;
};
/* -------------------------------------------------------------------------- */
// specialization for the case in which input and output types are the same
template <class T, template <class> class ret, bool filtered>
struct SingleType : public TypeTraits<T, ret<T>, ElementTypeMapArray<T>> {};
/* -------------------------------------------------------------------------- */
// same as before but for filtered data
template <class T, template <class> class ret>
struct SingleType<T, ret, true>
: public TypeTraits<T, ret<T>, ElementTypeMapArrayFilter<T>> {};
/* -------------------------------------------------------------------------- */
// specialization for the case in which input and output types are different
template <class it_type, class data_type, template <class> class ret,
bool filtered>
struct DualType : public TypeTraits<data_type, ret<data_type>,
ElementTypeMapArray<it_type>> {};
/* -------------------------------------------------------------------------- */
// same as before but for filtered data
template <class it_type, class data_type, template <class> class ret>
struct DualType<it_type, data_type, ret, true>
: public TypeTraits<data_type, ret<data_type>,
ElementTypeMapArrayFilter<it_type>> {};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_DUMPER_TYPE_TRAITS_HH__ */
diff --git a/src/io/dumper/dumper_variable.hh b/src/io/dumper/dumper_variable.hh
index 5d322273b..7ff1228b6 100644
--- a/src/io/dumper/dumper_variable.hh
+++ b/src/io/dumper/dumper_variable.hh
@@ -1,119 +1,120 @@
/**
* @file dumper_variable.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Jun 04 2013
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief template of variable
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH__
#define __AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumper {
/* --------------------------------------------------------------------------
*/
/// Variable interface
class VariableBase {
public:
VariableBase() = default;
virtual ~VariableBase() = default;
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) = 0;
};
/* --------------------------------------------------------------------------
*/
template <typename T, bool is_scal = std::is_arithmetic<T>::value>
class Variable : public VariableBase {
public:
Variable(const T & t) : vari(t) {}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addVariable(id, *this);
}
const T & operator[](UInt i) const { return vari[i]; }
UInt getDim() { return vari.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const T & vari;
};
/* --------------------------------------------------------------------------
*/
template <typename T> class Variable<Vector<T>, false> : public VariableBase {
public:
Variable(const Vector<T> & t) : vari(t) {}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addVariable(id, *this);
}
const T & operator[](UInt i) const { return vari[i]; }
UInt getDim() { return vari.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const Vector<T> & vari;
};
/* --------------------------------------------------------------------------
*/
template <typename T> class Variable<T, true> : public VariableBase {
public:
Variable(const T & t) : vari(t) {}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addVariable(id, *this);
}
const T & operator[](__attribute__((unused)) UInt i) const { return vari; }
UInt getDim() { return 1; }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const T & vari;
};
} // namespace dumper
} // namespace akantu
#endif /* __AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH__ */
diff --git a/src/io/mesh_io.cc b/src/io/mesh_io.cc
index cdc56a716..23e96bb8a 100644
--- a/src/io/mesh_io.cc
+++ b/src/io/mesh_io.cc
@@ -1,148 +1,147 @@
/**
* @file mesh_io.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Jun 01 2015
+ * @date last modification: Thu Feb 01 2018
*
* @brief common part for all mesh io classes
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
#include "aka_common.hh"
#include "aka_iterators.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIO::MeshIO() {
canReadSurface = false;
canReadExtendedData = false;
}
/* -------------------------------------------------------------------------- */
MeshIO::~MeshIO() = default;
/* -------------------------------------------------------------------------- */
std::unique_ptr<MeshIO> MeshIO::getMeshIO(const std::string & filename,
const MeshIOType & type) {
MeshIOType t = type;
if (type == _miot_auto) {
std::string::size_type idx = filename.rfind('.');
std::string ext;
if (idx != std::string::npos) {
ext = filename.substr(idx + 1);
}
if (ext == "msh") {
t = _miot_gmsh;
} else if (ext == "diana") {
t = _miot_diana;
} else if (ext == "inp") {
t = _miot_abaqus;
} else
AKANTU_EXCEPTION("Cannot guess the type of file of "
<< filename << " (ext " << ext << "). "
<< "Please provide the MeshIOType to the read function");
}
switch (t) {
case _miot_gmsh:
return std::make_unique<MeshIOMSH>();
#if defined(AKANTU_STRUCTURAL_MECHANICS)
case _miot_gmsh_struct:
return std::make_unique<MeshIOMSHStruct>();
#endif
case _miot_diana:
return std::make_unique<MeshIODiana>();
case _miot_abaqus:
return std::make_unique<MeshIOAbaqus>();
default:
return nullptr;
}
}
/* -------------------------------------------------------------------------- */
void MeshIO::read(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
std::unique_ptr<MeshIO> mesh_io = getMeshIO(filename, type);
mesh_io->read(filename, mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIO::write(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
std::unique_ptr<MeshIO> mesh_io = getMeshIO(filename, type);
mesh_io->write(filename, mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIO::constructPhysicalNames(const std::string & tag_name, Mesh & mesh) {
if (!phys_name_map.empty()) {
for (Mesh::type_iterator type_it = mesh.firstType();
type_it != mesh.lastType(); ++type_it) {
auto & name_vec =
mesh.getDataPointer<std::string>("physical_names", *type_it);
const auto & tags_vec = mesh.getData<UInt>(tag_name, *type_it);
for (auto pair : zip(tags_vec, name_vec)) {
auto tag = std::get<0>(pair);
auto & name = std::get<1>(pair);
auto map_it = phys_name_map.find(tag);
if (map_it == phys_name_map.end()) {
std::stringstream sstm;
sstm << tag;
name = sstm.str();
} else {
name = map_it->second;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void MeshIO::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
if (phys_name_map.size()) {
stream << space << "Physical map:" << std::endl;
for (auto & pair : phys_name_map) {
stream << space << pair.first << ": " << pair.second << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/mesh_io.hh b/src/io/mesh_io.hh
index 5e4860613..5ff6aa2f8 100644
--- a/src/io/mesh_io.hh
+++ b/src/io/mesh_io.hh
@@ -1,118 +1,117 @@
/**
* @file mesh_io.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Jun 01 2015
+ * @date last modification: Wed Aug 09 2017
*
* @brief interface of a mesh io class, reader and writer
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_IO_HH__
#define __AKANTU_MESH_IO_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIO();
virtual ~MeshIO();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void read(const std::string & filename, Mesh & mesh, const MeshIOType & type);
void write(const std::string & filename, Mesh & mesh,
const MeshIOType & type);
/// read a mesh from the file
virtual void read(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) Mesh & mesh) {}
/// write a mesh to a file
virtual void write(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) const Mesh & mesh) {}
/// function to request the manual construction of the physical names maps
virtual void constructPhysicalNames(const std::string & tag_name,
Mesh & mesh);
/// method to permit to be printed to a generic stream
virtual void printself(std::ostream & stream, int indent = 0) const;
/// static contruction of a meshio object
static std::unique_ptr<MeshIO> getMeshIO(const std::string & filename,
const MeshIOType & type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
std::map<UInt, std::string> & getPhysicalNameMap() { return phys_name_map; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
bool canReadSurface;
bool canReadExtendedData;
/// correspondance between a tag and physical names (if applicable)
std::map<UInt, std::string> phys_name_map;
};
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream, const MeshIO & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "mesh_io_abaqus.hh"
#include "mesh_io_diana.hh"
#include "mesh_io_msh.hh"
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "mesh_io_msh_struct.hh"
#endif
#endif /* __AKANTU_MESH_IO_HH__ */
diff --git a/src/io/mesh_io/mesh_io_abaqus.cc b/src/io/mesh_io/mesh_io_abaqus.cc
index a9f7714b4..fd16133b7 100644
--- a/src/io/mesh_io/mesh_io_abaqus.cc
+++ b/src/io/mesh_io/mesh_io_abaqus.cc
@@ -1,475 +1,475 @@
/**
* @file mesh_io_abaqus.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Fri Dec 11 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief read a mesh from an abaqus input file
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// std library header files
#include <fstream>
// akantu header files
#include "mesh.hh"
#include "mesh_io_abaqus.hh"
#include "mesh_utils.hh"
#include "element_group.hh"
#include "node_group.hh"
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/phoenix.hpp>
#include <boost/spirit/include/qi.hpp>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIOAbaqus::MeshIOAbaqus() = default;
/* -------------------------------------------------------------------------- */
MeshIOAbaqus::~MeshIOAbaqus() = default;
/* -------------------------------------------------------------------------- */
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace ascii = boost::spirit::ascii;
namespace lbs = boost::spirit::qi::labels;
namespace phx = boost::phoenix;
/* -------------------------------------------------------------------------- */
void element_read(Mesh & mesh, const ElementType & type, UInt id,
const std::vector<Int> & conn,
const std::map<UInt, UInt> & nodes_mapping,
std::map<UInt, Element> & elements_mapping) {
Vector<UInt> tmp_conn(Mesh::getNbNodesPerElement(type));
AKANTU_DEBUG_ASSERT(conn.size() == tmp_conn.size(),
"The nodes in the Abaqus file have too many coordinates"
<< " for the mesh you try to fill.");
mesh.addConnectivityType(type);
Array<UInt> & connectivity = mesh.getConnectivity(type);
UInt i = 0;
for (auto it = conn.begin(); it != conn.end(); ++it) {
auto nit = nodes_mapping.find(*it);
AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
"There is an unknown node in the connectivity.");
tmp_conn[i++] = nit->second;
}
Element el{type, connectivity.size(), _not_ghost};
elements_mapping[id] = el;
connectivity.push_back(tmp_conn);
}
void node_read(Mesh & mesh, UInt id, const std::vector<Real> & pos,
std::map<UInt, UInt> & nodes_mapping) {
Vector<Real> tmp_pos(mesh.getSpatialDimension());
UInt i = 0;
for (auto it = pos.begin(); it != pos.end() || i < mesh.getSpatialDimension();
++it)
tmp_pos[i++] = *it;
nodes_mapping[id] = mesh.getNbNodes();
mesh.getNodes().push_back(tmp_pos);
}
/* ------------------------------------------------------------------------ */
void add_element_to_group(ElementGroup * el_grp, UInt element,
const std::map<UInt, Element> & elements_mapping) {
auto eit = elements_mapping.find(element);
AKANTU_DEBUG_ASSERT(eit != elements_mapping.end(),
"There is an unknown element ("
<< element << ") in the in the ELSET "
<< el_grp->getName() << ".");
el_grp->add(eit->second, true, false);
}
ElementGroup * element_group_create(Mesh & mesh, const ID & name) {
auto eg_it = mesh.element_group_find(name);
if (eg_it != mesh.element_group_end()) {
return eg_it->second;
} else {
return &mesh.createElementGroup(name, _all_dimensions);
}
}
NodeGroup * node_group_create(Mesh & mesh, const ID & name) {
auto ng_it = mesh.node_group_find(name);
if (ng_it != mesh.node_group_end()) {
return ng_it->second;
} else {
return &mesh.createNodeGroup(name, mesh.getSpatialDimension());
}
}
void add_node_to_group(NodeGroup * node_grp, UInt node,
const std::map<UInt, UInt> & nodes_mapping) {
auto nit = nodes_mapping.find(node);
AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
"There is an unknown node in the in the NSET "
<< node_grp->getName() << ".");
node_grp->add(nit->second, false);
}
void optimize_group(NodeGroup * grp) { grp->optimize(); }
void optimize_element_group(ElementGroup * grp) { grp->optimize(); }
/* -------------------------------------------------------------------------- */
template <class Iterator> struct AbaqusSkipper : qi::grammar<Iterator> {
AbaqusSkipper() : AbaqusSkipper::base_type(skip, "abaqus_skipper") {
/* clang-format off */
skip
= (ascii::space - spirit::eol)
| "**" >> *(qi::char_ - spirit::eol) >> spirit::eol
;
/* clang-format on */
}
qi::rule<Iterator> skip;
};
/* -------------------------------------------------------------------------- */
template <class Iterator, typename Skipper = AbaqusSkipper<Iterator>>
struct AbaqusMeshGrammar : qi::grammar<Iterator, void(), Skipper> {
public:
AbaqusMeshGrammar(Mesh & mesh)
: AbaqusMeshGrammar::base_type(start, "abaqus_mesh_reader"), mesh(mesh) {
/* clang-format off */
start
= *(
(qi::char_('*')
> ( (qi::no_case[ qi::lit("node output") ] > any_section)
| (qi::no_case[ qi::lit("element output") ] > any_section)
| (qi::no_case[ qi::lit("node") ] > nodes)
| (qi::no_case[ qi::lit("element") ] > elements)
| (qi::no_case[ qi::lit("heading") ] > header)
| (qi::no_case[ qi::lit("elset") ] > elements_set)
| (qi::no_case[ qi::lit("nset") ] > nodes_set)
| (qi::no_case[ qi::lit("material") ] > material)
| (keyword > any_section)
)
)
| spirit::eol
)
;
header
= spirit::eol
> *any_line
;
nodes
= *(qi::char_(',') >> option)
>> spirit::eol
>> *( (qi::int_
> node_position) [ phx::bind(&node_read,
phx::ref(mesh),
lbs::_1,
lbs::_2,
phx::ref(abaqus_nodes_to_akantu)) ]
>> spirit::eol
)
;
elements
= (
( qi::char_(',') >> qi::no_case[qi::lit("type")] >> '='
>> abaqus_element_type [ lbs::_a = lbs::_1 ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> *( (qi::int_
> connectivity) [ phx::bind(&element_read,
phx::ref(mesh),
lbs::_a,
lbs::_1,
lbs::_2,
phx::cref(abaqus_nodes_to_akantu),
phx::ref(abaqus_elements_to_akantu)) ]
>> spirit::eol
)
;
elements_set
= (
(
( qi::char_(',') >> qi::no_case[ qi::lit("elset") ] >> '='
>> value [ lbs::_a = phx::bind<ElementGroup *>(&element_group_create,
phx::ref(mesh),
lbs::_1) ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> qi::skip
(qi::char_(',') | qi::space)
[ +(qi::int_ [ phx::bind(&add_element_to_group,
lbs::_a,
lbs::_1,
phx::cref(abaqus_elements_to_akantu)
)
]
)
]
) [ phx::bind(&optimize_element_group, lbs::_a) ]
;
nodes_set
= (
(
( qi::char_(',')
>> qi::no_case[ qi::lit("nset") ] >> '='
>> value [ lbs::_a = phx::bind<NodeGroup *>(&node_group_create, phx::ref(mesh), lbs::_1) ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> qi::skip
(qi::char_(',') | qi::space)
[ +(qi::int_ [ phx::bind(&add_node_to_group,
lbs::_a,
lbs::_1,
phx::cref(abaqus_nodes_to_akantu)
)
]
)
]
) [ phx::bind(&optimize_group, lbs::_a) ]
;
material
= (
( qi::char_(',') >> qi::no_case[ qi::lit("name") ] >> '='
>> value [ phx::push_back(phx::ref(material_names), lbs::_1) ]
)
^ *(qi::char_(',') >> option)
) >> spirit::eol;
;
node_position
= +(qi::char_(',') > real [ phx::push_back(lbs::_val, lbs::_1) ])
;
connectivity
= +(qi::char_(',') > qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ])
;
any_section
= *(qi::char_(',') >> option) > spirit::eol
> *any_line
;
any_line
= *(qi::char_ - spirit::eol - qi::char_('*')) >> spirit::eol
;
keyword
= qi::lexeme[ +(qi::char_ - (qi::char_('*') | spirit::eol)) ]
;
option
= key > -( '=' >> value );
key
= qi::char_("a-zA-Z_") >> *(qi::char_("a-zA-Z_0-9") | qi::char_('-'))
;
value
= key.alias()
;
BOOST_SPIRIT_DEBUG_NODE(start);
abaqus_element_type.add
#if defined(AKANTU_STRUCTURAL_MECHANICS)
("BE21" , _bernoulli_beam_2)
("BE31" , _bernoulli_beam_3)
#endif
("T3D2" , _segment_2) // Gmsh generates this elements
("T3D3" , _segment_3) // Gmsh generates this elements
("CPE3" , _triangle_3)
("CPS3" , _triangle_3)
("DC2D3" , _triangle_3)
("CPE6" , _triangle_6)
("CPS6" , _triangle_6)
("DC2D6" , _triangle_6)
("CPE4" , _quadrangle_4)
("CPS4" , _quadrangle_4)
("DC2D4" , _quadrangle_4)
("CPE8" , _quadrangle_8)
("CPS8" , _quadrangle_8)
("DC2D8" , _quadrangle_8)
("C3D4" , _tetrahedron_4)
("DC3D4" , _tetrahedron_4)
("C3D8" , _hexahedron_8)
("C3D8R" , _hexahedron_8)
("DC3D8" , _hexahedron_8)
("C3D10" , _tetrahedron_10)
("DC3D10", _tetrahedron_10);
#if !defined(AKANTU_NDEBUG) && defined(AKANTU_CORE_CXX_11)
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start .name("abaqus-start-rule");
connectivity .name("abaqus-connectivity");
node_position .name("abaqus-nodes-position");
nodes .name("abaqus-nodes");
any_section .name("abaqus-any_section");
header .name("abaqus-header");
material .name("abaqus-material");
elements .name("abaqus-elements");
elements_set .name("abaqus-elements-set");
nodes_set .name("abaqus-nodes-set");
key .name("abaqus-key");
value .name("abaqus-value");
option .name("abaqus-option");
keyword .name("abaqus-keyword");
any_line .name("abaqus-any-line");
abaqus_element_type.name("abaqus-element-type");
/* clang-format on */
}
public:
AKANTU_GET_MACRO(MaterialNames, material_names,
const std::vector<std::string> &);
/* ------------------------------------------------------------------------ */
/* Rules */
/* ------------------------------------------------------------------------ */
private:
qi::rule<Iterator, void(), Skipper> start;
qi::rule<Iterator, std::vector<int>(), Skipper> connectivity;
qi::rule<Iterator, std::vector<Real>(), Skipper> node_position;
qi::rule<Iterator, void(), Skipper> nodes, any_section, header, material;
qi::rule<Iterator, void(), qi::locals<ElementType>, Skipper> elements;
qi::rule<Iterator, void(), qi::locals<ElementGroup *>, Skipper> elements_set;
qi::rule<Iterator, void(), qi::locals<NodeGroup *>, Skipper> nodes_set;
qi::rule<Iterator, std::string(), Skipper> key, value, option, keyword,
any_line;
qi::real_parser<Real, qi::real_policies<Real>> real;
qi::symbols<char, ElementType> abaqus_element_type;
/* ------------------------------------------------------------------------ */
/* Mambers */
/* ------------------------------------------------------------------------ */
private:
/// reference to the mesh to read
Mesh & mesh;
/// correspondance between the numbering of nodes in the abaqus file and in
/// the akantu mesh
std::map<UInt, UInt> abaqus_nodes_to_akantu;
/// correspondance between the element number in the abaqus file and the
/// Element in the akantu mesh
std::map<UInt, Element> abaqus_elements_to_akantu;
/// list of the material names
std::vector<std::string> material_names;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
void MeshIOAbaqus::read(const std::string & filename, Mesh & mesh) {
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
std::ifstream infile;
infile.open(filename.c_str());
if (!infile.good()) {
AKANTU_ERROR("Cannot open file " << filename);
}
std::string storage; // We will read the contents here.
infile.unsetf(std::ios::skipws); // No white space skipping!
std::copy(std::istream_iterator<char>(infile), std::istream_iterator<char>(),
std::back_inserter(storage));
using iterator_t = std::string::const_iterator;
using skipper = AbaqusSkipper<iterator_t>;
using grammar = AbaqusMeshGrammar<iterator_t, skipper>;
grammar g(mesh);
skipper ws;
iterator_t iter = storage.begin();
iterator_t end = storage.end();
qi::phrase_parse(iter, end, g, ws);
MeshAccessor mesh_accessor(mesh);
for (auto & mat_name : g.getMaterialNames()) {
auto eg_it = mesh.element_group_find(mat_name);
auto & eg = *eg_it->second;
if (eg_it != mesh.element_group_end()) {
for (auto & type : eg.elementTypes()) {
Array<std::string> & abaqus_material =
mesh_accessor.getData<std::string>("abaqus_material", type);
for (auto elem : eg.getElements(type)) {
abaqus_material(elem) = mat_name;
}
}
}
}
mesh_accessor.setNbGlobalNodes(mesh.getNodes().size());
MeshUtils::fillElementToSubElementsData(mesh);
}
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_abaqus.hh b/src/io/mesh_io/mesh_io_abaqus.hh
index 5feea6314..305eb2d93 100644
--- a/src/io/mesh_io/mesh_io_abaqus.hh
+++ b/src/io/mesh_io/mesh_io_abaqus.hh
@@ -1,60 +1,59 @@
/**
* @file mesh_io_abaqus.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
- * @date last modification: Tue Jun 30 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief read a mesh from an abaqus input file
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_accessor.hh"
#include "mesh_io.hh"
#ifndef __AKANTU_MESH_IO_ABAQUS_HH__
#define __AKANTU_MESH_IO_ABAQUS_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
class MeshIOAbaqus : public MeshIO {
public:
MeshIOAbaqus();
~MeshIOAbaqus() override;
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
// virtual void write(const std::string & filename, const Mesh & mesh);
private:
/// correspondence between msh element types and akantu element types
std::map<std::string, ElementType> _abaqus_to_akantu_element_types;
};
} // akantu
#endif /* __AKANTU_MESH_IO_ABAQUS_HH__ */
diff --git a/src/io/mesh_io/mesh_io_diana.cc b/src/io/mesh_io/mesh_io_diana.cc
index 634226ac0..80a3bc957 100644
--- a/src/io/mesh_io/mesh_io_diana.cc
+++ b/src/io/mesh_io/mesh_io_diana.cc
@@ -1,602 +1,601 @@
/**
* @file mesh_io_diana.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
*
* @date creation: Sat Mar 26 2011
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief handles diana meshes
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_io_diana.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <string.h>
/* -------------------------------------------------------------------------- */
#include <stdio.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIODiana::MeshIODiana() {
canReadSurface = true;
canReadExtendedData = true;
_diana_to_akantu_element_types["T9TM"] = _triangle_3;
_diana_to_akantu_element_types["CT6CM"] = _triangle_6;
_diana_to_akantu_element_types["Q12TM"] = _quadrangle_4;
_diana_to_akantu_element_types["CQ8CM"] = _quadrangle_8;
_diana_to_akantu_element_types["TP18L"] = _pentahedron_6;
_diana_to_akantu_element_types["CTP45"] = _pentahedron_15;
_diana_to_akantu_element_types["TE12L"] = _tetrahedron_4;
_diana_to_akantu_element_types["HX24L"] = _hexahedron_8;
_diana_to_akantu_element_types["CHX60"] = _hexahedron_20;
_diana_to_akantu_mat_prop["YOUNG"] = "E";
_diana_to_akantu_mat_prop["DENSIT"] = "rho";
_diana_to_akantu_mat_prop["POISON"] = "nu";
std::map<std::string, ElementType>::iterator it;
for (it = _diana_to_akantu_element_types.begin();
it != _diana_to_akantu_element_types.end(); ++it) {
UInt nb_nodes = Mesh::getNbNodesPerElement(it->second);
auto * tmp = new UInt[nb_nodes];
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->second) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 8;
tmp[2] = 0;
tmp[3] = 6;
tmp[4] = 1;
tmp[5] = 7;
tmp[6] = 11;
tmp[7] = 9;
tmp[8] = 10;
tmp[9] = 5;
tmp[10] = 14;
tmp[11] = 3;
tmp[12] = 12;
tmp[13] = 4;
tmp[14] = 13;
break;
case _hexahedron_20:
tmp[0] = 5;
tmp[1] = 16;
tmp[2] = 4;
tmp[3] = 19;
tmp[4] = 7;
tmp[5] = 18;
tmp[6] = 6;
tmp[7] = 17;
tmp[8] = 13;
tmp[9] = 12;
tmp[10] = 15;
tmp[11] = 14;
tmp[12] = 1;
tmp[13] = 8;
tmp[14] = 0;
tmp[15] = 11;
tmp[16] = 3;
tmp[17] = 10;
tmp[18] = 2;
tmp[19] = 9;
break;
default:
// nothing to change
break;
}
_read_order[it->second] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIODiana::~MeshIODiana() = default;
/* -------------------------------------------------------------------------- */
inline void my_getline(std::ifstream & infile, std::string & line) {
std::getline(infile, line); // read the line
size_t pos = line.find('\r'); /// remove the extra \r if needed
line = line.substr(0, pos);
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::read(const std::string & filename, Mesh & mesh) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt first_node_number = std::numeric_limits<UInt>::max();
diana_element_number_to_elements.clear();
if (!infile.good()) {
AKANTU_ERROR("Cannot open file " << filename);
}
while (infile.good()) {
my_getline(infile, line);
/// read all nodes
if (line == "'COORDINATES'") {
line = readCoordinates(infile, mesh, first_node_number);
}
/// read all elements
if (line == "'ELEMENTS'") {
line = readElements(infile, mesh, first_node_number);
}
/// read the material properties and write a .dat file
if (line == "'MATERIALS'") {
line = readMaterial(infile, filename);
}
/// read the material properties and write a .dat file
if (line == "'GROUPS'") {
line = readGroups(infile, mesh, first_node_number);
}
}
infile.close();
mesh_accessor.setNbGlobalNodes(mesh.getNbNodes());
MeshUtils::fillElementToSubElementsData(mesh);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::write(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) const Mesh & mesh) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readCoordinates(std::ifstream & infile, Mesh & mesh,
UInt & first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
std::string line;
UInt index;
Vector<Real> coord(3);
do {
my_getline(infile, line);
if ("'ELEMENTS'" == line)
break;
std::stringstream sstr_node(line);
sstr_node >> index >> coord(0) >> coord(1) >> coord(2);
first_node_number = first_node_number < index ? first_node_number : index;
nodes.push_back(coord);
} while (true);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
UInt MeshIODiana::readInterval(std::stringstream & line,
std::set<UInt> & interval) {
UInt first;
line >> first;
if (line.fail()) {
return 0;
}
interval.insert(first);
UInt second;
int dash;
dash = line.get();
if (dash == '-') {
line >> second;
interval.insert(second);
return 2;
}
if (line.fail())
line.clear(std::ios::eofbit); // in case of get at end of the line
else
line.unget();
return 1;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readGroups(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
bool reading_nodes_group = false;
while (line != "'SUPPORTS'") {
if (line == "NODES") {
reading_nodes_group = true;
my_getline(infile, line);
}
if (line == "ELEMEN") {
reading_nodes_group = false;
my_getline(infile, line);
}
auto * str = new std::stringstream(line);
UInt id;
std::string name;
char c;
*str >> id >> name >> c;
auto * list_ids = new Array<UInt>(0, 1, name);
UInt s = 1;
bool end = false;
while (!end) {
while (!str->eof() && s != 0) {
std::set<UInt> interval;
s = readInterval(*str, interval);
auto it = interval.begin();
if (s == 1)
list_ids->push_back(*it);
if (s == 2) {
UInt first = *it;
++it;
UInt second = *it;
for (UInt i = first; i <= second; ++i) {
list_ids->push_back(i);
}
}
}
if (str->fail())
end = true;
else {
my_getline(infile, line);
delete str;
str = new std::stringstream(line);
}
}
delete str;
if (reading_nodes_group) {
NodeGroup & ng = mesh.createNodeGroup(name);
for (UInt i = 0; i < list_ids->size(); ++i) {
UInt node = (*list_ids)(i)-first_node_number;
ng.add(node, false);
}
delete list_ids;
} else {
ElementGroup & eg = mesh.createElementGroup(name);
for (UInt i = 0; i < list_ids->size(); ++i) {
Element & elem = diana_element_number_to_elements[(*list_ids)(i)];
if (elem.type != _not_defined)
eg.add(elem, false, false);
}
eg.optimize();
delete list_ids;
}
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readElements(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
if ("CONNECTIVITY" == line) {
line = readConnectivity(infile, mesh, first_node_number);
}
/// read the line corresponding to the materials
if ("MATERIALS" == line) {
line = readMaterialElement(infile, mesh);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readConnectivity(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Int index;
std::string lline;
std::string diana_type;
ElementType akantu_type, akantu_type_old = _not_defined;
Array<UInt> * connectivity = nullptr;
UInt node_per_element = 0;
Element elem;
UInt * read_order = nullptr;
while (true) {
my_getline(infile, lline);
// std::cerr << lline << std::endl;
std::stringstream sstr_elem(lline);
if (lline == "MATERIALS")
break;
/// traiter les coordonnees
sstr_elem >> index;
sstr_elem >> diana_type;
akantu_type = _diana_to_akantu_element_types[diana_type];
if (akantu_type == _not_defined)
continue;
if (akantu_type != akantu_type_old) {
connectivity = &(mesh_accessor.getConnectivity(akantu_type));
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
read_order = _read_order[akantu_type];
}
Vector<UInt> local_connect(node_per_element);
// used if element is written on two lines
UInt j_last = 0;
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
// check s'il y a pas plus rien après un certain point
if (sstr_elem.fail()) {
sstr_elem.clear();
sstr_elem.ignore();
break;
}
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
j_last = j;
}
// check if element is written in two lines
if (j_last != (node_per_element - 1)) {
// if this is the case, read on more line
my_getline(infile, lline);
std::stringstream sstr_elem(lline);
for (UInt j = (j_last + 1); j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
}
}
connectivity->push_back(local_connect);
elem.type = akantu_type;
elem.element = connectivity->size() - 1;
diana_element_number_to_elements[index] = elem;
akantu_number_to_diana_number[elem] = index;
}
AKANTU_DEBUG_OUT();
return lline;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterialElement(std::ifstream & infile,
Mesh & mesh) {
AKANTU_DEBUG_IN();
std::string line;
std::stringstream sstr_tag_name;
sstr_tag_name << "tag_" << 0;
Mesh::type_iterator it = mesh.firstType();
Mesh::type_iterator end = mesh.lastType();
for (; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
mesh.getDataPointer<UInt>("material", *it, _not_ghost, 1)
.resize(nb_element);
}
my_getline(infile, line);
while (line != "'MATERIALS'") {
line =
line.substr(line.find('/') + 1,
std::string::npos); // erase the first slash / of the line
char tutu[250];
strncpy(tutu, line.c_str(), 250);
AKANTU_DEBUG_WARNING("reading line " << line);
Array<UInt> temp_id(0, 2);
UInt mat;
while (true) {
std::stringstream sstr_intervals_elements(line);
Vector<UInt> id(2);
char temp;
while (sstr_intervals_elements.good()) {
sstr_intervals_elements >> id(0) >> temp >> id(1); // >> "/" >> mat;
if (!sstr_intervals_elements.fail())
temp_id.push_back(id);
}
if (sstr_intervals_elements.fail()) {
sstr_intervals_elements.clear();
sstr_intervals_elements.ignore();
sstr_intervals_elements >> mat;
break;
}
my_getline(infile, line);
}
// loop over elements
// UInt * temp_id_val = temp_id.storage();
for (UInt i = 0; i < temp_id.size(); ++i)
for (UInt j = temp_id(i, 0); j <= temp_id(i, 1); ++j) {
Element & element = diana_element_number_to_elements[j];
if (element.type == _not_defined)
continue;
UInt elem = element.element;
ElementType type = element.type;
Array<UInt> & data =
mesh.getDataPointer<UInt>("material", type, _not_ghost);
data(elem) = mat;
}
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterial(std::ifstream & infile,
const std::string & filename) {
AKANTU_DEBUG_IN();
std::stringstream mat_file_name;
mat_file_name << "material_" << filename;
std::ofstream material_file;
material_file.open(mat_file_name.str().c_str()); // mat_file_name.str());
UInt mat_index;
std::string line;
bool first_mat = true;
bool end = false;
UInt mat_id = 0;
using MatProp = std::map<std::string, Real>;
MatProp mat_prop;
do {
my_getline(infile, line);
std::stringstream sstr_material(line);
if (("'GROUPS'" == line) || ("'END'" == line)) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it)
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
material_file << "]" << std::endl;
mat_prop.clear();
}
end = true;
} else {
/// traiter les caractéristiques des matériaux
sstr_material >> mat_index;
if (!sstr_material.fail()) {
if (!first_mat) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it)
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
material_file << "]" << std::endl;
mat_prop.clear();
}
}
first_mat = false;
} else {
sstr_material.clear();
}
std::string prop_name;
sstr_material >> prop_name;
std::map<std::string, std::string>::iterator it;
it = _diana_to_akantu_mat_prop.find(prop_name);
if (it != _diana_to_akantu_mat_prop.end()) {
Real value;
sstr_material >> value;
mat_prop[it->second] = value;
} else {
AKANTU_DEBUG_INFO("In material reader, property " << prop_name
<< "not recognized");
}
}
} while (!end);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_diana.hh b/src/io/mesh_io/mesh_io_diana.hh
index a5bde0911..fde134690 100644
--- a/src/io/mesh_io/mesh_io_diana.hh
+++ b/src/io/mesh_io/mesh_io_diana.hh
@@ -1,109 +1,108 @@
/**
* @file mesh_io_diana.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Nov 19 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief diana mesh reader description
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_IO_DIANA_HH__
#define __AKANTU_MESH_IO_DIANA_HH__
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIODiana : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIODiana();
~MeshIODiana() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
void write(const std::string & filename, const Mesh & mesh) override;
private:
std::string readCoordinates(std::ifstream & infile, Mesh & mesh,
UInt & first_node_number);
std::string readElements(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readGroups(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readConnectivity(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readMaterialElement(std::ifstream & infile, Mesh & mesh);
std::string readMaterial(std::ifstream & infile,
const std::string & filename);
UInt readInterval(std::stringstream & line, std::set<UInt> & interval);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
std::map<std::string, ElementType> _diana_to_akantu_element_types;
std::map<std::string, std::string> _diana_to_akantu_mat_prop;
/// order in witch element as to be read, akantu_node_order =
/// _read_order[diana_node_order]
std::map<ElementType, UInt *> _read_order;
std::map<UInt, Element> diana_element_number_to_elements;
std::map<Element, UInt> akantu_number_to_diana_number;
};
} // akantu
#endif /* __AKANTU_MESH_IO_DIANA_HH__ */
diff --git a/src/io/mesh_io/mesh_io_msh.cc b/src/io/mesh_io/mesh_io_msh.cc
index 2f160815c..1e50bdaa5 100644
--- a/src/io/mesh_io/mesh_io_msh.cc
+++ b/src/io/mesh_io/mesh_io_msh.cc
@@ -1,972 +1,971 @@
/**
* @file mesh_io_msh.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Read/Write for MSH files generated by gmsh
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -----------------------------------------------------------------------------
Version (Legacy) 1.0
$NOD
number-of-nodes
node-number x-coord y-coord z-coord
...
$ENDNOD
$ELM
number-of-elements
elm-number elm-type reg-phys reg-elem number-of-nodes node-number-list
...
$ENDELM
-----------------------------------------------------------------------------
Version 2.1
$MeshFormat
version-number file-type data-size
$EndMeshFormat
$Nodes
number-of-nodes
node-number x-coord y-coord z-coord
...
$EndNodes
$Elements
number-of-elements
elm-number elm-type number-of-tags < tag > ... node-number-list
...
$EndElements
$PhysicalNames
number-of-names
physical-dimension physical-number "physical-name"
...
$EndPhysicalNames
$NodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
node-number value ...
...
$EndNodeData
$ElementData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number value ...
...
$EndElementData
$ElementNodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number number-of-nodes-per-element value ...
...
$ElementEndNodeData
-----------------------------------------------------------------------------
elem-type
1: 2-node line.
2: 3-node triangle.
3: 4-node quadrangle.
4: 4-node tetrahedron.
5: 8-node hexahedron.
6: 6-node prism.
7: 5-node pyramid.
8: 3-node second order line
9: 6-node second order triangle
10: 9-node second order quadrangle
11: 10-node second order tetrahedron
12: 27-node second order hexahedron
13: 18-node second order prism
14: 14-node second order pyramid
15: 1-node point.
16: 8-node second order quadrangle
17: 20-node second order hexahedron
18: 15-node second order prism
19: 13-node second order pyramid
20: 9-node third order incomplete triangle
21: 10-node third order triangle
22: 12-node fourth order incomplete triangle
23: 15-node fourth order triangle
24: 15-node fifth order incomplete triangle
25: 21-node fifth order complete triangle
26: 4-node third order edge
27: 5-node fourth order edge
28: 6-node fifth order edge
29: 20-node third order tetrahedron
30: 35-node fourth order tetrahedron
31: 56-node fifth order tetrahedron
-------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// The boost spirit is a work on the way it does not compile so I kept the
// current code. The current code does not handle files generated on Windows
// <CRLF>
// #include <boost/config/warning_disable.hpp>
// #include <boost/spirit/include/qi.hpp>
// #include <boost/spirit/include/phoenix_core.hpp>
// #include <boost/spirit/include/phoenix_fusion.hpp>
// #include <boost/spirit/include/phoenix_object.hpp>
// #include <boost/spirit/include/phoenix_container.hpp>
// #include <boost/spirit/include/phoenix_operator.hpp>
// #include <boost/spirit/include/phoenix_bind.hpp>
// #include <boost/spirit/include/phoenix_stl.hpp>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIOMSH::MeshIOMSH() {
canReadSurface = true;
canReadExtendedData = true;
_msh_nodes_per_elem[_msh_not_defined] = 0;
_msh_nodes_per_elem[_msh_segment_2] = 2;
_msh_nodes_per_elem[_msh_triangle_3] = 3;
_msh_nodes_per_elem[_msh_quadrangle_4] = 4;
_msh_nodes_per_elem[_msh_tetrahedron_4] = 4;
_msh_nodes_per_elem[_msh_hexahedron_8] = 8;
_msh_nodes_per_elem[_msh_prism_1] = 6;
_msh_nodes_per_elem[_msh_pyramid_1] = 1;
_msh_nodes_per_elem[_msh_segment_3] = 3;
_msh_nodes_per_elem[_msh_triangle_6] = 6;
_msh_nodes_per_elem[_msh_quadrangle_9] = 9;
_msh_nodes_per_elem[_msh_tetrahedron_10] = 10;
_msh_nodes_per_elem[_msh_hexahedron_27] = 27;
_msh_nodes_per_elem[_msh_hexahedron_20] = 20;
_msh_nodes_per_elem[_msh_prism_18] = 18;
_msh_nodes_per_elem[_msh_prism_15] = 15;
_msh_nodes_per_elem[_msh_pyramid_14] = 14;
_msh_nodes_per_elem[_msh_point] = 1;
_msh_nodes_per_elem[_msh_quadrangle_8] = 8;
_msh_to_akantu_element_types[_msh_not_defined] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2] = _segment_2;
_msh_to_akantu_element_types[_msh_triangle_3] = _triangle_3;
_msh_to_akantu_element_types[_msh_quadrangle_4] = _quadrangle_4;
_msh_to_akantu_element_types[_msh_tetrahedron_4] = _tetrahedron_4;
_msh_to_akantu_element_types[_msh_hexahedron_8] = _hexahedron_8;
_msh_to_akantu_element_types[_msh_prism_1] = _pentahedron_6;
_msh_to_akantu_element_types[_msh_pyramid_1] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_3] = _segment_3;
_msh_to_akantu_element_types[_msh_triangle_6] = _triangle_6;
_msh_to_akantu_element_types[_msh_quadrangle_9] = _not_defined;
_msh_to_akantu_element_types[_msh_tetrahedron_10] = _tetrahedron_10;
_msh_to_akantu_element_types[_msh_hexahedron_27] = _not_defined;
_msh_to_akantu_element_types[_msh_hexahedron_20] = _hexahedron_20;
_msh_to_akantu_element_types[_msh_prism_18] = _not_defined;
_msh_to_akantu_element_types[_msh_prism_15] = _pentahedron_15;
_msh_to_akantu_element_types[_msh_pyramid_14] = _not_defined;
_msh_to_akantu_element_types[_msh_point] = _point_1;
_msh_to_akantu_element_types[_msh_quadrangle_8] = _quadrangle_8;
_akantu_to_msh_element_types[_not_defined] = _msh_not_defined;
_akantu_to_msh_element_types[_segment_2] = _msh_segment_2;
_akantu_to_msh_element_types[_segment_3] = _msh_segment_3;
_akantu_to_msh_element_types[_triangle_3] = _msh_triangle_3;
_akantu_to_msh_element_types[_triangle_6] = _msh_triangle_6;
_akantu_to_msh_element_types[_tetrahedron_4] = _msh_tetrahedron_4;
_akantu_to_msh_element_types[_tetrahedron_10] = _msh_tetrahedron_10;
_akantu_to_msh_element_types[_quadrangle_4] = _msh_quadrangle_4;
_akantu_to_msh_element_types[_quadrangle_8] = _msh_quadrangle_8;
_akantu_to_msh_element_types[_hexahedron_8] = _msh_hexahedron_8;
_akantu_to_msh_element_types[_hexahedron_20] = _msh_hexahedron_20;
_akantu_to_msh_element_types[_pentahedron_6] = _msh_prism_1;
_akantu_to_msh_element_types[_pentahedron_15] = _msh_prism_15;
_akantu_to_msh_element_types[_point_1] = _msh_point;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
_akantu_to_msh_element_types[_bernoulli_beam_2] = _msh_segment_2;
_akantu_to_msh_element_types[_bernoulli_beam_3] = _msh_segment_2;
_akantu_to_msh_element_types[_discrete_kirchhoff_triangle_18] =
_msh_triangle_3;
#endif
std::map<ElementType, MSHElementType>::iterator it;
for (it = _akantu_to_msh_element_types.begin();
it != _akantu_to_msh_element_types.end(); ++it) {
UInt nb_nodes = _msh_nodes_per_elem[it->second];
std::vector<UInt> tmp(nb_nodes);
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->first) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_6:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
tmp[6] = 8;
tmp[8] = 11;
tmp[9] = 6;
tmp[10] = 9;
tmp[11] = 10;
tmp[12] = 14;
tmp[14] = 12;
break;
case _hexahedron_20:
tmp[9] = 11;
tmp[10] = 12;
tmp[11] = 9;
tmp[12] = 13;
tmp[13] = 10;
tmp[17] = 19;
tmp[18] = 17;
tmp[19] = 18;
break;
default:
// nothing to change
break;
}
_read_order[it->first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIOMSH::~MeshIOMSH() = default;
/* -------------------------------------------------------------------------- */
/* Spirit stuff */
/* -------------------------------------------------------------------------- */
// namespace _parser {
// namespace spirit = ::boost::spirit;
// namespace qi = ::boost::spirit::qi;
// namespace ascii = ::boost::spirit::ascii;
// namespace lbs = ::boost::spirit::qi::labels;
// namespace phx = ::boost::phoenix;
// /* ------------------------------------------------------------------------
// */
// /* Lazy functors */
// /* ------------------------------------------------------------------------
// */
// struct _Element {
// int index;
// std::vector<int> tags;
// std::vector<int> connectivity;
// ElementType type;
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_get_nb_nodes_ {
// template <class elem_type> struct result { typedef int type; };
// template <class elem_type> bool operator()(elem_type et) {
// return MeshIOMSH::_msh_nodes_per_elem[et];
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_element_ {
// template <class id_t, class tags_t, class elem_type, class conn_t>
// struct result {
// typedef _Element type;
// };
// template <class id_t, class tags_t, class elem_type, class conn_t>
// _Element operator()(id_t id, const elem_type & et, const tags_t & t,
// const conn_t & c) {
// _Element tmp_el;
// tmp_el.index = id;
// tmp_el.tags = t;
// tmp_el.connectivity = c;
// tmp_el.type = et;
// return tmp_el;
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_check_value_ {
// template <class T> struct result { typedef void type; };
// template <class T> void operator()(T v1, T v2) {
// if (v1 != v2) {
// AKANTU_EXCEPTION("The msh parser expected a "
// << v2 << " in the header bug got a " << v1);
// }
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_node_read_ {
// template <class Mesh, class ID, class V, class size, class Map>
// struct result {
// typedef bool type;
// };
// template <class Mesh, class ID, class V, class size, class Map>
// bool operator()(Mesh & mesh, const ID & id, const V & pos, size max,
// Map & nodes_mapping) const {
// Vector<Real> tmp_pos(mesh.getSpatialDimension());
// UInt i = 0;
// for (typename V::const_iterator it = pos.begin();
// it != pos.end() || i < mesh.getSpatialDimension(); ++it)
// tmp_pos[i++] = *it;
// nodes_mapping[id] = mesh.getNbNodes();
// mesh.getNodes().push_back(tmp_pos);
// return (mesh.getNbNodes() < UInt(max));
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_element_read_ {
// template <class Mesh, class EL, class size, class NodeMap, class ElemMap>
// struct result {
// typedef bool type;
// };
// template <class Mesh, class EL, class size, class NodeMap, class ElemMap>
// bool operator()(Mesh & mesh, const EL & element, size max,
// const NodeMap & nodes_mapping,
// ElemMap & elements_mapping) const {
// Vector<UInt> tmp_conn(Mesh::getNbNodesPerElement(element.type));
// AKANTU_DEBUG_ASSERT(element.connectivity.size() == tmp_conn.size(),
// "The element "
// << element.index
// << "in the MSH file has too many nodes.");
// mesh.addConnectivityType(element.type);
// Array<UInt> & connectivity = mesh.getConnectivity(element.type);
// UInt i = 0;
// for (std::vector<int>::const_iterator it =
// element.connectivity.begin();
// it != element.connectivity.end(); ++it) {
// typename NodeMap::const_iterator nit = nodes_mapping.find(*it);
// AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
// "There is an unknown node in the connectivity.");
// tmp_conn[i++] = nit->second;
// }
// ::akantu::Element el(element.type, connectivity.size());
// elements_mapping[element.index] = el;
// connectivity.push_back(tmp_conn);
// for (UInt i = 0; i < element.tags.size(); ++i) {
// std::stringstream tag_sstr;
// tag_sstr << "tag_" << i;
// Array<UInt> * data =
// mesh.template getDataPointer<UInt>(tag_sstr.str(), element.type,
// _not_ghost);
// data->push_back(element.tags[i]);
// }
// return (mesh.getNbElement() < UInt(max));
// }
// };
// /* ------------------------------------------------------------------------
// */
// template <class Iterator, typename Skipper = ascii::space_type>
// struct MshMeshGrammar : qi::grammar<Iterator, void(), Skipper> {
// public:
// MshMeshGrammar(Mesh & mesh)
// : MshMeshGrammar::base_type(start, "msh_mesh_reader"), mesh(mesh) {
// phx::function<lazy_element_> lazy_element;
// phx::function<lazy_get_nb_nodes_> lazy_get_nb_nodes;
// phx::function<lazy_check_value_> lazy_check_value;
// phx::function<lazy_node_read_> lazy_node_read;
// phx::function<lazy_element_read_> lazy_element_read;
// clang-format off
// start
// = *( known_section | unknown_section
// )
// ;
// known_section
// = qi::char_("$")
// >> sections [ lbs::_a = lbs::_1 ]
// >> qi::lazy(*lbs::_a)
// >> qi::lit("$End")
// //>> qi::lit(phx::ref(lbs::_a))
// ;
// unknown_section
// = qi::char_("$")
// >> qi::char_("") [ lbs::_a = lbs::_1 ]
// >> ignore_section
// >> qi::lit("$End")
// >> qi::lit(phx::val(lbs::_a))
// ;
// mesh_format // version followed by 0 or 1 for ascii or binary
// = version >> (
// ( qi::char_("0")
// >> qi::int_ [ lazy_check_value(lbs::_1, 8) ]
// )
// | ( qi::char_("1")
// >> qi::int_ [ lazy_check_value(lbs::_1, 8) ]
// >> qi::dword [ lazy_check_value(lbs::_1, 1) ]
// )
// )
// ;
// nodes
// = nodes_
// ;
// nodes_
// = qi::int_ [ lbs::_a = lbs::_1 ]
// > *(
// ( qi::int_ >> position ) [ lazy_node_read(phx::ref(mesh),
// lbs::_1,
// phx::cref(lbs::_2),
// lbs::_a,
// phx::ref(this->msh_nodes_to_akantu)) ]
// )
// ;
// element
// = elements_
// ;
// elements_
// = qi::int_ [ lbs::_a = lbs::_1 ]
// > qi::repeat(phx::ref(lbs::_a))[ element [ lazy_element_read(phx::ref(mesh),
// lbs::_1,
// phx::cref(lbs::_a),
// phx::cref(this->msh_nodes_to_akantu),
// phx::ref(this->msh_elemt_to_akantu)) ]]
// ;
// ignore_section
// = *(qi::char_ - qi::char_('$'))
// ;
// interpolation_scheme = ignore_section;
// element_data = ignore_section;
// node_data = ignore_section;
// version
// = qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ]
// >> *( qi::char_(".") >> qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ] )
// ;
// position
// = real [ phx::push_back(lbs::_val, lbs::_1) ]
// > real [ phx::push_back(lbs::_val, lbs::_1) ]
// > real [ phx::push_back(lbs::_val, lbs::_1) ]
// ;
// tags
// = qi::int_ [ lbs::_a = lbs::_1 ]
// > qi::repeat(phx::val(lbs::_a))[ qi::int_ [ phx::push_back(lbs::_val,
// lbs::_1) ] ]
// ;
// element
// = ( qi::int_ [ lbs::_a = lbs::_1 ]
// > msh_element_type [ lbs::_b = lazy_get_nb_nodes(lbs::_1) ]
// > tags [ lbs::_c = lbs::_1 ]
// > connectivity(lbs::_a) [ lbs::_d = lbs::_1 ]
// ) [ lbs::_val = lazy_element(lbs::_a,
// phx::cref(lbs::_b),
// phx::cref(lbs::_c),
// phx::cref(lbs::_d)) ]
// ;
// connectivity
// = qi::repeat(lbs::_r1)[ qi::int_ [ phx::push_back(lbs::_val,
// lbs::_1) ] ]
// ;
// sections.add
// ("MeshFormat", &mesh_format)
// ("Nodes", &nodes)
// ("Elements", &elements)
// ("PhysicalNames", &physical_names)
// ("InterpolationScheme", &interpolation_scheme)
// ("ElementData", &element_data)
// ("NodeData", &node_data);
// msh_element_type.add
// ("0" , _not_defined )
// ("1" , _segment_2 )
// ("2" , _triangle_3 )
// ("3" , _quadrangle_4 )
// ("4" , _tetrahedron_4 )
// ("5" , _hexahedron_8 )
// ("6" , _pentahedron_6 )
// ("7" , _not_defined )
// ("8" , _segment_3 )
// ("9" , _triangle_6 )
// ("10", _not_defined )
// ("11", _tetrahedron_10)
// ("12", _not_defined )
// ("13", _not_defined )
// ("14", _hexahedron_20 )
// ("15", _pentahedron_15)
// ("16", _not_defined )
// ("17", _point_1 )
// ("18", _quadrangle_8 );
// mesh_format .name("MeshFormat" );
// nodes .name("Nodes" );
// elements .name("Elements" );
// physical_names .name("PhysicalNames" );
// interpolation_scheme.name("InterpolationScheme");
// element_data .name("ElementData" );
// node_data .name("NodeData" );
// clang-format on
// }
// /* ----------------------------------------------------------------------
// */
// /* Rules */
// /* ----------------------------------------------------------------------
// */
// private:
// qi::symbols<char, ElementType> msh_element_type;
// qi::symbols<char, qi::rule<Iterator, void(), Skipper> *> sections;
// qi::rule<Iterator, void(), Skipper> start;
// qi::rule<Iterator, void(), Skipper, qi::locals<std::string> >
// unknown_section;
// qi::rule<Iterator, void(), Skipper, qi::locals<qi::rule<Iterator,
// Skipper> *> > known_section;
// qi::rule<Iterator, void(), Skipper> mesh_format, nodes, elements,
// physical_names, ignore_section,
// interpolation_scheme, element_data, node_data, any_line;
// qi::rule<Iterator, void(), Skipper, qi::locals<int> > nodes_;
// qi::rule<Iterator, void(), Skipper, qi::locals< int, int, vector<int>,
// vector<int> > > elements_;
// qi::rule<Iterator, std::vector<int>(), Skipper> version;
// qi::rule<Iterator, _Element(), Skipper, qi::locals<ElementType> >
// element;
// qi::rule<Iterator, std::vector<int>(), Skipper, qi::locals<int> > tags;
// qi::rule<Iterator, std::vector<int>(int), Skipper> connectivity;
// qi::rule<Iterator, std::vector<Real>(), Skipper> position;
// qi::real_parser<Real, qi::real_policies<Real> > real;
// /* ----------------------------------------------------------------------
// */
// /* Members */
// /* ----------------------------------------------------------------------
// */
// private:
// /// reference to the mesh to read
// Mesh & mesh;
// /// correspondance between the numbering of nodes in the abaqus file and
// in
// /// the akantu mesh
// std::map<UInt, UInt> msh_nodes_to_akantu;
// /// correspondance between the element number in the abaqus file and the
// /// Element in the akantu mesh
// std::map<UInt, Element> msh_elemt_to_akantu;
// };
// }
// /* --------------------------------------------------------------------------
// */
// void MeshIOAbaqus::read(const std::string& filename, Mesh& mesh) {
// namespace qi = boost::spirit::qi;
// namespace ascii = boost::spirit::ascii;
// std::ifstream infile;
// infile.open(filename.c_str());
// if(!infile.good()) {
// AKANTU_ERROR("Cannot open file " << filename);
// }
// std::string storage; // We will read the contents here.
// infile.unsetf(std::ios::skipws); // No white space skipping!
// std::copy(std::istream_iterator<char>(infile),
// std::istream_iterator<char>(),
// std::back_inserter(storage));
// typedef std::string::const_iterator iterator_t;
// typedef ascii::space_type skipper;
// typedef _parser::MshMeshGrammar<iterator_t, skipper> grammar;
// grammar g(mesh);
// skipper ws;
// iterator_t iter = storage.begin();
// iterator_t end = storage.end();
// qi::phrase_parse(iter, end, g, ws);
// this->setNbGlobalNodes(mesh, mesh.getNodes().size());
// MeshUtils::fillElementToSubElementsData(mesh);
// }
static void my_getline(std::ifstream & infile, std::string & str) {
std::string tmp_str;
std::getline(infile, tmp_str);
str = trim(tmp_str);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::read(const std::string & filename, Mesh & mesh) {
MeshAccessor mesh_accessor(mesh);
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt first_node_number = std::numeric_limits<UInt>::max(),
last_node_number = 0, file_format = 1, current_line = 0;
bool has_physical_names = false;
if (!infile.good()) {
AKANTU_EXCEPTION("Cannot open file " << filename);
}
while (infile.good()) {
my_getline(infile, line);
current_line++;
/// read the header
if (line == "$MeshFormat") {
my_getline(infile, line); /// the format line
std::stringstream sstr(line);
std::string version;
sstr >> version;
Int format;
sstr >> format;
if (format != 0)
AKANTU_ERROR("This reader can only read ASCII files.");
my_getline(infile, line); /// the end of block line
current_line += 2;
file_format = 2;
}
/// read the physical names
if (line == "$PhysicalNames") {
has_physical_names = true;
my_getline(infile, line); /// the format line
std::stringstream sstr(line);
UInt num_of_phys_names;
sstr >> num_of_phys_names;
for (UInt k(0); k < num_of_phys_names; k++) {
my_getline(infile, line);
std::stringstream sstr_phys_name(line);
UInt phys_name_id;
UInt phys_dim;
sstr_phys_name >> phys_dim >> phys_name_id;
std::size_t b = line.find('\"');
std::size_t e = line.rfind('\"');
std::string phys_name = line.substr(b + 1, e - b - 1);
phys_name_map[phys_name_id] = phys_name;
}
}
/// read all nodes
if (line == "$Nodes" || line == "$NOD") {
UInt nb_nodes;
my_getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_nodes;
current_line++;
Array<Real> & nodes = mesh_accessor.getNodes();
nodes.resize(nb_nodes);
mesh_accessor.setNbGlobalNodes(nb_nodes);
UInt index;
Real coord[3];
UInt spatial_dimension = nodes.getNbComponent();
/// for each node, read the coordinates
for (UInt i = 0; i < nb_nodes; ++i) {
UInt offset = i * spatial_dimension;
my_getline(infile, line);
std::stringstream sstr_node(line);
sstr_node >> index >> coord[0] >> coord[1] >> coord[2];
current_line++;
first_node_number = std::min(first_node_number, index);
last_node_number = std::max(last_node_number, index);
/// read the coordinates
for (UInt j = 0; j < spatial_dimension; ++j)
nodes.storage()[offset + j] = coord[j];
}
my_getline(infile, line); /// the end of block line
}
/// read all elements
if (line == "$Elements" || line == "$ELM") {
UInt nb_elements;
std::vector<UInt> read_order;
my_getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_elements;
current_line++;
Int index;
UInt msh_type;
ElementType akantu_type, akantu_type_old = _not_defined;
Array<UInt> * connectivity = nullptr;
UInt node_per_element = 0;
for (UInt i = 0; i < nb_elements; ++i) {
my_getline(infile, line);
std::stringstream sstr_elem(line);
current_line++;
sstr_elem >> index;
sstr_elem >> msh_type;
/// get the connectivity vector depending on the element type
akantu_type =
this->_msh_to_akantu_element_types[(MSHElementType)msh_type];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind "
<< msh_type << " at line " << current_line);
continue;
}
if (akantu_type != akantu_type_old) {
connectivity = &mesh_accessor.getConnectivity(akantu_type);
// connectivity->resize(0);
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
read_order = this->_read_order[akantu_type];
}
/// read tags informations
if (file_format == 2) {
UInt nb_tags;
sstr_elem >> nb_tags;
for (UInt j = 0; j < nb_tags; ++j) {
Int tag;
sstr_elem >> tag;
std::stringstream sstr_tag_name;
sstr_tag_name << "tag_" << j;
Array<UInt> & data = mesh.getDataPointer<UInt>(
sstr_tag_name.str(), akantu_type, _not_ghost);
data.push_back(tag);
}
} else if (file_format == 1) {
Int tag;
sstr_elem >> tag; // reg-phys
std::string tag_name = "tag_0";
Array<UInt> * data =
&mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
data->push_back(tag);
sstr_elem >> tag; // reg-elem
tag_name = "tag_1";
data = &mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
data->push_back(tag);
sstr_elem >> tag; // number-of-nodes
}
Vector<UInt> local_connect(node_per_element);
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
AKANTU_DEBUG_ASSERT(node_index <= last_node_number,
"Node number not in range : line "
<< current_line);
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
}
connectivity->push_back(local_connect);
}
my_getline(infile, line); /// the end of block line
}
if ((line[0] == '$') && (line.find("End") == std::string::npos)) {
AKANTU_DEBUG_WARNING("Unsuported block_kind " << line << " at line "
<< current_line);
}
}
// mesh.updateTypesOffsets(_not_ghost);
infile.close();
this->constructPhysicalNames("tag_0", mesh);
if (has_physical_names)
mesh.createGroupsFromMeshData<std::string>("physical_names");
MeshUtils::fillElementToSubElementsData(mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::write(const std::string & filename, const Mesh & mesh) {
std::ofstream outfile;
const Array<Real> & nodes = mesh.getNodes();
outfile.open(filename.c_str());
outfile << "$MeshFormat" << std::endl;
outfile << "2.1 0 8" << std::endl;
outfile << "$EndMeshFormat" << std::endl;
outfile << std::setprecision(std::numeric_limits<Real>::digits10);
outfile << "$Nodes" << std::endl;
outfile << nodes.size() << std::endl;
outfile << std::uppercase;
for (UInt i = 0; i < nodes.size(); ++i) {
Int offset = i * nodes.getNbComponent();
outfile << i + 1;
for (UInt j = 0; j < nodes.getNbComponent(); ++j) {
outfile << " " << nodes.storage()[offset + j];
}
for (UInt p = nodes.getNbComponent(); p < 3; ++p)
outfile << " " << 0.;
outfile << std::endl;
;
}
outfile << std::nouppercase;
outfile << "$EndNodes" << std::endl;
;
outfile << "$Elements" << std::endl;
;
Int nb_elements = 0;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
nb_elements += connectivity.size();
}
outfile << nb_elements << std::endl;
UInt element_idx = 1;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
UInt * tag[2] = {nullptr, nullptr};
if (mesh.hasData<UInt>("tag_0", type, _not_ghost)) {
const auto & data_tag_0 = mesh.getData<UInt>("tag_0", type, _not_ghost);
tag[0] = data_tag_0.storage();
}
if (mesh.hasData<UInt>("tag_1", type, _not_ghost)) {
const auto & data_tag_1 = mesh.getData<UInt>("tag_1", type, _not_ghost);
tag[1] = data_tag_1.storage();
}
for (UInt i = 0; i < connectivity.size(); ++i) {
UInt offset = i * connectivity.getNbComponent();
outfile << element_idx << " " << _akantu_to_msh_element_types[type]
<< " 2";
/// \todo write the real data in the file
for (UInt t = 0; t < 2; ++t)
if (tag[t])
outfile << " " << tag[t][i];
else
outfile << " 0";
for (UInt j = 0; j < connectivity.getNbComponent(); ++j) {
outfile << " " << connectivity.storage()[offset + j] + 1;
}
outfile << std::endl;
element_idx++;
}
}
outfile << "$EndElements" << std::endl;
;
outfile.close();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_msh.hh b/src/io/mesh_io/mesh_io_msh.hh
index 70c52f4c4..568f5cca6 100644
--- a/src/io/mesh_io/mesh_io_msh.hh
+++ b/src/io/mesh_io/mesh_io_msh.hh
@@ -1,110 +1,109 @@
/**
* @file mesh_io_msh.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Dec 07 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Read/Write for MSH files
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_IO_MSH_HH__
#define __AKANTU_MESH_IO_MSH_HH__
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIOMSH : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSH();
~MeshIOMSH() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
void write(const std::string & filename, const Mesh & mesh) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// MSH element types
enum MSHElementType {
_msh_not_defined = 0,
_msh_segment_2 = 1, // 2-node line.
_msh_triangle_3 = 2, // 3-node triangle.
_msh_quadrangle_4 = 3, // 4-node quadrangle.
_msh_tetrahedron_4 = 4, // 4-node tetrahedron.
_msh_hexahedron_8 = 5, // 8-node hexahedron.
_msh_prism_1 = 6, // 6-node prism.
_msh_pyramid_1 = 7, // 5-node pyramid.
_msh_segment_3 = 8, // 3-node second order line
_msh_triangle_6 = 9, // 6-node second order triangle
_msh_quadrangle_9 = 10, // 9-node second order quadrangle
_msh_tetrahedron_10 = 11, // 10-node second order tetrahedron
_msh_hexahedron_27 = 12, // 27-node second order hexahedron
_msh_prism_18 = 13, // 18-node second order prism
_msh_pyramid_14 = 14, // 14-node second order pyramid
_msh_point = 15, // 1-node point.
_msh_quadrangle_8 = 16, // 8-node second order quadrangle
_msh_hexahedron_20 = 17, // 20-node second order hexahedron
_msh_prism_15 = 18 // 15-node second order prism
};
#define MAX_NUMBER_OF_NODE_PER_ELEMENT 10 // tetrahedron of second order
/// order in witch element as to be read
std::map<ElementType, std::vector<UInt>> _read_order;
/// number of nodes per msh element
std::map<MSHElementType, UInt> _msh_nodes_per_elem;
/// correspondence between msh element types and akantu element types
std::map<MSHElementType, ElementType> _msh_to_akantu_element_types;
/// correspondence between akantu element types and msh element types
std::map<ElementType, MSHElementType> _akantu_to_msh_element_types;
};
} // akantu
#endif /* __AKANTU_MESH_IO_MSH_HH__ */
diff --git a/src/io/mesh_io/mesh_io_msh_struct.cc b/src/io/mesh_io/mesh_io_msh_struct.cc
index 96f3fbec8..55300ef69 100644
--- a/src/io/mesh_io/mesh_io_msh_struct.cc
+++ b/src/io/mesh_io/mesh_io_msh_struct.cc
@@ -1,80 +1,80 @@
/**
* @file mesh_io_msh_struct.cc
*
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Dec 07 2015
+ * @date last modification: Fri Jan 26 2018
*
* @brief Read/Write for MSH files generated by gmsh
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_io_msh_struct.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIOMSHStruct::MeshIOMSHStruct() : MeshIOMSH() {
canReadSurface = true;
canReadExtendedData = true;
_msh_to_akantu_element_types.clear();
_msh_to_akantu_element_types[_msh_not_defined] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2] = _bernoulli_beam_2;
_msh_to_akantu_element_types[_msh_triangle_3] =
_discrete_kirchhoff_triangle_18;
_akantu_to_msh_element_types.clear();
_akantu_to_msh_element_types[_not_defined] = _msh_not_defined;
_akantu_to_msh_element_types[_bernoulli_beam_2] = _msh_segment_2;
_akantu_to_msh_element_types[_bernoulli_beam_3] = _msh_segment_2;
_akantu_to_msh_element_types[_discrete_kirchhoff_triangle_18] =
_msh_triangle_3;
for (auto & kv_pair : _akantu_to_msh_element_types) {
UInt nb_nodes = _msh_nodes_per_elem[kv_pair.second];
std::vector<UInt> tmp(nb_nodes);
std::iota(tmp.begin(), tmp.end(), 0);
_read_order[kv_pair.first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
void MeshIOMSHStruct::read(const std::string & filename, Mesh & mesh) {
if (mesh.getSpatialDimension() == 2) {
_msh_to_akantu_element_types[_msh_segment_2] = _bernoulli_beam_2;
} else if (mesh.getSpatialDimension() == 3) {
_msh_to_akantu_element_types[_msh_segment_2] = _bernoulli_beam_3;
AKANTU_DEBUG_WARNING("The MeshIOMSHStruct is reading bernoulli beam 3D be "
"sure to provide the missing normals with the element "
"data \"extra_normal\"");
}
MeshIOMSH::read(filename, mesh);
}
} // akantu
diff --git a/src/io/mesh_io/mesh_io_msh_struct.hh b/src/io/mesh_io/mesh_io_msh_struct.hh
index b83045ce5..542d65743 100644
--- a/src/io/mesh_io/mesh_io_msh_struct.hh
+++ b/src/io/mesh_io/mesh_io_msh_struct.hh
@@ -1,54 +1,54 @@
/**
* @file mesh_io_msh_struct.hh
*
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Fri Jan 26 2018
*
* @brief Read/Write for MSH files
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_IO_MSH_STRUCT_HH__
#define __AKANTU_MESH_IO_MSH_STRUCT_HH__
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIOMSHStruct : public MeshIOMSH {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSHStruct();
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
};
} // akantu
#endif /* __AKANTU_MESH_IO_MSH_STRUCT_HH__ */
diff --git a/src/io/parser/algebraic_parser.hh b/src/io/parser/algebraic_parser.hh
index da97a2380..bfecaeb63 100644
--- a/src/io/parser/algebraic_parser.hh
+++ b/src/io/parser/algebraic_parser.hh
@@ -1,512 +1,512 @@
/**
* @file algebraic_parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Wed Nov 11 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief algebraic_parser definition of the grammar
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
// Boost
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/phoenix.hpp>
#include <boost/spirit/include/qi.hpp>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ALGEBRAIC_PARSER_HH__
#define __AKANTU_ALGEBRAIC_PARSER_HH__
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
namespace akantu {
namespace parser {
struct algebraic_error_handler_ {
template <typename, typename, typename> struct result {
using type = void;
};
template <typename Iterator>
void operator()(qi::info const & what, Iterator err_pos,
Iterator last) const {
AKANTU_EXCEPTION(
"Error! Expecting "
<< what // what failed?
<< " here: \""
<< std::string(err_pos, last) // iterators to error-pos, end
<< "\"");
}
};
static Real my_min(Real a, Real b) { return std::min(a, b); }
static Real my_max(Real a, Real b) { return std::max(a, b); }
static Real my_pow(Real a, Real b) { return std::pow(a, b); }
static Real eval_param(const ID & a, const ParserSection & section) {
return section.getParameter(a, _ppsc_current_and_parent_scope);
}
static Real unary_func(Real (*func)(Real), Real a) { return func(a); }
static Real binary_func(Real (*func)(Real, Real), Real a, Real b) {
return func(a, b);
}
template <class Iterator, typename Skipper = spirit::unused_type>
struct AlgebraicGrammar : qi::grammar<Iterator, Real(), Skipper> {
AlgebraicGrammar(const ParserSection & section)
: AlgebraicGrammar::base_type(start, "algebraic_grammar"),
section(section) {
// phx::function<lazy_pow_> lazy_pow;
// phx::function<lazy_unary_func_> lazy_unary_func;
// phx::function<lazy_binary_func_> lazy_binary_func;
// phx::function<lazy_eval_param_> lazy_eval_param;
/* clang-format off */
start
= expr.alias()
;
expr
= term [ lbs::_val = lbs::_1 ]
>> *( ('+' > term [ lbs::_val += lbs::_1 ])
| ('-' > term [ lbs::_val -= lbs::_1 ])
)
;
term
= factor [ lbs::_val = lbs::_1 ]
>> *( ('*' > factor [ lbs::_val *= lbs::_1 ])
| ('/' > factor [ lbs::_val /= lbs::_1 ])
)
;
factor
= number [ lbs::_val = lbs::_1 ]
>> *("**" > number [ lbs::_val = phx::bind(&my_pow, lbs::_val, lbs::_1) ])
;
number
= real [ lbs::_val = lbs::_1 ]
| ('-' > number [ lbs::_val = -lbs::_1 ])
| ('+' > number [ lbs::_val = lbs::_1 ])
| constant [ lbs::_val = lbs::_1 ]
| function [ lbs::_val = lbs::_1 ]
| ('(' > expr > ')') [ lbs::_val = lbs::_1 ]
| variable [ lbs::_val = lbs::_1 ]
;
function
= (qi::no_case[unary_function]
> '('
> expr
> ')') [ lbs::_val = phx::bind(&unary_func, lbs::_1, lbs::_2) ]
| (qi::no_case[binary_function]
> '(' >> expr
> ',' >> expr
> ')') [ lbs::_val = phx::bind(&binary_func ,lbs::_1, lbs::_2, lbs::_3) ]
;
variable
= key [ lbs::_val = phx::bind(&eval_param, lbs::_1, section) ]
;
key
= qi::no_skip[qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")] // coming from the InputFileGrammar
;
#ifndef M_PI
# define M_PI 3.14159265358979323846
#endif
#ifndef M_E
# define M_E 2.7182818284590452354
#endif
constant.add
("pi", M_PI)
("e", M_E);
unary_function.add
("abs" , &std::abs )
("acos" , &std::acos )
("asin" , &std::asin )
("atan" , &std::atan )
("ceil" , &std::ceil )
("cos" , &std::cos )
("cosh" , &std::cosh )
("exp" , &std::exp )
("floor" , &std::floor )
("log10" , &std::log10 )
("log" , &std::log )
("sin" , &std::sin )
("sinh" , &std::sinh )
("sqrt" , &std::sqrt )
("tan" , &std::tan )
("tanh" , &std::tanh )
("acosh" , &std::acosh )
("asinh" , &std::asinh )
("atanh" , &std::atanh )
("exp2" , &std::exp2 )
("expm1" , &std::expm1 )
("log1p" , &std::log1p )
("log2" , &std::log2 )
("erf" , &std::erf )
("erfc" , &std::erfc )
("lgamma", &std::lgamma)
("tgamma", &std::tgamma)
("trunc" , &std::trunc )
("round" , &std::round )
// ("crbt" , &std::crbt )
;
binary_function.add
("pow" , &std::pow )
("min" , &parser::my_min)
("max" , &parser::my_max)
("atan2", &std::atan2 )
("fmod" , &std::fmod )
("hypot", &std::hypot )
;
#if !defined(AKANTU_NDEBUG)
phx::function<algebraic_error_handler_> const error_handler = algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
expr .name("expression");
term .name("term");
factor .name("factor");
number .name("numerical-value");
variable.name("variable");
function.name("function");
constant.name("constants-list");
unary_function.name("unary-functions-list");
binary_function.name("binary-functions-list");
#if !defined AKANTU_NDEBUG
if(AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(expr);
qi::debug(term);
qi::debug(factor);
qi::debug(number);
qi::debug(variable);
qi::debug(function);
}
#endif
}
/* clang-format on */
private:
qi::rule<Iterator, Real(), Skipper> start;
qi::rule<Iterator, Real(), Skipper> expr;
qi::rule<Iterator, Real(), Skipper> term;
qi::rule<Iterator, Real(), Skipper> factor;
qi::rule<Iterator, Real(), Skipper> number;
qi::rule<Iterator, Real(), Skipper> variable;
qi::rule<Iterator, Real(), Skipper> function;
qi::rule<Iterator, std::string(), Skipper> key;
qi::real_parser<Real, qi::real_policies<Real>> real;
qi::symbols<char, Real> constant;
qi::symbols<char, Real (*)(Real)> unary_function;
qi::symbols<char, Real (*)(Real, Real)> binary_function;
const ParserSection & section;
};
/* ---------------------------------------------------------------------- */
/* Vector Parser */
/* ---------------------------------------------------------------------- */
struct parsable_vector {
operator Vector<Real>() {
Vector<Real> tmp(_cells.size());
auto it = _cells.begin();
for (UInt i = 0; it != _cells.end(); ++it, ++i)
tmp(i) = *it;
return tmp;
}
std::vector<Real> _cells;
};
inline std::ostream & operator<<(std::ostream & stream,
const parsable_vector & pv) {
stream << "pv[";
auto it = pv._cells.begin();
if (it != pv._cells.end()) {
stream << *it;
for (++it; it != pv._cells.end(); ++it)
stream << ", " << *it;
}
stream << "]";
return stream;
}
struct parsable_matrix {
operator Matrix<Real>() {
size_t cols = 0;
auto it_rows = _cells.begin();
for (; it_rows != _cells.end(); ++it_rows)
cols = std::max(cols, it_rows->_cells.size());
Matrix<Real> tmp(_cells.size(), _cells[0]._cells.size(), 0.);
it_rows = _cells.begin();
for (UInt i = 0; it_rows != _cells.end(); ++it_rows, ++i) {
auto it_cols = it_rows->_cells.begin();
for (UInt j = 0; it_cols != it_rows->_cells.end(); ++it_cols, ++j) {
tmp(i, j) = *it_cols;
}
}
return tmp;
}
std::vector<parsable_vector> _cells;
};
inline std::ostream & operator<<(std::ostream & stream,
const parsable_matrix & pm) {
stream << "pm[";
auto it = pm._cells.begin();
if (it != pm._cells.end()) {
stream << *it;
for (++it; it != pm._cells.end(); ++it)
stream << ", " << *it;
}
stream << "]";
return stream;
}
/* ---------------------------------------------------------------------- */
template <typename T1, typename T2>
static void cont_add(T1 & cont, T2 & value) {
cont._cells.push_back(value);
}
/* ---------------------------------------------------------------------- */
template <class Iterator, typename Skipper = spirit::unused_type>
struct VectorGrammar : qi::grammar<Iterator, parsable_vector(), Skipper> {
VectorGrammar(const ParserSection & section)
: VectorGrammar::base_type(start, "vector_algebraic_grammar"),
number(section) {
start = '[' > vector > ']';
vector =
(number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)] >>
*(',' >> number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)]))[lbs::_val = lbs::_a];
#if !defined(AKANTU_NDEBUG) && defined(AKANTU_CORE_CXX_11)
phx::function<algebraic_error_handler_> const error_handler =
algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start.name("start");
vector.name("vector");
number.name("value");
#if !defined AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(start);
qi::debug(vector);
}
#endif
}
private:
qi::rule<Iterator, parsable_vector(), Skipper> start;
qi::rule<Iterator, parsable_vector(), qi::locals<parsable_vector>, Skipper>
vector;
qi::rule<Iterator, Real(), Skipper> value;
AlgebraicGrammar<Iterator, Skipper> number;
};
/* ---------------------------------------------------------------------- */
static inline bool vector_eval(const ID & a, const ParserSection & section,
parsable_vector & result) {
std::string value = section.getParameter(a, _ppsc_current_and_parent_scope);
std::string::const_iterator b = value.begin();
std::string::const_iterator e = value.end();
parser::VectorGrammar<std::string::const_iterator, qi::space_type> grammar(
section);
return qi::phrase_parse(b, e, grammar, qi::space, result);
}
/* ---------------------------------------------------------------------- */
template <class Iterator, typename Skipper = spirit::unused_type>
struct MatrixGrammar : qi::grammar<Iterator, parsable_matrix(), Skipper> {
MatrixGrammar(const ParserSection & section)
: MatrixGrammar::base_type(start, "matrix_algebraic_grammar"),
vector(section) {
start = '[' >> matrix >> ']';
matrix =
(rows[phx::bind(&cont_add<parsable_matrix, parsable_vector>, lbs::_a,
lbs::_1)] >>
*(',' >> rows[phx::bind(&cont_add<parsable_matrix, parsable_vector>,
lbs::_a, lbs::_1)]))[lbs::_val = lbs::_a];
rows = eval_vector | vector;
eval_vector = (key[lbs::_pass = phx::bind(&vector_eval, lbs::_1, section,
lbs::_a)])[lbs::_val = lbs::_a];
key = qi::char_("a-zA-Z_") >>
*qi::char_("a-zA-Z_0-9") // coming from the InputFileGrammar
;
#if !defined(AKANTU_NDEBUG) && defined(AKANTU_CORE_CXX_11)
phx::function<algebraic_error_handler_> const error_handler =
algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start.name("matrix");
matrix.name("all_rows");
rows.name("rows");
vector.name("vector");
eval_vector.name("eval_vector");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(start);
qi::debug(matrix);
qi::debug(rows);
qi::debug(eval_vector);
qi::debug(key);
}
#endif
}
private:
qi::rule<Iterator, parsable_matrix(), Skipper> start;
qi::rule<Iterator, parsable_matrix(), qi::locals<parsable_matrix>, Skipper>
matrix;
qi::rule<Iterator, parsable_vector(), Skipper> rows;
qi::rule<Iterator, parsable_vector(), qi::locals<parsable_vector>, Skipper>
eval_vector;
qi::rule<Iterator, std::string(), Skipper> key;
VectorGrammar<Iterator, Skipper> vector;
};
/* ---------------------------------------------------------------------- */
/* Randon Generator */
/* ---------------------------------------------------------------------- */
struct ParsableRandomGenerator {
ParsableRandomGenerator(
Real base = Real(),
const RandomDistributionType & type = _rdt_not_defined,
const parsable_vector & parameters = parsable_vector())
: base(base), type(type), parameters(parameters) {}
Real base;
RandomDistributionType type;
parsable_vector parameters;
};
inline std::ostream & operator<<(std::ostream & stream,
const ParsableRandomGenerator & prg) {
stream << "prg[" << prg.base << " " << UInt(prg.type) << " "
<< prg.parameters << "]";
return stream;
}
/* ---------------------------------------------------------------------- */
template <class Iterator, typename Skipper = spirit::unused_type>
struct RandomGeneratorGrammar
: qi::grammar<Iterator, ParsableRandomGenerator(), Skipper> {
RandomGeneratorGrammar(const ParserSection & section)
: RandomGeneratorGrammar::base_type(start, "random_generator_grammar"),
number(section) {
start = generator.alias();
generator =
qi::hold[distribution[lbs::_val = lbs::_1]] |
number[lbs::_val = phx::construct<ParsableRandomGenerator>(lbs::_1)];
distribution = (number >> generator_type >> '[' >> generator_params >>
']')[lbs::_val = phx::construct<ParsableRandomGenerator>(
lbs::_1, lbs::_2, lbs::_3)];
generator_params =
(number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)] >>
*(',' > number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)]))[lbs::_val = lbs::_a];
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_ADD(r, data, elem) \
(BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 0, elem)), \
AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(BOOST_PP_TUPLE_ELEM(2, 0, elem)))
generator_type.add BOOST_PP_SEQ_FOR_EACH(
AKANTU_RANDOM_DISTRIBUTION_TYPE_ADD, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES);
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_ADD
#if !defined(AKANTU_NDEBUG) && defined(AKANTU_CORE_CXX_11)
phx::function<algebraic_error_handler_> const error_handler =
algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start.name("random-generator");
generator.name("random-generator");
distribution.name("random-distribution");
generator_type.name("generator-type");
generator_params.name("generator-parameters");
number.name("number");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(generator);
qi::debug(distribution);
qi::debug(generator_params);
}
#endif
}
private:
qi::rule<Iterator, ParsableRandomGenerator(), Skipper> start;
qi::rule<Iterator, ParsableRandomGenerator(), Skipper> generator;
qi::rule<Iterator, ParsableRandomGenerator(), Skipper> distribution;
qi::rule<Iterator, parsable_vector(), qi::locals<parsable_vector>, Skipper>
generator_params;
AlgebraicGrammar<Iterator, Skipper> number;
qi::symbols<char, RandomDistributionType> generator_type;
};
}
}
#endif /* __AKANTU_ALGEBRAIC_PARSER_HH__ */
diff --git a/src/io/parser/cppargparse/cppargparse.cc b/src/io/parser/cppargparse/cppargparse.cc
index 5c3280299..55ab84290 100644
--- a/src/io/parser/cppargparse/cppargparse.cc
+++ b/src/io/parser/cppargparse/cppargparse.cc
@@ -1,523 +1,523 @@
/**
* @file cppargparse.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
- * @date last modification: Wed Nov 11 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief implementation of the ArgumentParser
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cppargparse.hh"
#include <cstdlib>
#include <cstring>
#include <libgen.h>
#include <algorithm>
#include <iomanip>
#include <iostream>
#include <queue>
#include <sstream>
#include <string>
#include <exception>
#include <stdexcept>
#include <string.h>
namespace cppargparse {
/* -------------------------------------------------------------------------- */
static inline std::string to_upper(const std::string & str) {
std::string lstr = str;
std::transform(lstr.begin(), lstr.end(), lstr.begin(),
(int (*)(int))std::toupper);
return lstr;
}
/* -------------------------------------------------------------------------- */
/* ArgumentParser */
/* -------------------------------------------------------------------------- */
ArgumentParser::ArgumentParser() {
this->addArgument("-h;--help", "show this help message and exit", 0, _boolean,
false, true);
}
/* -------------------------------------------------------------------------- */
ArgumentParser::~ArgumentParser() {
for (auto it = arguments.begin(); it != arguments.end(); ++it) {
delete it->second;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::setParallelContext(int prank, int psize) {
this->prank = prank;
this->psize = psize;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::_exit(const std::string & msg, int status) {
if (prank == 0) {
if (msg != "") {
std::cerr << msg << std::endl;
std::cerr << std::endl;
}
this->print_help(std::cerr);
}
if (external_exit)
(*external_exit)(status);
else {
exit(status);
}
}
/* -------------------------------------------------------------------------- */
const ArgumentParser::Argument & ArgumentParser::
operator[](const std::string & name) const {
auto it = success_parsed.find(name);
if (it != success_parsed.end()) {
return *(it->second);
} else {
throw std::range_error("No argument named \'" + name +
"\' was found in the parsed argument," +
" make sur to specify it \'required\'" +
" or to give it a default value");
}
}
/* -------------------------------------------------------------------------- */
bool ArgumentParser::has(const std::string & name) const {
return (success_parsed.find(name) != success_parsed.end());
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type) {
_addArgument(name_or_flag, help, nargs, type);
}
/* -------------------------------------------------------------------------- */
ArgumentParser::_Argument &
ArgumentParser::_addArgument(const std::string & name, const std::string & help,
int nargs, ArgumentType type) {
_Argument * arg = nullptr;
switch (type) {
case _string: {
arg = new ArgumentStorage<std::string>();
break;
}
case _float: {
arg = new ArgumentStorage<double>();
break;
}
case _integer: {
arg = new ArgumentStorage<int>();
break;
}
case _boolean: {
arg = new ArgumentStorage<bool>();
break;
}
}
arg->help = help;
arg->nargs = nargs;
arg->type = type;
std::stringstream sstr(name);
std::string item;
std::vector<std::string> tmp_keys;
while (std::getline(sstr, item, ';')) {
tmp_keys.push_back(item);
}
int long_key = -1;
int short_key = -1;
bool problem = (tmp_keys.size() > 2) || (name == "");
for (auto it = tmp_keys.begin(); it != tmp_keys.end(); ++it) {
if (it->find("--") == 0) {
problem |= (long_key != -1);
long_key = it - tmp_keys.begin();
} else if (it->find("-") == 0) {
problem |= (long_key != -1);
short_key = it - tmp_keys.begin();
}
}
problem |= ((tmp_keys.size() == 2) && (long_key == -1 || short_key == -1));
if (problem) {
delete arg;
throw std::invalid_argument("Synthax of name or flags is not correct. "
"Possible synthax are \'-f\', \'-f;--foo\', "
"\'--foo\', \'bar\'");
}
if (long_key != -1) {
arg->name = tmp_keys[long_key];
arg->name.erase(0, 2);
} else if (short_key != -1) {
arg->name = tmp_keys[short_key];
arg->name.erase(0, 1);
} else {
arg->name = tmp_keys[0];
pos_args.push_back(arg);
arg->required = (nargs != _one_if_possible);
arg->is_positional = true;
}
arguments[arg->name] = arg;
if (!arg->is_positional) {
if (short_key != -1) {
std::string key = tmp_keys[short_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
if (long_key != -1) {
std::string key = tmp_keys[long_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
}
return *arg;
}
#if not HAVE_STRDUP
static char * strdup(const char * str) {
size_t len = strlen(str);
auto * x = (char *)malloc(len + 1); /* 1 for the null terminator */
if (!x)
return nullptr; /* malloc could not allocate memory */
memcpy(x, str, len + 1); /* copy the string into the new buffer */
return x;
}
#endif
/* -------------------------------------------------------------------------- */
void ArgumentParser::parse(int & argc, char **& argv, int flags,
bool parse_help) {
bool stop_in_not_parsed = flags & _stop_on_not_parsed;
bool remove_parsed = flags & _remove_parsed;
std::vector<std::string> argvs;
argvs.reserve(argc);
for (int i = 0; i < argc; ++i) {
argvs.emplace_back(argv[i]);
}
unsigned int current_position = 0;
if (this->program_name == "" && argc > 0) {
std::string prog = argvs[current_position];
const char * c_prog = prog.c_str();
char * c_prog_tmp = strdup(c_prog);
std::string base_prog(basename(c_prog_tmp));
this->program_name = base_prog;
std::free(c_prog_tmp);
}
std::queue<_Argument *> positional_queue;
for (auto it = pos_args.begin(); it != pos_args.end(); ++it)
positional_queue.push(*it);
std::vector<int> argvs_to_remove;
++current_position; // consume argv[0]
while (current_position < argvs.size()) {
std::string arg = argvs[current_position];
++current_position;
auto key_it = key_args.find(arg);
bool is_positional = false;
_Argument * argument_ptr = nullptr;
if (key_it == key_args.end()) {
if (positional_queue.empty()) {
if (stop_in_not_parsed)
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
continue;
} else {
argument_ptr = positional_queue.front();
is_positional = true;
--current_position;
}
} else {
argument_ptr = key_it->second;
}
if (remove_parsed && !is_positional && argument_ptr->name != "help") {
argvs_to_remove.push_back(current_position - 1);
}
_Argument & argument = *argument_ptr;
unsigned int min_nb_val = 0, max_nb_val = 0;
switch (argument.nargs) {
case _one_if_possible:
max_nb_val = 1;
break; // "?"
case _at_least_one:
min_nb_val = 1; // "+"
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it*/
case _any:
max_nb_val = argc - current_position;
break; // "*"
default:
min_nb_val = max_nb_val = argument.nargs; // "N"
}
std::vector<std::string> values;
unsigned int arg_consumed = 0;
if (max_nb_val <= (argc - current_position)) {
for (; arg_consumed < max_nb_val; ++arg_consumed) {
std::string v = argvs[current_position];
++current_position;
bool is_key = key_args.find(v) != key_args.end();
bool is_good_type = checkType(argument.type, v);
if (!is_key && is_good_type) {
values.push_back(v);
if (remove_parsed)
argvs_to_remove.push_back(current_position - 1);
} else {
// unconsume not parsed argument for optional
if (!is_positional || is_key)
--current_position;
break;
}
}
}
if (arg_consumed < min_nb_val) {
if (!is_positional) {
this->_exit("Not enought values for the argument " + argument.name +
" where provided",
EXIT_FAILURE);
} else {
if (stop_in_not_parsed)
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
}
} else {
if (is_positional)
positional_queue.pop();
if (!argument.parsed) {
success_parsed[argument.name] = &argument;
argument.parsed = true;
if ((argument.nargs == _one_if_possible || argument.nargs == 0) &&
arg_consumed == 0) {
if (argument.has_const)
argument.setToConst();
else if (argument.has_default)
argument.setToDefault();
} else {
argument.setValues(values);
}
} else {
this->_exit("Argument " + argument.name +
" already present in the list of argument",
EXIT_FAILURE);
}
}
}
for (auto ait = arguments.begin(); ait != arguments.end(); ++ait) {
_Argument & argument = *(ait->second);
if (!argument.parsed) {
if (argument.has_default) {
argument.setToDefault();
success_parsed[argument.name] = &argument;
}
if (argument.required) {
this->_exit("Argument " + argument.name + " required but not given!",
EXIT_FAILURE);
}
}
}
// removing the parsed argument if remove_parsed is true
if (argvs_to_remove.size()) {
std::vector<int>::const_iterator next_to_remove = argvs_to_remove.begin();
for (int i = 0, c = 0; i < argc; ++i) {
if (next_to_remove == argvs_to_remove.end() || i != *next_to_remove) {
argv[c] = argv[i];
++c;
} else {
if (next_to_remove != argvs_to_remove.end())
++next_to_remove;
}
}
argc -= argvs_to_remove.size();
}
this->argc = &argc;
this->argv = &argv;
if (this->arguments["help"]->parsed && parse_help) {
this->_exit();
}
}
/* -------------------------------------------------------------------------- */
bool ArgumentParser::checkType(ArgumentType type,
const std::string & value) const {
std::stringstream sstr(value);
switch (type) {
case _string: {
std::string s;
sstr >> s;
break;
}
case _float: {
double d;
sstr >> d;
break;
}
case _integer: {
int i;
sstr >> i;
break;
}
case _boolean: {
bool b;
sstr >> b;
break;
}
}
return (sstr.fail() == false);
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::printself(std::ostream & stream) const {
for (auto it = success_parsed.begin(); it != success_parsed.end(); ++it) {
const Argument & argument = *(it->second);
argument.printself(stream);
stream << std::endl;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage(std::ostream & stream) const {
stream << "Usage: " << this->program_name;
// print shorten usage
for (auto it = arguments.begin(); it != arguments.end(); ++it) {
const _Argument & argument = *(it->second);
if (!argument.is_positional) {
if (!argument.required)
stream << " [";
stream << argument.keys[0];
this->print_usage_nargs(stream, argument);
if (!argument.required)
stream << "]";
}
}
for (auto it = pos_args.begin(); it != pos_args.end(); ++it) {
const _Argument & argument = **it;
this->print_usage_nargs(stream, argument);
}
stream << std::endl;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage_nargs(std::ostream & stream,
const _Argument & argument) const {
std::string u_name = to_upper(argument.name);
switch (argument.nargs) {
case _one_if_possible:
stream << " [" << u_name << "]";
break;
case _at_least_one:
stream << " " << u_name;
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it */
case _any:
stream << " [" << u_name << " ...]";
break;
default:
for (int i = 0; i < argument.nargs; ++i) {
stream << " " << u_name;
}
}
}
void ArgumentParser::print_help(std::ostream & stream) const {
this->print_usage(stream);
if (!pos_args.empty()) {
stream << std::endl;
stream << "positional arguments:" << std::endl;
for (auto it = pos_args.begin(); it != pos_args.end(); ++it) {
const _Argument & argument = **it;
this->print_help_argument(stream, argument);
}
}
if (!key_args.empty()) {
stream << std::endl;
stream << "optional arguments:" << std::endl;
for (auto it = arguments.begin(); it != arguments.end(); ++it) {
const _Argument & argument = *(it->second);
if (!argument.is_positional) {
this->print_help_argument(stream, argument);
}
}
}
}
void ArgumentParser::print_help_argument(std::ostream & stream,
const _Argument & argument) const {
std::string key("");
if (argument.is_positional)
key = argument.name;
else {
std::stringstream sstr;
for (unsigned int i = 0; i < argument.keys.size(); ++i) {
if (i != 0)
sstr << ", ";
sstr << argument.keys[i];
this->print_usage_nargs(sstr, argument);
}
key = sstr.str();
}
stream << " " << std::left << std::setw(15) << key << " " << argument.help;
argument.printDefault(stream);
stream << std::endl;
}
}
diff --git a/src/io/parser/cppargparse/cppargparse.hh b/src/io/parser/cppargparse/cppargparse.hh
index 4a89f4c54..4608c9187 100644
--- a/src/io/parser/cppargparse/cppargparse.hh
+++ b/src/io/parser/cppargparse/cppargparse.hh
@@ -1,200 +1,200 @@
/**
* @file cppargparse.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Get the commandline options and store them as short, long and others
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <map>
#include <string>
#include <vector>
#ifndef __CPPARGPARSE_HH__
#define __CPPARGPARSE_HH__
/* -------------------------------------------------------------------------- */
namespace cppargparse {
/// define the types of the arguments
enum ArgumentType { _string, _integer, _float, _boolean };
/// Defines how many arguments to expect
enum ArgumentNargs { _one_if_possible = -1, _at_least_one = -2, _any = -3 };
/// Flags for the parse function of ArgumentParser
enum ParseFlags {
_no_flags = 0x0, ///< Default behavior
_stop_on_not_parsed = 0x1, ///< Stop on unknown arguments
_remove_parsed = 0x2 ///< Remove parsed arguments from argc argv
};
/// Helps to combine parse flags
inline ParseFlags operator|(const ParseFlags & a, const ParseFlags & b) {
auto tmp = ParseFlags(int(a) | int(b));
return tmp;
}
/* -------------------------------------------------------------------------- */
/**
* ArgumentParser is a class that mimics the Python argparse module
*/
class ArgumentParser {
public:
/// public definition of an argument
class Argument {
public:
Argument() : name(std::string()) {}
virtual ~Argument() = default;
virtual void printself(std::ostream & stream) const = 0;
template <class T> operator T() const;
std::string name;
};
/// constructor
ArgumentParser();
/// destroy everything
~ArgumentParser();
/// add an argument with a description
void addArgument(const std::string & name_or_flag, const std::string & help,
int nargs = 1, ArgumentType type = _string);
/// add an argument with an help and a default value
template <class T>
void addArgument(const std::string & name_or_flag, const std::string & help,
int nargs, ArgumentType type, T def);
/// add an argument with an help and a default + const value
template <class T>
void addArgument(const std::string & name_or_flag, const std::string & help,
int nargs, ArgumentType type, T def, T cons);
/// parse argc, argv
void parse(int & argc, char **& argv, int flags = _stop_on_not_parsed,
bool parse_help = true);
/// get the last argc parsed
int & getArgC() { return *(this->argc); }
/// get the last argv parsed
char **& getArgV() { return *(this->argv); }
/// print the content in the stream
void printself(std::ostream & stream) const;
/// print the help text
void print_help(std::ostream & stream = std::cout) const;
/// print the usage text
void print_usage(std::ostream & stream = std::cout) const;
/// set an external function to replace the exit function from the stdlib
void setExternalExitFunction(void (*external_exit)(int)) {
this->external_exit = external_exit;
}
/// accessor for a registered argument that was parsed, throw an exception if
/// the argument does not exist or was not set (parsed or default value)
const Argument & operator[](const std::string & name) const;
/// is the argument present
bool has(const std::string &) const;
/// set the parallel context to avoid multiple help messages in
/// multiproc/thread cases
void setParallelContext(int prank, int psize);
public:
/// Internal class describing the arguments
struct _Argument;
/// Stores that value of an argument
template <class T> class ArgumentStorage;
private:
/// Internal function to be used by the public addArgument
_Argument & _addArgument(const std::string & name_or_flag,
const std::string & description, int nargs,
ArgumentType type);
void _exit(const std::string & msg = "", int status = 0);
bool checkType(ArgumentType type, const std::string & value) const;
/// function to help to print help
void print_usage_nargs(std::ostream & stream,
const _Argument & argument) const;
/// function to help to print help
void print_help_argument(std::ostream & stream,
const _Argument & argument) const;
private:
/// public arguments storage
using Arguments = std::map<std::string, Argument *>;
/// internal arguments storage
using _Arguments = std::map<std::string, _Argument *>;
/// association key argument
using ArgumentKeyMap = std::map<std::string, _Argument *>;
/// position arguments
using PositionalArgument = std::vector<_Argument *>;
/// internal storage of arguments declared by the user
_Arguments arguments;
/// list of arguments successfully parsed
Arguments success_parsed;
/// keys associated to arguments
ArgumentKeyMap key_args;
/// positional arguments
PositionalArgument pos_args;
/// program name
std::string program_name;
/// exit function to use
void (*external_exit)(int){nullptr};
/// Parallel context, rank and size of communicator
int prank{0}, psize{1};
/// The last argc parsed (those are the modified version after parse)
int * argc;
/// The last argv parsed (those are the modified version after parse)
char *** argv;
};
}
inline std::ostream & operator<<(std::ostream & stream,
const cppargparse::ArgumentParser & argparse) {
argparse.printself(stream);
return stream;
}
#endif /* __CPPARGPARSE_HH__ */
#include "cppargparse_tmpl.hh"
diff --git a/src/io/parser/cppargparse/cppargparse_tmpl.hh b/src/io/parser/cppargparse/cppargparse_tmpl.hh
index c12727656..9dcad76df 100644
--- a/src/io/parser/cppargparse/cppargparse_tmpl.hh
+++ b/src/io/parser/cppargparse/cppargparse_tmpl.hh
@@ -1,240 +1,240 @@
/**
* @file cppargparse_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the templated part of the commandline argument
* parser
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include <stdexcept>
#ifndef __CPPARGPARSE_TMPL_HH__
#define __CPPARGPARSE_TMPL_HH__
namespace cppargparse {
/* -------------------------------------------------------------------------- */
/* Argument */
/* -------------------------------------------------------------------------- */
/// internal description of arguments
struct ArgumentParser::_Argument : public Argument {
_Argument() : Argument(), help(std::string()) {}
~_Argument() override = default;
void setValues(std::vector<std::string> & values) {
for (auto it = values.begin(); it != values.end(); ++it) {
this->addValue(*it);
}
}
virtual void addValue(std::string & value) = 0;
virtual void setToDefault() = 0;
virtual void setToConst() = 0;
std::ostream & printDefault(std::ostream & stream) const {
stream << std::boolalpha;
if (has_default) {
stream << " (default: ";
this->_printDefault(stream);
stream << ")";
}
if (has_const) {
stream << " (const: ";
this->_printConst(stream);
stream << ")";
}
return stream;
}
virtual std::ostream & _printDefault(std::ostream & stream) const = 0;
virtual std::ostream & _printConst(std::ostream & stream) const = 0;
std::string help;
int nargs{1};
ArgumentType type{_string};
bool required{false};
bool parsed{false};
bool has_default{false};
bool has_const{false};
std::vector<std::string> keys;
bool is_positional{false};
};
/* -------------------------------------------------------------------------- */
/// typed storage of the arguments
template <class T>
class ArgumentParser::ArgumentStorage : public ArgumentParser::_Argument {
public:
ArgumentStorage() : _default(T()), _const(T()), values(std::vector<T>()) {}
void addValue(std::string & value) override {
std::stringstream sstr(value);
T t;
sstr >> t;
values.push_back(t);
}
void setToDefault() override {
values.clear();
values.push_back(_default);
}
void setToConst() override {
values.clear();
values.push_back(_const);
}
void printself(std::ostream & stream) const override {
stream << this->name << " =";
stream << std::boolalpha; // for boolean
for (auto vit = this->values.begin(); vit != this->values.end(); ++vit) {
stream << " " << *vit;
}
}
std::ostream & _printDefault(std::ostream & stream) const override {
stream << _default;
return stream;
}
std::ostream & _printConst(std::ostream & stream) const override {
stream << _const;
return stream;
}
T _default;
T _const;
std::vector<T> values;
};
/* -------------------------------------------------------------------------- */
template <>
inline void
ArgumentParser::ArgumentStorage<std::string>::addValue(std::string & value) {
values.push_back(value);
}
template <class T> struct is_vector {
enum { value = false };
};
template <class T> struct is_vector<std::vector<T>> {
enum { value = true };
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_vector = cppargparse::is_vector<T>::value>
struct cast_helper {
static T cast(const ArgumentParser::Argument & arg) {
const auto & _arg =
dynamic_cast<const ArgumentParser::ArgumentStorage<T> &>(arg);
if (_arg.values.size() == 1) {
return _arg.values[0];
} else {
throw std::length_error("Not enougth or too many argument where passed "
"for the command line argument: " +
arg.name);
}
}
};
template <class T> struct cast_helper<T, true> {
static T cast(const ArgumentParser::Argument & arg) {
const auto & _arg =
dynamic_cast<const ArgumentParser::ArgumentStorage<T> &>(arg);
return _arg.values;
}
};
/* -------------------------------------------------------------------------- */
template <class T> ArgumentParser::Argument::operator T() const {
return cast_helper<T>::cast(*this);
}
template <> inline ArgumentParser::Argument::operator const char *() const {
return cast_helper<std::string>::cast(*this).c_str();
}
template <> inline ArgumentParser::Argument::operator unsigned int() const {
return cast_helper<int>::cast(*this);
}
template <class T>
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, T def) {
_Argument & arg = _addArgument(name_or_flag, help, nargs, type);
dynamic_cast<ArgumentStorage<T> &>(arg)._default = def;
arg.has_default = true;
}
template <class T>
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, T def, T cons) {
_Argument & arg = _addArgument(name_or_flag, help, nargs, type);
dynamic_cast<ArgumentStorage<T> &>(arg)._default = def;
arg.has_default = true;
dynamic_cast<ArgumentStorage<T> &>(arg)._const = cons;
arg.has_const = true;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ArgumentParser::addArgument<const char *>(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, const char * def) {
this->addArgument<std::string>(name_or_flag, help, nargs, type, def);
}
template <>
inline void
ArgumentParser::addArgument<unsigned int>(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, unsigned int def) {
this->addArgument<int>(name_or_flag, help, nargs, type, def);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ArgumentParser::addArgument<const char *>(
const std::string & name_or_flag, const std::string & help, int nargs,
ArgumentType type, const char * def, const char * cons) {
this->addArgument<std::string>(name_or_flag, help, nargs, type, def, cons);
}
template <>
inline void ArgumentParser::addArgument<unsigned int>(
const std::string & name_or_flag, const std::string & help, int nargs,
ArgumentType type, unsigned int def, unsigned int cons) {
this->addArgument<int>(name_or_flag, help, nargs, type, def, cons);
}
}
#endif /* __AKANTU_CPPARGPARSE_TMPL_HH__ */
diff --git a/src/io/parser/input_file_parser.hh b/src/io/parser/input_file_parser.hh
index 3826abca1..8de5904c9 100644
--- a/src/io/parser/input_file_parser.hh
+++ b/src/io/parser/input_file_parser.hh
@@ -1,268 +1,268 @@
/**
* @file input_file_parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Tue May 19 2015
+ * @date last modification: Mon Dec 18 2017
*
* @brief Grammar definition for the input files
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// Boost
/* -------------------------------------------------------------------------- */
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/phoenix_bind.hpp>
#include <boost/spirit/include/phoenix_core.hpp>
#include <boost/spirit/include/phoenix_fusion.hpp>
#include <boost/spirit/include/phoenix_operator.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/variant/recursive_variant.hpp>
#ifndef __AKANTU_INPUT_FILE_PARSER_HH__
#define __AKANTU_INPUT_FILE_PARSER_HH__
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
namespace akantu {
namespace parser {
struct error_handler_ {
template <typename, typename, typename, typename> struct result {
using type = void;
};
template <typename Iterator>
void operator()(qi::info const & what, Iterator err_pos, Iterator /*first*/,
Iterator /*last*/) const {
spirit::classic::file_position pos = err_pos.get_position();
AKANTU_EXCEPTION("Parse error [ "
<< "Expecting " << what << " instead of \"" << *err_pos
<< "\" ]"
<< " in file " << pos.file << " line " << pos.line
<< " column " << pos.column << std::endl
<< "'" << err_pos.get_currentline() << "'" << std::endl
<< std::setw(pos.column) << " "
<< "^- here");
}
private:
};
static ParserSection & create_subsection(
const ParserType & type, const boost::optional<std::string> & opt_name,
const boost::optional<std::string> & opt_option, ParserSection & sect) {
std::string option = "";
if (opt_option)
option = *opt_option;
static size_t id = 12;
std::string name = "anonymous_" + std::to_string(id++);
if (opt_name)
name = *opt_name;
ParserSection sect_tmp(name, type, option, sect);
return sect.addSubSection(sect_tmp);
}
template <typename Iter>
static bool create_parameter(boost::iterator_range<Iter> & rng,
std::string & value, ParserSection & sect) {
try {
std::string name(rng.begin(), rng.end());
name = trim(name);
spirit::classic::file_position pos = rng.begin().get_position();
ParserParameter param_tmp(name, value, sect);
param_tmp.setDebugInfo(pos.file, pos.line, pos.column);
sect.addParameter(param_tmp);
} catch (debug::Exception & e) {
return false;
}
return true;
}
static std::string concatenate(const std::string & t1,
const std::string & t2) {
return (t1 + t2);
}
/* ---------------------------------------------------------------------- */
/* Grammars definitions */
/* ---------------------------------------------------------------------- */
template <class Iterator>
struct InputFileGrammar
: qi::grammar<Iterator, void(), typename Skipper<Iterator>::type> {
InputFileGrammar(ParserSection * sect)
: InputFileGrammar::base_type(start, "input_file_grammar"),
parent_section(sect) {
/* clang-format off */
start
= mini_section(parent_section)
;
mini_section
= *(
entry (lbs::_r1)
| section(lbs::_r1)
)
;
entry
= (
qi::raw[key]
>> '='
> value
) [ lbs::_pass = phx::bind(&create_parameter<Iterator>,
lbs::_1,
lbs::_2,
*lbs::_r1) ]
;
section
= (
qi::no_case[section_type]
> qi::lexeme
[
-section_name
> -section_option
]
) [ lbs::_a = &phx::bind(&create_subsection,
lbs::_1,
phx::at_c<0>(lbs::_2),
phx::at_c<1>(lbs::_2),
*lbs::_r1) ]
> '['
> mini_section(lbs::_a)
> ']'
;
section_name
= qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")
;
section_option
= (+ascii::space >> section_name) [ lbs::_val = lbs::_2 ]
;
key
= qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")
;
value
= (
mono_line_value [ lbs::_a = phx::bind(&concatenate, lbs::_a, lbs::_1) ]
> *(
'\\' > mono_line_value [ lbs::_a = phx::bind(&concatenate, lbs::_a, lbs::_1) ]
)
) [ lbs::_val = lbs::_a ]
;
mono_line_value
= qi::lexeme
[
+(qi::char_ - (qi::char_('=') | spirit::eol | '#' | ';' | '\\'))
]
;
skipper
= ascii::space
| "#" >> *(qi::char_ - spirit::eol)
;
/* clang-format on */
#define AKANTU_SECTION_TYPE_ADD(r, data, elem) \
(BOOST_PP_STRINGIZE(elem), BOOST_PP_CAT(ParserType::_, elem))
section_type.add BOOST_PP_SEQ_FOR_EACH(AKANTU_SECTION_TYPE_ADD, _,
AKANTU_SECTION_TYPES);
#undef AKANTU_SECTION_TYPE_ADD
#if !defined(AKANTU_NDEBUG) && defined(AKANTU_CORE_CXX_11)
phx::function<error_handler_> const error_handler = error_handler_();
qi::on_error<qi::fail>(start,
error_handler(lbs::_4, lbs::_3, lbs::_1, lbs::_2));
#endif
section.name("section");
section_name.name("section-name");
section_option.name("section-option");
mini_section.name("section-content");
entry.name("parameter");
key.name("parameter-name");
value.name("parameter-value");
section_type.name("section-types-list");
mono_line_value.name("mono-line-value");
#if !defined AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
// qi::debug(section);
qi::debug(section_name);
qi::debug(section_option);
// qi::debug(mini_section);
// qi::debug(entry);
qi::debug(key);
qi::debug(value);
qi::debug(mono_line_value);
}
#endif
}
const std::string & getErrorMessage() const { return error_message; };
using skipper_type = typename Skipper<Iterator>::type;
skipper_type skipper;
private:
std::string error_message;
qi::rule<Iterator, void(ParserSection *), skipper_type> mini_section;
qi::rule<Iterator, void(ParserSection *), qi::locals<ParserSection *>,
skipper_type>
section;
qi::rule<Iterator, void(), skipper_type> start;
qi::rule<Iterator, std::string()> section_name;
qi::rule<Iterator, std::string()> section_option;
qi::rule<Iterator, void(ParserSection *), skipper_type> entry;
qi::rule<Iterator, std::string(), skipper_type> key;
qi::rule<Iterator, std::string(), qi::locals<std::string>, skipper_type>
value;
qi::rule<Iterator, std::string(), skipper_type> mono_line_value;
qi::symbols<char, ParserType> section_type;
ParserSection * parent_section;
};
}
} // akantu
#endif /* __AKANTU_INPUT_FILE_PARSER_HH__ */
diff --git a/src/io/parser/parameter_registry.cc b/src/io/parser/parameter_registry.cc
index 1e63f3127..69f2a0c47 100644
--- a/src/io/parser/parameter_registry.cc
+++ b/src/io/parser/parameter_registry.cc
@@ -1,154 +1,154 @@
/**
* @file parameter_registry.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Nov 13 2013
- * @date last modification: Thu Nov 19 2015
+ * @date creation: Wed May 04 2016
+ * @date last modification: Thu Feb 01 2018
*
* @brief Parameter Registry and derived classes implementation
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <utility>
#include "parameter_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
Parameter::Parameter() : name(""), description("") {}
/* -------------------------------------------------------------------------- */
Parameter::Parameter(std::string name, std::string description,
ParameterAccessType param_type)
: name(std::move(name)), description(std::move(description)),
param_type(param_type) {}
/* -------------------------------------------------------------------------- */
bool Parameter::isWritable() const { return param_type & _pat_writable; }
/* -------------------------------------------------------------------------- */
bool Parameter::isReadable() const { return param_type & _pat_readable; }
/* -------------------------------------------------------------------------- */
bool Parameter::isInternal() const { return param_type & _pat_internal; }
/* -------------------------------------------------------------------------- */
bool Parameter::isParsable() const { return param_type & _pat_parsable; }
/* -------------------------------------------------------------------------- */
void Parameter::setAccessType(ParameterAccessType ptype) {
this->param_type = ptype;
}
/* -------------------------------------------------------------------------- */
void Parameter::printself(std::ostream & stream) const {
stream << " ";
if (isInternal())
stream << "iii";
else {
if (isReadable())
stream << "r";
else
stream << "-";
if (isWritable())
stream << "w";
else
stream << "-";
if (isParsable())
stream << "p";
else
stream << "-";
}
stream << " ";
std::stringstream sstr;
sstr << name;
UInt width = std::max(int(10 - sstr.str().length()), 0);
sstr.width(width);
if (description != "") {
sstr << " [" << description << "]";
}
stream << sstr.str();
width = std::max(int(50 - sstr.str().length()), 0);
stream.width(width);
stream << " : ";
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
ParameterRegistry::ParameterRegistry() = default;
/* -------------------------------------------------------------------------- */
ParameterRegistry::~ParameterRegistry() {
std::map<std::string, Parameter *>::iterator it, end;
for (it = params.begin(); it != params.end(); ++it) {
delete it->second;
it->second = NULL;
}
this->params.clear();
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
Parameters::const_iterator it;
for (it = params.begin(); it != params.end(); ++it) {
stream << space;
it->second->printself(stream);
}
SubRegisteries::const_iterator sub_it;
for (sub_it = sub_registries.begin(); sub_it != sub_registries.end();
++sub_it) {
stream << space << "Registry [" << std::endl;
sub_it->second->printself(stream, indent + 1);
stream << space << "]";
}
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::registerSubRegistry(const ID & id,
ParameterRegistry & registry) {
sub_registries[id] = ®istry;
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::setParameterAccessType(const std::string & name,
ParameterAccessType ptype) {
auto it = params.find(name);
if (it == params.end())
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
Parameter & param = *(it->second);
param.setAccessType(ptype);
}
} // akantu
diff --git a/src/io/parser/parameter_registry.hh b/src/io/parser/parameter_registry.hh
index af649bdc8..733883f78 100644
--- a/src/io/parser/parameter_registry.hh
+++ b/src/io/parser/parameter_registry.hh
@@ -1,222 +1,221 @@
/**
* @file parameter_registry.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
- * @date last modification: Thu Dec 17 2015
+ * @date last modification: Tue Jan 30 2018
*
* @brief Interface of the parameter registry
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PARAMETER_REGISTRY_HH__
#define __AKANTU_PARAMETER_REGISTRY_HH__
namespace akantu {
class ParserParameter;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Defines the access modes of parsable parameters
enum ParameterAccessType {
_pat_internal = 0x0001,
_pat_writable = 0x0010,
_pat_readable = 0x0100,
_pat_modifiable = 0x0110, //<_pat_readable | _pat_writable,
_pat_parsable = 0x1000,
_pat_parsmod = 0x1110 //< _pat_parsable | _pat_modifiable
};
/// Bit-wise operator between access modes
inline ParameterAccessType operator|(const ParameterAccessType & a,
const ParameterAccessType & b) {
auto tmp = ParameterAccessType(UInt(a) | UInt(b));
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T> class ParameterTyped;
/**
* Interface for the Parameter
*/
class Parameter {
public:
Parameter();
Parameter(std::string name, std::string description,
ParameterAccessType param_type);
virtual ~Parameter() = default;
/* ------------------------------------------------------------------------ */
bool isInternal() const;
bool isWritable() const;
bool isReadable() const;
bool isParsable() const;
void setAccessType(ParameterAccessType ptype);
/* ------------------------------------------------------------------------ */
template <typename T, typename V> void set(const V & value);
virtual void setAuto(const ParserParameter & param);
template <typename T> T & get();
template <typename T> const T & get() const;
virtual inline operator Real() const { throw std::bad_cast(); };
template <typename T> inline operator T() const;
/* ------------------------------------------------------------------------ */
virtual void printself(std::ostream & stream) const;
virtual const std::type_info & type() const = 0;
protected:
/// Returns const instance of templated sub-class ParameterTyped
template <typename T> const ParameterTyped<T> & getParameterTyped() const;
/// Returns instance of templated sub-class ParameterTyped
template <typename T> ParameterTyped<T> & getParameterTyped();
protected:
/// Name of parameter
std::string name;
private:
/// Description of parameter
std::string description;
/// Type of access
ParameterAccessType param_type{_pat_internal};
};
/* -------------------------------------------------------------------------- */
/* Typed Parameter */
/* -------------------------------------------------------------------------- */
/**
* Type parameter transfering a ParserParameter (string: string) to a typed
* parameter in the memory of the p
*/
template <typename T> class ParameterTyped : public Parameter {
public:
ParameterTyped(std::string name, std::string description,
ParameterAccessType param_type, T & param);
/* ------------------------------------------------------------------------ */
template <typename V> void setTyped(const V & value);
void setAuto(const ParserParameter & param) override;
T & getTyped();
const T & getTyped() const;
void printself(std::ostream & stream) const override;
inline operator Real() const override;
inline const std::type_info & type() const override { return typeid(T); }
private:
/// Value of parameter
T & param;
};
/* -------------------------------------------------------------------------- */
/* Parsable Interface */
/* -------------------------------------------------------------------------- */
/// Defines interface for classes to manipulate parsable parameters
class ParameterRegistry {
public:
ParameterRegistry();
virtual ~ParameterRegistry();
/* ------------------------------------------------------------------------ */
/// Add parameter to the params map
template <typename T>
void registerParam(std::string name, T & variable, ParameterAccessType type,
const std::string & description = "");
/// Add parameter to the params map (with default value)
template <typename T>
void registerParam(std::string name, T & variable, const T & default_value,
ParameterAccessType type,
const std::string & description = "");
/*------------------------------------------------------------------------- */
protected:
void registerSubRegistry(const ID & id, ParameterRegistry & registry);
/* ------------------------------------------------------------------------ */
public:
/// Set value to a parameter (with possible different type)
template <typename T, typename V>
void setMixed(const std::string & name, const V & value);
/// Set value to a parameter
template <typename T> void set(const std::string & name, const T & value);
/// Get value of a parameter
inline const Parameter & get(const std::string & name) const;
std::vector<ID> listParameters() const {
std::vector<ID> params;
for (auto & pair : this->params)
params.push_back(pair.first);
return params;
}
std::vector<ID> listSubRegisteries() const {
std::vector<ID> subs;
for (auto & pair : this->sub_registries)
subs.push_back(pair.first);
return subs;
}
protected:
template <typename T> T & get_(const std::string & name);
protected:
void setParameterAccessType(const std::string & name,
ParameterAccessType ptype);
/* ------------------------------------------------------------------------ */
virtual void printself(std::ostream & stream, int indent) const;
protected:
/// Parameters map
using Parameters = std::map<std::string, Parameter *>;
Parameters params;
/// list of sub-registries
using SubRegisteries = std::map<std::string, ParameterRegistry *>;
SubRegisteries sub_registries;
/// should accessor check in sub registries
bool consisder_sub{true};
};
} // akantu
#include "parameter_registry_tmpl.hh"
#endif /* __AKANTU_PARAMETER_REGISTRY_HH__ */
diff --git a/src/io/parser/parameter_registry_tmpl.hh b/src/io/parser/parameter_registry_tmpl.hh
index 935338739..dd9f00d4d 100644
--- a/src/io/parser/parameter_registry_tmpl.hh
+++ b/src/io/parser/parameter_registry_tmpl.hh
@@ -1,391 +1,390 @@
/**
* @file parameter_registry_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Aug 09 2012
- * @date last modification: Fri Mar 27 2015
+ * @date creation: Wed May 04 2016
+ * @date last modification: Tue Jan 30 2018
*
- * @brief implementation of the templated part of ParameterRegistry class and
+ * @brief implementation of the templated part of ParameterRegistry class and
* the derivated ones
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_error.hh"
#include "aka_iterators.hh"
#include "parameter_registry.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <string>
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PARAMETER_REGISTRY_TMPL_HH__
#define __AKANTU_PARAMETER_REGISTRY_TMPL_HH__
namespace akantu {
namespace debug {
class ParameterException : public Exception {
public:
ParameterException(const std::string & name, const std::string & message)
: Exception(message), name(name) {}
const std::string & name;
};
class ParameterUnexistingException : public ParameterException {
public:
ParameterUnexistingException(const std::string & name,
const ParameterRegistry & registery)
: ParameterException(
name, "Parameter " + name + " does not exists in this scope") {
auto && params = registery.listParameters();
this->_info =
std::accumulate(params.begin(), params.end(),
this->_info + "\n Possible parameters are: ",
[](auto && str, auto && param) {
static auto first = true;
auto && ret = str + (first ? " " : ", ") + param;
first = false;
return ret;
});
}
};
class ParameterAccessRightException : public ParameterException {
public:
ParameterAccessRightException(const std::string & name,
const std::string & perm)
: ParameterException(name, "Parameter " + name + " is not " + perm) {}
};
class ParameterWrongTypeException : public ParameterException {
public:
ParameterWrongTypeException(const std::string & name,
const std::type_info & wrong_type,
const std::type_info & type)
: ParameterException(name,
"Parameter " + name +
" type error, cannot convert " +
debug::demangle(type.name()) + " to " +
debug::demangle(wrong_type.name())) {}
};
} // namespace debug
/* -------------------------------------------------------------------------- */
template <typename T>
const ParameterTyped<T> & Parameter::getParameterTyped() const {
try {
const auto & tmp = dynamic_cast<const ParameterTyped<T> &>(*this);
return tmp;
} catch (std::bad_cast &) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterWrongTypeException(name, typeid(T), this->type()));
}
}
/* -------------------------------------------------------------------------- */
template <typename T> ParameterTyped<T> & Parameter::getParameterTyped() {
try {
auto & tmp = dynamic_cast<ParameterTyped<T> &>(*this);
return tmp;
} catch (std::bad_cast &) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterWrongTypeException(name, typeid(T), this->type()));
}
}
/* ------------------------------------------------------------------------ */
template <typename T, typename V> void Parameter::set(const V & value) {
if (!(isWritable()))
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "writable"));
ParameterTyped<T> & typed_param = getParameterTyped<T>();
typed_param.setTyped(value);
}
/* ------------------------------------------------------------------------ */
inline void Parameter::setAuto(__attribute__((unused))
const ParserParameter & value) {
if (!(isParsable()))
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "parsable"));
}
/* -------------------------------------------------------------------------- */
template <typename T> const T & Parameter::get() const {
if (!(isReadable()))
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "readable"));
const ParameterTyped<T> & typed_param = getParameterTyped<T>();
return typed_param.getTyped();
}
/* -------------------------------------------------------------------------- */
template <typename T> T & Parameter::get() {
ParameterTyped<T> & typed_param = getParameterTyped<T>();
if (!(isReadable()) || !(this->isWritable()))
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "accessible"));
return typed_param.getTyped();
}
/* -------------------------------------------------------------------------- */
template <typename T> inline Parameter::operator T() const {
return this->get<T>();
}
/* -------------------------------------------------------------------------- */
template <typename T>
ParameterTyped<T>::ParameterTyped(std::string name, std::string description,
ParameterAccessType param_type, T & param)
: Parameter(name, description, param_type), param(param) {}
/* -------------------------------------------------------------------------- */
template <typename T>
template <typename V>
void ParameterTyped<T>::setTyped(const V & value) {
param = value;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParameterTyped<T>::setAuto(const ParserParameter & value) {
Parameter::setAuto(value);
param = static_cast<T>(value);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<std::string>::setAuto(const ParserParameter & value) {
Parameter::setAuto(value);
param = value.getValue();
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<Vector<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Vector<Real> tmp = in_param;
if (param.size() == 0) {
param = tmp;
} else {
for (UInt i = 0; i < param.size(); ++i) {
param(i) = tmp(i);
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<Matrix<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Matrix<Real> tmp = in_param;
if (param.size() == 0) {
param = tmp;
} else {
for (UInt i = 0; i < param.rows(); ++i) {
for (UInt j = 0; j < param.cols(); ++j) {
param(i, j) = tmp(i, j);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T> const T & ParameterTyped<T>::getTyped() const {
return param;
}
/* -------------------------------------------------------------------------- */
template <typename T> T & ParameterTyped<T>::getTyped() { return param; }
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParameterTyped<T>::printself(std::ostream & stream) const {
Parameter::printself(stream);
stream << param << "\n";
}
/* -------------------------------------------------------------------------- */
template <typename T> class ParameterTyped<std::vector<T>> : public Parameter {
public:
ParameterTyped(std::string name, std::string description,
ParameterAccessType param_type, std::vector<T> & param)
: Parameter(name, description, param_type), param(param) {}
/* ------------------------------------------------------------------------ */
template <typename V> void setTyped(const V & value) { param = value; }
void setAuto(const ParserParameter & value) override {
Parameter::setAuto(value);
param.clear();
const std::vector<T> & tmp = value;
for (auto && z : tmp) {
param.emplace_back(z);
}
}
std::vector<T> & getTyped() { return param; }
const std::vector<T> & getTyped() const { return param; }
void printself(std::ostream & stream) const override {
Parameter::printself(stream);
stream << "[ ";
for (auto && v : param)
stream << v << " ";
stream << "]\n";
}
inline const std::type_info & type() const override {
return typeid(std::vector<T>);
}
private:
/// Value of parameter
std::vector<T> & param;
};
/* ------o--------------------------------------------------------------------
*/
template <>
inline void ParameterTyped<bool>::printself(std::ostream & stream) const {
Parameter::printself(stream);
stream << std::boolalpha << param << "\n";
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::registerParam(std::string name, T & variable,
ParameterAccessType type,
const std::string & description) {
auto it = params.find(name);
if (it != params.end())
AKANTU_CUSTOM_EXCEPTION(debug::ParameterException(
name, "Parameter named " + name + " already registered."));
auto * param = new ParameterTyped<T>(name, description, type, variable);
params[name] = param;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::registerParam(std::string name, T & variable,
const T & default_value,
ParameterAccessType type,
const std::string & description) {
variable = default_value;
registerParam(name, variable, type, description);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename V>
void ParameterRegistry::setMixed(const std::string & name, const V & value) {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
it->second->setMixed<T>(name, value);
}
} else {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
} else {
Parameter & param = *(it->second);
param.set<T>(value);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::set(const std::string & name, const T & value) {
this->template setMixed<T>(name, value);
}
/* -------------------------------------------------------------------------- */
template <typename T> T & ParameterRegistry::get_(const std::string & name) {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
try {
return it->second->get_<T>(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
Parameter & param = *(it->second);
return param.get<T>();
}
/* -------------------------------------------------------------------------- */
const Parameter & ParameterRegistry::get(const std::string & name) const {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
try {
return it->second->get(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
Parameter & param = *(it->second);
return param;
}
/* -------------------------------------------------------------------------- */
namespace {
namespace details {
template <class T, class R, class Enable = void> struct CastHelper {
static R convert(const T &) { throw std::bad_cast(); }
};
template <class T, class R>
struct CastHelper<T, R,
std::enable_if_t<std::is_convertible<T, R>::value>> {
static R convert(const T & val) { return val; }
};
} // namespace details
} // namespace
template <typename T> inline ParameterTyped<T>::operator Real() const {
if (not isReadable())
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "accessible"));
return details::CastHelper<T, Real>::convert(param);
}
} // namespace akantu
#endif /* __AKANTU_PARAMETER_REGISTRY_TMPL_HH__ */
diff --git a/src/io/parser/parsable.cc b/src/io/parser/parsable.cc
index 89b41a458..c779bd11f 100644
--- a/src/io/parser/parsable.cc
+++ b/src/io/parser/parsable.cc
@@ -1,109 +1,110 @@
/**
* @file parsable.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Thu Nov 19 2015
+ * @date last modification: Thu Feb 08 2018
*
* @brief Parsable implementation
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "parsable.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Parsable::Parsable(const ParserType & section_type, const ID & id)
: section_type(section_type), pid(id) {
this->consisder_sub = false;
}
/* -------------------------------------------------------------------------- */
Parsable::~Parsable() = default;
/* -------------------------------------------------------------------------- */
void Parsable::registerSubSection(const ParserType & type,
const std::string & name,
Parsable & sub_section) {
SubSectionKey key(type, name);
sub_sections[key] = &sub_section;
this->registerSubRegistry(name, sub_section);
}
/* -------------------------------------------------------------------------- */
void Parsable::parseParam(const ParserParameter & in_param) {
auto it = params.find(in_param.getName());
if (it == params.end()) {
if (Parser::isPermissive()) {
AKANTU_DEBUG_WARNING("No parameter named " << in_param.getName()
<< " registered in " << pid
<< ".");
return;
} else
AKANTU_EXCEPTION("No parameter named " << in_param.getName()
<< " registered in " << pid
<< ".");
}
Parameter & param = *(it->second);
param.setAuto(in_param);
}
/* -------------------------------------------------------------------------- */
void Parsable::parseSection(const ParserSection & section) {
if (section_type != section.getType())
AKANTU_EXCEPTION("The object "
<< pid << " is meant to parse section of type "
<< section_type << ", so it cannot parse section of type "
<< section.getType());
auto params = section.getParameters();
auto it = params.first;
for (; it != params.second; ++it) {
parseParam(*it);
}
auto sit = section.getSubSections().first;
for (; sit != section.getSubSections().second; ++sit) {
parseSubSection(*sit);
}
}
/* -------------------------------------------------------------------------- */
void Parsable::parseSubSection(const ParserSection & section) {
SubSectionKey key(section.getType(), section.getName());
auto it = sub_sections.find(key);
if (it != sub_sections.end()) {
it->second->parseSection(section);
} else if (!Parser::isPermissive()) {
AKANTU_EXCEPTION("No parsable defined for sub sections of type <"
<< key.first << "," << key.second << "> in " << pid);
} else {
AKANTU_DEBUG_WARNING("No parsable defined for sub sections of type <"
<< key.first << "," << key.second << "> in " << pid);
}
}
} // akantu
diff --git a/src/io/parser/parsable.hh b/src/io/parser/parsable.hh
index 5eb45a4e8..542c64769 100644
--- a/src/io/parser/parsable.hh
+++ b/src/io/parser/parsable.hh
@@ -1,74 +1,73 @@
/**
- * @file parameter_registry.hh
+ * @file parsable.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
- * @date last modification: Thu Dec 17 2015
+ * @date last modification: Fri Dec 08 2017
*
* @brief Interface of the parameter registry
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parameter_registry.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PARSABLE_HH__
#define __AKANTU_PARSABLE_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Parsable Interface */
/* -------------------------------------------------------------------------- */
/// Defines interface for classes to manipulate parsable parameters
class Parsable : public ParameterRegistry {
public:
Parsable(const ParserType & section_type, const ID & id = std::string());
~Parsable() override;
/// Add subsection to the sub_sections map
void registerSubSection(const ParserType & type, const std::string & name,
Parsable & sub_section);
/* ------------------------------------------------------------------------ */
public:
virtual void parseSection(const ParserSection & section);
virtual void parseSubSection(const ParserSection & section);
virtual void parseParam(const ParserParameter & parameter);
private:
ParserType section_type;
/// ID of parsable object
ID pid;
using SubSectionKey = std::pair<ParserType, std::string>;
using SubSections = std::map<SubSectionKey, Parsable *>;
/// Subsections map
SubSections sub_sections;
};
} // namespace akantu
#endif /* __AKANTU_PARSABLE_HH__ */
diff --git a/src/io/parser/parser.cc b/src/io/parser/parser.cc
index b21c0db0f..30b34ad8c 100644
--- a/src/io/parser/parser.cc
+++ b/src/io/parser/parser.cc
@@ -1,101 +1,101 @@
/**
* @file parser.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Wed Jan 13 2016
+ * @date last modification: Thu Feb 01 2018
*
* @brief implementation of the parser
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// STL
#include <fstream>
#include <iomanip>
#include <map>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ParserSection::~ParserSection() { this->clean(); }
/* -------------------------------------------------------------------------- */
ParserParameter & ParserSection::addParameter(const ParserParameter & param) {
if (parameters.find(param.getName()) != parameters.end())
AKANTU_EXCEPTION("The parameter \"" + param.getName() +
"\" is already defined in this section");
return (parameters
.insert(std::pair<std::string, ParserParameter>(param.getName(),
param))
.first->second);
}
/* -------------------------------------------------------------------------- */
ParserSection & ParserSection::addSubSection(const ParserSection & section) {
return ((sub_sections_by_type.insert(std::pair<ParserType, ParserSection>(
section.getType(), section)))
->second);
}
/* -------------------------------------------------------------------------- */
std::string Parser::getLastParsedFile() const { return last_parsed_file; }
/* -------------------------------------------------------------------------- */
void ParserSection::printself(std::ostream & stream,
unsigned int indent) const {
std::string space;
std::string ind = AKANTU_INDENT;
for (unsigned int i = 0; i < indent; i++, space += ind)
;
stream << space << "Section(" << this->type << ") " << this->name
<< (option != "" ? (" " + option) : "") << " [" << std::endl;
if (!this->parameters.empty()) {
stream << space << ind << "Parameters [" << std::endl;
auto pit = this->parameters.begin();
for (; pit != this->parameters.end(); ++pit) {
stream << space << ind << " + ";
pit->second.printself(stream);
stream << std::endl;
}
stream << space << ind << "]" << std::endl;
}
if (!this->sub_sections_by_type.empty()) {
stream << space << ind << "Subsections [" << std::endl;
auto sit = this->sub_sections_by_type.begin();
for (; sit != this->sub_sections_by_type.end(); ++sit)
sit->second.printself(stream, indent + 2);
stream << std::endl;
stream << space << ind << "]" << std::endl;
}
stream << space << "]" << std::endl;
}
} // akantu
diff --git a/src/io/parser/parser.hh b/src/io/parser/parser.hh
index d97850eef..c762f0493 100644
--- a/src/io/parser/parser.hh
+++ b/src/io/parser/parser.hh
@@ -1,506 +1,506 @@
/**
* @file parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Wed Jan 13 2016
+ * @date last modification: Fri Dec 08 2017
*
* @brief File parser interface
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PARSER_HH__
#define __AKANTU_PARSER_HH__
namespace akantu {
// clang-format off
#define AKANTU_SECTION_TYPES \
(cohesive_inserter) \
(contact) \
(embedded_interface) \
(friction) \
(global) \
(heat) \
(integration_scheme) \
(material) \
(mesh) \
(model) \
(model_solver) \
(neighborhood) \
(neighborhoods) \
(non_linear_solver) \
(non_local) \
(rules) \
(solver) \
(time_step_solver) \
(user) \
(weight_function) \
(not_defined)
// clang-format on
/// Defines the possible section types
AKANTU_ENUM_DECLARE(ParserType, AKANTU_SECTION_TYPES)
AKANTU_ENUM_OUTPUT_STREAM(ParserType, AKANTU_SECTION_TYPES)
AKANTU_ENUM_INPUT_STREAM(ParserType, AKANTU_SECTION_TYPES)
/// Defines the possible search contexts/scopes (for parameter search)
enum ParserParameterSearchCxt {
_ppsc_current_scope = 0x1,
_ppsc_parent_scope = 0x2,
_ppsc_current_and_parent_scope = 0x3
};
/* ------------------------------------------------------------------------ */
/* Parameters Class */
/* ------------------------------------------------------------------------ */
class ParserSection;
/// @brief The ParserParameter objects represent the end of tree branches as
/// they
/// are the different informations contained in the input file.
class ParserParameter {
public:
ParserParameter()
: name(std::string()), value(std::string()), dbg_filename(std::string()) {
}
ParserParameter(const std::string & name, const std::string & value,
const ParserSection & parent_section)
: parent_section(&parent_section), name(name), value(value),
dbg_filename(std::string()) {}
ParserParameter(const ParserParameter & param) = default;
virtual ~ParserParameter() = default;
/// Get parameter name
const std::string & getName() const { return name; }
/// Get parameter value
const std::string & getValue() const { return value; }
/// Set info for debug output
void setDebugInfo(const std::string & filename, UInt line, UInt column) {
dbg_filename = filename;
dbg_line = line;
dbg_column = column;
}
template <typename T> inline operator T() const;
// template <typename T> inline operator Vector<T>() const;
// template <typename T> inline operator Matrix<T>() const;
/// Print parameter info in stream
void printself(std::ostream & stream,
__attribute__((unused)) unsigned int indent = 0) const {
stream << name << ": " << value << " (" << dbg_filename << ":" << dbg_line
<< ":" << dbg_column << ")";
}
private:
void setParent(const ParserSection & sect) { parent_section = § }
friend class ParserSection;
private:
/// Pointer to the parent section
const ParserSection * parent_section{nullptr};
/// Name of the parameter
std::string name;
/// Value of the parameter
std::string value;
/// File for debug output
std::string dbg_filename;
/// Position of parameter in parsed file
UInt dbg_line, dbg_column;
};
/* ------------------------------------------------------------------------ */
/* Sections Class */
/* ------------------------------------------------------------------------ */
/// ParserSection represents a branch of the parsing tree.
class ParserSection {
public:
using SubSections = std::multimap<ParserType, ParserSection>;
using Parameters = std::map<std::string, ParserParameter>;
private:
using const_section_iterator_ = SubSections::const_iterator;
public:
/* ------------------------------------------------------------------------ */
/* SubSection iterator */
/* ------------------------------------------------------------------------ */
/// Iterator on sections
class const_section_iterator {
public:
using iterator_category = std::forward_iterator_tag;
using value_type = ParserSection;
using pointer = ParserSection *;
using reference = ParserSection &;
const_section_iterator() = default;
const_section_iterator(const const_section_iterator_ & it) : it(it) {}
const_section_iterator(const const_section_iterator & other) = default;
const_section_iterator &
operator=(const const_section_iterator & other) = default;
const ParserSection & operator*() const { return it->second; }
const ParserSection * operator->() const { return &(it->second); }
bool operator==(const const_section_iterator & other) const {
return it == other.it;
}
bool operator!=(const const_section_iterator & other) const {
return it != other.it;
}
const_section_iterator & operator++() {
++it;
return *this;
}
const_section_iterator operator++(int) {
const_section_iterator tmp = *this;
operator++();
return tmp;
}
private:
const_section_iterator_ it;
};
/* ------------------------------------------------------------------------ */
/* Parameters iterator */
/* ------------------------------------------------------------------------ */
/// Iterator on parameters
class const_parameter_iterator {
public:
const_parameter_iterator(const const_parameter_iterator & other) = default;
const_parameter_iterator(const Parameters::const_iterator & it) : it(it) {}
const_parameter_iterator &
operator=(const const_parameter_iterator & other) {
if (this != &other) {
it = other.it;
}
return *this;
}
const ParserParameter & operator*() const { return it->second; }
const ParserParameter * operator->() { return &(it->second); };
bool operator==(const const_parameter_iterator & other) const {
return it == other.it;
}
bool operator!=(const const_parameter_iterator & other) const {
return it != other.it;
}
const_parameter_iterator & operator++() {
++it;
return *this;
}
const_parameter_iterator operator++(int) {
const_parameter_iterator tmp = *this;
operator++();
return tmp;
}
private:
Parameters::const_iterator it;
};
/* ---------------------------------------------------------------------- */
ParserSection() : name(std::string()) {}
ParserSection(const std::string & name, ParserType type)
: parent_section(nullptr), name(name), type(type) {}
ParserSection(const std::string & name, ParserType type,
const std::string & option,
const ParserSection & parent_section)
: parent_section(&parent_section), name(name), type(type),
option(option) {}
ParserSection(const ParserSection & section)
: parent_section(section.parent_section), name(section.name),
type(section.type), option(section.option),
parameters(section.parameters),
sub_sections_by_type(section.sub_sections_by_type) {
setChldrenPointers();
}
ParserSection & operator=(const ParserSection & other) {
if (&other != this) {
parent_section = other.parent_section;
name = other.name;
type = other.type;
option = other.option;
parameters = other.parameters;
sub_sections_by_type = other.sub_sections_by_type;
setChldrenPointers();
}
return *this;
}
virtual ~ParserSection();
virtual void printself(std::ostream & stream, unsigned int indent = 0) const;
/* ---------------------------------------------------------------------- */
/* Creation functions */
/* ---------------------------------------------------------------------- */
public:
ParserParameter & addParameter(const ParserParameter & param);
ParserSection & addSubSection(const ParserSection & section);
protected:
/// Clean ParserSection content
void clean() {
parameters.clear();
sub_sections_by_type.clear();
}
private:
void setChldrenPointers() {
for (auto && param_pair : this->parameters)
param_pair.second.setParent(*this);
for (auto && sub_sect_pair : this->sub_sections_by_type)
sub_sect_pair.second.setParent(*this);
}
/* ---------------------------------------------------------------------- */
/* Accessors */
/* ---------------------------------------------------------------------- */
public:
class SubSectionsRange
: public std::pair<const_section_iterator, const_section_iterator> {
public:
SubSectionsRange(const const_section_iterator & first,
const const_section_iterator & second)
: std::pair<const_section_iterator, const_section_iterator>(first,
second) {}
auto begin() { return this->first; }
auto end() { return this->second; }
};
/// Get begin and end iterators on subsections of certain type
auto getSubSections(ParserType type = ParserType::_not_defined) const {
if (type != ParserType::_not_defined) {
auto range = sub_sections_by_type.equal_range(type);
return SubSectionsRange(range.first, range.second);
} else {
return SubSectionsRange(sub_sections_by_type.begin(),
sub_sections_by_type.end());
}
}
/// Get number of subsections of certain type
UInt getNbSubSections(ParserType type = ParserType::_not_defined) const {
if (type != ParserType::_not_defined) {
return this->sub_sections_by_type.count(type);
} else {
return this->sub_sections_by_type.size();
}
}
/// Get begin and end iterators on parameters
auto getParameters() const {
return std::pair<const_parameter_iterator, const_parameter_iterator>(
parameters.begin(), parameters.end());
}
/* ---------------------------------------------------------------------- */
/// Get parameter within specified context
const ParserParameter & getParameter(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
Parameters::const_iterator it;
if (search_ctx & _ppsc_current_scope)
it = parameters.find(name);
if (it == parameters.end()) {
if ((search_ctx & _ppsc_parent_scope) && parent_section)
return parent_section->getParameter(name, search_ctx);
else {
AKANTU_SILENT_EXCEPTION(
"The parameter " << name
<< " has not been found in the specified context");
}
}
return it->second;
}
/* ------------------------------------------------------------------------ */
/// Get parameter within specified context, with a default value in case the
/// parameter does not exists
template <class T>
const T getParameter(
const std::string & name, const T & default_value,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
try {
T tmp = this->getParameter(name, search_ctx);
return tmp;
} catch (debug::Exception &) {
return default_value;
}
}
/* ------------------------------------------------------------------------ */
/// Check if parameter exists within specified context
bool hasParameter(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
Parameters::const_iterator it;
if (search_ctx & _ppsc_current_scope)
it = parameters.find(name);
if (it == parameters.end()) {
if ((search_ctx & _ppsc_parent_scope) && parent_section)
return parent_section->hasParameter(name, search_ctx);
else {
return false;
}
}
return true;
}
/* --------------------------------------------------------------------------
*/
/// Get value of given parameter in context
template <class T>
T getParameterValue(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
const ParserParameter & tmp_param = getParameter(name, search_ctx);
T t = tmp_param;
return t;
}
/* --------------------------------------------------------------------------
*/
/// Get section name
const std::string getName() const { return name; }
/// Get section type
ParserType getType() const { return type; }
/// Get section option
const std::string getOption(const std::string & def = "") const {
return option != "" ? option : def;
}
protected:
void setParent(const ParserSection & sect) { parent_section = § }
/* ---------------------------------------------------------------------- */
/* Members */
/* ---------------------------------------------------------------------- */
private:
/// Pointer to the parent section
const ParserSection * parent_section{nullptr};
/// Name of section
std::string name;
/// Type of section, see AKANTU_SECTION_TYPES
ParserType type{ParserType::_not_defined};
/// Section option
std::string option;
/// Map of parameters in section
Parameters parameters;
/// Multi-map of subsections
SubSections sub_sections_by_type;
};
/* ------------------------------------------------------------------------ */
/* Parser Class */
/* ------------------------------------------------------------------------ */
/// Root of parsing tree, represents the global ParserSection
class Parser : public ParserSection {
public:
Parser() : ParserSection("global", ParserType::_global) {}
void parse(const std::string & filename);
std::string getLastParsedFile() const;
static bool isPermissive() { return permissive_parser; }
public:
/// Parse real scalar
static Real parseReal(const std::string & value,
const ParserSection & section);
/// Parse real vector
static Vector<Real> parseVector(const std::string & value,
const ParserSection & section);
/// Parse real matrix
static Matrix<Real> parseMatrix(const std::string & value,
const ParserSection & section);
/// Parse real random parameter
static RandomParameter<Real>
parseRandomParameter(const std::string & value,
const ParserSection & section);
protected:
/// General parse function
template <class T, class Grammar>
static T parseType(const std::string & value, Grammar & grammar);
protected:
// friend class Parsable;
static bool permissive_parser;
std::string last_parsed_file;
};
inline std::ostream & operator<<(std::ostream & stream,
const ParserParameter & _this) {
_this.printself(stream);
return stream;
}
inline std::ostream & operator<<(std::ostream & stream,
const ParserSection & section) {
section.printself(stream);
return stream;
}
} // akantu
namespace std {
template <> struct iterator_traits<::akantu::Parser::const_section_iterator> {
using iterator_category = input_iterator_tag;
using value_type = ::akantu::ParserParameter;
using difference_type = ptrdiff_t;
using pointer = const ::akantu::ParserParameter *;
using reference = const ::akantu::ParserParameter &;
};
}
#include "parser_tmpl.hh"
#endif /* __AKANTU_PARSER_HH__ */
diff --git a/src/io/parser/parser_grammar_tmpl.hh b/src/io/parser/parser_grammar_tmpl.hh
index 9174f2529..d957801b7 100644
--- a/src/io/parser/parser_grammar_tmpl.hh
+++ b/src/io/parser/parser_grammar_tmpl.hh
@@ -1,81 +1,82 @@
/**
* @file parser_grammar_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 11 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief implementation of the templated part of ParsableParam Parsable and
* ParsableParamTyped
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
//#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/classic_position_iterator.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/spirit/include/support_multi_pass.hpp>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PARSER_GRAMMAR_TMPL_HH
#define AKANTU_PARSER_GRAMMAR_TMPL_HH
namespace akantu {
namespace qi = boost::spirit::qi;
/* -------------------------------------------------------------------------- */
template <class T, class Grammar>
T Parser::parseType(const std::string & value, Grammar & grammar) {
using boost::spirit::ascii::space;
std::string::const_iterator b = value.begin();
std::string::const_iterator e = value.end();
T resultat = T();
bool res = false;
try {
res = qi::phrase_parse(b, e, grammar, space, resultat);
} catch (debug::Exception & ex) {
AKANTU_EXCEPTION("Could not parse '"
<< value << "' as a " << debug::demangle(typeid(T).name())
<< ", an unknown error append '" << ex.what());
}
if (!res || (b != e)) {
AKANTU_EXCEPTION("Could not parse '"
<< value << "' as a " << debug::demangle(typeid(T).name())
<< ", an unknown error append '"
<< std::string(value.begin(), b) << "<HERE>"
<< std::string(b, e) << "'");
}
return resultat;
}
namespace parser {
template <class Iterator> struct Skipper {
using type = qi::rule<Iterator, void()>;
};
}
} // akantu
#endif // AKANTU_PARSER_GRAMMAR_TMPL_HH
diff --git a/src/io/parser/parser_input_files.cc b/src/io/parser/parser_input_files.cc
index 06d388c56..c3016a000 100644
--- a/src/io/parser/parser_input_files.cc
+++ b/src/io/parser/parser_input_files.cc
@@ -1,119 +1,119 @@
/**
* @file parser_input_files.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 11 2015
- * @date last modification: Wed Jan 13 2016
+ * @date last modification: Wed Nov 08 2017
*
* @brief implementation of the parser
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
- // is only gnu
+// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "input_file_parser.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void Parser::parse(const std::string & filename) {
this->clean();
std::ifstream input(filename.c_str());
if (!input.good()) {
AKANTU_EXCEPTION("Could not open file " << filename << "!");
}
input.unsetf(std::ios::skipws);
// wrap istream into iterator
spirit::istream_iterator fwd_begin(input);
spirit::istream_iterator fwd_end;
// wrap forward iterator with position iterator, to record the position
using pos_iterator_type =
spirit::classic::position_iterator2<spirit::istream_iterator>;
pos_iterator_type position_begin(fwd_begin, fwd_end, filename);
pos_iterator_type position_end;
// parse
parser::InputFileGrammar<pos_iterator_type> ag(this);
bool result = qi::phrase_parse(position_begin, position_end, ag, ag.skipper);
if (!result || position_begin != position_end) {
spirit::classic::file_position pos = position_begin.get_position();
AKANTU_EXCEPTION("Parse error [ "
<< ag.getErrorMessage() << " ]"
<< " in file " << filename << " line " << pos.line
<< " column " << pos.column << std::endl
<< "'" << position_begin.get_currentline() << "'"
<< std::endl
<< std::setw(pos.column) << " "
<< "^- here");
}
try {
bool permissive = getParameter("permissive_parser", _ppsc_current_scope);
permissive_parser = permissive;
AKANTU_DEBUG_INFO("Parser switched permissive mode to "
<< std::boolalpha << permissive_parser);
} catch (debug::Exception & e) {
}
last_parsed_file = filename;
input.close();
}
} // akantu
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
- // is only gnu
+// is only gnu
#elif defined(__GNUG__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic pop
#else
#pragma GCC diagnostic warning "-Wunused-local-typedefs"
#endif
#endif
diff --git a/src/io/parser/parser_random.cc b/src/io/parser/parser_random.cc
index 40b05fe81..46714a06e 100644
--- a/src/io/parser/parser_random.cc
+++ b/src/io/parser/parser_random.cc
@@ -1,109 +1,109 @@
/**
* @file parser_random.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Feb 21 2013
- * @date last modification: Mon Dec 07 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Sun Jul 09 2017
*
* @brief implementation of the parser
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "algebraic_parser.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
RandomParameter<Real>
Parser::parseRandomParameter(const std::string & value,
const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::RandomGeneratorGrammar<std::string::const_iterator, space_type>
grammar(section);
grammar.name("random_grammar");
parser::ParsableRandomGenerator rg =
Parser::parseType<parser::ParsableRandomGenerator>(value, grammar);
Vector<Real> params = rg.parameters;
switch (rg.type) {
case _rdt_not_defined:
return RandomParameter<Real>(rg.base,
std::uniform_real_distribution<Real>(0, 0));
case _rdt_uniform:
return RandomParameter<Real>(
rg.base, std::uniform_real_distribution<Real>(params(0), params(1)));
case _rdt_exponential:
return RandomParameter<Real>(
rg.base, std::exponential_distribution<Real>(params(0)));
case _rdt_gamma:
return RandomParameter<Real>(
rg.base, std::gamma_distribution<Real>(params(0), params(1)));
case _rdt_weibull:
return RandomParameter<Real>(
rg.base, std::weibull_distribution<Real>(params(1), params(0)));
case _rdt_extreme_value:
return RandomParameter<Real>(
rg.base, std::extreme_value_distribution<Real>(params(0), params(1)));
case _rdt_normal:
return RandomParameter<Real>(
rg.base, std::normal_distribution<Real>(params(0), params(1)));
case _rdt_lognormal:
return RandomParameter<Real>(
rg.base, std::lognormal_distribution<Real>(params(0), params(1)));
case _rdt_chi_squared:
return RandomParameter<Real>(
rg.base, std::chi_squared_distribution<Real>(params(0)));
case _rdt_cauchy:
return RandomParameter<Real>(
rg.base, std::cauchy_distribution<Real>(params(0), params(1)));
case _rdt_fisher_f:
return RandomParameter<Real>(
rg.base, std::fisher_f_distribution<Real>(params(0), params(1)));
case _rdt_student_t:
return RandomParameter<Real>(rg.base,
std::student_t_distribution<Real>(params(0)));
default:
AKANTU_EXCEPTION("This is an unknown random distribution in the parser");
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/parser/parser_real.cc b/src/io/parser/parser_real.cc
index 423307831..0c8471c13 100644
--- a/src/io/parser/parser_real.cc
+++ b/src/io/parser/parser_real.cc
@@ -1,63 +1,63 @@
/**
* @file parser_real.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Feb 21 2013
- * @date last modification: Wed Nov 11 2015
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Mon Jun 19 2017
*
* @brief implementation of the parser
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
- // is only gnu
+// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "algebraic_parser.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Real Parser::parseReal(const std::string & value,
const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::AlgebraicGrammar<std::string::const_iterator, space_type> grammar(
section);
grammar.name("algebraic_grammar");
return Parser::parseType<Real>(value, grammar);
}
} // akantu
diff --git a/src/io/parser/parser_tmpl.hh b/src/io/parser/parser_tmpl.hh
index c65c8d82c..f3ba422c9 100644
--- a/src/io/parser/parser_tmpl.hh
+++ b/src/io/parser/parser_tmpl.hh
@@ -1,111 +1,112 @@
/**
* @file parser_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Wed Apr 22 2015
+ * @date last modification: Mon Dec 18 2017
*
* @brief Implementation of the parser templated methods
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include <regex>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> inline ParserParameter::operator T() const {
T t;
std::stringstream sstr(value);
sstr >> t;
if (sstr.bad())
AKANTU_EXCEPTION("No known conversion of a ParserParameter \""
<< name << "\" to the type " << typeid(T).name());
return t;
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator const char *() const {
return value.c_str();
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator Real() const {
return Parser::parseReal(value, *parent_section);
}
/* --------------------------------------------------------- -----------------
*/
template <> inline ParserParameter::operator bool() const {
bool b;
std::stringstream sstr(value);
sstr >> std::boolalpha >> b;
if (sstr.fail()) {
sstr.clear();
sstr >> std::noboolalpha >> b;
}
return b;
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator std::vector<std::string>() const {
std::vector<std::string> tmp;
auto string =
std::regex_replace(value, std::regex("[[:space:]]|\\[|\\]"), "");
std::smatch sm;
while (std::regex_search(string, sm, std::regex("[^,]+"))) {
tmp.push_back(sm.str());
string = sm.suffix();
}
return tmp;
}
/* --------------------------------------------------------- -----------------
*/
template <> inline ParserParameter::operator Vector<Real>() const {
return Parser::parseVector(value, *parent_section);
}
/* --------------------------------------------------------- -----------------
*/
template <> inline ParserParameter::operator Vector<UInt>() const {
Vector<Real> tmp = Parser::parseVector(value, *parent_section);
Vector<UInt> tmp_uint(tmp.size());
for (UInt i = 0; i < tmp.size(); ++i) {
tmp_uint(i) = UInt(tmp(i));
}
return tmp_uint;
}
/* --------------------------------------------------------- -----------------
*/
template <> inline ParserParameter::operator Matrix<Real>() const {
return Parser::parseMatrix(value, *parent_section);
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator RandomParameter<Real>() const {
return Parser::parseRandomParameter(value, *parent_section);
}
} // akantu
diff --git a/src/io/parser/parser_types.cc b/src/io/parser/parser_types.cc
index 34bde6424..2b60bfdbd 100644
--- a/src/io/parser/parser_types.cc
+++ b/src/io/parser/parser_types.cc
@@ -1,75 +1,75 @@
/**
* @file parser_types.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Feb 21 2013
- * @date last modification: Wed Nov 11 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Mon Jun 19 2017
*
* @brief implementation of the parser
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
- // is only gnu
+// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "algebraic_parser.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Vector<Real> Parser::parseVector(const std::string & value,
const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::VectorGrammar<std::string::const_iterator, space_type> grammar(
section);
grammar.name("vector_grammar");
return Parser::parseType<parser::parsable_vector>(value, grammar);
}
/* -------------------------------------------------------------------------- */
Matrix<Real> Parser::parseMatrix(const std::string & value,
const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::MatrixGrammar<std::string::const_iterator, space_type> grammar(
section);
grammar.name("matrix_grammar");
return Parser::parseType<parser::parsable_matrix>(value, grammar);
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/mesh/element_group.cc b/src/mesh/element_group.cc
index 9f0158d7a..ded48bb53 100644
--- a/src/mesh/element_group.cc
+++ b/src/mesh/element_group.cc
@@ -1,203 +1,203 @@
/**
* @file element_group.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Mon Jan 22 2018
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_csr.hh"
#include "dumpable.hh"
#include "dumpable_inline_impl.hh"
#include "group_manager.hh"
#include "group_manager_inline_impl.cc"
#include "mesh.hh"
#include "mesh_utils.hh"
#include <algorithm>
#include <iterator>
#include <sstream>
#include "element_group.hh"
#if defined(AKANTU_USE_IOHELPER)
#include "dumper_iohelper_paraview.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
ElementGroup::ElementGroup(const std::string & group_name, const Mesh & mesh,
NodeGroup & node_group, UInt dimension,
const std::string & id, const MemoryID & mem_id)
: Memory(id, mem_id), mesh(mesh), name(group_name),
elements("elements", id, mem_id), node_group(node_group),
dimension(dimension) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_USE_IOHELPER)
this->registerDumper<DumperParaview>("paraview_" + group_name, group_name,
true);
this->addDumpFilteredMesh(mesh, elements, node_group.getNodes(), dimension);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::empty() { elements.free(); }
/* -------------------------------------------------------------------------- */
void ElementGroup::append(const ElementGroup & other_group) {
AKANTU_DEBUG_IN();
node_group.append(other_group.node_group);
/// loop on all element types in all dimensions
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
type_iterator it =
other_group.firstType(_all_dimensions, ghost_type, _ek_not_defined);
type_iterator last =
other_group.lastType(_all_dimensions, ghost_type, _ek_not_defined);
for (; it != last; ++it) {
ElementType type = *it;
const Array<UInt> & other_elem_list =
other_group.elements(type, ghost_type);
UInt nb_other_elem = other_elem_list.size();
Array<UInt> * elem_list;
UInt nb_elem = 0;
/// create current type if doesn't exists, otherwise get information
if (elements.exists(type, ghost_type)) {
elem_list = &elements(type, ghost_type);
nb_elem = elem_list->size();
} else {
elem_list = &(elements.alloc(0, 1, type, ghost_type));
}
/// append new elements to current list
elem_list->resize(nb_elem + nb_other_elem);
std::copy(other_elem_list.begin(), other_elem_list.end(),
elem_list->begin() + nb_elem);
/// remove duplicates
std::sort(elem_list->begin(), elem_list->end());
Array<UInt>::iterator<> end =
std::unique(elem_list->begin(), elem_list->end());
elem_list->resize(end - elem_list->begin());
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "ElementGroup [" << std::endl;
stream << space << " + name: " << name << std::endl;
stream << space << " + dimension: " << dimension << std::endl;
elements.printself(stream, indent + 1);
node_group.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ElementGroup::optimize() {
// increasing the locality of data when iterating on the element of a group
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
ElementList::type_iterator it =
elements.firstType(_all_dimensions, ghost_type);
ElementList::type_iterator last =
elements.lastType(_all_dimensions, ghost_type);
for (; it != last; ++it) {
Array<UInt> & els = elements(*it, ghost_type);
std::sort(els.begin(), els.end());
Array<UInt>::iterator<> end = std::unique(els.begin(), els.end());
els.resize(end - els.begin());
}
}
node_group.optimize();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::fillFromNodeGroup() {
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(this->mesh, node_to_elem, this->dimension);
std::set<Element> seen;
Array<UInt>::const_iterator<> itn = this->node_group.begin();
Array<UInt>::const_iterator<> endn = this->node_group.end();
for (; itn != endn; ++itn) {
CSR<Element>::iterator ite = node_to_elem.begin(*itn);
CSR<Element>::iterator ende = node_to_elem.end(*itn);
for (; ite != ende; ++ite) {
const Element & elem = *ite;
if (this->dimension != _all_dimensions &&
this->dimension != Mesh::getSpatialDimension(elem.type))
continue;
if (seen.find(elem) != seen.end())
continue;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(elem.type);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
this->mesh.getConnectivity(elem.type, elem.ghost_type)
.begin(nb_nodes_per_element);
const Vector<UInt> & conn = conn_it[elem.element];
UInt count = 0;
for (UInt n = 0; n < conn.size(); ++n) {
count +=
(this->node_group.getNodes().find(conn(n)) != UInt(-1) ? 1 : 0);
}
if (count == nb_nodes_per_element)
this->add(elem);
seen.insert(elem);
}
}
this->optimize();
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/mesh/element_group.hh b/src/mesh/element_group.hh
index fe47dc7d2..64615adaf 100644
--- a/src/mesh/element_group.hh
+++ b/src/mesh/element_group.hh
@@ -1,190 +1,190 @@
/**
* @file element_group.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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 "dumpable.hh"
#include "element_type_map.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_GROUP_HH__
#define __AKANTU_ELEMENT_GROUP_HH__
namespace akantu {
class Mesh;
class Element;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
class ElementGroup : private Memory, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementGroup(const std::string & name, const Mesh & mesh,
NodeGroup & node_group, UInt dimension = _all_dimensions,
const std::string & id = "element_group",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Type definitions */
/* ------------------------------------------------------------------------ */
public:
using ElementList = ElementTypeMapArray<UInt>;
using NodeList = Array<UInt>;
/* ------------------------------------------------------------------------ */
/* Element iterator */
/* ------------------------------------------------------------------------ */
using type_iterator = ElementList::type_iterator;
inline type_iterator firstType(UInt dim = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & kind = _ek_regular) const;
inline type_iterator lastType(UInt dim = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & kind = _ek_regular) const;
#ifndef SWIG
template <typename... pack>
inline decltype(auto) elementTypes(pack &&... _pack) const {
return elements.elementTypes(_pack...);
}
#endif
using const_element_iterator = Array<UInt>::const_iterator<UInt>;
inline const_element_iterator
begin(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
inline const_element_iterator
end(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// empty the element group
void empty();
/// append another group to this group
/// BE CAREFUL: it doesn't conserve the element order
void append(const ElementGroup & other_group);
/// add an element to the group. By default the it does not add the nodes to
/// the group
inline void add(const Element & el, bool add_nodes = false,
bool check_for_duplicate = true);
/// \todo fix the default for add_nodes : make it coherent with the other
/// method
inline void add(const ElementType & type, UInt element,
const GhostType & ghost_type = _not_ghost,
bool add_nodes = true, bool check_for_duplicate = true);
inline void addNode(UInt node_id, bool check_for_duplicate = true);
inline void removeNode(UInt node_id);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// fill the elements based on the underlying node group.
virtual void fillFromNodeGroup();
// sort and remove duplicated values
void optimize();
private:
inline void addElement(const ElementType & elem_type, UInt elem_id,
const GhostType & ghost_type);
friend class GroupManager;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
const Array<UInt> &
getElements(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
AKANTU_GET_MACRO(Elements, elements, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(Nodes, node_group.getNodes(), const Array<UInt> &);
AKANTU_GET_MACRO(NodeGroup, node_group, const NodeGroup &);
AKANTU_GET_MACRO_NOT_CONST(NodeGroup, node_group, NodeGroup &);
AKANTU_GET_MACRO(Dimension, dimension, UInt);
AKANTU_GET_MACRO(Name, name, std::string);
inline UInt getNbNodes() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Mesh to which this group belongs
const Mesh & mesh;
/// name of the group
std::string name;
/// list of elements composing the group
ElementList elements;
/// sub list of nodes which are composing the elements
NodeGroup & node_group;
/// group dimension
UInt dimension;
/// empty arry for the iterator to work when an element type not present
Array<UInt> empty_elements;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ElementGroup & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "element.hh"
#include "element_group_inline_impl.cc"
#endif /* __AKANTU_ELEMENT_GROUP_HH__ */
diff --git a/src/mesh/element_group_inline_impl.cc b/src/mesh/element_group_inline_impl.cc
index bd084f56c..7ae8b3750 100644
--- a/src/mesh/element_group_inline_impl.cc
+++ b/src/mesh/element_group_inline_impl.cc
@@ -1,146 +1,146 @@
/**
* @file element_group_inline_impl.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Sun Aug 13 2017
*
- * @brief Stores information relevent to the notion of domain boundary and
+ * @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_GROUP_INLINE_IMPL_CC__
#define __AKANTU_ELEMENT_GROUP_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void ElementGroup::add(const Element & el, bool add_nodes,
bool check_for_duplicate) {
this->add(el.type, el.element, el.ghost_type, add_nodes, check_for_duplicate);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::add(const ElementType & type, UInt element,
const GhostType & ghost_type, bool add_nodes,
bool check_for_duplicate) {
addElement(type, element, ghost_type);
if (add_nodes) {
Array<UInt>::const_vector_iterator it =
mesh.getConnectivity(type, ghost_type)
.begin(mesh.getNbNodesPerElement(type)) +
element;
const Vector<UInt> & conn = *it;
for (UInt i = 0; i < conn.size(); ++i)
addNode(conn[i], check_for_duplicate);
}
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::addNode(UInt node_id, bool check_for_duplicate) {
node_group.add(node_id, check_for_duplicate);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::removeNode(UInt node_id) {
node_group.remove(node_id);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::addElement(const ElementType & elem_type,
UInt elem_id,
const GhostType & ghost_type) {
if (!(elements.exists(elem_type, ghost_type))) {
elements.alloc(0, 1, elem_type, ghost_type);
}
elements(elem_type, ghost_type).push_back(elem_id);
this->dimension = UInt(
std::max(Int(this->dimension), Int(mesh.getSpatialDimension(elem_type))));
}
/* -------------------------------------------------------------------------- */
inline UInt ElementGroup::getNbNodes() const { return node_group.size(); }
/* -------------------------------------------------------------------------- */
inline ElementGroup::type_iterator
ElementGroup::firstType(UInt dim, const GhostType & ghost_type,
const ElementKind & kind) const {
return elements.firstType(dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::type_iterator
ElementGroup::lastType(UInt dim, const GhostType & ghost_type,
const ElementKind & kind) const {
return elements.lastType(dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_element_iterator
ElementGroup::begin(const ElementType & type,
const GhostType & ghost_type) const {
if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type).begin();
} else {
return empty_elements.begin();
}
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_element_iterator
ElementGroup::end(const ElementType & type,
const GhostType & ghost_type) const {
if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type).end();
} else {
return empty_elements.end();
}
}
/* -------------------------------------------------------------------------- */
inline const Array<UInt> &
ElementGroup::getElements(const ElementType & type,
const GhostType & ghost_type) const {
if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type);
} else {
return empty_elements;
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_ELEMENT_GROUP_INLINE_IMPL_CC__ */
diff --git a/src/mesh/element_type_map.cc b/src/mesh/element_type_map.cc
index ee0fc8cca..83fccc3a9 100644
--- a/src/mesh/element_type_map.cc
+++ b/src/mesh/element_type_map.cc
@@ -1,71 +1,73 @@
/**
* @file element_type_map.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jun 27 2017
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Tue Feb 20 2018
*
- * @brief A Documented file.
+ * @brief A Documented file.
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
FEEngineElementTypeMapArrayInitializer::FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine, UInt nb_component, UInt spatial_dimension,
const GhostType & ghost_type, const ElementKind & element_kind)
: MeshElementTypeMapArrayInitializer(
fe_engine.getMesh(), nb_component,
spatial_dimension == UInt(-2)
? fe_engine.getMesh().getSpatialDimension()
: spatial_dimension,
ghost_type, element_kind, true, false),
fe_engine(fe_engine) {}
FEEngineElementTypeMapArrayInitializer::FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine,
const ElementTypeMapArrayInitializer::CompFunc & nb_component,
UInt spatial_dimension, const GhostType & ghost_type,
const ElementKind & element_kind)
: MeshElementTypeMapArrayInitializer(
fe_engine.getMesh(), nb_component,
spatial_dimension == UInt(-2)
? fe_engine.getMesh().getSpatialDimension()
: spatial_dimension,
ghost_type, element_kind, true, false),
fe_engine(fe_engine) {}
UInt FEEngineElementTypeMapArrayInitializer::size(
const ElementType & type) const {
return MeshElementTypeMapArrayInitializer::size(type) *
fe_engine.getNbIntegrationPoints(type, this->ghost_type);
}
FEEngineElementTypeMapArrayInitializer::ElementTypesIteratorHelper
FEEngineElementTypeMapArrayInitializer::elementTypes() const {
return this->fe_engine.elementTypes(spatial_dimension, ghost_type,
element_kind);
}
} // namespace akantu
diff --git a/src/mesh/element_type_map.hh b/src/mesh/element_type_map.hh
index f3aefd368..4853569a7 100644
--- a/src/mesh/element_type_map.hh
+++ b/src/mesh/element_type_map.hh
@@ -1,449 +1,449 @@
/**
* @file element_type_map.hh
*
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
- * @date last modification: Fri Oct 02 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief storage class by element type
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_memory.hh"
#include "aka_named_argument.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_TYPE_MAP_HH__
#define __AKANTU_ELEMENT_TYPE_MAP_HH__
namespace akantu {
class FEEngine;
} // namespace akantu
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(all_ghost_types);
DECLARE_NAMED_ARGUMENT(default_value);
DECLARE_NAMED_ARGUMENT(element_kind);
DECLARE_NAMED_ARGUMENT(ghost_type);
DECLARE_NAMED_ARGUMENT(nb_component);
DECLARE_NAMED_ARGUMENT(nb_component_functor);
DECLARE_NAMED_ARGUMENT(with_nb_element);
DECLARE_NAMED_ARGUMENT(with_nb_nodes_per_element);
DECLARE_NAMED_ARGUMENT(spatial_dimension);
DECLARE_NAMED_ARGUMENT(do_not_default);
} // namespace
template <class Stored, typename SupportType = ElementType>
class ElementTypeMap;
/* -------------------------------------------------------------------------- */
/* ElementTypeMapBase */
/* -------------------------------------------------------------------------- */
/// Common non templated base class for the ElementTypeMap class
class ElementTypeMapBase {
public:
virtual ~ElementTypeMapBase() = default;
};
/* -------------------------------------------------------------------------- */
/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
class ElementTypeMap : public ElementTypeMapBase {
public:
ElementTypeMap();
~ElementTypeMap() override;
inline static std::string printType(const SupportType & type,
const GhostType & ghost_type);
/*! Tests whether a type is present in the object
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return true if the type is present. */
inline bool exists(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline const Stored &
operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline Stored & operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map. THIS METHOD IS
* NOT ARRAY SAFE, when using ElementTypeMapArray, use setArray instead
* @param data to insert
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
template <typename U>
inline Stored & operator()(U && insertee, const SupportType & type,
const GhostType & ghost_type = _not_ghost);
public:
/// print helper
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
/*! iterator allows to iterate over type-data pairs of the map. The interface
* expects the SupportType to be ElementType. */
using DataMap = std::map<SupportType, Stored>;
class type_iterator
: private std::iterator<std::forward_iterator_tag, const SupportType> {
public:
using value_type = const SupportType;
using pointer = const SupportType *;
using reference = const SupportType &;
protected:
using DataMapIterator =
typename ElementTypeMap<Stored>::DataMap::const_iterator;
public:
type_iterator(DataMapIterator & list_begin, DataMapIterator & list_end,
UInt dim, ElementKind ek);
type_iterator(const type_iterator & it);
type_iterator() = default;
inline reference operator*();
inline reference operator*() const;
inline type_iterator & operator++();
type_iterator operator++(int);
inline bool operator==(const type_iterator & other) const;
inline bool operator!=(const type_iterator & other) const;
type_iterator & operator=(const type_iterator & other);
private:
DataMapIterator list_begin;
DataMapIterator list_end;
UInt dim;
ElementKind kind;
};
/// helper class to use in range for constructions
class ElementTypesIteratorHelper {
public:
using Container = ElementTypeMap<Stored, SupportType>;
using iterator = typename Container::type_iterator;
ElementTypesIteratorHelper(const Container & container, UInt dim,
GhostType ghost_type, ElementKind kind)
: container(std::cref(container)), dim(dim), ghost_type(ghost_type),
kind(kind) {}
template <typename... pack>
ElementTypesIteratorHelper(const Container & container, use_named_args_t,
pack &&... _pack)
: ElementTypesIteratorHelper(
container, OPTIONAL_NAMED_ARG(spatial_dimension, _all_dimensions),
OPTIONAL_NAMED_ARG(ghost_type, _not_ghost),
OPTIONAL_NAMED_ARG(element_kind, _ek_regular)) {}
ElementTypesIteratorHelper(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
operator=(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
operator=(ElementTypesIteratorHelper &&) = default;
iterator begin() {
return container.get().firstType(dim, ghost_type, kind);
}
iterator end() { return container.get().lastType(dim, ghost_type, kind); }
private:
std::reference_wrapper<const Container> container;
UInt dim;
GhostType ghost_type;
ElementKind kind;
};
private:
ElementTypesIteratorHelper
elementTypesImpl(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
template <typename... pack>
ElementTypesIteratorHelper
elementTypesImpl(const use_named_args_t & /*unused*/, pack &&... _pack) const;
public:
/*!
* \param _spatial_dimension optional: filter for elements of given spatial
* dimension
* \param _ghost_type optional: filter for a certain ghost_type
* \param _element_kind optional: filter for elements of given kind
*/
template <typename... pack>
std::enable_if_t<are_named_argument<pack...>::value,
ElementTypesIteratorHelper>
elementTypes(pack &&... _pack) const {
return elementTypesImpl(use_named_args,
std::forward<decltype(_pack)>(_pack)...);
}
template <typename... pack>
std::enable_if_t<not are_named_argument<pack...>::value,
ElementTypesIteratorHelper>
elementTypes(pack &&... _pack) const {
return elementTypesImpl(std::forward<decltype(_pack)>(_pack)...);
}
public:
/*! Get an iterator to the beginning of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the first stored data matching the filters
* or an iterator to the end of the map if none match*/
inline type_iterator firstType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
/*! Get an iterator to the end of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the last stored data matching the filters
* or an iterator to the end of the map if none match */
inline type_iterator lastType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
protected:
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline DataMap & getData(GhostType ghost_type);
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline const DataMap & getData(GhostType ghost_type) const;
/* ------------------------------------------------------------------------ */
protected:
DataMap data;
DataMap ghost_data;
};
/* -------------------------------------------------------------------------- */
/* Some typedefs */
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
class ElementTypeMapArray : public ElementTypeMap<Array<T> *, SupportType>,
public Memory {
public:
using type = T;
using array_type = Array<T>;
protected:
using parent = ElementTypeMap<Array<T> *, SupportType>;
using DataMap = typename parent::DataMap;
public:
using type_iterator = typename parent::type_iterator;
/// standard assigment (copy) operator
void operator=(const ElementTypeMapArray &) = delete;
ElementTypeMapArray(const ElementTypeMapArray &) = delete;
/// explicit copy
void copy(const ElementTypeMapArray & other);
/*! Constructor
* @param id optional: identifier (string)
* @param parent_id optional: parent identifier. for organizational purposes
* only
* @param memory_id optional: choose a specific memory, defaults to memory 0
*/
ElementTypeMapArray(const ID & id = "by_element_type_array",
const ID & parent_id = "no_parent",
const MemoryID & memory_id = 0)
: parent(), Memory(parent_id + ":" + id, memory_id), name(id){};
/*! allocate memory for a new array
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map
* @param ghost_type whether to add the field to the data map or the
* ghost_data map
* @return a reference to the allocated array */
inline Array<T> & alloc(UInt size, UInt nb_component,
const SupportType & type,
const GhostType & ghost_type,
const T & default_value = T());
/*! allocate memory for a new array in both the data and the ghost_data map
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map*/
inline void alloc(UInt size, UInt nb_component, const SupportType & type,
const T & default_value = T());
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a reference to the array */
inline const Array<T> &
operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const;
/// access the data of an element, this combine the map and array accessor
inline const T & operator()(const Element & element,
UInt component = 0) const;
/// access the data of an element, this combine the map and array accessor
inline T & operator()(const Element & element, UInt component = 0);
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a const reference to the array */
inline Array<T> & operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map.
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @param vect the vector to include into the map
* @return stored data corresponding to type. */
inline void setArray(const SupportType & type, const GhostType & ghost_type,
const Array<T> & vect);
/*! frees all memory related to the data*/
inline void free();
/*! set all values in the ElementTypeMap to zero*/
inline void clear();
/*! set all values in the ElementTypeMap to value */
template <typename ST> inline void set(const ST & value);
/*! deletes and reorders entries in the stored arrays
* @param new_numbering a ElementTypeMapArray of new indices. UInt(-1)
* indicates
* deleted entries. */
inline void
onElementsRemoved(const ElementTypeMapArray<UInt> & new_numbering);
/// text output helper
void printself(std::ostream & stream, int indent = 0) const override;
/*! set the id
* @param id the new name
*/
inline void setID(const ID & id) { this->id = id; }
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
ElementTypeMap<UInt> nb_components;
for (auto & type : this->elementTypes(dim, ghost_type, kind)) {
UInt nb_comp = (*this)(type, ghost_type).getNbComponent();
nb_components(type, ghost_type) = nb_comp;
}
return nb_components;
}
/* ------------------------------------------------------------------------ */
/* more evolved allocators */
/* ------------------------------------------------------------------------ */
public:
/// initialize the arrays in accordance to a functor
template <class Func>
void initialize(const Func & f, const T & default_value, bool do_not_default);
/// initialize with sizes and number of components in accordance of a mesh
/// content
template <typename... pack>
void initialize(const Mesh & mesh, pack &&... _pack);
/// initialize with sizes and number of components in accordance of a fe
/// engine content (aka integration points)
template <typename... pack>
void initialize(const FEEngine & fe_engine, pack &&... _pack);
/* ------------------------------------------------------------------------ */
/* Accesssors */
/* ------------------------------------------------------------------------ */
public:
/// get the name of the internal field
AKANTU_GET_MACRO(Name, name, ID);
/// name of the elment type map: e.g. connectivity, grad_u
ID name;
};
/// to store data Array<Real> by element type
using ElementTypeMapReal = ElementTypeMapArray<Real>;
/// to store data Array<Int> by element type
using ElementTypeMapInt = ElementTypeMapArray<Int>;
/// to store data Array<UInt> by element type
using ElementTypeMapUInt = ElementTypeMapArray<UInt, ElementType>;
/// Map of data of type UInt stored in a mesh
using UIntDataMap = std::map<std::string, Array<UInt> *>;
using ElementTypeMapUIntDataMap = ElementTypeMap<UIntDataMap, ElementType>;
} // namespace akantu
#endif /* __AKANTU_ELEMENT_TYPE_MAP_HH__ */
diff --git a/src/mesh/element_type_map_filter.hh b/src/mesh/element_type_map_filter.hh
index 81c6ab58b..834469672 100644
--- a/src/mesh/element_type_map_filter.hh
+++ b/src/mesh/element_type_map_filter.hh
@@ -1,307 +1,307 @@
/**
* @file element_type_map_filter.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Fri Dec 18 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Filtered version based on a an akantu::ElementGroup of a
* akantu::ElementTypeMap
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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_BY_ELEMENT_TYPE_FILTER_HH__
#define __AKANTU_BY_ELEMENT_TYPE_FILTER_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* ArrayFilter */
/* -------------------------------------------------------------------------- */
template <typename T> class ArrayFilter {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
/// standard iterator
template <typename R = T> class iterator {
inline bool operator!=(__attribute__((unused)) iterator<R> & other) {
throw;
};
inline bool operator==(__attribute__((unused)) iterator<R> & other) {
throw;
};
inline iterator<R> & operator++() { throw; };
inline T operator*() {
throw;
return T();
};
};
/// const iterator
template <template <class S> class original_iterator, typename Shape,
typename filter_iterator>
class const_iterator {
public:
UInt getCurrentIndex() {
return (*this->filter_it * this->nb_item_per_elem +
this->sub_element_counter);
}
inline const_iterator() = default;
inline const_iterator(const original_iterator<Shape> & origin_it,
const filter_iterator & filter_it,
UInt nb_item_per_elem)
: origin_it(origin_it), filter_it(filter_it),
nb_item_per_elem(nb_item_per_elem), sub_element_counter(0){};
inline bool operator!=(const_iterator & other) const {
return !((*this) == other);
}
inline bool operator==(const_iterator & other) const {
return (this->origin_it == other.origin_it &&
this->filter_it == other.filter_it &&
this->sub_element_counter == other.sub_element_counter);
}
inline bool operator!=(const const_iterator & other) const {
return !((*this) == other);
}
inline bool operator==(const const_iterator & other) const {
return (this->origin_it == other.origin_it &&
this->filter_it == other.filter_it &&
this->sub_element_counter == other.sub_element_counter);
}
inline const_iterator & operator++() {
++sub_element_counter;
if (sub_element_counter == nb_item_per_elem) {
sub_element_counter = 0;
++filter_it;
}
return *this;
};
inline Shape operator*() {
return origin_it[nb_item_per_elem * (*filter_it) + sub_element_counter];
};
private:
original_iterator<Shape> origin_it;
filter_iterator filter_it;
/// the number of item per element
UInt nb_item_per_elem;
/// counter for every sub element group
UInt sub_element_counter;
};
using vector_iterator = iterator<Vector<T>>;
using array_type = Array<T>;
using const_vector_iterator =
const_iterator<array_type::template const_iterator, Vector<T>,
Array<UInt>::const_iterator<UInt>>;
using value_type = typename array_type::value_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ArrayFilter(const Array<T> & array, const Array<UInt> & filter,
UInt nb_item_per_elem)
: array(array), filter(filter), nb_item_per_elem(nb_item_per_elem){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
const_vector_iterator begin_reinterpret(UInt n, UInt new_size) const {
AKANTU_DEBUG_ASSERT(
n * new_size == this->getNbComponent() * this->size(),
"The new values for size ("
<< new_size << ") and nb_component (" << n
<< ") are not compatible with the one of this array("
<< this->size() << "," << this->getNbComponent() << ")");
UInt new_full_array_size = this->array.size() * array.getNbComponent() / n;
UInt new_nb_item_per_elem = this->nb_item_per_elem;
if (new_size != 0 && n != 0)
new_nb_item_per_elem = this->array.getNbComponent() *
this->filter.size() * this->nb_item_per_elem /
(n * new_size);
return const_vector_iterator(
this->array.begin_reinterpret(n, new_full_array_size),
this->filter.begin(), new_nb_item_per_elem);
};
const_vector_iterator end_reinterpret(UInt n, UInt new_size) const {
AKANTU_DEBUG_ASSERT(
n * new_size == this->getNbComponent() * this->size(),
"The new values for size ("
<< new_size << ") and nb_component (" << n
<< ") are not compatible with the one of this array("
<< this->size() << "," << this->getNbComponent() << ")");
UInt new_full_array_size =
this->array.size() * this->array.getNbComponent() / n;
UInt new_nb_item_per_elem = this->nb_item_per_elem;
if (new_size != 0 && n != 0)
new_nb_item_per_elem = this->array.getNbComponent() *
this->filter.size() * this->nb_item_per_elem /
(n * new_size);
return const_vector_iterator(
this->array.begin_reinterpret(n, new_full_array_size),
this->filter.end(), new_nb_item_per_elem);
};
vector_iterator begin_reinterpret(UInt, UInt) { throw; };
vector_iterator end_reinterpret(UInt, UInt) { throw; };
/// return the size of the filtered array which is the filter size
UInt size() const { return this->filter.size() * this->nb_item_per_elem; };
/// the number of components of the filtered array
UInt getNbComponent() const { return this->array.getNbComponent(); };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// reference to array of data
const Array<T> & array;
/// reference to the filter used to select elements
const Array<UInt> & filter;
/// the number of item per element
UInt nb_item_per_elem;
};
/* -------------------------------------------------------------------------- */
/* ElementTypeMapFilter */
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType = ElementType>
class ElementTypeMapArrayFilter {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using type = T;
using array_type = ArrayFilter<T>;
using value_type = typename array_type::value_type;
using type_iterator =
typename ElementTypeMapArray<UInt, SupportType>::type_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementTypeMapArrayFilter(
const ElementTypeMapArray<T, SupportType> & array,
const ElementTypeMapArray<UInt, SupportType> & filter,
const ElementTypeMap<UInt, SupportType> & nb_data_per_elem)
: array(array), filter(filter), nb_data_per_elem(nb_data_per_elem) {}
ElementTypeMapArrayFilter(
const ElementTypeMapArray<T, SupportType> & array,
const ElementTypeMapArray<UInt, SupportType> & filter)
: array(array), filter(filter) {}
~ElementTypeMapArrayFilter() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
inline const ArrayFilter<T>
operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const {
if (filter.exists(type, ghost_type)) {
if (nb_data_per_elem.exists(type, ghost_type))
return ArrayFilter<T>(array(type, ghost_type), filter(type, ghost_type),
nb_data_per_elem(type, ghost_type) /
array(type, ghost_type).getNbComponent());
else
return ArrayFilter<T>(array(type, ghost_type), filter(type, ghost_type),
1);
} else {
return ArrayFilter<T>(empty_array, empty_filter, 1);
}
};
inline type_iterator firstType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
return filter.firstType(dim, ghost_type, kind);
};
inline type_iterator lastType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
return filter.lastType(dim, ghost_type, kind);
};
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
return this->array.getNbComponents(dim, ghost_type, kind);
};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
std::string getID() {
return std::string("filtered:" + this->array().getID());
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
const ElementTypeMapArray<T, SupportType> & array;
const ElementTypeMapArray<UInt, SupportType> & filter;
ElementTypeMap<UInt> nb_data_per_elem;
/// Empty array to be able to return consistent filtered arrays
Array<T> empty_array;
Array<UInt> empty_filter;
};
} // namespace akantu
#endif /* __AKANTU_BY_ELEMENT_TYPE_FILTER_HH__ */
diff --git a/src/mesh/element_type_map_tmpl.hh b/src/mesh/element_type_map_tmpl.hh
index 6793158a1..2afd4aa37 100644
--- a/src/mesh/element_type_map_tmpl.hh
+++ b/src/mesh/element_type_map_tmpl.hh
@@ -1,747 +1,747 @@
/**
* @file element_type_map_tmpl.hh
*
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
- * @date last modification: Fri Oct 02 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief implementation of template functions of the ElementTypeMap and
* ElementTypeMapArray classes
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
#include "element_type_map.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include "element_type_conversion.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_TYPE_MAP_TMPL_HH__
#define __AKANTU_ELEMENT_TYPE_MAP_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline std::string
ElementTypeMap<Stored, SupportType>::printType(const SupportType & type,
const GhostType & ghost_type) {
std::stringstream sstr;
sstr << "(" << ghost_type << ":" << type << ")";
return sstr.str();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::exists(
const SupportType & type, const GhostType & ghost_type) const {
return this->getData(ghost_type).find(type) !=
this->getData(ghost_type).end();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline const Stored & ElementTypeMap<Stored, SupportType>::
operator()(const SupportType & type, const GhostType & ghost_type) const {
auto it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end())
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMap::printType(type, ghost_type)
<< " in this ElementTypeMap<"
<< debug::demangle(typeid(Stored).name())
<< "> class");
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline Stored & ElementTypeMap<Stored, SupportType>::
operator()(const SupportType & type, const GhostType & ghost_type) {
return this->getData(ghost_type)[type];
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
template <typename U>
inline Stored & ElementTypeMap<Stored, SupportType>::
operator()(U && insertee, const SupportType & type,
const GhostType & ghost_type) {
auto it = this->getData(ghost_type).find(type);
if (it != this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("Element of type "
<< ElementTypeMap::printType(type, ghost_type)
<< " already in this ElementTypeMap<"
<< debug::demangle(typeid(Stored).name())
<< "> class");
} else {
auto & data = this->getData(ghost_type);
const auto & res =
data.insert(std::make_pair(type, std::forward<U>(insertee)));
it = res.first;
}
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::DataMap &
ElementTypeMap<Stored, SupportType>::getData(GhostType ghost_type) {
if (ghost_type == _not_ghost)
return data;
return ghost_data;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline const typename ElementTypeMap<Stored, SupportType>::DataMap &
ElementTypeMap<Stored, SupportType>::getData(GhostType ghost_type) const {
if (ghost_type == _not_ghost)
return data;
return ghost_data;
}
/* -------------------------------------------------------------------------- */
/// Works only if stored is a pointer to a class with a printself method
template <class Stored, typename SupportType>
void ElementTypeMap<Stored, SupportType>::printself(std::ostream & stream,
int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "ElementTypeMap<" << debug::demangle(typeid(Stored).name())
<< "> [" << std::endl;
for (auto gt : ghost_types) {
const DataMap & data = getData(gt);
for (auto & pair : data) {
stream << space << space << ElementTypeMap::printType(pair.first, gt)
<< std::endl;
}
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::ElementTypeMap() = default;
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::~ElementTypeMap() = default;
/* -------------------------------------------------------------------------- */
/* ElementTypeMapArray */
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
void ElementTypeMapArray<T, SupportType>::copy(
const ElementTypeMapArray & other) {
for (auto ghost_type : ghost_types) {
for (auto type :
this->elementTypes(_all_dimensions, ghost_types, _ek_not_defined)) {
const auto & array_to_copy = other(type, ghost_type);
auto & array =
this->alloc(0, array_to_copy.getNbComponent(), type, ghost_type);
array.copy(array_to_copy);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline Array<T> & ElementTypeMapArray<T, SupportType>::alloc(
UInt size, UInt nb_component, const SupportType & type,
const GhostType & ghost_type, const T & default_value) {
std::string ghost_id = "";
if (ghost_type == _ghost)
ghost_id = ":ghost";
Array<T> * tmp;
auto it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end()) {
std::stringstream sstr;
sstr << this->id << ":" << type << ghost_id;
tmp = &(Memory::alloc<T>(sstr.str(), size, nb_component, default_value));
std::stringstream sstrg;
sstrg << ghost_type;
// tmp->setTag(sstrg.str());
this->getData(ghost_type)[type] = tmp;
} else {
AKANTU_DEBUG_INFO(
"The vector "
<< this->id << this->printType(type, ghost_type)
<< " already exists, it is resized instead of allocated.");
tmp = it->second;
it->second->resize(size);
}
return *tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void
ElementTypeMapArray<T, SupportType>::alloc(UInt size, UInt nb_component,
const SupportType & type,
const T & default_value) {
this->alloc(size, nb_component, type, _not_ghost, default_value);
this->alloc(size, nb_component, type, _ghost, default_value);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::free() {
AKANTU_DEBUG_IN();
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
for (auto & pair : data) {
dealloc(pair.second->getID());
}
data.clear();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::clear() {
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
for (auto & vect : data) {
vect.second->clear();
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
template <typename ST>
inline void ElementTypeMapArray<T, SupportType>::set(const ST & value) {
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
for (auto & vect : data) {
vect.second->set(value);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline const Array<T> & ElementTypeMapArray<T, SupportType>::
operator()(const SupportType & type, const GhostType & ghost_type) const {
auto it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end())
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMapArray::printType(type, ghost_type)
<< " in this const ElementTypeMapArray<"
<< debug::demangle(typeid(T).name()) << "> class(\""
<< this->id << "\")");
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline Array<T> & ElementTypeMapArray<T, SupportType>::
operator()(const SupportType & type, const GhostType & ghost_type) {
auto it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end())
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMapArray::printType(type, ghost_type)
<< " in this ElementTypeMapArray<"
<< debug::demangle(typeid(T).name())
<< "> class (\"" << this->id << "\")");
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void
ElementTypeMapArray<T, SupportType>::setArray(const SupportType & type,
const GhostType & ghost_type,
const Array<T> & vect) {
auto it = this->getData(ghost_type).find(type);
if (AKANTU_DEBUG_TEST(dblWarning) && it != this->getData(ghost_type).end() &&
it->second != &vect) {
AKANTU_DEBUG_WARNING(
"The Array "
<< this->printType(type, ghost_type)
<< " is already registred, this call can lead to a memory leak.");
}
this->getData(ghost_type)[type] = &(const_cast<Array<T> &>(vect));
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::onElementsRemoved(
const ElementTypeMapArray<UInt> & new_numbering) {
for (auto gt : ghost_types) {
for (auto & type :
new_numbering.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
auto support_type = convertType<ElementType, SupportType>(type);
if (this->exists(support_type, gt)) {
const auto & renumbering = new_numbering(type, gt);
if (renumbering.size() == 0)
continue;
auto & vect = this->operator()(support_type, gt);
auto nb_component = vect.getNbComponent();
Array<T> tmp(renumbering.size(), nb_component);
UInt new_size = 0;
for (UInt i = 0; i < vect.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
memcpy(tmp.storage() + new_i * nb_component,
vect.storage() + i * nb_component, nb_component * sizeof(T));
++new_size;
}
}
tmp.resize(new_size);
vect.copy(tmp);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
void ElementTypeMapArray<T, SupportType>::printself(std::ostream & stream,
int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "ElementTypeMapArray<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
for (UInt g = _not_ghost; g <= _ghost; ++g) {
auto gt = (GhostType)g;
const DataMap & data = this->getData(gt);
typename DataMap::const_iterator it;
for (it = data.begin(); it != data.end(); ++it) {
stream << space << space << ElementTypeMapArray::printType(it->first, gt)
<< " [" << std::endl;
it->second->printself(stream, indent + 3);
stream << space << space << " ]" << std::endl;
}
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/* SupportType Iterator */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::type_iterator::type_iterator(
DataMapIterator & list_begin, DataMapIterator & list_end, UInt dim,
ElementKind ek)
: list_begin(list_begin), list_end(list_end), dim(dim), kind(ek) {}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::type_iterator::type_iterator(
const type_iterator & it)
: list_begin(it.list_begin), list_end(it.list_end), dim(it.dim),
kind(it.kind) {}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::type_iterator &
ElementTypeMap<Stored, SupportType>::type_iterator::
operator=(const type_iterator & it) {
if (this != &it) {
list_begin = it.list_begin;
list_end = it.list_end;
dim = it.dim;
kind = it.kind;
}
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator::reference
ElementTypeMap<Stored, SupportType>::type_iterator::operator*() {
return list_begin->first;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator::reference
ElementTypeMap<Stored, SupportType>::type_iterator::operator*() const {
return list_begin->first;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator &
ElementTypeMap<Stored, SupportType>::type_iterator::operator++() {
++list_begin;
while ((list_begin != list_end) &&
(((dim != _all_dimensions) &&
(dim != Mesh::getSpatialDimension(list_begin->first))) ||
((kind != _ek_not_defined) &&
(kind != Mesh::getKind(list_begin->first)))))
++list_begin;
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::type_iterator
ElementTypeMap<Stored, SupportType>::type_iterator::operator++(int) {
type_iterator tmp(*this);
operator++();
return tmp;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::type_iterator::
operator==(const type_iterator & other) const {
return this->list_begin == other.list_begin;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::type_iterator::
operator!=(const type_iterator & other) const {
return this->list_begin != other.list_begin;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::ElementTypesIteratorHelper
ElementTypeMap<Stored, SupportType>::elementTypesImpl(UInt dim,
GhostType ghost_type,
ElementKind kind) const {
return ElementTypesIteratorHelper(*this, dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
template <typename... pack>
typename ElementTypeMap<Stored, SupportType>::ElementTypesIteratorHelper
ElementTypeMap<Stored, SupportType>::elementTypesImpl(
const use_named_args_t & unused, pack &&... _pack) const {
return ElementTypesIteratorHelper(*this, unused, _pack...);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator
ElementTypeMap<Stored, SupportType>::firstType(UInt dim, GhostType ghost_type,
ElementKind kind) const {
typename DataMap::const_iterator b, e;
b = getData(ghost_type).begin();
e = getData(ghost_type).end();
// loop until the first valid type
while ((b != e) &&
(((dim != _all_dimensions) &&
(dim != Mesh::getSpatialDimension(b->first))) ||
((kind != _ek_not_defined) && (kind != Mesh::getKind(b->first)))))
++b;
return typename ElementTypeMap<Stored, SupportType>::type_iterator(b, e, dim,
kind);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator
ElementTypeMap<Stored, SupportType>::lastType(UInt dim, GhostType ghost_type,
ElementKind kind) const {
typename DataMap::const_iterator e;
e = getData(ghost_type).end();
return typename ElementTypeMap<Stored, SupportType>::type_iterator(e, e, dim,
kind);
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Stored, typename SupportType>
inline std::ostream &
operator<<(std::ostream & stream,
const ElementTypeMap<Stored, SupportType> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
class ElementTypeMapArrayInitializer {
protected:
using CompFunc = std::function<UInt(const ElementType &, const GhostType &)>;
public:
ElementTypeMapArrayInitializer(const CompFunc & comp_func,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_regular)
: comp_func(comp_func), spatial_dimension(spatial_dimension),
ghost_type(ghost_type), element_kind(element_kind) {}
const GhostType & ghostType() const { return ghost_type; }
virtual UInt nbComponent(const ElementType & type) const {
return comp_func(type, ghostType());
}
protected:
CompFunc comp_func;
UInt spatial_dimension;
GhostType ghost_type;
ElementKind element_kind;
};
/* -------------------------------------------------------------------------- */
class MeshElementTypeMapArrayInitializer
: public ElementTypeMapArrayInitializer {
using CompFunc = ElementTypeMapArrayInitializer::CompFunc;
public:
MeshElementTypeMapArrayInitializer(
const Mesh & mesh, UInt nb_component = 1,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_regular,
bool with_nb_element = false, bool with_nb_nodes_per_element = false)
: MeshElementTypeMapArrayInitializer(
mesh,
[nb_component](const ElementType &, const GhostType &) -> UInt {
return nb_component;
},
spatial_dimension, ghost_type, element_kind, with_nb_element,
with_nb_nodes_per_element) {}
MeshElementTypeMapArrayInitializer(
const Mesh & mesh, const CompFunc & comp_func,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_regular,
bool with_nb_element = false, bool with_nb_nodes_per_element = false)
: ElementTypeMapArrayInitializer(comp_func, spatial_dimension, ghost_type,
element_kind),
mesh(mesh), with_nb_element(with_nb_element),
with_nb_nodes_per_element(with_nb_nodes_per_element) {}
decltype(auto) elementTypes() const {
return mesh.elementTypes(this->spatial_dimension, this->ghost_type,
this->element_kind);
}
virtual UInt size(const ElementType & type) const {
if (with_nb_element)
return mesh.getNbElement(type, this->ghost_type);
return 0;
}
UInt nbComponent(const ElementType & type) const override {
UInt res = ElementTypeMapArrayInitializer::nbComponent(type);
if (with_nb_nodes_per_element)
return (res * mesh.getNbNodesPerElement(type));
return res;
}
protected:
const Mesh & mesh;
bool with_nb_element;
bool with_nb_nodes_per_element;
};
/* -------------------------------------------------------------------------- */
class FEEngineElementTypeMapArrayInitializer
: public MeshElementTypeMapArrayInitializer {
public:
FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine, UInt nb_component = 1,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_regular);
FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine,
const ElementTypeMapArrayInitializer::CompFunc & nb_component,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_regular);
UInt size(const ElementType & type) const override;
using ElementTypesIteratorHelper =
ElementTypeMapArray<Real, ElementType>::ElementTypesIteratorHelper;
ElementTypesIteratorHelper elementTypes() const;
protected:
const FEEngine & fe_engine;
};
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
template <class Func>
void ElementTypeMapArray<T, SupportType>::initialize(const Func & f,
const T & default_value,
bool do_not_default) {
auto ghost_type = f.ghostType();
for (auto & type : f.elementTypes()) {
if (not this->exists(type, ghost_type))
if (do_not_default) {
auto & array = this->alloc(0, f.nbComponent(type), type, ghost_type);
array.resize(f.size(type));
} else {
this->alloc(f.size(type), f.nbComponent(type), type, ghost_type,
default_value);
}
else {
auto & array = this->operator()(type, ghost_type);
if (not do_not_default)
array.resize(f.size(type), default_value);
else
array.resize(f.size(type));
}
}
}
/* -------------------------------------------------------------------------- */
/**
* All parameters are named optionals
* \param _nb_component a functor giving the number of components per
* (ElementType, GhostType) pair or a scalar giving a unique number of
* components
* regardless of type
* \param _spatial_dimension a filter for the elements of a specific dimension
* \param _element_kind filter with element kind (_ek_regular, _ek_structural,
* ...)
* \param _with_nb_element allocate the arrays with the number of elements for
* each
* type in the mesh
* \param _with_nb_nodes_per_element multiply the number of components by the
* number of nodes per element
* \param _default_value default inital value
* \param _do_not_default do not initialize the allocated arrays
* \param _ghost_type filter a type of ghost
*/
template <typename T, typename SupportType>
template <typename... pack>
void ElementTypeMapArray<T, SupportType>::initialize(const Mesh & mesh,
pack &&... _pack) {
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _casper);
bool all_ghost_types = requested_ghost_type == _casper;
for (auto ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types))
continue;
// This thing should have a UInt or functor type
auto && nb_components = OPTIONAL_NAMED_ARG(nb_component, 1);
auto functor = MeshElementTypeMapArrayInitializer(
mesh, std::forward<decltype(nb_components)>(nb_components),
OPTIONAL_NAMED_ARG(spatial_dimension, mesh.getSpatialDimension()),
ghost_type, OPTIONAL_NAMED_ARG(element_kind, _ek_regular),
OPTIONAL_NAMED_ARG(with_nb_element, false),
OPTIONAL_NAMED_ARG(with_nb_nodes_per_element, false));
this->initialize(functor, OPTIONAL_NAMED_ARG(default_value, T()),
OPTIONAL_NAMED_ARG(do_not_default, false));
}
}
/* -------------------------------------------------------------------------- */
/**
* All parameters are named optionals
* \param _nb_component a functor giving the number of components per
* (ElementType, GhostType) pair or a scalar giving a unique number of
* components
* regardless of type
* \param _spatial_dimension a filter for the elements of a specific dimension
* \param _element_kind filter with element kind (_ek_regular, _ek_structural,
* ...)
* \param _default_value default inital value
* \param _do_not_default do not initialize the allocated arrays
* \param _ghost_type filter a specific ghost type
* \param _all_ghost_types get all ghost types
*/
template <typename T, typename SupportType>
template <typename... pack>
void ElementTypeMapArray<T, SupportType>::initialize(const FEEngine & fe_engine,
pack &&... _pack) {
bool all_ghost_types = OPTIONAL_NAMED_ARG(all_ghost_types, true);
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _not_ghost);
for (auto ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types))
continue;
auto && nb_components = OPTIONAL_NAMED_ARG(nb_component, 1);
auto functor = FEEngineElementTypeMapArrayInitializer(
fe_engine, std::forward<decltype(nb_components)>(nb_components),
OPTIONAL_NAMED_ARG(spatial_dimension, UInt(-2)), ghost_type,
OPTIONAL_NAMED_ARG(element_kind, _ek_regular));
this->initialize(functor, OPTIONAL_NAMED_ARG(default_value, T()),
OPTIONAL_NAMED_ARG(do_not_default, false));
}
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
inline T & ElementTypeMapArray<T, SupportType>::
operator()(const Element & element, UInt component) {
return this->operator()(element.type, element.ghost_type)(element.element,
component);
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
inline const T & ElementTypeMapArray<T, SupportType>::
operator()(const Element & element, UInt component) const {
return this->operator()(element.type, element.ghost_type)(element.element,
component);
}
} // namespace akantu
#endif /* __AKANTU_ELEMENT_TYPE_MAP_TMPL_HH__ */
diff --git a/src/mesh/group_manager.cc b/src/mesh/group_manager.cc
index a18c02007..98c067ce4 100644
--- a/src/mesh/group_manager.cc
+++ b/src/mesh/group_manager.cc
@@ -1,1040 +1,1040 @@
/**
* @file group_manager.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Mon Aug 17 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Stores information about ElementGroup and NodeGroup
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "group_manager.hh"
#include "aka_csr.hh"
#include "data_accessor.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iterator>
#include <list>
#include <numeric>
#include <queue>
#include <sstream>
#include <utility>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
GroupManager::GroupManager(const Mesh & mesh, const ID & id,
const MemoryID & mem_id)
: id(id), memory_id(mem_id), mesh(mesh) {
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
GroupManager::~GroupManager() {
auto eit = element_groups.begin();
auto eend = element_groups.end();
for (; eit != eend; ++eit)
delete (eit->second);
auto nit = node_groups.begin();
auto nend = node_groups.end();
for (; nit != nend; ++nit)
delete (nit->second);
}
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::createNodeGroup(const std::string & group_name,
bool replace_group) {
AKANTU_DEBUG_IN();
auto it = node_groups.find(group_name);
if (it != node_groups.end()) {
if (replace_group) {
it->second->empty();
AKANTU_DEBUG_OUT();
return *(it->second);
} else
AKANTU_EXCEPTION(
"Trying to create a node group that already exists:" << group_name);
}
std::stringstream sstr;
sstr << this->id << ":" << group_name << "_node_group";
NodeGroup * node_group =
new NodeGroup(group_name, mesh, sstr.str(), memory_id);
node_groups[group_name] = node_group;
AKANTU_DEBUG_OUT();
return *node_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
NodeGroup &
GroupManager::createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & source_node_group,
T & filter) {
AKANTU_DEBUG_IN();
NodeGroup & node_group = this->createNodeGroup(group_name);
node_group.append(source_node_group);
if (T::type == FilterFunctor::_node_filter_functor) {
node_group.applyNodeFilter(filter);
} else {
AKANTU_ERROR("ElementFilter cannot be applied to NodeGroup yet."
<< " Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
return node_group;
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyNodeGroup(const std::string & group_name) {
AKANTU_DEBUG_IN();
auto nit = node_groups.find(group_name);
auto nend = node_groups.end();
if (nit != nend) {
delete (nit->second);
node_groups.erase(nit);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
bool replace_group) {
AKANTU_DEBUG_IN();
NodeGroup & new_node_group =
createNodeGroup(group_name + "_nodes", replace_group);
auto it = element_groups.find(group_name);
if (it != element_groups.end()) {
if (replace_group) {
it->second->empty();
AKANTU_DEBUG_OUT();
return *(it->second);
} else
AKANTU_EXCEPTION("Trying to create a element group that already exists:"
<< group_name);
}
std::stringstream sstr;
sstr << this->id << ":" << group_name << "_element_group";
ElementGroup * element_group = new ElementGroup(
group_name, mesh, new_node_group, dimension, sstr.str(), memory_id);
std::stringstream sstr_nodes;
sstr_nodes << group_name << "_nodes";
node_groups[sstr_nodes.str()] = &new_node_group;
element_groups[group_name] = element_group;
AKANTU_DEBUG_OUT();
return *element_group;
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyElementGroup(const std::string & group_name,
bool destroy_node_group) {
AKANTU_DEBUG_IN();
auto eit = element_groups.find(group_name);
auto eend = element_groups.end();
if (eit != eend) {
if (destroy_node_group)
destroyNodeGroup(eit->second->getNodeGroup().getName());
delete (eit->second);
element_groups.erase(eit);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyAllElementGroups(bool destroy_node_groups) {
AKANTU_DEBUG_IN();
auto eit = element_groups.begin();
auto eend = element_groups.end();
for (; eit != eend; ++eit) {
if (destroy_node_groups)
destroyNodeGroup(eit->second->getNodeGroup().getName());
delete (eit->second);
}
element_groups.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
NodeGroup & node_group) {
AKANTU_DEBUG_IN();
if (element_groups.find(group_name) != element_groups.end())
AKANTU_EXCEPTION(
"Trying to create a element group that already exists:" << group_name);
ElementGroup * element_group =
new ElementGroup(group_name, mesh, node_group, dimension,
id + ":" + group_name + "_element_group", memory_id);
element_groups[group_name] = element_group;
AKANTU_DEBUG_OUT();
return *element_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementGroup & GroupManager::createFilteredElementGroup(
const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter) {
AKANTU_DEBUG_IN();
ElementGroup * element_group = nullptr;
if (T::type == FilterFunctor::_node_filter_functor) {
NodeGroup & filtered_node_group = this->createFilteredNodeGroup(
group_name + "_nodes", node_group, filter);
element_group =
&(this->createElementGroup(group_name, dimension, filtered_node_group));
} else if (T::type == FilterFunctor::_element_filter_functor) {
AKANTU_ERROR(
"Cannot handle an ElementFilter yet. Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
return *element_group;
}
/* -------------------------------------------------------------------------- */
class ClusterSynchronizer : public DataAccessor<Element> {
using DistantIDs = std::set<std::pair<UInt, UInt>>;
public:
ClusterSynchronizer(GroupManager & group_manager, UInt element_dimension,
std::string cluster_name_prefix,
ElementTypeMapArray<UInt> & element_to_fragment,
const ElementSynchronizer & element_synchronizer,
UInt nb_cluster)
: group_manager(group_manager), element_dimension(element_dimension),
cluster_name_prefix(std::move(cluster_name_prefix)),
element_to_fragment(element_to_fragment),
element_synchronizer(element_synchronizer), nb_cluster(nb_cluster) {}
UInt synchronize() {
Communicator & comm = Communicator::getStaticCommunicator();
UInt rank = comm.whoAmI();
UInt nb_proc = comm.getNbProc();
/// find starting index to renumber local clusters
Array<UInt> nb_cluster_per_proc(nb_proc);
nb_cluster_per_proc(rank) = nb_cluster;
comm.allGather(nb_cluster_per_proc);
starting_index = std::accumulate(nb_cluster_per_proc.begin(),
nb_cluster_per_proc.begin() + rank, 0);
UInt global_nb_fragment =
std::accumulate(nb_cluster_per_proc.begin() + rank,
nb_cluster_per_proc.end(), starting_index);
/// create the local to distant cluster pairs with neighbors
element_synchronizer.synchronizeOnce(*this, _gst_gm_clusters);
/// count total number of pairs
Array<int> nb_pairs(nb_proc); // This is potentially a bug for more than
// 2**31 pairs, but due to a all gatherv after
// it must be int to match MPI interfaces
nb_pairs(rank) = distant_ids.size();
comm.allGather(nb_pairs);
UInt total_nb_pairs = std::accumulate(nb_pairs.begin(), nb_pairs.end(), 0);
/// generate pairs global array
UInt local_pair_index =
std::accumulate(nb_pairs.storage(), nb_pairs.storage() + rank, 0);
Array<UInt> total_pairs(total_nb_pairs, 2);
for (auto & ids : distant_ids) {
total_pairs(local_pair_index, 0) = ids.first;
total_pairs(local_pair_index, 1) = ids.second;
++local_pair_index;
}
/// communicate pairs to all processors
nb_pairs *= 2;
comm.allGatherV(total_pairs, nb_pairs);
/// renumber clusters
/// generate fragment list
std::vector<std::set<UInt>> global_clusters;
UInt total_nb_cluster = 0;
Array<bool> is_fragment_in_cluster(global_nb_fragment, 1, false);
std::queue<UInt> fragment_check_list;
while (total_pairs.size() != 0) {
/// create a new cluster
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster = global_clusters[total_nb_cluster - 1];
UInt first_fragment = total_pairs(0, 0);
UInt second_fragment = total_pairs(0, 1);
total_pairs.erase(0);
fragment_check_list.push(first_fragment);
fragment_check_list.push(second_fragment);
while (!fragment_check_list.empty()) {
UInt current_fragment = fragment_check_list.front();
UInt * total_pairs_end = total_pairs.storage() + total_pairs.size() * 2;
UInt * fragment_found =
std::find(total_pairs.storage(), total_pairs_end, current_fragment);
if (fragment_found != total_pairs_end) {
UInt position = fragment_found - total_pairs.storage();
UInt pair = position / 2;
UInt other_index = (position + 1) % 2;
fragment_check_list.push(total_pairs(pair, other_index));
total_pairs.erase(pair);
} else {
fragment_check_list.pop();
current_cluster.insert(current_fragment);
is_fragment_in_cluster(current_fragment) = true;
}
}
}
/// add to FragmentToCluster all local fragments
for (UInt c = 0; c < global_nb_fragment; ++c) {
if (!is_fragment_in_cluster(c)) {
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster =
global_clusters[total_nb_cluster - 1];
current_cluster.insert(c);
}
}
/// reorganize element groups to match global clusters
for (UInt c = 0; c < global_clusters.size(); ++c) {
/// create new element group corresponding to current cluster
std::stringstream sstr;
sstr << cluster_name_prefix << "_" << c;
ElementGroup & cluster =
group_manager.createElementGroup(sstr.str(), element_dimension, true);
auto it = global_clusters[c].begin();
auto end = global_clusters[c].end();
/// append to current element group all fragments that belong to
/// the same cluster if they exist
for (; it != end; ++it) {
Int local_index = *it - starting_index;
if (local_index < 0 || local_index >= Int(nb_cluster))
continue;
std::stringstream tmp_sstr;
tmp_sstr << "tmp_" << cluster_name_prefix << "_" << local_index;
auto eg_it = group_manager.element_group_find(tmp_sstr.str());
AKANTU_DEBUG_ASSERT(eg_it != group_manager.element_group_end(),
"Temporary fragment \"" << tmp_sstr.str()
<< "\" not found");
cluster.append(*(eg_it->second));
group_manager.destroyElementGroup(tmp_sstr.str(), true);
}
}
return total_nb_cluster;
}
private:
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag == _gst_gm_clusters)
return elements.size() * sizeof(UInt);
return 0;
}
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag != _gst_gm_clusters)
return;
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
const Element & el = *el_it;
/// for each element pack its global cluster index
buffer << element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
}
}
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override {
if (tag != _gst_gm_clusters)
return;
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
UInt distant_cluster;
buffer >> distant_cluster;
const Element & el = *el_it;
UInt local_cluster =
element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
distant_ids.insert(std::make_pair(local_cluster, distant_cluster));
}
}
private:
GroupManager & group_manager;
UInt element_dimension;
std::string cluster_name_prefix;
ElementTypeMapArray<UInt> & element_to_fragment;
const ElementSynchronizer & element_synchronizer;
UInt nb_cluster;
DistantIDs distant_ids;
UInt starting_index;
};
/* -------------------------------------------------------------------------- */
/// \todo this function doesn't work in 1D
UInt GroupManager::createBoundaryGroupFromGeometry() {
UInt spatial_dimension = mesh.getSpatialDimension();
return createClusters(spatial_dimension - 1, "boundary");
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::createClusters(
UInt element_dimension, Mesh & mesh_facets, std::string cluster_name_prefix,
const GroupManager::ClusteringFilter & filter) {
return createClusters(element_dimension, std::move(cluster_name_prefix),
filter, mesh_facets);
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::createClusters(
UInt element_dimension, std::string cluster_name_prefix,
const GroupManager::ClusteringFilter & filter) {
std::unique_ptr<Mesh> mesh_facets;
if (!mesh_facets && element_dimension > 0) {
MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
mesh_facets = std::make_unique<Mesh>(mesh.getSpatialDimension(),
mesh_accessor.getNodesSharedPtr(),
"mesh_facets_for_clusters");
mesh_facets->defineMeshParent(mesh);
MeshUtils::buildAllFacets(mesh, *mesh_facets, element_dimension,
element_dimension - 1);
}
return createClusters(element_dimension, std::move(cluster_name_prefix),
filter, *mesh_facets);
}
/* -------------------------------------------------------------------------- */
//// \todo if needed element list construction can be optimized by
//// templating the filter class
UInt GroupManager::createClusters(UInt element_dimension,
const std::string & cluster_name_prefix,
const GroupManager::ClusteringFilter & filter,
Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
UInt nb_proc = mesh.getCommunicator().getNbProc();
std::string tmp_cluster_name_prefix = cluster_name_prefix;
ElementTypeMapArray<UInt> * element_to_fragment = nullptr;
if (nb_proc > 1 && mesh.isDistributed()) {
element_to_fragment =
new ElementTypeMapArray<UInt>("element_to_fragment", id, memory_id);
element_to_fragment->initialize(
mesh, _nb_component = 1, _spatial_dimension = element_dimension,
_element_kind = _ek_not_defined, _with_nb_element = true);
// mesh.initElementTypeMapArray(*element_to_fragment, 1, element_dimension,
// false, _ek_not_defined, true);
tmp_cluster_name_prefix = "tmp_" + tmp_cluster_name_prefix;
}
ElementTypeMapArray<bool> seen_elements("seen_elements", id, memory_id);
seen_elements.initialize(mesh, _spatial_dimension = element_dimension,
_element_kind = _ek_not_defined,
_with_nb_element = true);
// mesh.initElementTypeMapArray(seen_elements, 1, element_dimension, false,
// _ek_not_defined, true);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Element el;
el.ghost_type = ghost_type;
Mesh::type_iterator type_it =
mesh.firstType(element_dimension, ghost_type, _ek_not_defined);
Mesh::type_iterator type_end =
mesh.lastType(element_dimension, ghost_type, _ek_not_defined);
for (; type_it != type_end; ++type_it) {
el.type = *type_it;
UInt nb_element = mesh.getNbElement(*type_it, ghost_type);
Array<bool> & seen_elements_array = seen_elements(el.type, ghost_type);
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
if (!filter(el))
seen_elements_array(e) = true;
}
}
}
Array<bool> checked_node(mesh.getNbNodes(), 1, false);
UInt nb_cluster = 0;
/// keep looping until all elements are seen
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Element uns_el;
uns_el.ghost_type = ghost_type;
Mesh::type_iterator type_it =
mesh.firstType(element_dimension, ghost_type, _ek_not_defined);
Mesh::type_iterator type_end =
mesh.lastType(element_dimension, ghost_type, _ek_not_defined);
for (; type_it != type_end; ++type_it) {
uns_el.type = *type_it;
Array<bool> & seen_elements_vec =
seen_elements(uns_el.type, uns_el.ghost_type);
for (UInt e = 0; e < seen_elements_vec.size(); ++e) {
// skip elements that have been already seen
if (seen_elements_vec(e) == true)
continue;
// set current element
uns_el.element = e;
seen_elements_vec(e) = true;
/// create a new cluster
std::stringstream sstr;
sstr << tmp_cluster_name_prefix << "_" << nb_cluster;
ElementGroup & cluster =
createElementGroup(sstr.str(), element_dimension, true);
++nb_cluster;
// point element are cluster by themself
if (element_dimension == 0) {
cluster.add(uns_el);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(uns_el.type);
Vector<UInt> connect =
mesh.getConnectivity(uns_el.type, uns_el.ghost_type)
.begin(nb_nodes_per_element)[uns_el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node);
checked_node(node) = true;
}
}
continue;
}
std::queue<Element> element_to_add;
element_to_add.push(uns_el);
/// keep looping until current cluster is complete (no more
/// connected elements)
while (!element_to_add.empty()) {
/// take first element and erase it in the queue
Element el = element_to_add.front();
element_to_add.pop();
/// if parallel, store cluster index per element
if (nb_proc > 1 && mesh.isDistributed())
(*element_to_fragment)(el.type, el.ghost_type)(el.element) =
nb_cluster - 1;
/// add current element to the cluster
cluster.add(el);
const Array<Element> & element_to_facet =
mesh_facets.getSubelementToElement(el.type, el.ghost_type);
UInt nb_facet_per_element = element_to_facet.getNbComponent();
for (UInt f = 0; f < nb_facet_per_element; ++f) {
const Element & facet = element_to_facet(el.element, f);
if (facet == ElementNull)
continue;
const std::vector<Element> & connected_elements =
mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
for (UInt elem = 0; elem < connected_elements.size(); ++elem) {
const Element & check_el = connected_elements[elem];
// check if this element has to be skipped
if (check_el == ElementNull || check_el == el)
continue;
Array<bool> & seen_elements_vec_current =
seen_elements(check_el.type, check_el.ghost_type);
if (seen_elements_vec_current(check_el.element) == false) {
seen_elements_vec_current(check_el.element) = true;
element_to_add.push(check_el);
}
}
}
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
Vector<UInt> connect = mesh.getConnectivity(el.type, el.ghost_type)
.begin(nb_nodes_per_element)[el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node, false);
checked_node(node) = true;
}
}
}
}
}
}
if (nb_proc > 1 && mesh.isDistributed()) {
ClusterSynchronizer cluster_synchronizer(
*this, element_dimension, cluster_name_prefix, *element_to_fragment,
this->mesh.getElementSynchronizer(), nb_cluster);
nb_cluster = cluster_synchronizer.synchronize();
delete element_to_fragment;
}
if (mesh.isDistributed())
this->synchronizeGroupNames();
AKANTU_DEBUG_OUT();
return nb_cluster;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void GroupManager::createGroupsFromMeshData(const std::string & dataset_name) {
std::set<std::string> group_names;
const ElementTypeMapArray<T> & datas = mesh.getData<T>(dataset_name);
using type_iterator = typename ElementTypeMapArray<T>::type_iterator;
std::map<std::string, UInt> group_dim;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
type_iterator type_it = datas.firstType(_all_dimensions, *gt);
type_iterator type_end = datas.lastType(_all_dimensions, *gt);
for (; type_it != type_end; ++type_it) {
const Array<T> & dataset = datas(*type_it, *gt);
UInt nb_element = mesh.getNbElement(*type_it, *gt);
AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
"Not the same number of elements ("
<< *type_it << ":" << *gt
<< ") in the map from MeshData ("
<< dataset.size() << ") " << dataset_name
<< " and in the mesh (" << nb_element << ")!");
for (UInt e(0); e < nb_element; ++e) {
std::stringstream sstr;
sstr << dataset(e);
std::string gname = sstr.str();
group_names.insert(gname);
auto it = group_dim.find(gname);
if (it == group_dim.end()) {
group_dim[gname] = mesh.getSpatialDimension(*type_it);
} else {
it->second = std::max(it->second, mesh.getSpatialDimension(*type_it));
}
}
}
}
auto git = group_names.begin();
auto gend = group_names.end();
for (; git != gend; ++git)
createElementGroup(*git, group_dim[*git]);
if (mesh.isDistributed())
this->synchronizeGroupNames();
Element el;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
el.ghost_type = *gt;
type_iterator type_it = datas.firstType(_all_dimensions, *gt);
type_iterator type_end = datas.lastType(_all_dimensions, *gt);
for (; type_it != type_end; ++type_it) {
el.type = *type_it;
const Array<T> & dataset = datas(*type_it, *gt);
UInt nb_element = mesh.getNbElement(*type_it, *gt);
AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
"Not the same number of elements in the map from "
"MeshData and in the mesh!");
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(el.type);
Array<UInt>::const_iterator<Vector<UInt>> cit =
mesh.getConnectivity(*type_it, *gt).begin(nb_nodes_per_element);
for (UInt e(0); e < nb_element; ++e, ++cit) {
el.element = e;
std::stringstream sstr;
sstr << dataset(e);
ElementGroup & group = getElementGroup(sstr.str());
group.add(el, false, false);
const Vector<UInt> & connect = *cit;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connect[n];
group.addNode(node, false);
}
}
}
}
git = group_names.begin();
for (; git != gend; ++git) {
getElementGroup(*git).optimize();
}
}
template void GroupManager::createGroupsFromMeshData<std::string>(
const std::string & dataset_name);
template void
GroupManager::createGroupsFromMeshData<UInt>(const std::string & dataset_name);
/* -------------------------------------------------------------------------- */
void GroupManager::createElementGroupFromNodeGroup(
const std::string & name, const std::string & node_group_name,
UInt dimension) {
NodeGroup & node_group = getNodeGroup(node_group_name);
ElementGroup & group = createElementGroup(name, dimension, node_group);
group.fillFromNodeGroup();
}
/* -------------------------------------------------------------------------- */
void GroupManager::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "GroupManager [" << std::endl;
std::set<std::string> node_group_seen;
for (auto it(element_group_begin()); it != element_group_end(); ++it) {
it->second->printself(stream, indent + 1);
node_group_seen.insert(it->second->getNodeGroup().getName());
}
for (auto it(node_group_begin()); it != node_group_end(); ++it) {
if (node_group_seen.find(it->second->getName()) == node_group_seen.end())
it->second->printself(stream, indent + 1);
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::getNbElementGroups(UInt dimension) const {
if (dimension == _all_dimensions)
return element_groups.size();
auto it = element_groups.begin();
auto end = element_groups.end();
UInt count = 0;
for (; it != end; ++it)
count += (it->second->getDimension() == dimension);
return count;
}
/* -------------------------------------------------------------------------- */
void GroupManager::checkAndAddGroups(CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
UInt nb_node_group;
buffer >> nb_node_group;
AKANTU_DEBUG_INFO("Received " << nb_node_group << " node group names");
for (UInt ng = 0; ng < nb_node_group; ++ng) {
std::string node_group_name;
buffer >> node_group_name;
if (node_groups.find(node_group_name) == node_groups.end()) {
this->createNodeGroup(node_group_name);
}
AKANTU_DEBUG_INFO("Received node goup name: " << node_group_name);
}
UInt nb_element_group;
buffer >> nb_element_group;
AKANTU_DEBUG_INFO("Received " << nb_element_group << " element group names");
for (UInt eg = 0; eg < nb_element_group; ++eg) {
std::string element_group_name;
buffer >> element_group_name;
std::string node_group_name;
buffer >> node_group_name;
UInt dim;
buffer >> dim;
AKANTU_DEBUG_INFO("Received element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with node group "
<< node_group_name);
NodeGroup & node_group = *node_groups[node_group_name];
if (element_groups.find(element_group_name) == element_groups.end()) {
this->createElementGroup(element_group_name, dim, node_group);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::fillBufferWithGroupNames(
DynamicCommunicationBuffer & comm_buffer) const {
AKANTU_DEBUG_IN();
// packing node group names;
UInt nb_groups = this->node_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " node group names");
auto nnames_it = node_groups.begin();
auto nnames_end = node_groups.end();
for (; nnames_it != nnames_end; ++nnames_it) {
std::string node_group_name = nnames_it->first;
comm_buffer << node_group_name;
AKANTU_DEBUG_INFO("Sending node goupe name: " << node_group_name);
}
// packing element group names with there associated node group name
nb_groups = this->element_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " element group names");
auto gnames_it = this->element_groups.begin();
auto gnames_end = this->element_groups.end();
for (; gnames_it != gnames_end; ++gnames_it) {
ElementGroup & element_group = *(gnames_it->second);
std::string element_group_name = gnames_it->first;
std::string node_group_name = element_group.getNodeGroup().getName();
UInt dim = element_group.getDimension();
comm_buffer << element_group_name;
comm_buffer << node_group_name;
comm_buffer << dim;
AKANTU_DEBUG_INFO("Sending element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with the node group "
<< node_group_name);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::synchronizeGroupNames() {
AKANTU_DEBUG_IN();
const Communicator & comm = mesh.getCommunicator();
Int nb_proc = comm.getNbProc();
Int my_rank = comm.whoAmI();
if (nb_proc == 1)
return;
if (my_rank == 0) {
for (Int p = 1; p < nb_proc; ++p) {
CommunicationStatus status;
comm.probe<char>(p, p, status);
AKANTU_DEBUG_INFO("Got " << printMemorySize<char>(status.size())
<< " from proc " << p);
CommunicationBuffer recv_buffer(status.size());
comm.receive(recv_buffer, p, p);
this->checkAndAddGroups(recv_buffer);
}
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
UInt buffer_size = comm_buffer.size();
comm.broadcast(buffer_size, 0);
AKANTU_DEBUG_INFO("Initiating broadcast with "
<< printMemorySize<char>(comm_buffer.size()));
comm.broadcast(comm_buffer, 0);
} else {
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
AKANTU_DEBUG_INFO("Sending " << printMemorySize<char>(comm_buffer.size())
<< " to proc " << 0);
comm.send(comm_buffer, 0, my_rank);
UInt buffer_size = 0;
comm.broadcast(buffer_size, 0);
AKANTU_DEBUG_INFO("Receiving broadcast with "
<< printMemorySize<char>(comm_buffer.size()));
CommunicationBuffer recv_buffer(buffer_size);
comm.broadcast(recv_buffer, 0);
this->checkAndAddGroups(recv_buffer);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
const ElementGroup &
GroupManager::getElementGroup(const std::string & name) const {
auto it = element_group_find(name);
if (it == element_group_end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::getElementGroup(const std::string & name) {
auto it = element_group_find(name);
if (it == element_group_end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
const NodeGroup & GroupManager::getNodeGroup(const std::string & name) const {
auto it = node_group_find(name);
if (it == node_group_end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::getNodeGroup(const std::string & name) {
auto it = node_group_find(name);
if (it == node_group_end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
} // namespace akantu
diff --git a/src/mesh/group_manager.hh b/src/mesh/group_manager.hh
index 56998407b..242dd2ef4 100644
--- a/src/mesh/group_manager.hh
+++ b/src/mesh/group_manager.hh
@@ -1,316 +1,316 @@
/**
* @file group_manager.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Mon Nov 16 2015
+ * @date last modification: Wed Feb 07 2018
*
* @brief Stores information relevent to the notion of element and nodes
- *groups.
+ * groups.
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GROUP_MANAGER_HH__
#define __AKANTU_GROUP_MANAGER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementGroup;
class NodeGroup;
class Mesh;
class Element;
class ElementSynchronizer;
template <bool> class CommunicationBufferTemplated;
namespace dumper {
class Field;
}
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
class GroupManager {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
#ifdef SWIGPYTHON
public:
using ElementGroups = std::map<std::string, ElementGroup *>;
using NodeGroups = std::map<std::string, NodeGroup *>;
private:
#else
using ElementGroups = std::map<std::string, ElementGroup *>;
using NodeGroups = std::map<std::string, NodeGroup *>;
#endif
public:
using GroupManagerTypeSet = std::set<ElementType>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GroupManager(const Mesh & mesh, const ID & id = "group_manager",
const MemoryID & memory_id = 0);
virtual ~GroupManager();
/* ------------------------------------------------------------------------ */
/* Groups iterators */
/* ------------------------------------------------------------------------ */
public:
using node_group_iterator = NodeGroups::iterator;
using element_group_iterator = ElementGroups::iterator;
using const_node_group_iterator = NodeGroups::const_iterator;
using const_element_group_iterator = ElementGroups::const_iterator;
#ifndef SWIG
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(group_type, function, \
param_in, param_out) \
inline BOOST_PP_CAT(BOOST_PP_CAT(const_, group_type), _iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) const { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}; \
\
inline BOOST_PP_CAT(group_type, _iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(group_type, function) \
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION( \
group_type, function, BOOST_PP_EMPTY(), BOOST_PP_EMPTY())
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(element_group, find,
const std::string & name, name);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(node_group, find,
const std::string & name, name);
#endif
/* ------------------------------------------------------------------------ */
/* Clustering filter */
/* ------------------------------------------------------------------------ */
public:
class ClusteringFilter {
public:
virtual bool operator()(const Element &) const { return true; }
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create an empty node group
NodeGroup & createNodeGroup(const std::string & group_name,
bool replace_group = false);
/// create a node group from another node group but filtered
template <typename T>
NodeGroup & createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & node_group, T & filter);
/// destroy a node group
void destroyNodeGroup(const std::string & group_name);
/// create an element group and the associated node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension = _all_dimensions,
bool replace_group = false);
/// create an element group from another element group but filtered
template <typename T>
ElementGroup &
createFilteredElementGroup(const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter);
/// destroy an element group and the associated node group
void destroyElementGroup(const std::string & group_name,
bool destroy_node_group = false);
/// destroy all element groups and the associated node groups
void destroyAllElementGroups(bool destroy_node_groups = false);
/// create a element group using an existing node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension, NodeGroup & node_group);
/// create groups based on values stored in a given mesh data
template <typename T>
void createGroupsFromMeshData(const std::string & dataset_name);
/// create boundaries group by a clustering algorithm \todo extend to parallel
UInt createBoundaryGroupFromGeometry();
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension, Mesh & mesh_facets,
std::string cluster_name_prefix = "cluster",
const ClusteringFilter & filter = ClusteringFilter());
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension,
std::string cluster_name_prefix = "cluster",
const ClusteringFilter & filter = ClusteringFilter());
private:
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension,
const std::string & cluster_name_prefix,
const ClusteringFilter & filter, Mesh & mesh_facets);
public:
/// Create an ElementGroup based on a NodeGroup
void createElementGroupFromNodeGroup(const std::string & name,
const std::string & node_group,
UInt dimension = _all_dimensions);
virtual void printself(std::ostream & stream, int indent = 0) const;
/// this function insure that the group names are present on all processors
/// /!\ it is a SMP call
void synchronizeGroupNames();
/// register an elemental field to the given group name (overloading for
/// ElementalPartionField)
#ifndef SWIG
template <typename T, template <bool> class dump_type>
dumper::Field * createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// ElementalField)
template <typename T, template <class> class ret_type,
template <class, template <class> class, bool> class dump_type>
dumper::Field * createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// MaterialInternalField)
template <typename T,
/// type of InternalMaterialField
template <typename, bool filtered> class dump_type>
dumper::Field * createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name,
UInt spatial_dimension,
const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem);
template <typename type, bool flag, template <class, bool> class ftype>
dumper::Field * createNodalField(const ftype<type, flag> * field,
const std::string & group_name,
UInt padding_size = 0);
template <typename type, bool flag, template <class, bool> class ftype>
dumper::Field * createStridedNodalField(const ftype<type, flag> * field,
const std::string & group_name,
UInt size, UInt stride,
UInt padding_size);
protected:
/// fill a buffer with all the group names
void fillBufferWithGroupNames(
CommunicationBufferTemplated<false> & comm_buffer) const;
/// take a buffer and create the missing groups localy
void checkAndAddGroups(CommunicationBufferTemplated<true> & buffer);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline dumper::Field *
createElementalField(const field_type & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
const ElementTypeMap<UInt> & nb_data_per_elem);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline dumper::Field *
createElementalFilteredField(const field_type & field,
const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem);
#endif
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(ElementGroups, element_groups, const ElementGroups &);
const ElementGroup & getElementGroup(const std::string & name) const;
const NodeGroup & getNodeGroup(const std::string & name) const;
ElementGroup & getElementGroup(const std::string & name);
NodeGroup & getNodeGroup(const std::string & name);
UInt getNbElementGroups(UInt dimension = _all_dimensions) const;
UInt getNbNodeGroups() { return node_groups.size(); };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id to create element and node groups
ID id;
/// memory_id to create element and node groups
MemoryID memory_id;
/// list of the node groups managed
NodeGroups node_groups;
/// list of the element groups managed
ElementGroups element_groups;
/// Mesh to which the element belongs
const Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const GroupManager & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* __AKANTU_GROUP_MANAGER_HH__ */
diff --git a/src/mesh/group_manager_inline_impl.cc b/src/mesh/group_manager_inline_impl.cc
index 9629a5279..bfb9d0f6a 100644
--- a/src/mesh/group_manager_inline_impl.cc
+++ b/src/mesh/group_manager_inline_impl.cc
@@ -1,205 +1,205 @@
/**
* @file group_manager_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_field.hh"
#include "element_group.hh"
#include "element_type_map_filter.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_nodal_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, template <bool> class dump_type>
dumper::Field * GroupManager::createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
if (field_ptr == nullptr)
return nullptr;
if (group_name == "all")
return this->createElementalField<dump_type<false>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
else
return this->createElementalFilteredField<dump_type<true>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <class> class T2,
template <class, template <class> class, bool> class dump_type>
dumper::Field * GroupManager::createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
if (field_ptr == nullptr)
return nullptr;
if (group_name == "all")
return this->createElementalField<dump_type<T, T2, false>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
else
return this->createElementalFilteredField<dump_type<T, T2, true>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename T2, bool filtered>
class dump_type> ///< type of InternalMaterialField
dumper::Field *
GroupManager::createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name,
UInt spatial_dimension,
const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
if (field_ptr == nullptr)
return nullptr;
if (group_name == "all")
return this->createElementalField<dump_type<T, false>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
else
return this->createElementalFilteredField<dump_type<T, true>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename dump_type, typename field_type>
dumper::Field * GroupManager::createElementalField(
const field_type & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
const ElementTypeMap<UInt> & nb_data_per_elem) {
const field_type * field_ptr = &field;
if (field_ptr == nullptr)
return nullptr;
if (group_name != "all")
throw;
dumper::Field * dumper =
new dump_type(field, spatial_dimension, _not_ghost, kind);
dumper->setNbDataPerElem(nb_data_per_elem);
return dumper;
}
/* -------------------------------------------------------------------------- */
template <typename dump_type, typename field_type>
dumper::Field * GroupManager::createElementalFilteredField(
const field_type & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const field_type * field_ptr = &field;
if (field_ptr == nullptr)
return nullptr;
if (group_name == "all")
throw;
using T = typename field_type::type;
ElementGroup & group = this->getElementGroup(group_name);
UInt dim = group.getDimension();
if (dim != spatial_dimension)
throw;
const ElementTypeMapArray<UInt> & elemental_filter = group.getElements();
auto * filtered = new ElementTypeMapArrayFilter<T>(field, elemental_filter,
nb_data_per_elem);
dumper::Field * dumper = new dump_type(*filtered, dim, _not_ghost, kind);
dumper->setNbDataPerElem(nb_data_per_elem);
return dumper;
}
/* -------------------------------------------------------------------------- */
template <typename type, bool flag, template <class, bool> class ftype>
dumper::Field * GroupManager::createNodalField(const ftype<type, flag> * field,
const std::string & group_name,
UInt padding_size) {
if (field == nullptr)
return nullptr;
if (group_name == "all") {
using DumpType = typename dumper::NodalField<type, false>;
auto * dumper = new DumpType(*field, 0, 0, nullptr);
dumper->setPadding(padding_size);
return dumper;
} else {
ElementGroup & group = this->getElementGroup(group_name);
const Array<UInt> * nodal_filter = &(group.getNodes());
using DumpType = typename dumper::NodalField<type, true>;
auto * dumper = new DumpType(*field, 0, 0, nodal_filter);
dumper->setPadding(padding_size);
return dumper;
}
return nullptr;
}
/* -------------------------------------------------------------------------- */
template <typename type, bool flag, template <class, bool> class ftype>
dumper::Field *
GroupManager::createStridedNodalField(const ftype<type, flag> * field,
const std::string & group_name, UInt size,
UInt stride, UInt padding_size) {
if (field == NULL)
return nullptr;
if (group_name == "all") {
using DumpType = typename dumper::NodalField<type, false>;
auto * dumper = new DumpType(*field, size, stride, NULL);
dumper->setPadding(padding_size);
return dumper;
} else {
ElementGroup & group = this->getElementGroup(group_name);
const Array<UInt> * nodal_filter = &(group.getNodes());
using DumpType = typename dumper::NodalField<type, true>;
auto * dumper = new DumpType(*field, size, stride, nodal_filter);
dumper->setPadding(padding_size);
return dumper;
}
return nullptr;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif
diff --git a/src/mesh/mesh.cc b/src/mesh/mesh.cc
index bb13d8b62..cc63c5fd2 100644
--- a/src/mesh/mesh.cc
+++ b/src/mesh/mesh.cc
@@ -1,570 +1,569 @@
/**
* @file mesh.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Jan 22 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief class handling meshes
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "group_manager_inline_impl.cc"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "facet_synchronizer.hh"
#include "mesh_utils_distribution.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_field.hh"
#include "dumper_internal_material_field.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <limits>
#include <sstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id,
Communicator & communicator)
: Memory(id, memory_id),
GroupManager(*this, id + ":group_manager", memory_id),
nodes_type(0, 1, id + ":nodes_type"),
connectivities("connectivities", id, memory_id),
ghosts_counters("ghosts_counters", id, memory_id),
normals("normals", id, memory_id), spatial_dimension(spatial_dimension),
lower_bounds(spatial_dimension, 0.), upper_bounds(spatial_dimension, 0.),
size(spatial_dimension, 0.), local_lower_bounds(spatial_dimension, 0.),
local_upper_bounds(spatial_dimension, 0.),
mesh_data("mesh_data", id, memory_id), communicator(&communicator) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, Communicator & communicator, const ID & id,
const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id, communicator) {
AKANTU_DEBUG_IN();
this->nodes =
std::make_shared<Array<Real>>(0, spatial_dimension, id + ":coordinates");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, Communicator::getStaticCommunicator(), id,
memory_id) {}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const std::shared_ptr<Array<Real>> & nodes,
const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id,
Communicator::getStaticCommunicator()) {
this->nodes = nodes;
this->nb_global_nodes = this->nodes->size();
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
void Mesh::getBarycenters(Array<Real> & barycenter, const ElementType & type,
const GhostType & ghost_type) const {
barycenter.resize(getNbElement(type, ghost_type));
for (auto && data : enumerate(make_view(barycenter, spatial_dimension))) {
getBarycenter(Element{type, UInt(std::get<0>(data)), ghost_type},
std::get<1>(data));
}
}
/* -------------------------------------------------------------------------- */
Mesh & Mesh::initMeshFacets(const ID & id) {
AKANTU_DEBUG_IN();
if (!mesh_facets) {
mesh_facets = std::make_unique<Mesh>(spatial_dimension, this->nodes,
getID() + ":" + id, getMemoryID());
mesh_facets->mesh_parent = this;
mesh_facets->is_mesh_facets = true;
MeshUtils::buildAllFacets(*this, *mesh_facets, 0);
if (mesh.isDistributed()) {
mesh_facets->is_distributed = true;
mesh_facets->element_synchronizer = std::make_unique<FacetSynchronizer>(
*mesh_facets, mesh.getElementSynchronizer());
}
/// transfers the the mesh physical names to the mesh facets
if (not this->hasData("physical_names")) {
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
if (not mesh_facets->hasData("physical_names")) {
mesh_facets->registerData<std::string>("physical_names");
}
auto & mesh_phys_data = this->getData<std::string>("physical_names");
auto & phys_data = mesh_facets->getData<std::string>("physical_names");
phys_data.initialize(*mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
ElementTypeMapArray<Real> barycenters(getID(), "temporary_barycenters");
barycenters.initialize(*mesh_facets, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
for (auto && ghost_type : ghost_types) {
for (auto && type :
barycenters.elementTypes(spatial_dimension - 1, ghost_type)) {
mesh_facets->getBarycenters(barycenters(type, ghost_type), type,
ghost_type);
}
}
for_each_element(
mesh,
[&](auto && element) {
Vector<Real> barycenter(spatial_dimension);
mesh.getBarycenter(element, barycenter);
auto norm_barycenter = barycenter.norm();
auto tolerance = Math::getTolerance();
if (norm_barycenter > tolerance)
tolerance *= norm_barycenter;
const auto & element_to_facet = mesh_facets->getElementToSubelement(
element.type, element.ghost_type);
Vector<Real> barycenter_facet(spatial_dimension);
auto range =
enumerate(make_view(barycenters(element.type, element.ghost_type),
spatial_dimension));
#ifndef AKANTU_NDEBUG
auto min_dist = std::numeric_limits<Real>::max();
#endif
// this is a spacial search coded the most inefficient way.
auto facet =
std::find_if(range.begin(), range.end(), [&](auto && data) {
auto facet = std::get<0>(data);
if (element_to_facet(facet)[1] == ElementNull)
return false;
auto norm_distance = barycenter.distance(std::get<1>(data));
#ifndef AKANTU_NDEBUG
min_dist = std::min(min_dist, norm_distance);
#endif
return (norm_distance < tolerance);
});
if (facet == range.end()) {
AKANTU_DEBUG_INFO("The element "
<< element
<< " did not find its associated facet in the "
"mesh_facets! Try to decrease math tolerance. "
"The closest element was at a distance of "
<< min_dist);
return;
}
// set physical name
phys_data(Element{element.type, UInt(std::get<0>(*facet)),
element.ghost_type}) = mesh_phys_data(element);
},
_spatial_dimension = spatial_dimension - 1);
mesh_facets->createGroupsFromMeshData<std::string>("physical_names");
}
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
/* -------------------------------------------------------------------------- */
void Mesh::defineMeshParent(const Mesh & mesh) {
AKANTU_DEBUG_IN();
this->mesh_parent = &mesh;
this->is_mesh_facets = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::~Mesh() = default;
/* -------------------------------------------------------------------------- */
void Mesh::read(const std::string & filename, const MeshIOType & mesh_io_type) {
MeshIO mesh_io;
mesh_io.read(filename, *this, mesh_io_type);
type_iterator it =
this->firstType(spatial_dimension, _not_ghost, _ek_not_defined);
type_iterator last =
this->lastType(spatial_dimension, _not_ghost, _ek_not_defined);
if (it == last)
AKANTU_EXCEPTION(
"The mesh contained in the file "
<< filename << " does not seem to be of the good dimension."
<< " No element of dimension " << spatial_dimension << " where read.");
this->nb_global_nodes = this->nodes->size();
this->computeBoundingBox();
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
}
/* -------------------------------------------------------------------------- */
void Mesh::write(const std::string & filename,
const MeshIOType & mesh_io_type) {
MeshIO mesh_io;
mesh_io.write(filename, *this, mesh_io_type);
}
/* -------------------------------------------------------------------------- */
void Mesh::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Mesh [" << std::endl;
stream << space << " + id : " << getID() << std::endl;
stream << space << " + spatial dimension : " << this->spatial_dimension
<< std::endl;
stream << space << " + nodes [" << std::endl;
nodes->printself(stream, indent + 2);
stream << space << " + connectivities [" << std::endl;
connectivities.printself(stream, indent + 2);
stream << space << " ]" << std::endl;
GroupManager::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void Mesh::computeBoundingBox() {
AKANTU_DEBUG_IN();
for (UInt k = 0; k < spatial_dimension; ++k) {
local_lower_bounds(k) = std::numeric_limits<double>::max();
local_upper_bounds(k) = -std::numeric_limits<double>::max();
}
for (UInt i = 0; i < nodes->size(); ++i) {
// if(!isPureGhostNode(i))
for (UInt k = 0; k < spatial_dimension; ++k) {
local_lower_bounds(k) = std::min(local_lower_bounds[k], (*nodes)(i, k));
local_upper_bounds(k) = std::max(local_upper_bounds[k], (*nodes)(i, k));
}
}
if (this->is_distributed) {
Matrix<Real> reduce_bounds(spatial_dimension, 2);
for (UInt k = 0; k < spatial_dimension; ++k) {
reduce_bounds(k, 0) = local_lower_bounds(k);
reduce_bounds(k, 1) = -local_upper_bounds(k);
}
communicator->allReduce(reduce_bounds, SynchronizerOperation::_min);
for (UInt k = 0; k < spatial_dimension; ++k) {
lower_bounds(k) = reduce_bounds(k, 0);
upper_bounds(k) = -reduce_bounds(k, 1);
}
} else {
this->lower_bounds = this->local_lower_bounds;
this->upper_bounds = this->local_upper_bounds;
}
size = upper_bounds - lower_bounds;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Mesh::initNormals() {
normals.initialize(*this, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_element_kind = _ek_not_defined);
}
/* -------------------------------------------------------------------------- */
void Mesh::getGlobalConnectivity(
ElementTypeMapArray<UInt> & global_connectivity) {
AKANTU_DEBUG_IN();
for (auto && ghost_type : ghost_types) {
for (auto type :
global_connectivity.elementTypes(_spatial_dimension = _all_dimensions,
_element_kind = _ek_not_defined, _ghost_type = ghost_type)) {
if (not connectivities.exists(type, ghost_type))
continue;
auto & local_conn = connectivities(type, ghost_type);
auto & g_connectivity = global_connectivity(type, ghost_type);
UInt nb_nodes = local_conn.size() * local_conn.getNbComponent();
if (not nodes_global_ids && is_mesh_facets) {
std::transform(
local_conn.begin_reinterpret(nb_nodes),
local_conn.end_reinterpret(nb_nodes),
g_connectivity.begin_reinterpret(nb_nodes),
[& node_ids = *mesh_parent->nodes_global_ids](UInt l)->UInt {
return node_ids(l);
});
} else {
std::transform(local_conn.begin_reinterpret(nb_nodes),
local_conn.end_reinterpret(nb_nodes),
g_connectivity.begin_reinterpret(nb_nodes),
[& node_ids = *nodes_global_ids](UInt l)->UInt {
return node_ids(l);
});
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Mesh::getGroupDumper(const std::string & dumper_name,
const std::string & group_name) {
if (group_name == "all")
return this->getDumper(dumper_name);
else
return element_groups[group_name]->getDumper(dumper_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementTypeMap<UInt> Mesh::getNbDataPerElem(ElementTypeMapArray<T> & arrays,
const ElementKind & element_kind) {
ElementTypeMap<UInt> nb_data_per_elem;
for (auto type : elementTypes(spatial_dimension, _not_ghost, element_kind)) {
UInt nb_elements = this->getNbElement(type);
auto & array = arrays(type);
nb_data_per_elem(type) = array.getNbComponent() * array.size();
nb_data_per_elem(type) /= nb_elements;
}
return nb_data_per_elem;
}
/* -------------------------------------------------------------------------- */
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<Real> & array,
const ElementKind & element_kind);
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<UInt> & array,
const ElementKind & element_kind);
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
template <typename T>
dumper::Field *
Mesh::createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind) {
dumper::Field * field = nullptr;
ElementTypeMapArray<T> * internal = nullptr;
try {
internal = &(this->getData<T>(field_id));
} catch (...) {
return nullptr;
}
ElementTypeMap<UInt> nb_data_per_elem =
this->getNbDataPerElem(*internal, element_kind);
field = this->createElementalField<T, dumper::InternalMaterialField>(
*internal, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
return field;
}
template dumper::Field *
Mesh::createFieldFromAttachedData<Real>(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
template dumper::Field *
Mesh::createFieldFromAttachedData<UInt>(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
#endif
/* -------------------------------------------------------------------------- */
void Mesh::distribute() {
this->distribute(Communicator::getStaticCommunicator());
}
/* -------------------------------------------------------------------------- */
void Mesh::distribute(Communicator & communicator) {
AKANTU_DEBUG_ASSERT(is_distributed == false,
"This mesh is already distribute");
this->communicator = &communicator;
this->element_synchronizer = std::make_unique<ElementSynchronizer>(
*this, this->getID() + ":element_synchronizer", this->getMemoryID(),
true);
this->node_synchronizer = std::make_unique<NodeSynchronizer>(
*this, this->getID() + ":node_synchronizer", this->getMemoryID(), true);
Int psize = this->communicator->getNbProc();
#ifdef AKANTU_USE_SCOTCH
Int prank = this->communicator->whoAmI();
if (prank == 0) {
MeshPartitionScotch partition(*this, spatial_dimension);
partition.partitionate(psize);
MeshUtilsDistribution::distributeMeshCentralized(*this, 0, partition);
} else {
MeshUtilsDistribution::distributeMeshCentralized(*this, 0);
}
#else
if (!(psize == 1)) {
AKANTU_ERROR("Cannot distribute a mesh without a partitioning tool");
}
#endif
this->is_distributed = true;
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
void Mesh::getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements) {
for (const auto & node : node_list)
for (const auto & element : *nodes_to_elements[node])
elements.push_back(element);
}
/* -------------------------------------------------------------------------- */
void Mesh::fillNodesToElements() {
Element e;
UInt nb_nodes = nodes->size();
for (UInt n = 0; n < nb_nodes; ++n) {
if (this->nodes_to_elements[n])
this->nodes_to_elements[n]->clear();
else
this->nodes_to_elements[n] = std::make_unique<std::set<Element>>();
}
for (auto ghost_type : ghost_types) {
e.ghost_type = ghost_type;
for (const auto & type :
elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
e.type = type;
UInt nb_element = this->getNbElement(type, ghost_type);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
connectivities(type, ghost_type)
.begin(Mesh::getNbNodesPerElement(type));
for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
e.element = el;
const Vector<UInt> & conn = *conn_it;
for (UInt n = 0; n < conn.size(); ++n)
nodes_to_elements[conn(n)]->insert(e);
}
}
}
}
/* -------------------------------------------------------------------------- */
void Mesh::eraseElements(const Array<Element> & elements) {
ElementTypeMap<UInt> last_element;
RemovedElementsEvent event(*this);
auto & remove_list = event.getList();
auto & new_numbering = event.getNewNumbering();
for (auto && el : elements) {
if (el.ghost_type != _not_ghost) {
auto & count = ghosts_counters(el);
--count;
if (count > 0)
continue;
}
remove_list.push_back(el);
if (not last_element.exists(el.type, el.ghost_type)) {
UInt nb_element = mesh.getNbElement(el.type, el.ghost_type);
last_element(nb_element - 1, el.type, el.ghost_type);
auto & numbering =
new_numbering.alloc(nb_element, 1, el.type, el.ghost_type);
for (auto && pair : enumerate(numbering)) {
std::get<1>(pair) = std::get<0>(pair);
}
}
UInt & pos = last_element(el.type, el.ghost_type);
auto & numbering = new_numbering(el.type, el.ghost_type);
numbering(el.element) = UInt(-1);
numbering(pos) = el.element;
--pos;
}
this->sendEvent(event);
}
} // namespace akantu
diff --git a/src/mesh/mesh.hh b/src/mesh/mesh.hh
index ffdd11510..c1d47f15e 100644
--- a/src/mesh/mesh.hh
+++ b/src/mesh/mesh.hh
@@ -1,613 +1,612 @@
/**
* @file mesh.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Mon Feb 19 2018
*
* @brief the class representing the meshes
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_HH__
#define __AKANTU_MESH_HH__
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_event_handler_manager.hh"
#include "aka_memory.hh"
#include "dumpable.hh"
#include "element.hh"
#include "element_class.hh"
#include "element_type_map.hh"
#include "group_manager.hh"
#include "mesh_data.hh"
#include "mesh_events.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
class Communicator;
class ElementSynchronizer;
class NodeSynchronizer;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Mesh */
/* -------------------------------------------------------------------------- */
/**
* @class Mesh this contain the coordinates of the nodes in the Mesh.nodes
* Array, and the connectivity. The connectivity are stored in by element
* types.
*
* In order to loop on all element you have to loop on all types like this :
* @code{.cpp}
for(auto & type : mesh.elementTypes()) {
UInt nb_element = mesh.getNbElement(type);
const Array<UInt> & conn = mesh.getConnectivity(type);
for(UInt e = 0; e < nb_element; ++e) {
...
}
}
or
for_each_element(mesh, [](Element & element) {
std::cout << element << std::endl
});
@endcode
*/
class Mesh : protected Memory,
public EventHandlerManager<MeshEventHandler>,
public GroupManager,
public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
/// default constructor used for chaining, the last parameter is just to
/// differentiate constructors
Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id,
Communicator & communicator);
public:
/// constructor that create nodes coordinates array
Mesh(UInt spatial_dimension, const ID & id = "mesh",
const MemoryID & memory_id = 0);
/// mesh not distributed and not using the default communicator
Mesh(UInt spatial_dimension, Communicator & communicator,
const ID & id = "mesh", const MemoryID & memory_id = 0);
/// constructor that use an existing nodes coordinates array, by knowing its
/// ID
// Mesh(UInt spatial_dimension, const ID & nodes_id, const ID & id,
// const MemoryID & memory_id = 0);
/**
* constructor that use an existing nodes coordinates
* array, by getting the vector of coordinates
*/
Mesh(UInt spatial_dimension, const std::shared_ptr<Array<Real>> & nodes,
const ID & id = "mesh", const MemoryID & memory_id = 0);
~Mesh() override;
/// @typedef ConnectivityTypeList list of the types present in a Mesh
using ConnectivityTypeList = std::set<ElementType>;
/// read the mesh from a file
void read(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
/// write the mesh to a file
void write(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
private:
/// initialize the connectivity to NULL and other stuff
void init();
/// function that computes the bounding box (fills xmin, xmax)
void computeBoundingBox();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// patitionate the mesh among the processors involved in their computation
virtual void distribute(Communicator & communicator);
virtual void distribute();
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// extract coordinates of nodes from an element
template <typename T>
inline void extractNodalValuesFromElement(const Array<T> & nodal_values,
T * elemental_values,
UInt * connectivity, UInt n_nodes,
UInt nb_degree_of_freedom) const;
// /// extract coordinates of nodes from a reversed element
// inline void extractNodalCoordinatesFromPBCElement(Real * local_coords,
// UInt * connectivity,
// UInt n_nodes);
/// add a Array of connectivity for the type <type>.
inline void addConnectivityType(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
template <class Event> inline void sendEvent(Event & event) {
// if(event.getList().size() != 0)
EventHandlerManager<MeshEventHandler>::sendEvent<Event>(event);
}
/// prepare the event to remove the elements listed
void eraseElements(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
template <typename T>
inline void removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering);
/// initialize normals
void initNormals();
/// init facets' mesh
Mesh & initMeshFacets(const ID & id = "mesh_facets");
/// define parent mesh
void defineMeshParent(const Mesh & mesh);
/// get global connectivity array
void getGlobalConnectivity(ElementTypeMapArray<UInt> & global_connectivity);
public:
void getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements);
private:
/// fills the nodes_to_elements structure
void fillNodesToElements();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the id of the mesh
AKANTU_GET_MACRO(ID, Memory::id, const ID &);
/// get the id of the mesh
AKANTU_GET_MACRO(MemoryID, Memory::memory_id, const MemoryID &);
/// get the spatial dimension of the mesh = number of component of the
/// coordinates
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the nodes Array aka coordinates
AKANTU_GET_MACRO(Nodes, *nodes, const Array<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Nodes, *nodes, Array<Real> &);
/// get the normals for the elements
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Normals, normals, Real);
/// get the number of nodes
AKANTU_GET_MACRO(NbNodes, nodes->size(), UInt);
/// get the Array of global ids of the nodes (only used in parallel)
AKANTU_GET_MACRO(GlobalNodesIds, *nodes_global_ids, const Array<UInt> &);
AKANTU_GET_MACRO_NOT_CONST(GlobalNodesIds, *nodes_global_ids, Array<UInt> &);
/// get the global id of a node
inline UInt getNodeGlobalId(UInt local_id) const;
/// get the global id of a node
inline UInt getNodeLocalId(UInt global_id) const;
/// get the global number of nodes
inline UInt getNbGlobalNodes() const;
/// get the nodes type Array
AKANTU_GET_MACRO(NodesType, nodes_type, const Array<NodeType> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(NodesType, nodes_type, Array<NodeType> &);
public:
inline NodeType getNodeType(UInt local_id) const;
/// say if a node is a pure ghost node
inline bool isPureGhostNode(UInt n) const;
/// say if a node is pur local or master node
inline bool isLocalOrMasterNode(UInt n) const;
inline bool isLocalNode(UInt n) const;
inline bool isMasterNode(UInt n) const;
inline bool isSlaveNode(UInt n) const;
AKANTU_GET_MACRO(LowerBounds, lower_bounds, const Vector<Real> &);
AKANTU_GET_MACRO(UpperBounds, upper_bounds, const Vector<Real> &);
AKANTU_GET_MACRO(LocalLowerBounds, local_lower_bounds, const Vector<Real> &);
AKANTU_GET_MACRO(LocalUpperBounds, local_upper_bounds, const Vector<Real> &);
/// get the connectivity Array for a given type
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO(Connectivities, connectivities,
const ElementTypeMapArray<UInt> &);
/// get the number of element of a type in the mesh
inline UInt getNbElement(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// get the number of element for a given ghost_type and a given dimension
inline UInt getNbElement(const UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & kind = _ek_not_defined) const;
// /// get the connectivity list either for the elements or the ghost elements
// inline const ConnectivityTypeList &
// getConnectivityTypeList(const GhostType & ghost_type = _not_ghost) const;
/// compute the barycenter of a given element
private:
inline void getBarycenter(UInt element, const ElementType & type,
Real * barycenter,
GhostType ghost_type = _not_ghost) const;
public:
inline void getBarycenter(const Element & element,
Vector<Real> & barycenter) const;
void getBarycenters(Array<Real> & barycenter, const ElementType & type,
const GhostType & ghost_type) const;
#ifndef SWIG
/// get the element connected to a subelement
const auto & getElementToSubelement() const;
/// get the element connected to a subelement
const auto &
getElementToSubelement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get the element connected to a subelement
auto & getElementToSubelement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// get the subelement connected to an element
const auto &
getSubelementToElement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get the subelement connected to an element
auto & getSubelementToElement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
#endif
/// register a new ElementalTypeMap in the MeshData
template <typename T>
inline ElementTypeMapArray<T> & registerData(const std::string & data_name);
template <typename T>
inline bool hasData(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get a name field associated to the mesh
template <typename T>
inline const Array<T> &
getData(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get a name field associated to the mesh
template <typename T>
inline Array<T> & getData(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// tells if the data data_name is contained in the mesh or not
inline bool hasData(const ID & data_name) const;
/// get a name field associated to the mesh
template <typename T>
inline const ElementTypeMapArray<T> & getData(const ID & data_name) const;
/// get a name field associated to the mesh
template <typename T>
inline ElementTypeMapArray<T> & getData(const ID & data_name);
template <typename T>
ElementTypeMap<UInt> getNbDataPerElem(ElementTypeMapArray<T> & array,
const ElementKind & element_kind);
template <typename T>
dumper::Field * createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
/// templated getter returning the pointer to data in MeshData (modifiable)
template <typename T>
inline Array<T> &
getDataPointer(const std::string & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost,
UInt nb_component = 1, bool size_to_nb_element = true,
bool resize_with_parent = false);
/// Facets mesh accessor
inline const Mesh & getMeshFacets() const;
inline Mesh & getMeshFacets();
/// Parent mesh accessor
inline const Mesh & getMeshParent() const;
inline bool isMeshFacets() const { return this->is_mesh_facets; }
/// defines is the mesh is distributed or not
inline bool isDistributed() const { return this->is_distributed; }
#ifndef SWIG
/// return the dumper from a group and and a dumper name
DumperIOHelper & getGroupDumper(const std::string & dumper_name,
const std::string & group_name);
#endif
/* ------------------------------------------------------------------------ */
/* Wrappers on ElementClass functions */
/* ------------------------------------------------------------------------ */
public:
/// get the number of nodes per element for a given element type
static inline UInt getNbNodesPerElement(const ElementType & type);
/// get the number of nodes per element for a given element type considered as
/// a first order element
static inline ElementType getP1ElementType(const ElementType & type);
/// get the kind of the element type
static inline ElementKind getKind(const ElementType & type);
/// get spatial dimension of a type of element
static inline UInt getSpatialDimension(const ElementType & type);
/// get number of facets of a given element type
static inline UInt getNbFacetsPerElement(const ElementType & type);
/// get number of facets of a given element type
static inline UInt getNbFacetsPerElement(const ElementType & type, UInt t);
#ifndef SWIG
/// get local connectivity of a facet for a given facet type
static inline auto getFacetLocalConnectivity(const ElementType & type,
UInt t = 0);
/// get connectivity of facets for a given element
inline auto getFacetConnectivity(const Element & element, UInt t = 0) const;
#endif
/// get the number of type of the surface element associated to a given
/// element type
static inline UInt getNbFacetTypes(const ElementType & type, UInt t = 0);
#ifndef SWIG
/// get the type of the surface element associated to a given element
static inline constexpr auto getFacetType(const ElementType & type,
UInt t = 0);
/// get all the type of the surface element associated to a given element
static inline constexpr auto getAllFacetTypes(const ElementType & type);
#endif
/// get the number of nodes in the given element list
static inline UInt getNbNodesPerElementList(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
using type_iterator = ElementTypeMapArray<UInt, ElementType>::type_iterator;
using ElementTypesIteratorHelper =
ElementTypeMapArray<UInt, ElementType>::ElementTypesIteratorHelper;
template <typename... pack>
ElementTypesIteratorHelper elementTypes(pack &&... _pack) const;
inline type_iterator firstType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.firstType(dim, ghost_type, kind);
}
inline type_iterator lastType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.lastType(dim, ghost_type, kind);
}
AKANTU_GET_MACRO(ElementSynchronizer, *element_synchronizer,
const ElementSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(ElementSynchronizer, *element_synchronizer,
ElementSynchronizer &);
AKANTU_GET_MACRO(NodeSynchronizer, *node_synchronizer,
const NodeSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(NodeSynchronizer, *node_synchronizer,
NodeSynchronizer &);
// AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, StaticCommunicator
// &);
#ifndef SWIG
AKANTU_GET_MACRO(Communicator, *communicator, const auto &);
AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, auto &);
#endif
/* ------------------------------------------------------------------------ */
/* Private methods for friends */
/* ------------------------------------------------------------------------ */
private:
friend class MeshAccessor;
AKANTU_GET_MACRO(NodesPointer, *nodes, Array<Real> &);
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline Array<UInt> & getNodesGlobalIdsPointer();
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline Array<NodeType> & getNodesTypePointer();
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
inline Array<UInt> &
getConnectivityPointer(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/// get the ghost element counter
inline Array<UInt> &
getGhostsCounters(const ElementType & type,
const GhostType & ghost_type = _ghost) {
AKANTU_DEBUG_ASSERT(ghost_type != _not_ghost,
"No ghost counter for _not_ghost elements");
return ghosts_counters(type, ghost_type);
}
/// get a pointer to the element_to_subelement Array for the given type and
/// create it if necessary
inline Array<std::vector<Element>> &
getElementToSubelementPointer(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
inline Array<Element> &
getSubelementToElementPointer(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
AKANTU_GET_MACRO_NOT_CONST(MeshData, mesh_data, MeshData &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// array of the nodes coordinates
std::shared_ptr<Array<Real>> nodes;
/// global node ids
std::unique_ptr<Array<UInt>> nodes_global_ids;
/// node type, -3 pure ghost, -2 master for the node, -1 normal node, i in
/// [0-N] slave node and master is proc i
Array<NodeType> nodes_type;
/// global number of nodes;
UInt nb_global_nodes{0};
/// all class of elements present in this mesh (for heterogenous meshes)
ElementTypeMapArray<UInt> connectivities;
/// count the references on ghost elements
ElementTypeMapArray<UInt> ghosts_counters;
/// map to normals for all class of elements present in this mesh
ElementTypeMapArray<Real> normals;
/// list of all existing types in the mesh
// ConnectivityTypeList type_set;
/// the spatial dimension of this mesh
UInt spatial_dimension{0};
/// types offsets
// Array<UInt> types_offsets;
// /// list of all existing types in the mesh
// ConnectivityTypeList ghost_type_set;
// /// ghost types offsets
// Array<UInt> ghost_types_offsets;
/// min of coordinates
Vector<Real> lower_bounds;
/// max of coordinates
Vector<Real> upper_bounds;
/// size covered by the mesh on each direction
Vector<Real> size;
/// local min of coordinates
Vector<Real> local_lower_bounds;
/// local max of coordinates
Vector<Real> local_upper_bounds;
/// Extra data loaded from the mesh file
MeshData mesh_data;
/// facets' mesh
std::unique_ptr<Mesh> mesh_facets;
/// parent mesh (this is set for mesh_facets meshes)
const Mesh * mesh_parent{nullptr};
/// defines if current mesh is mesh_facets or not
bool is_mesh_facets{false};
/// defines if the mesh is centralized or distributed
bool is_distributed{false};
/// Communicator on which mesh is distributed
Communicator * communicator;
/// Element synchronizer
std::unique_ptr<ElementSynchronizer> element_synchronizer;
/// Node synchronizer
std::unique_ptr<NodeSynchronizer> node_synchronizer;
using NodesToElements = std::vector<std::unique_ptr<std::set<Element>>>;
/// This info is stored to simplify the dynamic changes
NodesToElements nodes_to_elements;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Mesh & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
#include "element_type_map_tmpl.hh"
#include "mesh_inline_impl.cc"
#endif /* __AKANTU_MESH_HH__ */
diff --git a/src/mesh/mesh_accessor.hh b/src/mesh/mesh_accessor.hh
index 402286b60..9ac501700 100644
--- a/src/mesh/mesh_accessor.hh
+++ b/src/mesh/mesh_accessor.hh
@@ -1,135 +1,137 @@
/**
* @file mesh_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jun 30 2015
+ * @date last modification: Tue Sep 19 2017
*
* @brief this class allow to access some private member of mesh it is used for
* IO for examples
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_ACCESSOR_HH__
#define __AKANTU_MESH_ACCESSOR_HH__
namespace akantu {
class NodeSynchronizer;
class ElementSynchronizer;
} // namespace akantu
namespace akantu {
class MeshAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit MeshAccessor(Mesh & mesh) : _mesh(mesh) {}
virtual ~MeshAccessor() = default;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the global number of nodes
inline UInt getNbGlobalNodes() const { return this->_mesh.nb_global_nodes; }
/// set the global number of nodes
inline void setNbGlobalNodes(UInt nb_global_nodes) {
this->_mesh.nb_global_nodes = nb_global_nodes;
}
/// set the mesh as being distributed
inline void setDistributed() { this->_mesh.is_distributed = true; }
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline auto & getNodesGlobalIds() {
return this->_mesh.getNodesGlobalIdsPointer();
}
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline auto & getNodesType() { return this->_mesh.getNodesTypePointer(); }
/// get a pointer to the coordinates Array
inline auto & getNodes() { return this->_mesh.getNodesPointer(); }
/// get a pointer to the coordinates Array
inline auto getNodesSharedPtr() { return this->_mesh.nodes; }
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
inline auto & getConnectivity(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return this->_mesh.getConnectivityPointer(type, ghost_type);
}
/// get the ghost element counter
inline auto & getGhostsCounters(const ElementType & type,
const GhostType & ghost_type = _ghost) {
return this->_mesh.getGhostsCounters(type, ghost_type);
}
/// get a pointer to the element_to_subelement Array for the given type and
/// create it if necessary
inline auto &
getElementToSubelement(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return this->_mesh.getElementToSubelementPointer(type, ghost_type);
}
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
inline auto &
getSubelementToElement(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return this->_mesh.getSubelementToElementPointer(type, ghost_type);
}
template <typename T>
inline auto &
getData(const std::string & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost, UInt nb_component = 1,
bool size_to_nb_element = true, bool resize_with_parent = false) {
return this->_mesh.getDataPointer<T>(data_name, el_type, ghost_type,
nb_component, size_to_nb_element,
resize_with_parent);
}
auto & getMeshData() { return this->_mesh.getMeshData(); }
/// get the node synchonizer
auto & getNodeSynchronizer() { return *this->_mesh.node_synchronizer; }
/// get the element synchonizer
auto & getElementSynchronizer() { return *this->_mesh.element_synchronizer; }
private:
Mesh & _mesh;
};
} // namespace akantu
#endif /* __AKANTU_MESH_ACCESSOR_HH__ */
diff --git a/src/mesh/mesh_data.cc b/src/mesh/mesh_data.cc
index 88022e988..ead9bcf7c 100644
--- a/src/mesh/mesh_data.cc
+++ b/src/mesh/mesh_data.cc
@@ -1,48 +1,47 @@
/**
* @file mesh_data.cc
*
* @author Dana Christen <dana.christen@gmail.com>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Mon Jun 19 2017
*
* @brief Stores generic data loaded from the mesh file
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "mesh_data.hh"
#include "mesh.hh"
namespace akantu {
MeshData::MeshData(const ID & _id, const ID & parent_id,
const MemoryID & mem_id)
: Memory(parent_id + ":" + _id, mem_id) {}
MeshData::~MeshData() {
ElementalDataMap::iterator it, end;
for (it = elemental_data.begin(); it != elemental_data.end(); ++it) {
delete it->second;
}
}
} // akantu
diff --git a/src/mesh/mesh_data.hh b/src/mesh/mesh_data.hh
index 029af4fe9..45650efae 100644
--- a/src/mesh/mesh_data.hh
+++ b/src/mesh/mesh_data.hh
@@ -1,153 +1,153 @@
/**
* @file mesh_data.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Thu Nov 05 2015
+ * @date last modification: Mon Dec 18 2017
*
* @brief Stores generic data loaded from the mesh file
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_DATA_HH__
#define __AKANTU_MESH_DATA_HH__
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "element_type_map.hh"
#include <map>
#include <string>
/* -------------------------------------------------------------------------- */
namespace akantu {
#define AKANTU_MESH_DATA_TYPES \
((_tc_int, Int))((_tc_uint, UInt))((_tc_real, Real))( \
(_tc_element, Element))((_tc_std_string, std::string))( \
(_tc_std_vector_element, std::vector<Element>))
#define AKANTU_MESH_DATA_TUPLE_FIRST_ELEM(s, data, elem) \
BOOST_PP_TUPLE_ELEM(2, 0, elem)
enum MeshDataTypeCode : int {
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_MESH_DATA_TUPLE_FIRST_ELEM, ,
AKANTU_MESH_DATA_TYPES)),
_tc_unknown
};
class MeshData : public Memory {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
using TypeCode = MeshDataTypeCode;
using ElementalDataMap = std::map<std::string, ElementTypeMapBase *>;
using StringVector = std::vector<std::string>;
using TypeCodeMap = std::map<std::string, TypeCode>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshData(const ID & id = "mesh_data", const ID & parent_id = "",
const MemoryID & memory_id = 0);
~MeshData() override;
/* ------------------------------------------------------------------------ */
/* Methods and accessors */
/* ------------------------------------------------------------------------ */
public:
/// Register new elemental data (and alloc data) with check if the name is
/// new
template <typename T> void registerElementalData(const ID & name);
inline void registerElementalData(const ID & name, TypeCode type);
/// tells if the given array exists
template <typename T>
bool hasDataArray(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// tells if the given data exists
bool hasData(const ID & data_name) const;
/// Get an existing elemental data array
template <typename T>
const Array<T> &
getElementalDataArray(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
template <typename T>
Array<T> & getElementalDataArray(const ID & data_name,
const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// Get an elemental data array, if it does not exist: allocate it
template <typename T>
Array<T> &
getElementalDataArrayAlloc(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost,
UInt nb_component = 1);
/// get the names of the data stored in elemental_data
inline void getTagNames(StringVector & tags, const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// get the type of the data stored in elemental_data
template <typename T> TypeCode getTypeCode() const;
inline TypeCode getTypeCode(const ID & name) const;
template <typename T>
inline UInt getNbComponentTemplated(const ID & name,
const ElementType & el_type,
const GhostType & ghost_type) const;
inline UInt getNbComponent(const ID & name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// Get an existing elemental data
template <typename T>
const ElementTypeMapArray<T> & getElementalData(const ID & name) const;
template <typename T>
ElementTypeMapArray<T> & getElementalData(const ID & name);
private:
/// Register new elemental data (add alloc data)
template <typename T>
ElementTypeMapArray<T> * allocElementalData(const ID & name);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Map when elemental data is stored as ElementTypeMap
ElementalDataMap elemental_data;
/// Map when elementalType of the data stored in elemental_data
TypeCodeMap typecode_map;
};
} // akantu
#include "mesh_data_tmpl.hh"
#undef AKANTU_MESH_DATA_TUPLE_FIRST_ELEM
#endif /* __AKANTU_MESH_DATA_HH__ */
diff --git a/src/mesh/mesh_data_tmpl.hh b/src/mesh/mesh_data_tmpl.hh
index 6cd581045..7de088649 100644
--- a/src/mesh/mesh_data_tmpl.hh
+++ b/src/mesh/mesh_data_tmpl.hh
@@ -1,275 +1,276 @@
/**
* @file mesh_data_tmpl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Thu Nov 05 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Stores generic data loaded from the mesh file
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh_data.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_DATA_TMPL_HH__
#define __AKANTU_MESH_DATA_TMPL_HH__
namespace akantu {
#define MESH_DATA_GET_TYPE(r, data, type) \
template <> \
inline MeshDataTypeCode \
MeshData::getTypeCode<BOOST_PP_TUPLE_ELEM(2, 1, type)>() const { \
return BOOST_PP_TUPLE_ELEM(2, 0, type); \
}
/* -------------------------------------------------------------------------- */
// get the type of the data stored in elemental_data
template <typename T> inline MeshDataTypeCode MeshData::getTypeCode() const {
AKANTU_ERROR("Type " << debug::demangle(typeid(T).name())
<< "not implemented by MeshData.");
}
/* -------------------------------------------------------------------------- */
BOOST_PP_SEQ_FOR_EACH(MESH_DATA_GET_TYPE, void, AKANTU_MESH_DATA_TYPES)
#undef MESH_DATA_GET_TYPE
inline MeshDataTypeCode MeshData::getTypeCode(const ID & name) const {
auto it = typecode_map.find(name);
if (it == typecode_map.end())
AKANTU_EXCEPTION("No dataset named " << name << " found.");
return it->second;
}
/* -------------------------------------------------------------------------- */
// Register new elemental data templated (and alloc data) with check if the
// name is new
template <typename T> void MeshData::registerElementalData(const ID & name) {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
allocElementalData<T>(name);
} else {
AKANTU_DEBUG_INFO("Data named " << name << " already registered.");
}
}
/* -------------------------------------------------------------------------- */
// Register new elemental data of a given MeshDataTypeCode with check if the
// name is new
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
registerElementalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(name); \
break; \
}
inline void MeshData::registerElementalData(const ID & name,
MeshDataTypeCode type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, name,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Type " << type << "not implemented by MeshData.");
}
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
/// Register new elemental data (and alloc data)
template <typename T>
ElementTypeMapArray<T> * MeshData::allocElementalData(const ID & name) {
auto * dataset = new ElementTypeMapArray<T>(name, id, memory_id);
elemental_data[name] = dataset;
typecode_map[name] = getTypeCode<T>();
return dataset;
}
/* -------------------------------------------------------------------------- */
template <typename T>
const ElementTypeMapArray<T> &
MeshData::getElementalData(const ID & name) const {
auto it = elemental_data.find(name);
if (it == elemental_data.end())
AKANTU_EXCEPTION("No dataset named " << name << " found.");
return dynamic_cast<const ElementTypeMapArray<T> &>(*(it->second));
}
/* -------------------------------------------------------------------------- */
// Get an existing elemental data
template <typename T>
ElementTypeMapArray<T> & MeshData::getElementalData(const ID & name) {
auto it = elemental_data.find(name);
if (it == elemental_data.end())
AKANTU_EXCEPTION("No dataset named " << name << " found.");
return dynamic_cast<ElementTypeMapArray<T> &>(*(it->second));
}
/* -------------------------------------------------------------------------- */
template <typename T>
bool MeshData::hasDataArray(const ID & name, const ElementType & elem_type,
const GhostType & ghost_type) const {
auto it = elemental_data.find(name);
if (it == elemental_data.end())
return false;
auto & elem_map = dynamic_cast<const ElementTypeMapArray<T> &>(*(it->second));
return elem_map.exists(elem_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool MeshData::hasData(const ID & name) const {
auto it = elemental_data.find(name);
return (it != elemental_data.end());
}
/* -------------------------------------------------------------------------- */
template <typename T>
const Array<T> &
MeshData::getElementalDataArray(const ID & name, const ElementType & elem_type,
const GhostType & ghost_type) const {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
AKANTU_EXCEPTION("Data named " << name
<< " not registered for type: " << elem_type
<< " - ghost_type:" << ghost_type << "!");
}
return dynamic_cast<const ElementTypeMapArray<T> &>(*(it->second))(
elem_type, ghost_type);
}
template <typename T>
Array<T> & MeshData::getElementalDataArray(const ID & name,
const ElementType & elem_type,
const GhostType & ghost_type) {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
AKANTU_EXCEPTION("Data named " << name
<< " not registered for type: " << elem_type
<< " - ghost_type:" << ghost_type << "!");
}
return dynamic_cast<ElementTypeMapArray<T> &>(*(it->second))(elem_type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
// Get an elemental data array, if it does not exist: allocate it
template <typename T>
Array<T> & MeshData::getElementalDataArrayAlloc(const ID & name,
const ElementType & elem_type,
const GhostType & ghost_type,
UInt nb_component) {
auto it = elemental_data.find(name);
ElementTypeMapArray<T> * dataset;
if (it == elemental_data.end()) {
dataset = allocElementalData<T>(name);
} else {
dataset = dynamic_cast<ElementTypeMapArray<T> *>(it->second);
}
AKANTU_DEBUG_ASSERT(
getTypeCode<T>() == typecode_map.find(name)->second,
"Function getElementalDataArrayAlloc called with the wrong type!");
if (!(dataset->exists(elem_type, ghost_type))) {
dataset->alloc(0, nb_component, elem_type, ghost_type);
}
return (*dataset)(elem_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
nb_comp = getNbComponentTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>( \
name, el_type, ghost_type); \
break; \
}
inline UInt MeshData::getNbComponent(const ID & name,
const ElementType & el_type,
const GhostType & ghost_type) const {
auto it = typecode_map.find(name);
UInt nb_comp(0);
if (it == typecode_map.end()) {
AKANTU_EXCEPTION("Could not determine the type held in dataset "
<< name << " for type: " << el_type
<< " - ghost_type:" << ghost_type << ".");
}
MeshDataTypeCode type = it->second;
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, name,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR(
"Could not call the correct instance of getNbComponentTemplated.");
break;
}
return nb_comp;
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
template <typename T>
inline UInt
MeshData::getNbComponentTemplated(const ID & name, const ElementType & el_type,
const GhostType & ghost_type) const {
return getElementalDataArray<T>(name, el_type, ghost_type).getNbComponent();
}
/* -------------------------------------------------------------------------- */
// get the names of the data stored in elemental_data
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
ElementTypeMapArray<BOOST_PP_TUPLE_ELEM(2, 1, elem)> * dataset; \
dataset = \
dynamic_cast<ElementTypeMapArray<BOOST_PP_TUPLE_ELEM(2, 1, elem)> *>( \
it->second); \
exists = dataset->exists(el_type, ghost_type); \
break; \
}
inline void MeshData::getTagNames(StringVector & tags,
const ElementType & el_type,
const GhostType & ghost_type) const {
tags.clear();
bool exists(false);
auto it = elemental_data.begin();
auto it_end = elemental_data.end();
for (; it != it_end; ++it) {
MeshDataTypeCode type = getTypeCode(it->first);
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not determine the proper type to (dynamic-)cast.");
break;
}
if (exists) {
tags.push_back(it->first);
}
}
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_MESH_DATA_TMPL_HH__ */
diff --git a/src/mesh/mesh_events.hh b/src/mesh/mesh_events.hh
index 53f8f0d9a..a654c4f5e 100644
--- a/src/mesh/mesh_events.hh
+++ b/src/mesh/mesh_events.hh
@@ -1,198 +1,198 @@
/**
* @file mesh_events.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 20 2015
- * @date last modification: Mon Dec 07 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Classes corresponding to mesh events type
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <utility>
#include "aka_array.hh"
#include "element.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_EVENTS_HH__
#define __AKANTU_MESH_EVENTS_HH__
namespace akantu {
/// akantu::MeshEvent is the base event for meshes
template <class Entity> class MeshEvent {
public:
virtual ~MeshEvent() = default;
/// Get the list of entity modified by the event nodes or elements
const Array<Entity> & getList() const { return list; }
/// Get the list of entity modified by the event nodes or elements
Array<Entity> & getList() { return list; }
protected:
Array<Entity> list;
};
class Mesh;
/// akantu::MeshEvent related to new nodes in the mesh
class NewNodesEvent : public MeshEvent<UInt> {
public:
~NewNodesEvent() override = default;
};
/// akantu::MeshEvent related to nodes removed from the mesh
class RemovedNodesEvent : public MeshEvent<UInt> {
public:
~RemovedNodesEvent() override = default;
inline RemovedNodesEvent(const Mesh & mesh);
/// Get the new numbering following suppression of nodes from nodes arrays
AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering, Array<UInt> &);
/// Get the new numbering following suppression of nodes from nodes arrays
AKANTU_GET_MACRO(NewNumbering, new_numbering, const Array<UInt> &);
private:
Array<UInt> new_numbering;
};
/// akantu::MeshEvent related to new elements in the mesh
class NewElementsEvent : public MeshEvent<Element> {
public:
~NewElementsEvent() override = default;
};
/// akantu::MeshEvent related to elements removed from the mesh
class RemovedElementsEvent : public MeshEvent<Element> {
public:
~RemovedElementsEvent() override = default;
inline RemovedElementsEvent(const Mesh & mesh,
const ID & new_numbering_id = "new_numbering");
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO(NewNumbering, new_numbering,
const ElementTypeMapArray<UInt> &);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering,
ElementTypeMapArray<UInt> &);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(NewNumbering, new_numbering, UInt);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(NewNumbering, new_numbering, UInt);
protected:
ElementTypeMapArray<UInt> new_numbering;
};
/// akantu::MeshEvent for element that changed in some sort, can be seen as a
/// combination of removed and added elements
class ChangedElementsEvent : public RemovedElementsEvent {
public:
~ChangedElementsEvent() override = default;
inline ChangedElementsEvent(
const Mesh & mesh, ID new_numbering_id = "changed_event:new_numbering")
: RemovedElementsEvent(mesh, std::move(new_numbering_id)){};
AKANTU_GET_MACRO(ListOld, list, const Array<Element> &);
AKANTU_GET_MACRO_NOT_CONST(ListOld, list, Array<Element> &);
AKANTU_GET_MACRO(ListNew, new_list, const Array<Element> &);
AKANTU_GET_MACRO_NOT_CONST(ListNew, new_list, Array<Element> &);
protected:
Array<Element> new_list;
};
/* -------------------------------------------------------------------------- */
class MeshEventHandler {
public:
virtual ~MeshEventHandler() = default;
/* ------------------------------------------------------------------------ */
/* Internal code */
/* ------------------------------------------------------------------------ */
private:
/// send a akantu::NewNodesEvent
inline void sendEvent(const NewNodesEvent & event) {
onNodesAdded(event.getList(), event);
}
/// send a akantu::RemovedNodesEvent
inline void sendEvent(const RemovedNodesEvent & event) {
onNodesRemoved(event.getList(), event.getNewNumbering(), event);
}
/// send a akantu::NewElementsEvent
inline void sendEvent(const NewElementsEvent & event) {
onElementsAdded(event.getList(), event);
}
/// send a akantu::RemovedElementsEvent
inline void sendEvent(const RemovedElementsEvent & event) {
onElementsRemoved(event.getList(), event.getNewNumbering(), event);
}
/// send a akantu::ChangedElementsEvent
inline void sendEvent(const ChangedElementsEvent & event) {
onElementsChanged(event.getListOld(), event.getListNew(),
event.getNewNumbering(), event);
}
template <class EventHandler> friend class EventHandlerManager;
/* ------------------------------------------------------------------------ */
/* Interface */
/* ------------------------------------------------------------------------ */
public:
/// function to implement to react on akantu::NewNodesEvent
virtual void onNodesAdded(const Array<UInt> & /*nodes_list*/,
const NewNodesEvent & /*event*/) {
AKANTU_TO_IMPLEMENT();
}
/// function to implement to react on akantu::RemovedNodesEvent
virtual void onNodesRemoved(const Array<UInt> & /*nodes_list*/,
const Array<UInt> & /*new_numbering*/,
const RemovedNodesEvent & /*event*/) {
AKANTU_TO_IMPLEMENT();
}
/// function to implement to react on akantu::NewElementsEvent
virtual void onElementsAdded(const Array<Element> & /*elements_list*/,
const NewElementsEvent & /*event*/) {
AKANTU_TO_IMPLEMENT();
}
/// function to implement to react on akantu::RemovedElementsEvent
virtual void
onElementsRemoved(const Array<Element> & /*elements_list*/,
const ElementTypeMapArray<UInt> & /*new_numbering*/,
const RemovedElementsEvent & /*event*/) {
AKANTU_TO_IMPLEMENT();
}
/// function to implement to react on akantu::ChangedElementsEvent
virtual void
onElementsChanged(const Array<Element> & /*old_elements_list*/,
const Array<Element> & /*new_elements_list*/,
const ElementTypeMapArray<UInt> & /*new_numbering*/,
const ChangedElementsEvent & /*event*/) {
AKANTU_TO_IMPLEMENT();
}
};
} // akantu
#endif /* __AKANTU_MESH_EVENTS_HH__ */
diff --git a/src/mesh/mesh_filter.hh b/src/mesh/mesh_filter.hh
index 59420e63d..3607f549d 100644
--- a/src/mesh/mesh_filter.hh
+++ b/src/mesh/mesh_filter.hh
@@ -1,73 +1,72 @@
/**
* @file mesh_filter.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Dec 18 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief the class representing the meshes
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_FILTER_HH__
#define __AKANTU_MESH_FILTER_HH__
/* -------------------------------------------------------------------------- */
#include "element.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Filter Functors */
/* -------------------------------------------------------------------------- */
/// struct for the possible filter functors
struct FilterFunctor {
enum Type { _node_filter_functor, _element_filter_functor };
};
/// class (functor) for the node filter
class NodeFilterFunctor : public FilterFunctor {
public:
bool operator()(__attribute__((unused)) UInt node) { AKANTU_TO_IMPLEMENT(); }
public:
static const Type type = _node_filter_functor;
};
/// class (functor) for the element filter
class ElementFilterFunctor : public FilterFunctor {
public:
bool operator()(__attribute__((unused)) const Element & element) {
AKANTU_TO_IMPLEMENT();
}
public:
static const Type type = _element_filter_functor;
};
} // akantu
#endif /* __AKANTU_MESH_FILTER_HH__ */
diff --git a/src/mesh/mesh_inline_impl.cc b/src/mesh/mesh_inline_impl.cc
index fd19d3982..2e4b756b5 100644
--- a/src/mesh/mesh_inline_impl.cc
+++ b/src/mesh/mesh_inline_impl.cc
@@ -1,637 +1,636 @@
/**
* @file mesh_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jul 15 2010
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Mon Dec 18 2017
*
* @brief Implementation of the inline functions of the mesh class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "element_class.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_INLINE_IMPL_CC__
#define __AKANTU_MESH_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
inline ElementKind Element::kind() const { return Mesh::getKind(type); }
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename... pack>
Mesh::ElementTypesIteratorHelper Mesh::elementTypes(pack &&... _pack) const {
return connectivities.elementTypes(_pack...);
}
/* -------------------------------------------------------------------------- */
inline RemovedNodesEvent::RemovedNodesEvent(const Mesh & mesh)
: new_numbering(mesh.getNbNodes(), 1, "new_numbering") {}
/* -------------------------------------------------------------------------- */
inline RemovedElementsEvent::RemovedElementsEvent(const Mesh & mesh,
const ID & new_numbering_id)
: new_numbering(new_numbering_id, mesh.getID(), mesh.getMemoryID()) {}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<NewElementsEvent>(NewElementsEvent & event) {
this->nodes_to_elements.resize(nodes->size());
for (const auto & elem : event.getList()) {
const Array<UInt> & conn = connectivities(elem.type, elem.ghost_type);
UInt nb_nodes_per_elem = this->getNbNodesPerElement(elem.type);
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = conn(elem.element, n);
if (not nodes_to_elements[node])
nodes_to_elements[node] = std::make_unique<std::set<Element>>();
nodes_to_elements[node]->insert(elem);
}
}
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <> inline void Mesh::sendEvent<NewNodesEvent>(NewNodesEvent & event) {
this->computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
Mesh::sendEvent<RemovedElementsEvent>(RemovedElementsEvent & event) {
this->connectivities.onElementsRemoved(event.getNewNumbering());
this->fillNodesToElements();
this->computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<RemovedNodesEvent>(RemovedNodesEvent & event) {
const auto & new_numbering = event.getNewNumbering();
this->removeNodesFromArray(*nodes, new_numbering);
if (nodes_global_ids)
this->removeNodesFromArray(*nodes_global_ids, new_numbering);
if (nodes_type.size() != 0)
this->removeNodesFromArray(nodes_type, new_numbering);
if (not nodes_to_elements.empty()) {
std::vector<std::unique_ptr<std::set<Element>>> tmp(
nodes_to_elements.size());
auto it = nodes_to_elements.begin();
UInt new_nb_nodes = 0;
for (auto new_i : new_numbering) {
if (new_i != UInt(-1)) {
tmp[new_i] = std::move(*it);
++new_nb_nodes;
}
++it;
}
tmp.resize(new_nb_nodes);
std::move(tmp.begin(), tmp.end(), nodes_to_elements.begin());
}
computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering) {
Array<T> tmp(vect.size(), vect.getNbComponent());
UInt nb_component = vect.getNbComponent();
UInt new_nb_nodes = 0;
for (UInt i = 0; i < new_numbering.size(); ++i) {
UInt new_i = new_numbering(i);
if (new_i != UInt(-1)) {
T * to_copy = vect.storage() + i * nb_component;
std::uninitialized_copy(to_copy, to_copy + nb_component,
tmp.storage() + new_i * nb_component);
++new_nb_nodes;
}
}
tmp.resize(new_nb_nodes);
vect.copy(tmp);
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> & Mesh::getNodesGlobalIdsPointer() {
AKANTU_DEBUG_IN();
if (not nodes_global_ids) {
nodes_global_ids = std::make_unique<Array<UInt>>(
nodes->size(), 1, getID() + ":nodes_global_ids");
for (auto && global_ids : enumerate(*nodes_global_ids)) {
std::get<1>(global_ids) = std::get<0>(global_ids);
}
}
AKANTU_DEBUG_OUT();
return *nodes_global_ids;
}
/* -------------------------------------------------------------------------- */
inline Array<NodeType> & Mesh::getNodesTypePointer() {
AKANTU_DEBUG_IN();
if (nodes_type.size() == 0) {
nodes_type.resize(nodes->size());
nodes_type.set(_nt_normal);
}
AKANTU_DEBUG_OUT();
return nodes_type;
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> &
Mesh::getConnectivityPointer(const ElementType & type,
const GhostType & ghost_type) {
if (connectivities.exists(type, ghost_type))
return connectivities(type, ghost_type);
if (ghost_type != _not_ghost) {
ghosts_counters.alloc(0, 1, type, ghost_type, 1);
}
AKANTU_DEBUG_INFO("The connectivity vector for the type " << type
<< " created");
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
return connectivities.alloc(0, nb_nodes_per_element, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<std::vector<Element>> &
Mesh::getElementToSubelementPointer(const ElementType & type,
const GhostType & ghost_type) {
return getDataPointer<std::vector<Element>>("element_to_subelement", type,
ghost_type, 1, true);
}
/* -------------------------------------------------------------------------- */
inline Array<Element> &
Mesh::getSubelementToElementPointer(const ElementType & type,
const GhostType & ghost_type) {
auto & array = getDataPointer<Element>(
"subelement_to_element", type, ghost_type, getNbFacetsPerElement(type),
true, is_mesh_facets);
array.set(ElementNull);
return array;
}
/* -------------------------------------------------------------------------- */
inline const auto & Mesh::getElementToSubelement() const {
return getData<std::vector<Element>>("element_to_subelement");
}
/* -------------------------------------------------------------------------- */
inline const auto &
Mesh::getElementToSubelement(const ElementType & type,
const GhostType & ghost_type) const {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline auto & Mesh::getElementToSubelement(const ElementType & type,
const GhostType & ghost_type) {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const auto &
Mesh::getSubelementToElement(const ElementType & type,
const GhostType & ghost_type) const {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline auto & Mesh::getSubelementToElement(const ElementType & type,
const GhostType & ghost_type) {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> &
Mesh::getDataPointer(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type, UInt nb_component,
bool size_to_nb_element, bool resize_with_parent) {
Array<T> & tmp = mesh_data.getElementalDataArrayAlloc<T>(
data_name, el_type, ghost_type, nb_component);
if (size_to_nb_element) {
if (resize_with_parent)
tmp.resize(mesh_parent->getNbElement(el_type, ghost_type));
else
tmp.resize(this->getNbElement(el_type, ghost_type));
} else {
tmp.resize(0);
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline bool Mesh::hasData(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type) const {
return mesh_data.hasDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const Array<T> & Mesh::getData(const ID & data_name,
const ElementType & el_type,
const GhostType & ghost_type) const {
return mesh_data.getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> & Mesh::getData(const ID & data_name,
const ElementType & el_type,
const GhostType & ghost_type) {
return mesh_data.getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::hasData(const ID & data_name) const {
return mesh_data.hasData(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const ElementTypeMapArray<T> &
Mesh::getData(const ID & data_name) const {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> & Mesh::getData(const ID & data_name) {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> & Mesh::registerData(const ID & data_name) {
this->mesh_data.registerElementalData<T>(data_name);
return this->getData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const ElementType & type,
const GhostType & ghost_type) const {
try {
const Array<UInt> & conn = connectivities(type, ghost_type);
return conn.size();
} catch (...) {
return 0;
}
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & kind) const {
AKANTU_DEBUG_ASSERT(spatial_dimension <= 3 || spatial_dimension == UInt(-1),
"spatial_dimension is " << spatial_dimension
<< " and is greater than 3 !");
UInt nb_element = 0;
for (auto type : elementTypes(spatial_dimension, ghost_type, kind))
nb_element += getNbElement(type, ghost_type);
return nb_element;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(UInt element, const ElementType & type,
Real * barycenter, GhostType ghost_type) const {
UInt * conn_val = getConnectivity(type, ghost_type).storage();
UInt nb_nodes_per_element = getNbNodesPerElement(type);
auto * local_coord = new Real[spatial_dimension * nb_nodes_per_element];
UInt offset = element * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
memcpy(local_coord + n * spatial_dimension,
nodes->storage() + conn_val[offset + n] * spatial_dimension,
spatial_dimension * sizeof(Real));
}
Math::barycenter(local_coord, nb_nodes_per_element, spatial_dimension,
barycenter);
delete[] local_coord;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(const Element & element,
Vector<Real> & barycenter) const {
getBarycenter(element.element, element.type, barycenter.storage(),
element.ghost_type);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElement(const ElementType & type) {
UInt nb_nodes_per_element = 0;
#define GET_NB_NODES_PER_ELEMENT(type) \
nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_NODES_PER_ELEMENT);
#undef GET_NB_NODES_PER_ELEMENT
return nb_nodes_per_element;
}
/* -------------------------------------------------------------------------- */
inline ElementType Mesh::getP1ElementType(const ElementType & type) {
ElementType p1_type = _not_defined;
#define GET_P1_TYPE(type) p1_type = ElementClass<type>::getP1ElementType()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_P1_TYPE);
#undef GET_P1_TYPE
return p1_type;
}
/* -------------------------------------------------------------------------- */
inline ElementKind Mesh::getKind(const ElementType & type) {
ElementKind kind = _ek_not_defined;
#define GET_KIND(type) kind = ElementClass<type>::getKind()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_KIND);
#undef GET_KIND
return kind;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getSpatialDimension(const ElementType & type) {
UInt spatial_dimension = 0;
#define GET_SPATIAL_DIMENSION(type) \
spatial_dimension = ElementClass<type>::getSpatialDimension()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SPATIAL_DIMENSION);
#undef GET_SPATIAL_DIMENSION
return spatial_dimension;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetTypes(const ElementType & type,
__attribute__((unused)) UInt t) {
UInt nb = 0;
#define GET_NB_FACET_TYPE(type) nb = ElementClass<type>::getNbFacetTypes()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET_TYPE);
#undef GET_NB_FACET_TYPE
return nb;
}
/* -------------------------------------------------------------------------- */
inline constexpr auto Mesh::getFacetType(const ElementType & type, UInt t) {
#define GET_FACET_TYPE(type) return ElementClass<type>::getFacetType(t);
AKANTU_BOOST_ALL_ELEMENT_SWITCH_NO_DEFAULT(GET_FACET_TYPE);
#undef GET_FACET_TYPE
return _not_defined;
}
/* -------------------------------------------------------------------------- */
inline constexpr auto Mesh::getAllFacetTypes(const ElementType & type) {
#define GET_FACET_TYPE(type) return ElementClass<type>::getFacetTypes();
AKANTU_BOOST_ALL_ELEMENT_SWITCH_NO_DEFAULT(GET_FACET_TYPE);
#undef GET_FACET_TYPE
return ElementClass<_not_defined>::getFacetTypes();
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(const ElementType & type) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) n_facet = ElementClass<type>::getNbFacetsPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(const ElementType & type, UInt t) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) \
n_facet = ElementClass<type>::getNbFacetsPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline auto Mesh::getFacetLocalConnectivity(const ElementType & type, UInt t) {
AKANTU_DEBUG_IN();
#define GET_FACET_CON(type) \
AKANTU_DEBUG_OUT(); \
return ElementClass<type>::getFacetLocalConnectivityPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_CON);
#undef GET_FACET_CON
AKANTU_DEBUG_OUT();
return ElementClass<_not_defined>::getFacetLocalConnectivityPerElement(0);
// This avoid a compilation warning but will certainly
// also cause a segfault if reached
}
/* -------------------------------------------------------------------------- */
inline auto Mesh::getFacetConnectivity(const Element & element, UInt t) const {
AKANTU_DEBUG_IN();
Matrix<const UInt> local_facets(getFacetLocalConnectivity(element.type, t));
Matrix<UInt> facets(local_facets.rows(), local_facets.cols());
const Array<UInt> & conn = connectivities(element.type, element.ghost_type);
for (UInt f = 0; f < facets.rows(); ++f) {
for (UInt n = 0; n < facets.cols(); ++n) {
facets(f, n) = conn(element.element, local_facets(f, n));
}
}
AKANTU_DEBUG_OUT();
return facets;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::extractNodalValuesFromElement(
const Array<T> & nodal_values, T * local_coord, UInt * connectivity,
UInt n_nodes, UInt nb_degree_of_freedom) const {
for (UInt n = 0; n < n_nodes; ++n) {
memcpy(local_coord + n * nb_degree_of_freedom,
nodal_values.storage() + connectivity[n] * nb_degree_of_freedom,
nb_degree_of_freedom * sizeof(T));
}
}
/* -------------------------------------------------------------------------- */
inline void Mesh::addConnectivityType(const ElementType & type,
const GhostType & ghost_type) {
getConnectivityPointer(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPureGhostNode(UInt n) const {
return nodes_type.size() ? (nodes_type(n) == _nt_pure_gost) : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalOrMasterNode(UInt n) const {
return nodes_type.size()
? (nodes_type(n) == _nt_master) || (nodes_type(n) == _nt_normal)
: true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalNode(UInt n) const {
return nodes_type.size() ? nodes_type(n) == _nt_normal : true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isMasterNode(UInt n) const {
return nodes_type.size() ? nodes_type(n) == _nt_master : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isSlaveNode(UInt n) const {
return nodes_type.size() ? nodes_type(n) >= 0 : false;
}
/* -------------------------------------------------------------------------- */
inline NodeType Mesh::getNodeType(UInt local_id) const {
return nodes_type.size() ? nodes_type(local_id) : _nt_normal;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeGlobalId(UInt local_id) const {
return nodes_global_ids ? (*nodes_global_ids)(local_id) : local_id;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeLocalId(UInt global_id) const {
AKANTU_DEBUG_ASSERT(nodes_global_ids != nullptr,
"The global ids are note set.");
return nodes_global_ids->find(global_id);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbGlobalNodes() const {
return nodes_global_ids ? nb_global_nodes : nodes->size();
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElementList(const Array<Element> & elements) {
UInt nb_nodes_per_element = 0;
UInt nb_nodes = 0;
ElementType current_element_type = _not_defined;
Array<Element>::const_iterator<Element> el_it = elements.begin();
Array<Element>::const_iterator<Element> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
const Element & el = *el_it;
if (el.type != current_element_type) {
current_element_type = el.type;
nb_nodes_per_element = Mesh::getNbNodesPerElement(current_element_type);
}
nb_nodes += nb_nodes_per_element;
}
return nb_nodes;
}
/* -------------------------------------------------------------------------- */
inline Mesh & Mesh::getMeshFacets() {
if (!this->mesh_facets)
AKANTU_SILENT_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshFacets() const {
if (!this->mesh_facets)
AKANTU_SILENT_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshParent() const {
if (!this->mesh_parent)
AKANTU_SILENT_EXCEPTION(
"No parent mesh is defined! This is only valid in a mesh_facets");
return *this->mesh_parent;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_MESH_INLINE_IMPL_CC__ */
diff --git a/src/mesh/mesh_iterators.hh b/src/mesh/mesh_iterators.hh
index 3d040e6a7..270f5a1fc 100644
--- a/src/mesh/mesh_iterators.hh
+++ b/src/mesh/mesh_iterators.hh
@@ -1,302 +1,303 @@
/**
-
* @file mesh_iterators.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Wed Aug 09 2017
+ * @date creation: Thu Jul 16 2015
+ * @date last modification: Wed Jan 31 2018
*
- * @brief Set of helper classes to have fun with range based for
+ * @brief Set of helper classes to have fun with range based for
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "aka_static_if.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_ITERATORS_HH__
#define __AKANTU_MESH_ITERATORS_HH__
namespace akantu {
class MeshElementsByTypes {
using elements_iterator = Array<Element>::scalar_iterator;
public:
explicit MeshElementsByTypes(const Array<Element> & elements) {
this->elements.copy(elements);
std::sort(this->elements.begin(), this->elements.end());
}
/* ------------------------------------------------------------------------ */
class MeshElementsRange {
public:
MeshElementsRange() = default;
MeshElementsRange(const elements_iterator & begin,
const elements_iterator & end)
: type((*begin).type), ghost_type((*begin).ghost_type), begin(begin),
end(end) {}
AKANTU_GET_MACRO(Type, type, const ElementType &);
AKANTU_GET_MACRO(GhostType, ghost_type, const GhostType &);
const Array<UInt> & getElements() {
elements.resize(end - begin);
auto el_it = elements.begin();
for (auto it = begin; it != end; ++it, ++el_it) {
*el_it = it->element;
}
return elements;
}
private:
ElementType type{_not_defined};
GhostType ghost_type{_casper};
elements_iterator begin;
elements_iterator end;
Array<UInt> elements;
};
/* ------------------------------------------------------------------------ */
class iterator {
struct element_comparator {
bool operator()(const Element & lhs, const Element & rhs) const {
return ((rhs == ElementNull) ||
std::tie(lhs.ghost_type, lhs.type) <
std::tie(rhs.ghost_type, rhs.type));
}
};
public:
iterator(const iterator &) = default;
iterator(const elements_iterator & first, const elements_iterator & last)
: range(std::equal_range(first, last, *first, element_comparator())),
first(first), last(last) {}
decltype(auto) operator*() const {
return MeshElementsRange(range.first, range.second);
}
iterator operator++() {
first = range.second;
range = std::equal_range(first, last, *first, element_comparator());
return *this;
}
bool operator==(const iterator & other) const {
return (first == other.first and last == other.last);
}
bool operator!=(const iterator & other) const {
return (not operator==(other));
}
private:
std::pair<elements_iterator, elements_iterator> range;
elements_iterator first;
elements_iterator last;
};
iterator begin() { return iterator(elements.begin(), elements.end()); }
iterator end() { return iterator(elements.end(), elements.end()); }
private:
Array<Element> elements;
};
/* -------------------------------------------------------------------------- */
namespace mesh_iterators {
namespace details {
template <class internal_iterator> class delegated_iterator {
public:
using value_type = std::remove_pointer_t<
typename internal_iterator::value_type::second_type>;
using difference_type = std::ptrdiff_t;
using pointer = value_type *;
using reference = value_type &;
using iterator_category = std::input_iterator_tag;
explicit delegated_iterator(internal_iterator it) : it(std::move(it)) {}
decltype(auto) operator*() {
return std::forward<decltype(*(it->second))>(*(it->second));
}
delegated_iterator operator++() {
++it;
return *this;
}
bool operator==(const delegated_iterator & other) const {
return other.it == it;
}
bool operator!=(const delegated_iterator & other) const {
return other.it != it;
}
private:
internal_iterator it;
};
template <class GroupManager> class ElementGroupsIterable {
public:
explicit ElementGroupsIterable(GroupManager && group_manager)
: group_manager(std::forward<GroupManager>(group_manager)) {}
size_t size() { return group_manager.getNbElementGroups(); }
decltype(auto) begin() {
return delegated_iterator<decltype(
group_manager.element_group_begin())>(
group_manager.element_group_begin());
}
decltype(auto) begin() const {
return delegated_iterator<decltype(
group_manager.element_group_begin())>(
group_manager.element_group_begin());
}
decltype(auto) end() {
return delegated_iterator<decltype(group_manager.element_group_end())>(
group_manager.element_group_end());
}
decltype(auto) end() const {
return delegated_iterator<decltype(group_manager.element_group_end())>(
group_manager.element_group_end());
}
private:
GroupManager && group_manager;
};
template <class GroupManager> class NodeGroupsIterable {
public:
explicit NodeGroupsIterable(GroupManager && group_manager)
: group_manager(std::forward<GroupManager>(group_manager)) {}
size_t size() { return group_manager.getNbNodeGroups(); }
decltype(auto) begin() {
return delegated_iterator<decltype(group_manager.node_group_begin())>(
group_manager.node_group_begin());
}
decltype(auto) begin() const {
return delegated_iterator<decltype(group_manager.node_group_begin())>(
group_manager.node_group_begin());
}
decltype(auto) end() {
return delegated_iterator<decltype(group_manager.node_group_end())>(
group_manager.node_group_end());
}
decltype(auto) end() const {
return delegated_iterator<decltype(group_manager.node_group_end())>(
group_manager.node_group_end());
}
private:
GroupManager && group_manager;
};
} // namespace details
} // namespace mesh_iterators
template <class GroupManager>
decltype(auto) ElementGroupsIterable(GroupManager && group_manager) {
return mesh_iterators::details::ElementGroupsIterable<GroupManager>(
group_manager);
}
template <class GroupManager>
decltype(auto) NodeGroupsIterable(GroupManager && group_manager) {
return mesh_iterators::details::NodeGroupsIterable<GroupManager>(
group_manager);
}
/* -------------------------------------------------------------------------- */
template <class Func>
void for_each_element(UInt nb_elements, const Array<UInt> & filter_elements,
Func && function) {
if (filter_elements != empty_filter) {
std::for_each(filter_elements.begin(), filter_elements.end(),
std::forward<Func>(function));
} else {
auto && range = arange(nb_elements);
std::for_each(range.begin(), range.end(), std::forward<Func>(function));
}
}
namespace {
DECLARE_NAMED_ARGUMENT(element_filter);
}
/* -------------------------------------------------------------------------- */
template <class Func, typename... pack>
void for_each_element(const Mesh & mesh, Func && function, pack &&... _pack) {
auto requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _casper);
const ElementTypeMapArray<UInt> * filter =
OPTIONAL_NAMED_ARG(element_filter, nullptr);
bool all_ghost_types = requested_ghost_type == _casper;
auto spatial_dimension =
OPTIONAL_NAMED_ARG(spatial_dimension, mesh.getSpatialDimension());
auto element_kind = OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined);
for (auto ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types))
continue;
auto element_types =
mesh.elementTypes(spatial_dimension, ghost_type, element_kind);
if (filter) {
element_types =
filter->elementTypes(spatial_dimension, ghost_type, element_kind);
}
for (auto type : element_types) {
const Array<UInt> * filter_array;
if (filter) {
filter_array = &((*filter)(type, ghost_type));
} else {
filter_array = &empty_filter;
}
auto nb_elements = mesh.getNbElement(type, ghost_type);
for_each_element(nb_elements, *filter_array, [&](auto && el) {
auto element = Element{type, el, ghost_type};
std::forward<Func>(function)(element);
});
}
}
}
} // namespace akantu
#endif /* __AKANTU_MESH_ITERATORS_HH__ */
diff --git a/src/mesh/node_group.cc b/src/mesh/node_group.cc
index 45ab104a8..5ece1d1d0 100644
--- a/src/mesh/node_group.cc
+++ b/src/mesh/node_group.cc
@@ -1,99 +1,98 @@
/**
* @file node_group.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Thu Feb 01 2018
*
* @brief Implementation of the node group
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_group.hh"
#include "dumpable.hh"
#include "dumpable_inline_impl.hh"
#include "mesh.hh"
#if defined(AKANTU_USE_IOHELPER)
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeGroup::NodeGroup(const std::string & name, const Mesh & mesh,
const std::string & id, const MemoryID & memory_id)
: Memory(id, memory_id), name(name),
node_group(alloc<UInt>(std::string(this->id + ":nodes"), 0, 1)) {
#if defined(AKANTU_USE_IOHELPER)
this->registerDumper<DumperParaview>("paraview_" + name, name, true);
this->getDumper().registerField(
"positions", new dumper::NodalField<Real, true>(mesh.getNodes(), 0, 0,
&this->getNodes()));
#endif
}
/* -------------------------------------------------------------------------- */
NodeGroup::~NodeGroup() = default;
/* -------------------------------------------------------------------------- */
void NodeGroup::empty() { node_group.resize(0); }
/* -------------------------------------------------------------------------- */
void NodeGroup::optimize() {
std::sort(node_group.begin(), node_group.end());
Array<UInt>::iterator<> end =
std::unique(node_group.begin(), node_group.end());
node_group.resize(end - node_group.begin());
}
/* -------------------------------------------------------------------------- */
void NodeGroup::append(const NodeGroup & other_group) {
AKANTU_DEBUG_IN();
UInt nb_nodes = node_group.size();
/// append new nodes to current list
node_group.resize(nb_nodes + other_group.node_group.size());
std::copy(other_group.node_group.begin(), other_group.node_group.end(),
node_group.begin() + nb_nodes);
optimize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeGroup::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NodeGroup [" << std::endl;
stream << space << " + name: " << name << std::endl;
node_group.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
} // akantu
diff --git a/src/mesh/node_group.hh b/src/mesh/node_group.hh
index 8eb5f5d51..f3b36be81 100644
--- a/src/mesh/node_group.hh
+++ b/src/mesh/node_group.hh
@@ -1,132 +1,131 @@
/**
* @file node_group.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Node group definition
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_memory.hh"
#include "dumpable.hh"
#include "mesh_filter.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NODE_GROUP_HH__
#define __AKANTU_NODE_GROUP_HH__
namespace akantu {
class NodeGroup : public Memory, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NodeGroup(const std::string & name, const Mesh & mesh,
const std::string & id = "node_group",
const MemoryID & memory_id = 0);
~NodeGroup() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
using const_node_iterator = Array<UInt>::const_iterator<UInt>;
/// empty the node group
void empty();
/// iterator to the beginning of the node group
inline const_node_iterator begin() const;
/// iterator to the end of the node group
inline const_node_iterator end() const;
/// add a node and give the local position through an iterator
inline const_node_iterator add(UInt node, bool check_for_duplicate = true);
/// remove a node
inline void remove(UInt node);
#ifndef SWIG
inline decltype(auto) find(UInt node) const { return node_group.find(node); }
#endif
/// remove duplicated nodes
void optimize();
/// append a group to current one
void append(const NodeGroup & other_group);
/// apply a filter on current node group
template <typename T> void applyNodeFilter(T & filter);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(Nodes, node_group, Array<UInt> &);
AKANTU_GET_MACRO(Nodes, node_group, const Array<UInt> &);
AKANTU_GET_MACRO(Name, name, const std::string &);
/// give the number of nodes in the current group
inline UInt size() const;
UInt * storage() { return node_group.storage(); };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// name of the group
std::string name;
/// list of nodes in the group
Array<UInt> & node_group;
/// reference to the mesh in question
// const Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NodeGroup & _this) {
_this.printself(stream);
return stream;
}
} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "node_group_inline_impl.cc"
#endif /* __AKANTU_NODE_GROUP_HH__ */
diff --git a/src/mesh/node_group_inline_impl.cc b/src/mesh/node_group_inline_impl.cc
index c165570f9..49665377d 100644
--- a/src/mesh/node_group_inline_impl.cc
+++ b/src/mesh/node_group_inline_impl.cc
@@ -1,99 +1,98 @@
/**
* @file node_group_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Sun Aug 13 2017
*
* @brief Node group inline function definitions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::begin() const {
return node_group.begin();
}
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::end() const {
return node_group.end();
}
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::add(UInt node,
bool check_for_duplicate) {
if (check_for_duplicate) {
const_node_iterator it = std::find(begin(), end(), node);
if (it == node_group.end()) {
node_group.push_back(node);
return (node_group.end() - 1);
}
return it;
} else {
node_group.push_back(node);
return (node_group.end() - 1);
}
}
/* -------------------------------------------------------------------------- */
inline void NodeGroup::remove(UInt node) {
Array<UInt>::iterator<> it = this->node_group.begin();
Array<UInt>::iterator<> end = this->node_group.end();
AKANTU_DEBUG_ASSERT(it != end, "The node group is empty!!");
for (; it != node_group.end(); ++it) {
if (*it == node) {
it = node_group.erase(it);
}
}
AKANTU_DEBUG_ASSERT(it != end, "The node was not found!");
}
/* -------------------------------------------------------------------------- */
inline UInt NodeGroup::size() const { return node_group.size(); }
/* -------------------------------------------------------------------------- */
struct FilterFunctor;
template <typename T> void NodeGroup::applyNodeFilter(T & filter) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(T::type == FilterFunctor::_node_filter_functor,
"NodeFilter can only apply node filter functor");
Array<UInt>::iterator<> it = this->node_group.begin();
for (; it != node_group.end(); ++it) {
/// filter == true -> keep node
if (!filter(*it)) {
it = node_group.erase(it);
}
}
AKANTU_DEBUG_OUT();
}
} // akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.cc b/src/mesh_utils/cohesive_element_inserter.cc
index 7be630cf2..43a36eacb 100644
--- a/src/mesh_utils/cohesive_element_inserter.cc
+++ b/src/mesh_utils/cohesive_element_inserter.cc
@@ -1,281 +1,282 @@
/**
* @file cohesive_element_inserter.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
- * @date last modification: Sun Oct 04 2015
+ * @date last modification: Mon Feb 19 2018
*
* @brief Cohesive element inserter functions
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "global_ids_updater.hh"
#include "mesh_iterators.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <limits>
/* -------------------------------------------------------------------------- */
namespace akantu {
CohesiveElementInserter::CohesiveElementInserter(Mesh & mesh, const ID & id)
: Parsable(ParserType::_cohesive_inserter), id(id), mesh(mesh),
mesh_facets(mesh.initMeshFacets()),
insertion_facets("insertion_facets", id),
insertion_limits(mesh.getSpatialDimension(), 2),
check_facets("check_facets", id) {
this->registerParam("cohesive_surfaces", physical_groups, _pat_parsable,
"List of groups to consider for insertion");
this->registerParam("bounding_box", insertion_limits, _pat_parsable,
"Global limit for insertion");
UInt spatial_dimension = mesh.getSpatialDimension();
MeshUtils::resetFacetToDouble(mesh_facets);
/// init insertion limits
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
insertion_limits(dim, 0) = std::numeric_limits<Real>::max() * Real(-1.);
insertion_limits(dim, 1) = std::numeric_limits<Real>::max();
}
insertion_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = false);
}
/* -------------------------------------------------------------------------- */
CohesiveElementInserter::~CohesiveElementInserter() = default;
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::parseSection(const ParserSection & section) {
Parsable::parseSection(section);
if (is_extrinsic)
limitCheckFacets(this->check_facets);
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::limitCheckFacets() {
limitCheckFacets(this->check_facets);
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::setLimit(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);
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertIntrinsicElements() {
limitCheckFacets(insertion_facets);
return insertElements();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::limitCheckFacets(
ElementTypeMapArray<bool> & check_facets) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
check_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = true);
check_facets.set(true);
// remove the pure ghost elements
for_each_element(
mesh_facets,
[&](auto && facet) {
const auto & element_to_facet = mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
auto & left = element_to_facet[0];
auto & right = element_to_facet[1];
if (right == ElementNull ||
(left.ghost_type == _ghost && right.ghost_type == _ghost)) {
check_facets(facet) = false;
return;
}
if (left.kind() == _ek_cohesive or right.kind() == _ek_cohesive) {
check_facets(facet) = false;
}
},
_spatial_dimension = spatial_dimension - 1);
Vector<Real> bary_facet(spatial_dimension);
// set the limits to the bounding box
for_each_element(mesh_facets,
[&](auto && facet) {
auto & need_check = check_facets(facet);
if (not need_check)
return;
mesh_facets.getBarycenter(facet, bary_facet);
UInt coord_in_limit = 0;
while (coord_in_limit < spatial_dimension &&
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)
need_check = false;
},
_spatial_dimension = spatial_dimension - 1);
if (not mesh_facets.hasData("physical_names")) {
AKANTU_DEBUG_ASSERT(
physical_groups.size() == 0,
"No physical names in the mesh but insertion limited to a group");
AKANTU_DEBUG_OUT();
return;
}
const auto & physical_ids =
mesh_facets.getData<std::string>("physical_names");
// set the limits to the physical surfaces
for_each_element(mesh_facets,
[&](auto && facet) {
auto & need_check = check_facets(facet);
if (not need_check)
return;
const auto & physical_id = physical_ids(facet);
auto it = find(physical_groups.begin(),
physical_groups.end(), physical_id);
need_check = (it != physical_groups.end());
},
_spatial_dimension = spatial_dimension - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertElements(bool only_double_facets) {
CohesiveNewNodesEvent node_event;
NewElementsEvent element_event;
Array<UInt> new_pairs(0, 2);
UInt nb_new_elements = MeshUtils::insertCohesiveElements(
mesh, mesh_facets, insertion_facets, new_pairs, element_event.getList(),
only_double_facets);
UInt nb_new_nodes = new_pairs.size();
node_event.getList().reserve(nb_new_nodes);
node_event.getOldNodesList().reserve(nb_new_nodes);
for (UInt n = 0; n < nb_new_nodes; ++n) {
node_event.getList().push_back(new_pairs(n, 1));
node_event.getOldNodesList().push_back(new_pairs(n, 0));
}
if (mesh.isDistributed()) {
/// update nodes type
updateNodesType(mesh, node_event);
updateNodesType(mesh_facets, node_event);
/// update global ids
nb_new_nodes = this->updateGlobalIDs(node_event);
/// compute total number of new elements
const auto & comm = mesh.getCommunicator();
comm.allReduce(nb_new_elements, SynchronizerOperation::_sum);
}
if (nb_new_nodes > 0)
mesh.sendEvent(node_event);
if (nb_new_elements > 0) {
updateInsertionFacets();
// mesh.updateTypesOffsets(_not_ghost);
mesh.sendEvent(element_event);
MeshUtils::resetFacetToDouble(mesh_facets);
}
if (mesh.isDistributed()) {
/// update global ids
this->synchronizeGlobalIDs(node_event);
}
return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::updateInsertionFacets() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (auto && facet_gt : ghost_types) {
for (auto && facet_type :
mesh_facets.elementTypes(spatial_dimension - 1, facet_gt)) {
auto & ins_facets = insertion_facets(facet_type, facet_gt);
// this is the intrinsic case
if (not is_extrinsic)
continue;
auto & f_check = check_facets(facet_type, facet_gt);
for (auto && pair : zip(ins_facets, f_check)) {
bool & ins = std::get<0>(pair);
bool & check = std::get<1>(pair);
if (ins)
ins = check = false;
}
}
}
// resize for the newly added facets
insertion_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = false);
// resize for the newly added facets
if (is_extrinsic) {
check_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = false);
} else {
insertion_facets.set(false);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.hh b/src/mesh_utils/cohesive_element_inserter.hh
index faa0481e3..688f1888e 100644
--- a/src/mesh_utils/cohesive_element_inserter.hh
+++ b/src/mesh_utils/cohesive_element_inserter.hh
@@ -1,192 +1,194 @@
/**
* @file cohesive_element_inserter.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
- * @date last modification: Fri Oct 02 2015
+ * @date last modification: Sun Feb 04 2018
*
* @brief Cohesive element inserter
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "mesh_utils.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
#define __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
namespace akantu {
class GlobalIdsUpdater;
class FacetSynchronizer;
} // akantu
namespace akantu {
class CohesiveElementInserter : public DataAccessor<Element>, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
CohesiveElementInserter(Mesh & mesh,
const ID & id = "cohesive_element_inserter");
~CohesiveElementInserter() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set range limitation for intrinsic cohesive element insertion
void setLimit(SpacialDirection axis, Real first_limit, Real second_limit);
/// insert intrinsic cohesive elements in a predefined range
UInt insertIntrinsicElements();
/// insert extrinsic cohesive elements (returns the number of new
/// cohesive elements)
UInt insertElements(bool only_double_facets = false);
/// limit check facets to match given insertion limits
void limitCheckFacets();
protected:
/// init parallel variables
void initParallel(ElementSynchronizer & element_synchronizer);
void parseSection(const ParserSection & section) override;
protected:
/// internal version of limitCheckFacets
void limitCheckFacets(ElementTypeMapArray<bool> & check_facets);
/// update facet insertion arrays after facets doubling
void updateInsertionFacets();
/// update nodes type and global ids for parallel simulations
/// (locally, within each processor)
UInt updateGlobalIDs(NewNodesEvent & node_event);
/// synchronize the global ids among the processors in parallel simulations
void synchronizeGlobalIDs(NewNodesEvent & node_event);
/// update nodes type
void updateNodesType(Mesh & mesh, NewNodesEvent & node_event);
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
template <bool pack_mode>
inline void
packUnpackGlobalConnectivity(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
template <bool pack_mode>
inline void
packUnpackGroupedInsertionData(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(InsertionFacetsByElement, insertion_facets,
ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO(InsertionFacetsByElement, insertion_facets,
const ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(InsertionFacets, insertion_facets, bool);
AKANTU_GET_MACRO(CheckFacets, check_facets,
const ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO(MeshFacets, mesh_facets, const Mesh &);
AKANTU_GET_MACRO_NOT_CONST(MeshFacets, mesh_facets, Mesh &);
AKANTU_SET_MACRO(IsExtrinsic, is_extrinsic, bool);
public:
friend class SolidMechanicsModelCohesive;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// object id
ID id;
/// main mesh where to insert cohesive elements
Mesh & mesh;
/// mesh containing facets
Mesh & mesh_facets;
/// list of facets where to insert elements
ElementTypeMapArray<bool> insertion_facets;
/// limits for element insertion
Matrix<Real> insertion_limits;
/// list of groups to consider for insertion, ignored if empty
std::vector<ID> physical_groups;
/// vector containing facets in which extrinsic cohesive elements can be
/// inserted
ElementTypeMapArray<bool> check_facets;
/// global connectivity ids updater
std::unique_ptr<GlobalIdsUpdater> global_ids_updater;
/// is this inserter used in extrinsic
bool is_extrinsic{false};
};
class CohesiveNewNodesEvent : public NewNodesEvent {
public:
CohesiveNewNodesEvent() = default;
~CohesiveNewNodesEvent() override = default;
AKANTU_GET_MACRO_NOT_CONST(OldNodesList, old_nodes, Array<UInt> &);
AKANTU_GET_MACRO(OldNodesList, old_nodes, const Array<UInt> &);
private:
Array<UInt> old_nodes;
};
} // akantu
#include "cohesive_element_inserter_inline_impl.cc"
#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__ */
diff --git a/src/mesh_utils/cohesive_element_inserter_inline_impl.cc b/src/mesh_utils/cohesive_element_inserter_inline_impl.cc
index 65255ff86..d53f12d16 100644
--- a/src/mesh_utils/cohesive_element_inserter_inline_impl.cc
+++ b/src/mesh_utils/cohesive_element_inserter_inline_impl.cc
@@ -1,105 +1,121 @@
/**
* @file cohesive_element_inserter_inline_impl.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
+ * @date creation: Wed Nov 05 2014
+ * @date last modification: Fri Dec 08 2017
*
* @brief Cohesive element inserter inline functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
*/
+
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_CC__
#define __AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt
CohesiveElementInserter::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (tag == _gst_ce_groups) {
size = elements.size() * (sizeof(bool) + sizeof(unsigned int));
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void
CohesiveElementInserter::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (tag == _gst_ce_groups)
packUnpackGroupedInsertionData<true>(buffer, elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void
CohesiveElementInserter::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (tag == _gst_ce_groups)
packUnpackGroupedInsertionData<false>(buffer, elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool pack_mode>
inline void CohesiveElementInserter::packUnpackGroupedInsertionData(
CommunicationBuffer & buffer, const Array<Element> & elements) const {
AKANTU_DEBUG_IN();
auto current_element_type = _not_defined;
auto current_ghost_type = _casper;
auto & physical_names = mesh_facets.registerData<UInt>("physical_names");
Array<bool> * vect = nullptr;
Array<UInt> * vect2 = nullptr;
for (const auto & el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect =
&const_cast<Array<bool> &>(insertion_facets(el.type, el.ghost_type));
vect2 = &(physical_names(el.type, el.ghost_type));
}
Vector<bool> data(vect->storage() + el.element, 1);
Vector<unsigned int> data2(vect2->storage() + el.element, 1);
if (pack_mode) {
buffer << data;
buffer << data2;
} else {
buffer >> data;
buffer >> data2;
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_CC__ */
diff --git a/src/mesh_utils/cohesive_element_inserter_parallel.cc b/src/mesh_utils/cohesive_element_inserter_parallel.cc
index a8e5cac48..a61281338 100644
--- a/src/mesh_utils/cohesive_element_inserter_parallel.cc
+++ b/src/mesh_utils/cohesive_element_inserter_parallel.cc
@@ -1,77 +1,93 @@
/**
* @file cohesive_element_inserter_parallel.cc
*
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
+ * @date creation: Wed Nov 05 2014
+ * @date last modification: Fri Dec 08 2017
*
* @brief Parallel functions for the cohesive element inserter
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
#include "global_ids_updater.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::initParallel(ElementSynchronizer & synchronizer) {
global_ids_updater = std::make_unique<GlobalIdsUpdater>(mesh, synchronizer);
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::updateNodesType(Mesh & mesh,
NewNodesEvent & node_event) {
AKANTU_DEBUG_IN();
auto & cohesive_node_event =
dynamic_cast<CohesiveNewNodesEvent &>(node_event);
auto & new_nodes = cohesive_node_event.getList();
auto & old_nodes = cohesive_node_event.getOldNodesList();
UInt local_nb_new_nodes = new_nodes.size();
MeshAccessor mesh_accessor(mesh);
auto & nodes_type = mesh_accessor.getNodesType();
UInt nb_old_nodes = nodes_type.size();
nodes_type.resize(nb_old_nodes + local_nb_new_nodes);
for (auto && data : zip(old_nodes, new_nodes)) {
UInt old_node, new_node;
std::tie(old_node, new_node) = data;
nodes_type(new_node) = nodes_type(old_node);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::updateGlobalIDs(NewNodesEvent & node_event) {
AKANTU_DEBUG_IN();
Array<UInt> & doubled_nodes = node_event.getList();
UInt total_nb_new_nodes =
global_ids_updater->updateGlobalIDsLocally(doubled_nodes.size());
AKANTU_DEBUG_OUT();
return total_nb_new_nodes;
}
void CohesiveElementInserter::synchronizeGlobalIDs(
NewNodesEvent & /*node_event*/) {
AKANTU_DEBUG_IN();
global_ids_updater->synchronizeGlobalIDs();
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/global_ids_updater.cc b/src/mesh_utils/global_ids_updater.cc
index bd3ae404d..5f0198e60 100644
--- a/src/mesh_utils/global_ids_updater.cc
+++ b/src/mesh_utils/global_ids_updater.cc
@@ -1,57 +1,56 @@
/**
* @file global_ids_updater.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Fri Oct 02 2015
+ * @date last modification: Fri Dec 08 2017
*
* @brief Functions of the GlobalIdsUpdater
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "global_ids_updater.hh"
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
UInt GlobalIdsUpdater::updateGlobalIDs(UInt old_nb_nodes) {
UInt total_nb_new_nodes = this->updateGlobalIDsLocally(old_nb_nodes);
this->synchronizeGlobalIDs();
return total_nb_new_nodes;
}
UInt GlobalIdsUpdater::updateGlobalIDsLocally(UInt old_nb_nodes) {
UInt total_nb_new_nodes =
MeshUtils::updateLocalMasterGlobalConnectivity(mesh, old_nb_nodes);
return total_nb_new_nodes;
}
void GlobalIdsUpdater::synchronizeGlobalIDs() {
this->synchronizer.synchronizeOnce(*this, _gst_giu_global_conn);
}
} // akantu
diff --git a/src/mesh_utils/global_ids_updater.hh b/src/mesh_utils/global_ids_updater.hh
index bc2b6199a..5869c99b4 100644
--- a/src/mesh_utils/global_ids_updater.hh
+++ b/src/mesh_utils/global_ids_updater.hh
@@ -1,100 +1,102 @@
/**
* @file global_ids_updater.hh
*
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Oct 02 2015
+ * @date last modification: Fri Dec 08 2017
*
* @brief Class that updates the global ids of new nodes that are
* inserted in the mesh. The functions in this class must be called
* after updating the node types
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GLOBAL_IDS_UPDATER_HH__
#define __AKANTU_GLOBAL_IDS_UPDATER_HH__
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer;
} // akantu
namespace akantu {
class GlobalIdsUpdater : public DataAccessor<Element> {
public:
GlobalIdsUpdater(Mesh & mesh, ElementSynchronizer & synchronizer)
: mesh(mesh), synchronizer(synchronizer) {}
/// function to update and synchronize the global connectivity of
/// new inserted nodes. It must be called after updating the node
/// types. (It calls in sequence the functions
/// updateGlobalIDsLocally and synchronizeGlobalIDs)
UInt updateGlobalIDs(UInt old_nb_nodes);
/// function to update the global connectivity (only locally) of new
/// inserted nodes. It must be called after updating the node types.
UInt updateGlobalIDsLocally(UInt old_nb_nodes);
/// function to synchronize the global connectivity of new inserted
/// nodes among the processors. It must be called after updating the
/// node types.
void synchronizeGlobalIDs();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
template <bool pack_mode>
inline void
packUnpackGlobalConnectivity(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
/// Reference to the mesh to update
Mesh & mesh;
/// distributed synchronizer to communicate the connectivity
ElementSynchronizer & synchronizer;
};
} // akantu
#include "global_ids_updater_inline_impl.cc"
#endif /* __AKANTU_GLOBAL_IDS_UPDATER_HH__ */
diff --git a/src/mesh_utils/global_ids_updater_inline_impl.cc b/src/mesh_utils/global_ids_updater_inline_impl.cc
index 77a4ffe24..4fc0e7b2b 100644
--- a/src/mesh_utils/global_ids_updater_inline_impl.cc
+++ b/src/mesh_utils/global_ids_updater_inline_impl.cc
@@ -1,132 +1,132 @@
/**
* @file global_ids_updater_inline_impl.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Oct 02 2015
- * @date last modification: Sun Oct 04 2015
+ * @date last modification: Sun Aug 13 2017
*
* @brief Implementation of the inline functions of GlobalIdsUpdater
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "global_ids_updater.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_CC__
#define __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt GlobalIdsUpdater::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
UInt size = 0;
if (elements.size() == 0)
return size;
if (tag == _gst_giu_global_conn)
size += Mesh::getNbNodesPerElementList(elements) * sizeof(UInt);
return size;
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_giu_global_conn)
packUnpackGlobalConnectivity<true>(buffer, elements);
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == _gst_giu_global_conn)
packUnpackGlobalConnectivity<false>(buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <bool pack_mode>
inline void GlobalIdsUpdater::packUnpackGlobalConnectivity(
CommunicationBuffer & buffer, const Array<Element> & elements) const {
AKANTU_DEBUG_IN();
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
Array<UInt>::const_vector_iterator conn_begin;
UInt nb_nodes_per_elem = 0;
UInt index;
Array<UInt> & global_nodes_ids = mesh.getGlobalNodesIds();
Array<Element>::const_scalar_iterator it = elements.begin();
Array<Element>::const_scalar_iterator end = elements.end();
for (; it != end; ++it) {
const 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;
const Array<UInt> & connectivity =
mesh.getConnectivity(current_element_type, current_ghost_type);
nb_nodes_per_elem = connectivity.getNbComponent();
conn_begin = connectivity.begin(nb_nodes_per_elem);
}
/// get element connectivity
const Vector<UInt> current_conn = conn_begin[el.element];
/// loop on all connectivity nodes
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = current_conn(n);
if (pack_mode) {
/// if node is local or master pack its global id, otherwise
/// dummy data
if (mesh.isLocalOrMasterNode(node))
index = global_nodes_ids(node);
else
index = UInt(-1);
buffer << index;
} else {
buffer >> index;
/// update slave nodes' index
if (index != UInt(-1) && mesh.isSlaveNode(node))
global_nodes_ids(node) = index;
}
}
}
AKANTU_DEBUG_OUT();
}
} // akantu
#endif /* __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_CC__ */
diff --git a/src/mesh_utils/mesh_partition.cc b/src/mesh_utils/mesh_partition.cc
index d7a27e34f..7bb771e62 100644
--- a/src/mesh_utils/mesh_partition.cc
+++ b/src/mesh_utils/mesh_partition.cc
@@ -1,434 +1,433 @@
/**
* @file mesh_partition.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 17 2010
- * @date last modification: Fri Jan 22 2016
+ * @date last modification: Wed Jan 24 2018
*
* @brief implementation of common part of all partitioner
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_partition.hh"
#include "aka_iterators.hh"
#include "aka_types.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <numeric>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshPartition::MeshPartition(const Mesh & mesh, UInt spatial_dimension,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(mesh), spatial_dimension(spatial_dimension),
partitions("partition", id, memory_id),
ghost_partitions("ghost_partition", id, memory_id),
ghost_partitions_offset("ghost_partition_offset", id, memory_id),
saved_connectivity("saved_connectivity", id, memory_id) {
AKANTU_DEBUG_IN();
UInt nb_total_element = 0;
for (auto && type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
linearized_offsets.push_back(std::make_pair(type, nb_total_element));
nb_total_element += mesh.getConnectivity(type).size();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MeshPartition::~MeshPartition() = default;
/* -------------------------------------------------------------------------- */
UInt MeshPartition::linearized(const Element & element) {
auto it =
std::find_if(linearized_offsets.begin(), linearized_offsets.end(),
[&element](auto & a) { return a.first == element.type; });
AKANTU_DEBUG_ASSERT(it != linearized_offsets.end(),
"A bug might be crawling around this corner...");
return (it->second + element.element);
}
/* -------------------------------------------------------------------------- */
Element MeshPartition::unlinearized(UInt lin_element) {
ElementType type{_not_defined};
UInt offset{0};
for (auto & pair : linearized_offsets) {
if (lin_element < pair.second)
continue;
std::tie(type, offset) = pair;
}
return Element{type, lin_element - offset, _not_ghost};
}
/* -------------------------------------------------------------------------- */
/**
* TODO this function should most probably be rewritten in a more modern way
* conversion in c++ of the GENDUALMETIS (mesh.c) function wrote by George in
* Metis (University of Minnesota)
*/
void MeshPartition::buildDualGraph(Array<Int> & dxadj, Array<Int> & dadjncy,
Array<Int> & edge_loads,
const EdgeLoadFunctor & edge_load_func) {
AKANTU_DEBUG_IN();
std::map<ElementType, std::tuple<const Array<UInt> *, UInt, UInt>>
connectivities;
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_total_element{0};
for (auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
auto type_p1 = mesh.getP1ElementType(type);
auto nb_nodes_per_element_p1 = mesh.getNbNodesPerElement(type_p1);
auto magic_number = mesh.getNbNodesPerElement(mesh.getFacetType(type_p1));
const auto & conn = mesh.getConnectivity(type, _not_ghost);
connectivities[type] =
std::make_tuple(&conn, nb_nodes_per_element_p1, magic_number);
nb_total_element += conn.size();
}
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem);
dxadj.resize(nb_total_element + 1);
/// initialize the dxadj array
auto dxadj_it = dxadj.begin();
for (auto & pair : connectivities) {
const auto & connectivity = *std::get<0>(pair.second);
auto nb_nodes_per_element_p1 = std::get<1>(pair.second);
std::fill_n(dxadj_it, connectivity.size(), nb_nodes_per_element_p1);
dxadj_it += connectivity.size();
}
/// convert the dxadj_val array in a csr one
for (UInt i = 1; i < nb_total_element; ++i)
dxadj(i) += dxadj(i - 1);
for (UInt i = nb_total_element; i > 0; --i)
dxadj(i) = dxadj(i - 1);
dxadj(0) = 0;
dadjncy.resize(2 * dxadj(nb_total_element));
edge_loads.resize(2 * dxadj(nb_total_element));
/// weight map to determine adjacency
std::unordered_map<UInt, UInt> weight_map;
for (auto & pair : connectivities) {
auto type = pair.first;
const auto & connectivity = *std::get<0>(pair.second);
auto nb_nodes_per_element = std::get<1>(pair.second);
auto magic_number = std::get<2>(pair.second);
Element element{type, 0, _not_ghost};
for (const auto & conn :
make_view(connectivity, connectivity.getNbComponent())) {
auto linearized_el = linearized(element);
/// fill the weight map
for (UInt n : arange(nb_nodes_per_element)) {
auto && node = conn(n);
for (auto k = node_to_elem.rbegin(node); k != node_to_elem.rend(node);
--k) {
auto & current_element = *k;
auto current_el = linearized(current_element);
AKANTU_DEBUG_ASSERT(current_el != UInt(-1),
"Linearized element not found");
if (current_el <= linearized_el)
break;
auto weight_map_insert =
weight_map.insert(std::make_pair(current_el, 1));
if (not weight_map_insert.second)
(weight_map_insert.first->second)++;
}
}
/// each element with a weight of the size of a facet are adjacent
for (auto & weight_pair : weight_map) {
auto & adjacent_el = weight_pair.first;
auto magic = weight_pair.second;
if (magic != magic_number)
continue;
#if defined(AKANTU_COHESIVE_ELEMENT)
/// Patch in order to prevent neighboring cohesive elements
/// from detecting each other
auto adjacent_element = unlinearized(adjacent_el);
auto el_kind = element.kind();
auto adjacent_el_kind = adjacent_element.kind();
if (el_kind == adjacent_el_kind && el_kind == _ek_cohesive)
continue;
#endif
UInt index_adj = dxadj(adjacent_el)++;
UInt index_lin = dxadj(linearized_el)++;
dadjncy(index_lin) = adjacent_el;
dadjncy(index_adj) = linearized_el;
}
element.element++;
weight_map.clear();
}
}
Int k_start = 0, linerized_el = 0, j = 0;
for (auto & pair : connectivities) {
const auto & connectivity = *std::get<0>(pair.second);
auto nb_nodes_per_element_p1 = std::get<1>(pair.second);
auto nb_element = connectivity.size();
for (UInt el = 0; el < nb_element; ++el, ++linerized_el) {
for (Int k = k_start; k < dxadj(linerized_el); ++k, ++j)
dadjncy(j) = dadjncy(k);
dxadj(linerized_el) = j;
k_start += nb_nodes_per_element_p1;
}
}
for (UInt i = nb_total_element; i > 0; --i)
dxadj(i) = dxadj(i - 1);
dxadj(0) = 0;
UInt adj = 0;
for (UInt i = 0; i < nb_total_element; ++i) {
UInt nb_adj = dxadj(i + 1) - dxadj(i);
for (UInt j = 0; j < nb_adj; ++j, ++adj) {
Int el_adj_id = dadjncy(dxadj(i) + j);
Element el = unlinearized(i);
Element el_adj = unlinearized(el_adj_id);
Int load = edge_load_func(el, el_adj);
edge_loads(adj) = load;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::fillPartitionInformation(
const Mesh & mesh, const Int * linearized_partitions) {
AKANTU_DEBUG_IN();
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem);
UInt linearized_el = 0;
for (auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
partitions.alloc(nb_element, 1, type, _not_ghost);
auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
ghost_partitions.alloc(0, 1, type, _ghost);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
UInt part = linearized_partitions[linearized_el];
partitions(type, _not_ghost)(el) = part;
std::list<UInt> list_adj_part;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity.storage()[el * nb_nodes_per_element + n];
CSR<Element>::iterator ne;
for (ne = node_to_elem.begin(node); ne != node_to_elem.end(node);
++ne) {
const Element & adj_element = *ne;
UInt adj_el = linearized(adj_element);
UInt adj_part = linearized_partitions[adj_el];
if (part != adj_part) {
list_adj_part.push_back(adj_part);
}
}
}
list_adj_part.sort();
list_adj_part.unique();
for (auto & adj_part : list_adj_part) {
ghost_part_csr.getRows().push_back(adj_part);
ghost_part_csr.rowOffset(el)++;
ghost_partitions(type, _ghost).push_back(adj_part);
ghost_partitions_offset(type, _ghost)(el)++;
}
}
ghost_part_csr.countToCSR();
/// convert the ghost_partitions_offset array in an offset array
Array<UInt> & ghost_partitions_offset_ptr =
ghost_partitions_offset(type, _ghost);
for (UInt i = 1; i < nb_element; ++i)
ghost_partitions_offset_ptr(i) += ghost_partitions_offset_ptr(i - 1);
for (UInt i = nb_element; i > 0; --i)
ghost_partitions_offset_ptr(i) = ghost_partitions_offset_ptr(i - 1);
ghost_partitions_offset_ptr(0) = 0;
}
// All Facets
for (Int sp = spatial_dimension - 1; sp >= 0; --sp) {
for (auto & type : mesh.elementTypes(sp, _not_ghost, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type);
partitions.alloc(nb_element, 1, type, _not_ghost);
AKANTU_DEBUG_INFO("Allocating partitions for " << type);
auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
ghost_partitions.alloc(0, 1, type, _ghost);
AKANTU_DEBUG_INFO("Allocating ghost_partitions for " << type);
const Array<std::vector<Element>> & elem_to_subelem =
mesh.getElementToSubelement(type, _not_ghost);
for (UInt i(0); i < mesh.getNbElement(type, _not_ghost);
++i) { // Facet loop
const std::vector<Element> & adjacent_elems = elem_to_subelem(i);
if (!adjacent_elems.empty()) {
Element min_elem{_max_element_type, std::numeric_limits<UInt>::max(),
*ghost_type_t::end()};
UInt min_part(std::numeric_limits<UInt>::max());
std::set<UInt> adjacent_parts;
for (UInt j(0); j < adjacent_elems.size(); ++j) {
UInt adjacent_elem_id = adjacent_elems[j].element;
UInt adjacent_elem_part =
partitions(adjacent_elems[j].type,
adjacent_elems[j].ghost_type)(adjacent_elem_id);
if (adjacent_elem_part < min_part) {
min_part = adjacent_elem_part;
min_elem = adjacent_elems[j];
}
adjacent_parts.insert(adjacent_elem_part);
}
partitions(type, _not_ghost)(i) = min_part;
auto git = ghost_partitions_csr(min_elem.type, _not_ghost)
.begin(min_elem.element);
auto gend = ghost_partitions_csr(min_elem.type, _not_ghost)
.end(min_elem.element);
for (; git != gend; ++git) {
adjacent_parts.insert(min_part);
}
adjacent_parts.erase(min_part);
for (auto & part : adjacent_parts) {
ghost_part_csr.getRows().push_back(part);
ghost_part_csr.rowOffset(i)++;
ghost_partitions(type, _ghost).push_back(part);
}
ghost_partitions_offset(type, _ghost)(i + 1) =
ghost_partitions_offset(type, _ghost)(i + 1) +
adjacent_elems.size();
} else {
partitions(type, _not_ghost)(i) = 0;
}
}
ghost_part_csr.countToCSR();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::tweakConnectivity(const Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
if (pairs.size() == 0)
return;
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);
for (; it != end; ++it) {
ElementType type = *it;
Array<UInt> & conn =
const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost));
UInt nb_nodes_per_element = conn.getNbComponent();
UInt nb_element = conn.size();
Array<UInt> & saved_conn = saved_connectivity.alloc(
nb_element, nb_nodes_per_element, type, _not_ghost);
saved_conn.copy(conn);
for (UInt i = 0; i < pairs.size(); ++i) {
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
if (pairs(i, 1) == conn(el, n))
conn(el, n) = pairs(i, 0);
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::restoreConnectivity() {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
for (auto && type : saved_connectivity.elementTypes(
spatial_dimension, _not_ghost, _ek_not_defined)) {
auto & conn = mesh_accessor.getConnectivity(type, _not_ghost);
auto & saved_conn = saved_connectivity(type, _not_ghost);
conn.copy(saved_conn);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
bool MeshPartition::hasPartitions(const ElementType & type,
const GhostType & ghost_type) {
return partitions.exists(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/mesh_utils/mesh_partition.hh b/src/mesh_utils/mesh_partition.hh
index 175c8c1ef..bd1b703f9 100644
--- a/src/mesh_utils/mesh_partition.hh
+++ b/src/mesh_utils/mesh_partition.hh
@@ -1,155 +1,154 @@
/**
* @file mesh_partition.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Sep 01 2015
+ * @date last modification: Tue Jan 23 2018
*
* @brief tools to partitionate a mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_PARTITION_HH__
#define __AKANTU_MESH_PARTITION_HH__
/* -------------------------------------------------------------------------- */
#include "aka_csr.hh"
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartition : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshPartition(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "MeshPartitioner",
const MemoryID & memory_id = 0);
~MeshPartition() override;
class EdgeLoadFunctor {
public:
virtual Int operator()(const Element & el1, const Element & el2) const
noexcept = 0;
};
class ConstEdgeLoadFunctor : public EdgeLoadFunctor {
public:
inline Int operator()(const Element &, const Element &) const
noexcept override {
return 1;
}
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// define a partition of the mesh
virtual void
partitionate(UInt nb_part,
const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
const Array<UInt> & pairs = Array<UInt>()) = 0;
/// reorder the nodes to reduce the filling during the factorization of a
/// matrix that has a profil based on the connectivity of the mesh
virtual void reorder() = 0;
/// fill the partitions array with a given linearized partition information
void fillPartitionInformation(const Mesh & mesh,
const Int * linearized_partitions);
protected:
/// build the dual graph of the mesh, for all element of spatial_dimension
void buildDualGraph(Array<Int> & dxadj, Array<Int> & dadjncy,
Array<Int> & edge_loads,
const EdgeLoadFunctor & edge_load_func);
/// tweak the mesh to handle the PBC pairs
void tweakConnectivity(const Array<UInt> & pairs);
/// restore the mesh that has been tweaked
void restoreConnectivity();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
bool hasPartitions(const ElementType & type, const GhostType & ghost_type);
AKANTU_GET_MACRO(Partitions, partitions, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Partition, partitions, UInt);
AKANTU_GET_MACRO(GhostPartitionCSR, ghost_partitions_csr,
const ElementTypeMap<CSR<UInt>> &);
AKANTU_GET_MACRO(NbPartition, nb_partitions, UInt);
AKANTU_SET_MACRO(NbPartition, nb_partitions, UInt);
protected:
UInt linearized(const Element & element);
Element unlinearized(UInt lin_element);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id
std::string id;
/// the mesh to partition
const Mesh & mesh;
/// dimension of the elements to consider in the mesh
UInt spatial_dimension;
/// number of partitions
UInt nb_partitions;
/// partition numbers
ElementTypeMapArray<UInt> partitions;
ElementTypeMap<CSR<UInt>> ghost_partitions_csr;
ElementTypeMapArray<UInt> ghost_partitions;
ElementTypeMapArray<UInt> ghost_partitions_offset;
Array<UInt> * permutation;
ElementTypeMapArray<UInt> saved_connectivity;
// vector of pair to ensure the iteration order
std::vector<std::pair<ElementType, UInt>> linearized_offsets;
};
} // namespace akantu
#ifdef AKANTU_USE_SCOTCH
#include "mesh_partition_scotch.hh"
#endif
#endif /* __AKANTU_MESH_PARTITION_HH__ */
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
index 78d5990bb..aad595cc1 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
+++ b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
@@ -1,141 +1,141 @@
/**
* @file mesh_partition_mesh_data.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Wed Nov 11 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief implementation of the MeshPartitionMeshData class
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "mesh_partition_mesh_data.hh"
#if !defined(AKANTU_NDEBUG)
#include <set>
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshPartitionMeshData::MeshPartitionMeshData(const Mesh & mesh,
UInt spatial_dimension,
const ID & id,
const MemoryID & memory_id)
: MeshPartition(mesh, spatial_dimension, id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MeshPartitionMeshData::MeshPartitionMeshData(
const Mesh & mesh, const ElementTypeMapArray<UInt> & mapping,
UInt spatial_dimension, const ID & id, const MemoryID & memory_id)
: MeshPartition(mesh, spatial_dimension, id, memory_id),
partition_mapping(&mapping) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::partitionate(UInt nb_part,
__attribute__((unused))
const EdgeLoadFunctor & edge_load_func,
const Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
tweakConnectivity(pairs);
nb_partitions = nb_part;
GhostType ghost_type = _not_ghost;
UInt spatial_dimension = mesh.getSpatialDimension();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(spatial_dimension, ghost_type, _ek_not_defined);
UInt linearized_el = 0;
UInt nb_elements = mesh.getNbElement(mesh.getSpatialDimension(), ghost_type);
auto * partition_list = new Int[nb_elements];
#if !defined(AKANTU_NDEBUG)
std::set<UInt> partitions;
#endif
for (; it != end; ++it) {
ElementType type = *it;
const Array<UInt> & partition_array =
(*partition_mapping)(type, ghost_type);
Array<UInt>::const_iterator<Vector<UInt>> p_it = partition_array.begin(1);
Array<UInt>::const_iterator<Vector<UInt>> p_end = partition_array.end(1);
AKANTU_DEBUG_ASSERT(UInt(p_end - p_it) ==
mesh.getNbElement(type, ghost_type),
"The partition mapping does not have the right number "
<< "of entries for type " << type
<< " and ghost type " << ghost_type << "."
<< " Tags=" << p_end - p_it
<< " Mesh=" << mesh.getNbElement(type, ghost_type));
for (; p_it != p_end; ++p_it, ++linearized_el) {
partition_list[linearized_el] = (*p_it)(0);
#if !defined(AKANTU_NDEBUG)
partitions.insert((*p_it)(0));
#endif
}
}
#if !defined(AKANTU_NDEBUG)
AKANTU_DEBUG_ASSERT(partitions.size() == nb_part,
"The number of real partitions does not match with the "
"number of asked partitions");
#endif
fillPartitionInformation(mesh, partition_list);
delete[] partition_list;
restoreConnectivity();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::reorder() { AKANTU_TO_IMPLEMENT(); }
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::setPartitionMapping(
const ElementTypeMapArray<UInt> & mapping) {
partition_mapping = &mapping;
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::setPartitionMappingFromMeshData(
const std::string & data_name) {
partition_mapping = &(mesh.getData<UInt>(data_name));
}
} // akantu
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
index d2405af38..efc3a394c 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
+++ b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
@@ -1,94 +1,93 @@
/**
* @file mesh_partition_mesh_data.hh
*
* @author Dana Christen <dana.christen@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief mesh partitioning based on data provided in the mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_PARTITION_MESH_DATA_HH__
#define __AKANTU_MESH_PARTITION_MESH_DATA_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_partition.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartitionMeshData : public MeshPartition {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshPartitionMeshData(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "MeshPartitionerMeshData",
const MemoryID & memory_id = 0);
MeshPartitionMeshData(const Mesh & mesh,
const ElementTypeMapArray<UInt> & mapping,
UInt spatial_dimension,
const ID & id = "MeshPartitionerMeshData",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void
partitionate(UInt nb_part,
const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
const Array<UInt> & pairs = Array<UInt>()) override;
void reorder() override;
void setPartitionMapping(const ElementTypeMapArray<UInt> & mapping);
void setPartitionMappingFromMeshData(const std::string & data_name);
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const ElementTypeMapArray<UInt> * partition_mapping;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_MESH_PARTITION_MESH_DATA_HH__ */
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc b/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
index 9d0cd28f1..f12652bff 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
+++ b/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
@@ -1,479 +1,479 @@
/**
* @file mesh_partition_scotch.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Jan 22 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief implementation of the MeshPartitionScotch class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh_partition_scotch.hh"
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "aka_static_if.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <cstdio>
#include <fstream>
/* -------------------------------------------------------------------------- */
#if !defined(AKANTU_USE_PTSCOTCH)
#ifndef AKANTU_SCOTCH_NO_EXTERN
extern "C" {
#endif // AKANTU_SCOTCH_NO_EXTERN
#include <scotch.h>
#ifndef AKANTU_SCOTCH_NO_EXTERN
}
#endif // AKANTU_SCOTCH_NO_EXTERN
#else // AKANTU_USE_PTSCOTCH
#include <ptscotch.h>
#endif // AKANTU_USE_PTSCOTCH
namespace akantu {
namespace {
constexpr int scotch_version = int(SCOTCH_VERSION);
}
/* -------------------------------------------------------------------------- */
MeshPartitionScotch::MeshPartitionScotch(const Mesh & mesh,
UInt spatial_dimension, const ID & id,
const MemoryID & memory_id)
: MeshPartition(mesh, spatial_dimension, id, memory_id) {
AKANTU_DEBUG_IN();
// check if the akantu types and Scotch one are consistent
static_assert(
sizeof(Int) == sizeof(SCOTCH_Num),
"The integer type of Akantu does not match the one from Scotch");
static_if(aka::bool_constant_v<scotch_version >= 6>)
.then([](auto && y) { SCOTCH_randomSeed(y); })
.else_([](auto && y) { srandom(y); })(
std::forward<UInt>(RandomGenerator<UInt>::seed()));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
static SCOTCH_Mesh * createMesh(const Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes = mesh.getNbNodes();
UInt total_nb_element = 0;
UInt nb_edge = 0;
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator end = mesh.lastType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
total_nb_element += nb_element;
nb_edge += nb_element * nb_nodes_per_element;
}
SCOTCH_Num vnodbas = 0;
SCOTCH_Num vnodnbr = nb_nodes;
SCOTCH_Num velmbas = vnodnbr;
SCOTCH_Num velmnbr = total_nb_element;
auto * verttab = new SCOTCH_Num[vnodnbr + velmnbr + 1];
SCOTCH_Num * vendtab = verttab + 1;
SCOTCH_Num * velotab = nullptr;
SCOTCH_Num * vnlotab = nullptr;
SCOTCH_Num * vlbltab = nullptr;
memset(verttab, 0, (vnodnbr + velmnbr + 1) * sizeof(SCOTCH_Num));
it = mesh.firstType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
if (Mesh::getSpatialDimension(type) != spatial_dimension)
continue;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
/// count number of occurrence of each node
for (UInt el = 0; el < nb_element; ++el) {
UInt * conn_val = connectivity.storage() + el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
verttab[*(conn_val++)]++;
}
}
}
/// convert the occurrence array in a csr one
for (UInt i = 1; i < nb_nodes; ++i)
verttab[i] += verttab[i - 1];
for (UInt i = nb_nodes; i > 0; --i)
verttab[i] = verttab[i - 1];
verttab[0] = 0;
/// rearrange element to get the node-element list
SCOTCH_Num edgenbr = verttab[vnodnbr] + nb_edge;
auto * edgetab = new SCOTCH_Num[edgenbr];
UInt linearized_el = 0;
it = mesh.firstType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
UInt * conn_val = connectivity.storage() + el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n)
edgetab[verttab[*(conn_val++)]++] = linearized_el + velmbas;
}
}
for (UInt i = nb_nodes; i > 0; --i)
verttab[i] = verttab[i - 1];
verttab[0] = 0;
SCOTCH_Num * verttab_tmp = verttab + vnodnbr + 1;
SCOTCH_Num * edgetab_tmp = edgetab + verttab[vnodnbr];
it = mesh.firstType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el) {
*verttab_tmp = *(verttab_tmp - 1) + nb_nodes_per_element;
verttab_tmp++;
UInt * conn = connectivity.storage() + el * nb_nodes_per_element;
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
*(edgetab_tmp++) = *(conn++) + vnodbas;
}
}
}
auto * meshptr = new SCOTCH_Mesh;
SCOTCH_meshInit(meshptr);
SCOTCH_meshBuild(meshptr, velmbas, vnodbas, velmnbr, vnodnbr, verttab,
vendtab, velotab, vnlotab, vlbltab, edgenbr, edgetab);
/// Check the mesh
AKANTU_DEBUG_ASSERT(SCOTCH_meshCheck(meshptr) == 0,
"Scotch mesh is not consistent");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save initial graph
FILE * fmesh = fopen("ScotchMesh.msh", "w");
SCOTCH_meshSave(meshptr, fmesh);
fclose(fmesh);
/// write geometry file
std::ofstream fgeominit;
fgeominit.open("ScotchMesh.xyz");
fgeominit << spatial_dimension << std::endl << nb_nodes << std::endl;
const Array<Real> & nodes = mesh.getNodes();
Real * nodes_val = nodes.storage();
for (UInt i = 0; i < nb_nodes; ++i) {
fgeominit << i << " ";
for (UInt s = 0; s < spatial_dimension; ++s)
fgeominit << *(nodes_val++) << " ";
fgeominit << std::endl;
;
}
fgeominit.close();
}
#endif
AKANTU_DEBUG_OUT();
return meshptr;
}
/* -------------------------------------------------------------------------- */
static void destroyMesh(SCOTCH_Mesh * meshptr) {
AKANTU_DEBUG_IN();
SCOTCH_Num velmbas, vnodbas, vnodnbr, velmnbr, *verttab, *vendtab, *velotab,
*vnlotab, *vlbltab, edgenbr, *edgetab, degrptr;
SCOTCH_meshData(meshptr, &velmbas, &vnodbas, &velmnbr, &vnodnbr, &verttab,
&vendtab, &velotab, &vnlotab, &vlbltab, &edgenbr, &edgetab,
°rptr);
delete[] verttab;
delete[] edgetab;
SCOTCH_meshExit(meshptr);
delete meshptr;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionScotch::partitionate(UInt nb_part,
const EdgeLoadFunctor & edge_load_func,
const Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
nb_partitions = nb_part;
tweakConnectivity(pairs);
AKANTU_DEBUG_INFO("Partitioning the mesh " << mesh.getID() << " in "
<< nb_part << " parts.");
Array<Int> dxadj;
Array<Int> dadjncy;
Array<Int> edge_loads;
buildDualGraph(dxadj, dadjncy, edge_loads, edge_load_func);
/// variables that will hold our structures in scotch format
SCOTCH_Graph scotch_graph;
SCOTCH_Strat scotch_strat;
/// description number and arrays for struct mesh for scotch
SCOTCH_Num baseval = 0; // base numbering for element and
// nodes (0 -> C , 1 -> fortran)
SCOTCH_Num vertnbr = dxadj.size() - 1; // number of vertexes
SCOTCH_Num * parttab; // array of partitions
SCOTCH_Num edgenbr = dxadj(vertnbr); // twice the number of "edges"
//(an "edge" bounds two nodes)
SCOTCH_Num * verttab = dxadj.storage(); // array of start indices in edgetab
SCOTCH_Num * vendtab = nullptr; // array of after-last indices in edgetab
SCOTCH_Num * velotab = nullptr; // integer load associated with
// every vertex ( optional )
SCOTCH_Num * edlotab = edge_loads.storage(); // integer load associated with
// every edge ( optional )
SCOTCH_Num * edgetab = dadjncy.storage(); // adjacency array of every vertex
SCOTCH_Num * vlbltab = nullptr; // vertex label array (optional)
/// Allocate space for Scotch arrays
parttab = new SCOTCH_Num[vertnbr];
/// Initialize the strategy structure
SCOTCH_stratInit(&scotch_strat);
/// Initialize the graph structure
SCOTCH_graphInit(&scotch_graph);
/// Build the graph from the adjacency arrays
SCOTCH_graphBuild(&scotch_graph, baseval, vertnbr, verttab, vendtab, velotab,
vlbltab, edgenbr, edgetab, edlotab);
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save initial graph
FILE * fgraphinit = fopen("GraphIniFile.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraphinit);
fclose(fgraphinit);
/// write geometry file
std::ofstream fgeominit;
fgeominit.open("GeomIniFile.xyz");
fgeominit << spatial_dimension << std::endl << vertnbr << std::endl;
const Array<Real> & nodes = mesh.getNodes();
Mesh::type_iterator f_it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_not_defined);
Mesh::type_iterator f_end =
mesh.lastType(spatial_dimension, _not_ghost, _ek_not_defined);
auto nodes_it = nodes.begin(spatial_dimension);
UInt out_linerized_el = 0;
for (; f_it != f_end; ++f_it) {
ElementType type = *f_it;
UInt nb_element = mesh.getNbElement(*f_it);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Vector<Real> mid(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mid.set(0.);
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity.storage()[nb_nodes_per_element * el + n];
mid += Vector<Real>(nodes_it[node]);
}
mid /= nb_nodes_per_element;
fgeominit << out_linerized_el++ << " ";
for (UInt s = 0; s < spatial_dimension; ++s)
fgeominit << mid[s] << " ";
fgeominit << std::endl;
;
}
}
fgeominit.close();
}
#endif
/// Check the graph
AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
"Graph to partition is not consistent");
/// Partition the mesh
SCOTCH_graphPart(&scotch_graph, nb_part, &scotch_strat, parttab);
/// Check the graph
AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
"Partitioned graph is not consistent");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save the partitioned graph
FILE * fgraph = fopen("GraphFile.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraph);
fclose(fgraph);
/// save the partition map
std::ofstream fmap;
fmap.open("MapFile.map");
fmap << vertnbr << std::endl;
for (Int i = 0; i < vertnbr; i++)
fmap << i << " " << parttab[i] << std::endl;
fmap.close();
}
#endif
/// free the scotch data structures
SCOTCH_stratExit(&scotch_strat);
SCOTCH_graphFree(&scotch_graph);
SCOTCH_graphExit(&scotch_graph);
fillPartitionInformation(mesh, parttab);
delete[] parttab;
restoreConnectivity();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionScotch::reorder() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Reordering the mesh " << mesh.getID());
SCOTCH_Mesh * scotch_mesh = createMesh(mesh);
UInt nb_nodes = mesh.getNbNodes();
SCOTCH_Strat scotch_strat;
// SCOTCH_Ordering scotch_order;
auto * permtab = new SCOTCH_Num[nb_nodes];
SCOTCH_Num * peritab = nullptr;
SCOTCH_Num cblknbr = 0;
SCOTCH_Num * rangtab = nullptr;
SCOTCH_Num * treetab = nullptr;
/// Initialize the strategy structure
SCOTCH_stratInit(&scotch_strat);
SCOTCH_Graph scotch_graph;
SCOTCH_graphInit(&scotch_graph);
SCOTCH_meshGraph(scotch_mesh, &scotch_graph);
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
FILE * fgraphinit = fopen("ScotchMesh.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraphinit);
fclose(fgraphinit);
}
#endif
/// Check the graph
// AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
// "Mesh to Graph is not consistent");
SCOTCH_graphOrder(&scotch_graph, &scotch_strat, permtab, peritab, &cblknbr,
rangtab, treetab);
SCOTCH_graphExit(&scotch_graph);
SCOTCH_stratExit(&scotch_strat);
destroyMesh(scotch_mesh);
/// Renumbering
UInt spatial_dimension = mesh.getSpatialDimension();
for (UInt g = _not_ghost; g <= _ghost; ++g) {
auto gt = (GhostType)g;
Mesh::type_iterator it = mesh.firstType(_all_dimensions, gt);
Mesh::type_iterator end = mesh.lastType(_all_dimensions, gt);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type, gt);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, gt);
UInt * conn = connectivity.storage();
for (UInt el = 0; el < nb_element * nb_nodes_per_element; ++el, ++conn) {
*conn = permtab[*conn];
}
}
}
/// \todo think of a in-place way to do it
auto * new_coordinates = new Real[spatial_dimension * nb_nodes];
Real * old_coordinates = mesh.getNodes().storage();
for (UInt i = 0; i < nb_nodes; ++i) {
memcpy(new_coordinates + permtab[i] * spatial_dimension,
old_coordinates + i * spatial_dimension,
spatial_dimension * sizeof(Real));
}
memcpy(old_coordinates, new_coordinates,
nb_nodes * spatial_dimension * sizeof(Real));
delete[] new_coordinates;
delete[] permtab;
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh b/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
index 2dc3e385b..abe747b96 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
+++ b/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
@@ -1,78 +1,77 @@
/**
* @file mesh_partition_scotch.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief mesh partitioning based on libScotch
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_PARTITION_SCOTCH_HH__
#define __AKANTU_MESH_PARTITION_SCOTCH_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_partition.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartitionScotch : public MeshPartition {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshPartitionScotch(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "mesh_partition_scotch",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void
partitionate(UInt nb_part,
const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
const Array<UInt> & pairs = Array<UInt>()) override;
void reorder() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // akantu
#endif /* __AKANTU_MESH_PARTITION_SCOTCH_HH__ */
diff --git a/src/mesh_utils/mesh_utils.cc b/src/mesh_utils/mesh_utils.cc
index 7883e4a37..cc68fe58f 100644
--- a/src/mesh_utils/mesh_utils.cc
+++ b/src/mesh_utils/mesh_utils.cc
@@ -1,2091 +1,2090 @@
/**
* @file mesh_utils.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Aug 20 2010
- * @date last modification: Fri Jan 22 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief All mesh utils necessary for various tasks
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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 "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#include <limits>
#include <numeric>
#include <queue>
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2Elements(const Mesh & mesh,
CSR<Element> & node_to_elem,
UInt spatial_dimension) {
AKANTU_DEBUG_IN();
if (spatial_dimension == _all_dimensions)
spatial_dimension = mesh.getSpatialDimension();
/// count number of occurrence of each node
UInt nb_nodes = mesh.getNbNodes();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
// AKANTU_DEBUG_ASSERT(
// mesh.firstType(spatial_dimension) != mesh.lastType(spatial_dimension),
// "Some elements must be found in right dimension to compute facets!");
for (auto && ghost_type : ghost_types) {
for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
auto conn_it = mesh.getConnectivity(type, ghost_type)
.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 (auto && ghost_type : ghost_types) {
e.ghost_type = ghost_type;
for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
e.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
auto conn_it = mesh.getConnectivity(type, ghost_type)
.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();
}
/* -------------------------------------------------------------------------- */
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).size();
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
/// count number of occurrence of each node
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n)
++node_to_elem.rowOffset(conn_val[el_offset + n]);
}
/// convert the occurrence array in a csr one
node_to_elem.countToCSR();
node_to_elem.resizeCols();
node_to_elem.beginInsertions();
/// save the element index in the node-element list
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
node_to_elem.insertInRow(conn_val[el_offset + n], el);
}
}
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacets(Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (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) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
buildAllFacets(mesh, mesh_facets, spatial_dimension, to_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt from_dimension, UInt to_dimension) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
mesh_facets.isMeshFacets(),
"The mesh_facets should be initialized with initMeshFacets");
/// generate facets
buildFacetsDimension(mesh, mesh_facets, false, from_dimension);
/// copy nodes type
MeshAccessor mesh_accessor_facets(mesh_facets);
mesh_accessor_facets.getNodesType().copy(mesh.getNodesType());
/// sort facets and generate sub-facets
for (UInt i = from_dimension - 1; i > to_dimension; --i) {
buildFacetsDimension(mesh_facets, mesh_facets, false, i);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacetsDimension(const Mesh & mesh, Mesh & mesh_facets,
bool boundary_only, UInt dimension) {
AKANTU_DEBUG_IN();
// save the current parent of mesh_facets and set it temporarly to mesh since
// mesh is the one containing the elements for which mesh_facets has the
// sub-elements
// example: if the function is called with mesh = mesh_facets
const Mesh * mesh_facets_parent = nullptr;
try {
mesh_facets_parent = &mesh_facets.getMeshParent();
} catch (...) {
}
mesh_facets.defineMeshParent(mesh);
MeshAccessor mesh_accessor(mesh_facets);
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<Real> & mesh_facets_nodes = mesh_facets.getNodes();
const auto mesh_facets_nodes_it = mesh_facets_nodes.begin(spatial_dimension);
CSR<Element> node_to_elem;
buildNode2Elements(mesh, node_to_elem, dimension);
Array<UInt> counter;
std::vector<Element> connected_elements;
// init the SubelementToElement data to improve performance
for (auto && ghost_type : ghost_types) {
for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
mesh_accessor.getSubelementToElement(type, ghost_type);
auto facet_types = mesh.getAllFacetTypes(type);
for (auto && ft : arange(facet_types.size())) {
auto facet_type = facet_types(ft);
mesh_accessor.getElementToSubelement(facet_type, ghost_type);
mesh_accessor.getConnectivity(facet_type, ghost_type);
}
}
}
const ElementSynchronizer * synchronizer = nullptr;
if (mesh.isDistributed()) {
synchronizer = &(mesh.getElementSynchronizer());
}
Element current_element;
for (auto && ghost_type : ghost_types) {
GhostType facet_ghost_type = ghost_type;
current_element.ghost_type = ghost_type;
for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
auto facet_types = mesh.getAllFacetTypes(type);
current_element.type = type;
for (auto && ft : arange(facet_types.size())) {
auto facet_type = facet_types(ft);
auto nb_element = mesh.getNbElement(type, ghost_type);
auto element_to_subelement =
&mesh_facets.getElementToSubelement(facet_type, ghost_type);
auto connectivity_facets =
&mesh_facets.getConnectivity(facet_type, ghost_type);
auto nb_facet_per_element = mesh.getNbFacetsPerElement(type, ft);
const auto & element_connectivity =
mesh.getConnectivity(type, ghost_type);
Matrix<const UInt> facet_local_connectivity(
mesh.getFacetLocalConnectivity(type, ft));
auto nb_nodes_per_facet = connectivity_facets->getNbComponent();
Vector<UInt> facet(nb_nodes_per_facet);
for (UInt el = 0; el < nb_element; ++el) {
current_element.element = el;
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
UInt local_el = 0;
auto first_node_elements = node_to_elem.begin(facet(0));
auto first_node_elements_end = node_to_elem.end(facet(0));
for (; first_node_elements != first_node_elements_end;
++first_node_elements, ++local_el) {
for (UInt n = 1; n < nb_nodes_per_facet; ++n) {
auto node_elements_begin = node_to_elem.begin(facet(n));
auto 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 (not(counter(el_f) == nb_nodes_per_facet - 1))
continue;
++nb_element_connected_to_facet;
minimum_el = std::min(minimum_el, real_el);
connected_elements.push_back(real_el);
}
if (minimum_el != current_element)
continue;
bool full_ghost_facet = false;
UInt n = 0;
while (n < nb_nodes_per_facet && mesh.isPureGhostNode(facet(n)))
++n;
if (n == nb_nodes_per_facet)
full_ghost_facet = true;
if (full_ghost_facet)
continue;
if (boundary_only and nb_element_connected_to_facet != 1)
continue;
std::vector<Element> elements;
// build elements_on_facets: linearized_el must come first
// in order to store the facet in the correct direction
// and avoid to invert the sign in the normal computation
elements.push_back(current_element);
if (nb_element_connected_to_facet == 1) { /// boundary facet
elements.push_back(ElementNull);
} else if (nb_element_connected_to_facet == 2) { /// internal facet
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] and
(gt[0] == _not_ghost or gt[1] == _not_ghost)) {
UInt prank[2];
for (UInt el = 0; el < 2; ++el) {
prank[el] = synchronizer->getRank(connected_elements[el]);
}
// ugly trick from Marco detected :P
bool ghost_one = (gt[0] != _ghost);
if (prank[ghost_one] > prank[!ghost_one])
facet_ghost_type = _not_ghost;
else
facet_ghost_type = _ghost;
connectivity_facets =
&mesh_facets.getConnectivity(facet_type, facet_ghost_type);
element_to_subelement = &mesh_facets.getElementToSubelement(
facet_type, facet_ghost_type);
}
} else { /// facet of facet
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->size() - 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)
continue;
Array<Element> & subelement_to_element =
mesh_facets.getSubelementToElement(loc_el.type,
loc_el.ghost_type);
UInt nb_facet_per_loc_element =
subelement_to_element.getNbComponent();
for (UInt f_in = 0; f_in < nb_facet_per_loc_element; ++f_in) {
auto & el = subelement_to_element(loc_el.element, f_in);
if (el.type != _not_defined)
continue;
el.type = facet_type;
el.element = current_facet;
el.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_accessor.getConnectivity(facet_type, facet_ghost_type);
element_to_subelement = &mesh_accessor.getElementToSubelement(
facet_type, facet_ghost_type);
}
}
}
}
}
}
// restore the parent of mesh_facet
if (mesh_facets_parent)
mesh_facets.defineMeshParent(*mesh_facets_parent);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberMeshNodes(Mesh & mesh,
Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type,
Array<UInt> & old_nodes_numbers) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
std::map<UInt, UInt> renumbering_map;
for (UInt i = 0; i < old_nodes_numbers.size(); ++i) {
renumbering_map[old_nodes_numbers(i)] = i;
}
/// renumber the nodes
renumberNodesInConnectivity(local_connectivities,
(nb_local_element + nb_ghost_element) *
nb_nodes_per_element,
renumbering_map);
old_nodes_numbers.resize(renumbering_map.size());
for (auto & renumber_pair : renumbering_map) {
old_nodes_numbers(renumber_pair.second) = renumber_pair.first;
}
renumbering_map.clear();
MeshAccessor mesh_accessor(mesh);
/// copy the renumbered connectivity to the right place
auto & local_conn = mesh_accessor.getConnectivity(type);
local_conn.resize(nb_local_element);
memcpy(local_conn.storage(), local_connectivities.storage(),
nb_local_element * nb_nodes_per_element * sizeof(UInt));
auto & ghost_conn = mesh_accessor.getConnectivity(type, _ghost);
ghost_conn.resize(nb_ghost_element);
std::memcpy(ghost_conn.storage(),
local_connectivities.storage() +
nb_local_element * nb_nodes_per_element,
nb_ghost_element * nb_nodes_per_element * sizeof(UInt));
auto & ghost_counter = mesh_accessor.getGhostsCounters(type, _ghost);
ghost_counter.resize(nb_ghost_element, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberNodesInConnectivity(
Array<UInt> & list_nodes, UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map) {
AKANTU_DEBUG_IN();
UInt * connectivity = list_nodes.storage();
UInt new_node_num = renumbering_map.size();
for (UInt n = 0; n < nb_nodes; ++n, ++connectivity) {
UInt & node = *connectivity;
auto it = renumbering_map.find(node);
if (it == renumbering_map.end()) {
UInt old_node = node;
renumbering_map[old_node] = new_node_num;
node = new_node_num;
++new_node_num;
} else {
node = it->second;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::purifyMesh(Mesh & mesh) {
AKANTU_DEBUG_IN();
std::map<UInt, UInt> renumbering_map;
RemovedNodesEvent remove_nodes(mesh);
Array<UInt> & nodes_removed = remove_nodes.getList();
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
auto 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);
Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_element(connectivity.size());
renumberNodesInConnectivity(
connectivity, nb_element * nb_nodes_per_element, renumbering_map);
}
}
Array<UInt> & new_numbering = remove_nodes.getNewNumbering();
std::fill(new_numbering.begin(), new_numbering.end(), UInt(-1));
auto it = renumbering_map.begin();
auto end = renumbering_map.end();
for (; it != end; ++it) {
new_numbering(it->first) = it->second;
}
for (UInt i = 0; i < new_numbering.size(); ++i) {
if (new_numbering(i) == UInt(-1))
nodes_removed.push_back(i);
}
mesh.sendEvent(remove_nodes);
AKANTU_DEBUG_OUT();
}
#if defined(AKANTU_COHESIVE_ELEMENT)
/* -------------------------------------------------------------------------- */
UInt MeshUtils::insertCohesiveElements(
Mesh & mesh, Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes, Array<Element> & new_elements,
bool only_double_facets) {
UInt spatial_dimension = mesh.getSpatialDimension();
UInt elements_to_insert = 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);
}
}
if (!only_double_facets)
updateCohesiveData(mesh, mesh_facets, new_elements);
}
return elements_to_insert;
}
#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.size();
UInt new_nb_nodes = old_nb_nodes + old_nodes.size();
UInt old_nb_doubled_nodes = doubled_nodes.size();
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.size();
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 = nullptr;
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.size();
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();
}
/* -------------------------------------------------------------------------- */
UInt MeshUtils::updateFacetToDouble(
Mesh & mesh_facets, const ElementTypeMapArray<bool> & facet_insertion) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
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 = nullptr;
for (UInt f = 0; f < f_insertion.size(); ++f) {
if (f_insertion(f) == false)
continue;
++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.size() - 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 nb_facets_to_double;
}
/* -------------------------------------------------------------------------- */
void MeshUtils::resetFacetToDouble(Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
for (UInt g = _not_ghost; g <= _ghost; ++g) {
auto 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.size();
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 = nullptr;
Array<UInt> * sf_to_double = nullptr;
Array<std::vector<Element>> * sf_to_subfacet_double = nullptr;
Array<std::vector<Element>> * f_to_subfacet_double = nullptr;
Array<std::vector<Element>> * el_to_subfacet_double = nullptr;
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 = nullptr;
UInt old_nb_facet = subfacet_to_facet.size() - 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 = nullptr;
/// 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;
MeshAccessor mesh_facets_accessor(mesh_facets);
for (auto gt_facet : ghost_types) {
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.size();
if (nb_facet_to_double == 0)
continue;
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
auto & facet_to_coh_element =
mesh_facets_accessor.getSubelementToElement(type_cohesive, gt_facet);
auto & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
auto & conn_cohesive = mesh.getConnectivity(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.size();
UInt new_nb_cohesive_elements = conn_cohesive.size() + nb_facet_to_double;
UInt old_nb_facet = element_to_facet.size() - 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.size();
new_elements.resize(new_elements_old_size + nb_facet_to_double);
Element c_element{type_cohesive, 0, gt_facet};
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.size();
UInt old_nb_facet = element_to_facet.size() - nb_facet_to_double;
UInt new_nb_facet = element_to_facet.size();
UInt old_nb_nodes = position.size();
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.size();
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.size();
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 = nullptr;
Array<std::vector<Element>> * f_to_subfacet_double = nullptr;
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.size();
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.size();
/// update subfacet_to_facet vector
ElementType type_facet = _not_defined;
GhostType gt_facet = _casper;
Array<Element> * subfacet_to_facet = nullptr;
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 = nullptr;
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.size();
Array<std::vector<Element>> & facet_to_subfacet =
mesh_facets.getElementToSubelement(type_subfacet, gt_subfacet);
Array<std::vector<Element>> * facet_to_subfacet_double = nullptr;
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.size();
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.size();
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.size();
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.size();
/// 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 = nullptr;
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("global_connectivity_tmp",
mesh_facets.getID(),
mesh_facets.getMemoryID());
global_connectivity_tmp.initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_ghost_type = gt_facet, _with_nb_nodes_per_element = true,
_with_nb_element = true);
mesh_facets.getGlobalConnectivity(global_connectivity_tmp);
/// loop on every facet
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
auto & connectivity = mesh_facets.getConnectivity(type_facet, gt_facet);
const auto & g_connectivity = global_connectivity(type_facet, gt_facet);
auto & el_to_f = mesh_facets.getElementToSubelement(type_facet, gt_facet);
auto & 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.size();
UInt nb_nodes_per_P1_facet =
Mesh::getNbNodesPerElement(Mesh::getP1ElementType(type_facet));
auto & global_conn_tmp = global_connectivity_tmp(type_facet, gt_facet);
auto conn_it = connectivity.begin(nb_nodes_per_facet);
auto gconn_tmp_it = global_conn_tmp.begin(nb_nodes_per_facet);
auto conn_glob_it = g_connectivity.begin(nb_nodes_per_facet);
auto subf_to_f = subfacet_to_facet.begin(nb_subfacet_per_facet);
auto * conn_tmp_pointer = new UInt[nb_nodes_per_facet];
Vector<UInt> conn_tmp(conn_tmp_pointer, nb_nodes_per_facet);
Element el_tmp;
auto * 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.getMemoryID());
barycenters.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = _all_dimensions);
// mesh.initElementTypeMapArray(barycenters, spatial_dimension,
// _all_dimensions);
Element element;
for (auto ghost_type : ghost_types) {
element.ghost_type = ghost_type;
for (auto & type : mesh.elementTypes(_all_dimensions, ghost_type)) {
element.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<Real> & barycenters_arr = barycenters(type, ghost_type);
barycenters_arr.resize(nb_element);
auto bary = barycenters_arr.begin(spatial_dimension);
auto bary_end = barycenters_arr.end(spatial_dimension);
for (UInt el = 0; bary != bary_end; ++bary, ++el) {
element.element = el;
mesh.getBarycenter(element, *bary);
}
}
}
MeshAccessor mesh_accessor(mesh);
for (Int sp(spatial_dimension); sp >= 1; --sp) {
if (mesh.getNbElement(sp) == 0)
continue;
for (auto ghost_type : ghost_types) {
for (auto & type : mesh.elementTypes(sp, ghost_type)) {
mesh_accessor.getSubelementToElement(type, ghost_type)
.resize(mesh.getNbElement(type, ghost_type));
mesh_accessor.getSubelementToElement(type, ghost_type).clear();
}
for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
mesh_accessor.getElementToSubelement(type, ghost_type)
.resize(mesh.getNbElement(type, ghost_type));
mesh.getElementToSubelement(type, ghost_type).clear();
}
}
CSR<Element> nodes_to_elements;
buildNode2Elements(mesh, nodes_to_elements, sp);
Element facet_element;
for (auto ghost_type : ghost_types) {
facet_element.ghost_type = ghost_type;
for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
facet_element.type = type;
auto & element_to_subelement =
mesh.getElementToSubelement(type, ghost_type);
const auto & connectivity = mesh.getConnectivity(type, ghost_type);
auto fit = connectivity.begin(mesh.getNbNodesPerElement(type));
auto fend = connectivity.end(mesh.getNbNodesPerElement(type));
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(type));
for (UInt n(0); n < nb_nodes_per_facet; ++n) {
auto eit = nodes_to_elements.begin(facet(n));
auto eend = nodes_to_elements.end(facet(n));
for (; eit != eend; ++eit) {
auto & elem = *eit;
auto 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;
auto cit = element_seen_counter.begin();
auto cend = element_seen_counter.end();
for (; cit != cend; ++cit) {
if (cit->second == nb_nodes_per_facet)
connected_elements.push_back(cit->first);
}
auto ceit = connected_elements.begin();
auto 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_accessor.getSubelementToElement(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 = nullptr;
const Array<UInt> * sf_connectivity = nullptr;
const Array<Element> * facet_to_element = nullptr;
const Array<Element> * subfacet_to_facet = nullptr;
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 = nullptr;
const Element * opposing_el = nullptr;
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;
}
/* -------------------------------------------------------------------------- */
UInt MeshUtils::updateLocalMasterGlobalConnectivity(Mesh & mesh,
UInt local_nb_new_nodes) {
const auto & comm = mesh.getCommunicator();
Int rank = comm.whoAmI();
Int nb_proc = comm.getNbProc();
if (nb_proc == 1)
return local_nb_new_nodes;
/// resize global ids array
Array<UInt> & nodes_global_ids = mesh.getGlobalNodesIds();
UInt old_nb_nodes = mesh.getNbNodes() - local_nb_new_nodes;
nodes_global_ids.resize(mesh.getNbNodes());
/// compute the number of global nodes based on the number of old nodes
Vector<UInt> old_local_master_nodes(nb_proc);
for (UInt n = 0; n < old_nb_nodes; ++n)
if (mesh.isLocalOrMasterNode(n))
++old_local_master_nodes(rank);
comm.allGather(old_local_master_nodes);
UInt old_global_nodes =
std::accumulate(old_local_master_nodes.storage(),
old_local_master_nodes.storage() + nb_proc, 0);
/// compute amount of local or master doubled nodes
Vector<UInt> local_master_nodes(nb_proc);
for (UInt n = old_nb_nodes; n < mesh.getNbNodes(); ++n)
if (mesh.isLocalOrMasterNode(n))
++local_master_nodes(rank);
comm.allGather(local_master_nodes);
/// update global number of nodes
UInt total_nb_new_nodes = std::accumulate(
local_master_nodes.storage(), local_master_nodes.storage() + nb_proc, 0);
if (total_nb_new_nodes == 0)
return 0;
/// set global ids of local and master nodes
UInt starting_index =
std::accumulate(local_master_nodes.storage(),
local_master_nodes.storage() + rank, old_global_nodes);
for (UInt n = old_nb_nodes; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n)) {
nodes_global_ids(n) = starting_index;
++starting_index;
}
}
MeshAccessor mesh_accessor(mesh);
mesh_accessor.setNbGlobalNodes(old_global_nodes + total_nb_new_nodes);
return total_nb_new_nodes;
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateElementalConnectivity(
Mesh & mesh, UInt old_node, UInt new_node,
const std::vector<Element> & element_list,
__attribute__((unused)) const std::vector<Element> * facet_list) {
AKANTU_DEBUG_IN();
ElementType el_type = _not_defined;
GhostType gt_type = _casper;
Array<UInt> * conn_elem = nullptr;
#if defined(AKANTU_COHESIVE_ELEMENT)
const Array<Element> * cohesive_facets = nullptr;
#endif
UInt nb_nodes_per_element = 0;
UInt * n_update = nullptr;
for (UInt el = 0; el < element_list.size(); ++el) {
const Element & elem = element_list[el];
if (elem.type == _not_defined)
continue;
if (elem.type != el_type || elem.ghost_type != gt_type) {
el_type = elem.type;
gt_type = elem.ghost_type;
conn_elem = &mesh.getConnectivity(el_type, gt_type);
nb_nodes_per_element = conn_elem->getNbComponent();
#if defined(AKANTU_COHESIVE_ELEMENT)
if (elem.kind() == _ek_cohesive)
cohesive_facets =
&mesh.getMeshFacets().getSubelementToElement(el_type, gt_type);
#endif
}
#if defined(AKANTU_COHESIVE_ELEMENT)
if (elem.kind() == _ek_cohesive) {
AKANTU_DEBUG_ASSERT(
facet_list != nullptr,
"Provide a facet list in order to update cohesive elements");
/// loop over cohesive element's facets
for (UInt f = 0, n = 0; f < 2; ++f, n += nb_nodes_per_element / 2) {
const Element & facet = (*cohesive_facets)(elem.element, f);
/// skip facets if not present in the list
if (std::find(facet_list->begin(), facet_list->end(), facet) ==
facet_list->end())
continue;
n_update = std::find(
conn_elem->storage() + elem.element * nb_nodes_per_element + n,
conn_elem->storage() + elem.element * nb_nodes_per_element + n +
nb_nodes_per_element / 2,
old_node);
AKANTU_DEBUG_ASSERT(n_update !=
conn_elem->storage() +
elem.element * nb_nodes_per_element + n +
nb_nodes_per_element / 2,
"Node not found in current element");
/// update connectivity
*n_update = new_node;
}
} else {
#endif
n_update =
std::find(conn_elem->storage() + elem.element * nb_nodes_per_element,
conn_elem->storage() + elem.element * nb_nodes_per_element +
nb_nodes_per_element,
old_node);
AKANTU_DEBUG_ASSERT(n_update !=
conn_elem->storage() +
elem.element * nb_nodes_per_element +
nb_nodes_per_element,
"Node not found in current element");
/// update connectivity
*n_update = new_node;
#if defined(AKANTU_COHESIVE_ELEMENT)
}
#endif
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/mesh_utils.hh b/src/mesh_utils/mesh_utils.hh
index f7af08129..51932d972 100644
--- a/src/mesh_utils/mesh_utils.hh
+++ b/src/mesh_utils/mesh_utils.hh
@@ -1,244 +1,243 @@
/**
* @file mesh_utils.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Oct 02 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief All mesh utils necessary for various tasks
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_UTILS_HH__
#define __AKANTU_MESH_UTILS_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshUtils {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build a CSR<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 of a given spatial dimension
static void buildNode2Elements(const Mesh & mesh, CSR<Element> & node_to_elem,
UInt spatial_dimension = _all_dimensions);
/// build a CSR<UInt> that contains for each node the number of
/// the connected elements of a given ElementType
static void
buildNode2ElementsElementTypeMap(const Mesh & mesh, CSR<UInt> & node_to_elem,
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);
/// build all the facets elements: boundary and internals and store them in
/// the mesh_facets
static void buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt to_dimension = 0);
/// build facets for a given spatial dimension
static void buildFacetsDimension(const Mesh & mesh, Mesh & mesh_facets,
bool boundary_only, UInt dimension);
/// take the local_connectivity array as the array of local and ghost
/// connectivity, renumber the nodes and set the connectivity of the mesh
static void renumberMeshNodes(Mesh & mesh, Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type, Array<UInt> & old_nodes);
/// compute pbc pair for a given direction
static void computePBCMap(const Mesh & mymesh, 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<ID, ID> & surface_pair,
std::map<UInt, UInt> & pbc_pair);
/// 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
/// @return number of facets that have been doubled
static UInt
insertCohesiveElements(Mesh & mesh, Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes,
Array<Element> & new_elements,
bool only_double_facets);
#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 = nullptr);
/// 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);
/// associate a node type to each segment in the mesh
// static void buildSegmentToNodeType(const Mesh & mesh, Mesh & mesh_facets);
/// update local and master global connectivity when new nodes are added
static UInt updateLocalMasterGlobalConnectivity(Mesh & mesh,
UInt old_nb_nodes);
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(Array<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
/// 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 = nullptr);
/// 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"
} // akantu
#endif /* __AKANTU_MESH_UTILS_HH__ */
diff --git a/src/mesh_utils/mesh_utils_distribution.cc b/src/mesh_utils/mesh_utils_distribution.cc
index c6e00425b..416eb5c45 100644
--- a/src/mesh_utils/mesh_utils_distribution.cc
+++ b/src/mesh_utils/mesh_utils_distribution.cc
@@ -1,172 +1,174 @@
/**
* @file mesh_utils_distribution.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Sun Oct 2 19:23:15 2016
+ * @date creation: Tue Nov 08 2016
+ * @date last modification: Tue Nov 07 2017
*
* @brief Implementation of the methods of mesh utils distribute
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh_utils_distribution.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "mesh_partition.hh"
#include "mesh_utils.hh"
#include "node_info_per_processor.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace MeshUtilsDistribution {
/* ------------------------------------------------------------------------ */
void distributeMeshCentralized(Mesh & mesh, UInt,
const MeshPartition & partition) {
MeshAccessor mesh_accessor(mesh);
ElementSynchronizer & element_synchronizer =
mesh_accessor.getElementSynchronizer();
NodeSynchronizer & node_synchronizer = mesh_accessor.getNodeSynchronizer();
const Communicator & comm = element_synchronizer.getCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
mesh_accessor.setNbGlobalNodes(mesh.getNbNodes());
auto & gids = mesh_accessor.getNodesGlobalIds();
if (nb_proc == 1)
return;
gids.resize(0);
mesh.synchronizeGroupNames();
AKANTU_DEBUG_ASSERT(
partition.getNbPartition() == nb_proc,
"The number of partition does not match the number of processors: "
<< partition.getNbPartition() << " != " << nb_proc);
/**
* connectivity and communications scheme construction
*/
UInt count = 0;
/* --- MAIN LOOP ON TYPES --- */
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
/// \todo change this ugly way to avoid a problem if an element
/// type is present in the mesh but not in the partitions
try {
partition.getPartition(type, _not_ghost);
} catch (...) {
continue;
}
MasterElementInfoPerProc proc_infos(element_synchronizer, count, my_rank,
type, partition);
proc_infos.synchronizeConnectivities();
proc_infos.synchronizePartitions();
proc_infos.synchronizeTags();
proc_infos.synchronizeGroups();
++count;
}
{ /// Ending the synchronization of elements by sending a stop message
MasterElementInfoPerProc proc_infos(element_synchronizer, count, my_rank,
_not_defined, partition);
++count;
}
/**
* Nodes synchronization
*/
MasterNodeInfoPerProc node_proc_infos(node_synchronizer, count, my_rank);
node_proc_infos.synchronizeNodes();
node_proc_infos.synchronizeTypes();
node_proc_infos.synchronizeGroups();
MeshUtils::fillElementToSubElementsData(mesh);
mesh_accessor.setDistributed();
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------ */
void distributeMeshCentralized(Mesh & mesh, UInt root) {
MeshAccessor mesh_accessor(mesh);
ElementSynchronizer & element_synchronizer =
mesh_accessor.getElementSynchronizer();
NodeSynchronizer & node_synchronizer = mesh_accessor.getNodeSynchronizer();
const Communicator & comm = element_synchronizer.getCommunicator();
UInt nb_proc = comm.getNbProc();
mesh_accessor.getNodesGlobalIds().resize(0);
if (nb_proc == 1)
return;
mesh.synchronizeGroupNames();
/**
* connectivity and communications scheme construction on distant
* processors
*/
UInt count = 0;
bool need_synchronize = true;
do {
/* --------<<<<-SIZE--------------------------------------------------- */
SlaveElementInfoPerProc proc_infos(element_synchronizer, count, root);
need_synchronize = proc_infos.needSynchronize();
if (need_synchronize) {
proc_infos.synchronizeConnectivities();
proc_infos.synchronizePartitions();
proc_infos.synchronizeTags();
proc_infos.synchronizeGroups();
}
++count;
} while (need_synchronize);
/**
* Nodes synchronization
*/
SlaveNodeInfoPerProc node_proc_infos(node_synchronizer, count, root);
node_proc_infos.synchronizeNodes();
node_proc_infos.synchronizeTypes();
node_proc_infos.synchronizeGroups();
MeshUtils::fillElementToSubElementsData(mesh);
mesh_accessor.setDistributed();
}
} // namespace MeshUtilsDistribution
} // namespace akantu
diff --git a/src/mesh_utils/mesh_utils_distribution.hh b/src/mesh_utils/mesh_utils_distribution.hh
index e498a6ae7..82112b2dc 100644
--- a/src/mesh_utils/mesh_utils_distribution.hh
+++ b/src/mesh_utils/mesh_utils_distribution.hh
@@ -1,54 +1,55 @@
/**
* @file mesh_utils_distribution.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Sun Oct 2 19:04:13 2016
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Sat Apr 01 2017
*
* @brief Mesh utils to distribute a mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_UTILS_DISTRIBUTION_HH__
#define __AKANTU_MESH_UTILS_DISTRIBUTION_HH__
namespace akantu {
class Mesh;
class MeshPartition;
} // akantu
namespace akantu {
namespace MeshUtilsDistribution {
/// Master call to distribute a mesh in a centralized manner (the UInt is just
/// to avoid some shitty access from the slave...)
void distributeMeshCentralized(Mesh & mesh, UInt,
const MeshPartition & partition);
/// Slave call to distribute a mesh in a centralized manner
void distributeMeshCentralized(Mesh & mesh, UInt root);
} // MeshUtilsDistribution
} // akantu
#endif /* __AKANTU_MESH_UTILS_DISTRIBUTION_HH__ */
diff --git a/src/mesh_utils/mesh_utils_inline_impl.cc b/src/mesh_utils/mesh_utils_inline_impl.cc
index 4c7c8bf27..0a48d9e57 100644
--- a/src/mesh_utils/mesh_utils_inline_impl.cc
+++ b/src/mesh_utils/mesh_utils_inline_impl.cc
@@ -1,82 +1,81 @@
/**
* @file mesh_utils_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Aug 20 2010
- * @date last modification: Fri Mar 20 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Mesh utils inline functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 bool MeshUtils::hasElement(const Array<UInt> & connectivity,
const Element & el,
const Vector<UInt> & nodes) {
UInt nb_nodes_per_element = connectivity.getNbComponent();
const Vector<UInt> el_nodes(connectivity.storage() +
el.element * nb_nodes_per_element,
nb_nodes_per_element);
UInt * el_nodes_end = el_nodes.storage() + nb_nodes_per_element;
UInt n = 0;
while (n < nodes.size() &&
std::find(el_nodes.storage(), el_nodes_end, nodes[n]) != el_nodes_end)
++n;
return (n == nodes.size());
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
inline bool
MeshUtils::removeElementsInVector(const std::vector<Element> & elem_to_remove,
std::vector<Element> & elem_list) {
if (elem_list.size() <= elem_to_remove.size())
return true;
auto el_it = elem_to_remove.begin();
auto el_last = elem_to_remove.end();
std::vector<Element>::iterator el_del;
UInt deletions = 0;
for (; el_it != el_last; ++el_it) {
el_del = std::find(elem_list.begin(), elem_list.end(), *el_it);
if (el_del != elem_list.end()) {
elem_list.erase(el_del);
++deletions;
}
}
AKANTU_DEBUG_ASSERT(deletions == 0 || deletions == elem_to_remove.size(),
"Not all elements have been erased");
return deletions == 0;
}
diff --git a/src/mesh_utils/mesh_utils_pbc.cc b/src/mesh_utils/mesh_utils_pbc.cc
index ac6a05a95..ad44e0ae7 100644
--- a/src/mesh_utils/mesh_utils_pbc.cc
+++ b/src/mesh_utils/mesh_utils_pbc.cc
@@ -1,300 +1,299 @@
/**
* @file mesh_utils_pbc.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Wed Feb 09 2011
- * @date last modification: Tue Sep 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief periodic boundary condition connectivity tweak
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/// class that sorts a set of nodes of same coordinates in 'dir' direction
class CoordinatesComparison {
public:
CoordinatesComparison(const UInt dimension, const UInt dir_1,
const UInt dir_2, Real normalization, Real tolerance,
const Array<Real> & coords)
: dim(dimension), dir_1(dir_1), dir_2(dir_2),
normalization(normalization), tolerance(tolerance),
coords_it(coords.begin(dim)) {}
// answers the question whether n2 is larger or equal to n1
bool operator()(const UInt n1, const UInt n2) {
Vector<Real> coords_n1 = coords_it[n1];
Vector<Real> coords_n2 = coords_it[n2];
return this->operator()(coords_n1, coords_n2);
}
bool operator()(const Vector<Real> & coords_n1,
const Vector<Real> & coords_n2) {
Real diff = coords_n1(dir_1) - coords_n2(dir_1);
;
if (dim == 2 || std::abs(diff) / normalization > tolerance)
return diff > 0. ? false : true;
else if (dim > 2) {
diff = coords_n1(dir_2) - coords_n2(dir_2);
;
return diff > 0 ? false : true;
}
return true;
}
private:
UInt dim;
UInt dir_1;
UInt dir_2;
Real normalization;
Real tolerance;
const Array<Real>::const_vector_iterator coords_it;
};
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh, const UInt dir,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_left;
Array<UInt> selected_right;
const UInt dim = mesh.getSpatialDimension();
auto it = mesh.getNodes().begin(dim);
auto end = mesh.getNodes().end(dim);
if (dim <= dir)
return;
const Vector<Real> & lower_bounds = mesh.getLowerBounds();
const Vector<Real> & upper_bounds = mesh.getUpperBounds();
AKANTU_DEBUG_INFO("min " << lower_bounds(dir));
AKANTU_DEBUG_INFO("max " << upper_bounds(dir));
for (UInt node = 0; it != end; ++it, ++node) {
const Vector<Real> & coords = *it;
AKANTU_DEBUG_TRACE("treating " << coords(dir));
if (Math::are_float_equal(coords(dir), lower_bounds(dir))) {
AKANTU_DEBUG_TRACE("pushing node " << node << " on the left side");
selected_left.push_back(node);
} else if (Math::are_float_equal(coords(dir), upper_bounds(dir))) {
selected_right.push_back(node);
AKANTU_DEBUG_TRACE("pushing node " << node << " on the right side");
}
}
AKANTU_DEBUG_INFO("found "
<< selected_left.size() << " and " << selected_right.size()
<< " nodes at each boundary for direction " << dir);
// match pairs
MeshUtils::matchPBCPairs(mesh, dir, selected_left, selected_right, pbc_pair);
}
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh,
const std::pair<ID, ID> & surface_pair,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_first;
Array<UInt> selected_second;
// find nodes on surfaces
const ElementGroup & first_surf = mesh.getElementGroup(surface_pair.first);
const ElementGroup & second_surf = mesh.getElementGroup(surface_pair.second);
// if this surface pair is not on this proc
if (first_surf.getNbNodes() == 0 || second_surf.getNbNodes() == 0) {
AKANTU_DEBUG_WARNING("computePBCMap has at least one surface without any "
"nodes. I will ignore it.");
return;
}
// copy nodes from element group
selected_first.copy(first_surf.getNodeGroup().getNodes());
selected_second.copy(second_surf.getNodeGroup().getNodes());
// coordinates
const Array<Real> & coords = mesh.getNodes();
const UInt dim = mesh.getSpatialDimension();
// variables to find min and max of surfaces
Real first_max[3], first_min[3];
Real second_max[3], second_min[3];
for (UInt i = 0; i < dim; ++i) {
first_min[i] = std::numeric_limits<Real>::max();
second_min[i] = std::numeric_limits<Real>::max();
first_max[i] = -std::numeric_limits<Real>::max();
second_max[i] = -std::numeric_limits<Real>::max();
}
// find min and max of surface nodes
for (auto it = selected_first.begin(); it != selected_first.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
if (first_min[i] > coords(*it, i))
first_min[i] = coords(*it, i);
if (first_max[i] < coords(*it, i))
first_max[i] = coords(*it, i);
}
}
for (auto it = selected_second.begin(); it != selected_second.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
if (second_min[i] > coords(*it, i))
second_min[i] = coords(*it, i);
if (second_max[i] < coords(*it, i))
second_max[i] = coords(*it, i);
}
}
// find direction of pbc
Int first_dir = -1;
#ifndef AKANTU_NDEBUG
Int second_dir = -2;
#endif
for (UInt i = 0; i < dim; ++i) {
if (Math::are_float_equal(first_min[i], first_max[i])) {
first_dir = i;
}
#ifndef AKANTU_NDEBUG
if (Math::are_float_equal(second_min[i], second_max[i])) {
second_dir = i;
}
#endif
}
AKANTU_DEBUG_ASSERT(first_dir == second_dir,
"Surface pair has not same direction. Surface "
<< surface_pair.first << " dir=" << first_dir
<< " ; Surface " << surface_pair.second
<< " dir=" << second_dir);
UInt dir = first_dir;
// match pairs
if (first_min[dir] < second_min[dir])
MeshUtils::matchPBCPairs(mesh, dir, selected_first, selected_second,
pbc_pair);
else
MeshUtils::matchPBCPairs(mesh, dir, selected_second, selected_first,
pbc_pair);
}
/* -------------------------------------------------------------------------- */
void MeshUtils::matchPBCPairs(const Mesh & mesh, const UInt dir,
Array<UInt> & selected_left,
Array<UInt> & selected_right,
std::map<UInt, UInt> & pbc_pair) {
// tolerance is that large because most meshers generate points coordinates
// with single precision only (it is the case of GMSH for instance)
Real tolerance = 1e-7;
const UInt dim = mesh.getSpatialDimension();
Real normalization = mesh.getUpperBounds()(dir) - mesh.getLowerBounds()(dir);
AKANTU_DEBUG_ASSERT(std::abs(normalization) > Math::getTolerance(),
"In matchPBCPairs: The normalization is zero. "
<< "Did you compute the bounding box of the mesh?");
auto odir_1 = UInt(-1), odir_2 = UInt(-1);
if (dim == 3) {
if (dir == _x) {
odir_1 = _y;
odir_2 = _z;
} else if (dir == _y) {
odir_1 = _x;
odir_2 = _z;
} else if (dir == _z) {
odir_1 = _x;
odir_2 = _y;
}
} else if (dim == 2) {
if (dir == _x) {
odir_1 = _y;
} else if (dir == _y) {
odir_1 = _x;
}
}
CoordinatesComparison compare_nodes(dim, odir_1, odir_2, normalization,
tolerance, mesh.getNodes());
std::sort(selected_left.begin(), selected_left.end(), compare_nodes);
std::sort(selected_right.begin(), selected_right.end(), compare_nodes);
auto it_left = selected_left.begin();
auto end_left = selected_left.end();
auto it_right = selected_right.begin();
auto end_right = selected_right.end();
auto nit = mesh.getNodes().begin(dim);
while ((it_left != end_left) && (it_right != end_right)) {
UInt i1 = *it_left;
UInt i2 = *it_right;
Vector<Real> coords1 = nit[i1];
Vector<Real> coords2 = nit[i2];
AKANTU_DEBUG_TRACE("do I pair? " << i1 << "(" << coords1 << ") with" << i2
<< "(" << coords2 << ") in direction "
<< dir);
Real dx = 0.0;
Real dy = 0.0;
if (dim >= 2)
dx = coords1(odir_1) - coords2(odir_1);
if (dim == 3)
dy = coords1(odir_2) - coords2(odir_2);
if (std::abs(dx * dx + dy * dy) / normalization < tolerance) {
// then i match these pairs
if (pbc_pair.count(i2)) {
i2 = pbc_pair[i2];
}
pbc_pair[i1] = i2;
AKANTU_DEBUG_TRACE("pairing " << i1 << "(" << coords1 << ") with" << i2
<< "(" << coords2 << ") in direction "
<< dir);
++it_left;
++it_right;
} else if (compare_nodes(coords1, coords2)) {
++it_left;
} else {
++it_right;
}
}
AKANTU_DEBUG_INFO("found " << pbc_pair.size() << " pairs for direction "
<< dir);
}
} // akantu
diff --git a/src/model/boundary_condition.hh b/src/model/boundary_condition.hh
index dd7775b2f..82a5b154b 100644
--- a/src/model/boundary_condition.hh
+++ b/src/model/boundary_condition.hh
@@ -1,101 +1,101 @@
/**
* @file boundary_condition.hh
*
* @author Dana Christen <dana.christen@gmail.com>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Dec 18 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief XXX
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BOUNDARY_CONDITION_HH__
#define __AKANTU_BOUNDARY_CONDITION_HH__
#include "aka_common.hh"
#include "boundary_condition_functor.hh"
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace akantu {
template <class ModelType> class BoundaryCondition {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
/* ------------------------------------------------------------------------ */
/* Constructors / Destructors / Initializers */
/* ------------------------------------------------------------------------ */
public:
BoundaryCondition() : model(nullptr) {}
/// Initialize the boundary conditions
void initBC(ModelType & ptr, Array<Real> & primal, Array<Real> & dual);
void initBC(ModelType & ptr, Array<Real> & primal,
Array<Real> & primal_increment, Array<Real> & dual);
/* ------------------------------------------------------------------------ */
/* Methods and accessors */
/* ------------------------------------------------------------------------ */
public:
// inline void initBoundaryCondition();
template <typename FunctorType>
/// Apply the boundary conditions
inline void applyBC(const FunctorType & func);
template <class FunctorType>
inline void applyBC(const FunctorType & func, const std::string & group_name);
template <class FunctorType>
inline void applyBC(const FunctorType & func,
const ElementGroup & element_group);
AKANTU_GET_MACRO_NOT_CONST(Model, *model, ModelType &);
AKANTU_GET_MACRO_NOT_CONST(Primal, *primal, Array<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Dual, *dual, Array<Real> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
template <class FunctorType, BC::Functor::Type type = FunctorType::type>
struct TemplateFunctionWrapper;
private:
ModelType * model;
Array<Real> * primal{nullptr};
Array<Real> * dual{nullptr};
Array<Real> * primal_increment{nullptr};
};
} // akantu
#include "boundary_condition_tmpl.hh"
#endif /* __AKANTU_BOUNDARY_CONDITION_HH__ */
diff --git a/src/model/boundary_condition_functor.hh b/src/model/boundary_condition_functor.hh
index 84cc245e3..4c54b5b09 100644
--- a/src/model/boundary_condition_functor.hh
+++ b/src/model/boundary_condition_functor.hh
@@ -1,217 +1,217 @@
/**
* @file boundary_condition_functor.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Definitions of the functors to apply boundary conditions
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "fe_engine.hh"
#include "integration_point.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__
#define __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
namespace BC {
using Axis = ::akantu::SpacialDirection;
struct Functor {
enum Type { _dirichlet, _neumann };
};
/* ------------------------------------------------------------------------ */
/* Dirichlet */
/* ------------------------------------------------------------------------ */
namespace Dirichlet {
/* ---------------------------------------------------------------------- */
class DirichletFunctor : public Functor {
protected:
DirichletFunctor() = default;
explicit DirichletFunctor(Axis ax) : axis(ax) {}
public:
void operator()(__attribute__((unused)) UInt node,
__attribute__((unused)) Vector<bool> & flags,
__attribute__((unused)) Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
AKANTU_TO_IMPLEMENT();
}
public:
static const Type type = _dirichlet;
protected:
Axis axis{_x};
};
/* ---------------------------------------------------------------------- */
class FlagOnly : public DirichletFunctor {
public:
explicit FlagOnly(Axis ax = _x) : DirichletFunctor(ax) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
};
/* ---------------------------------------------------------------------- */
class FreeBoundary : public DirichletFunctor {
public:
explicit FreeBoundary(Axis ax = _x) : DirichletFunctor(ax) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
};
/* ---------------------------------------------------------------------- */
class FixedValue : public DirichletFunctor {
public:
FixedValue(Real val, Axis ax = _x) : DirichletFunctor(ax), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
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;
};
/* ---------------------------------------------------------------------- */
class Increment : public DirichletFunctor {
public:
explicit Increment(const Vector<Real> & val)
: DirichletFunctor(_x), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
inline void setIncrement(const Vector<Real> & val) { this->value = val; }
protected:
Vector<Real> value;
};
} // end namespace Dirichlet
/* ------------------------------------------------------------------------ */
/* Neumann */
/* ------------------------------------------------------------------------ */
namespace Neumann {
/* ---------------------------------------------------------------------- */
class NeumannFunctor : public Functor {
protected:
NeumannFunctor() = default;
public:
virtual void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const = 0;
virtual ~NeumannFunctor() = default;
public:
static const Type type = _neumann;
};
/* ---------------------------------------------------------------------- */
class FromHigherDim : public NeumannFunctor {
public:
explicit FromHigherDim(const Matrix<Real> & mat) : bc_data(mat) {}
~FromHigherDim() override = default;
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const override;
protected:
Matrix<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FromSameDim : public NeumannFunctor {
public:
explicit FromSameDim(const Vector<Real> & vec) : bc_data(vec) {}
~FromSameDim() override = default;
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const override;
protected:
Vector<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FreeBoundary : public NeumannFunctor {
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const override;
};
} // end namespace Neumann
} // end namespace BC
} // akantu
#include "boundary_condition_functor_inline_impl.cc"
#endif /* __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__ */
diff --git a/src/model/boundary_condition_functor_inline_impl.cc b/src/model/boundary_condition_functor_inline_impl.cc
index abe306794..41a7d2b87 100644
--- a/src/model/boundary_condition_functor_inline_impl.cc
+++ b/src/model/boundary_condition_functor_inline_impl.cc
@@ -1,156 +1,158 @@
/**
* @file boundary_condition_functor_inline_impl.cc
*
* @author Dana Christen <dana.christen@gmail.com>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Mon Feb 19 2018
*
* @brief implementation of the BC::Functors
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "boundary_condition_functor.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_CC__
#define __AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_CC__
/* -------------------------------------------------------------------------- */
#define DIRICHLET_SANITY_CHECK \
AKANTU_DEBUG_ASSERT( \
coord.size() <= flags.size(), \
"The coordinates and flags vectors given to the boundary" \
<< " condition functor have different sizes!"); \
AKANTU_DEBUG_ASSERT( \
primal.size() <= coord.size(), \
"The primal vector and coordinates vector given" \
<< " to the boundary condition functor have different sizes!");
#define NEUMANN_SANITY_CHECK \
AKANTU_DEBUG_ASSERT( \
coord.size() <= normals.size(), \
"The coordinates and normals vectors given to the" \
<< " boundary condition functor have different sizes!"); \
AKANTU_DEBUG_ASSERT( \
dual.size() <= coord.size(), \
"The dual vector and coordinates vector given to" \
<< " the boundary condition functor have different sizes!");
namespace akantu {
namespace BC {
namespace Dirichlet {
/* ---------------------------------------------------------------------- */
inline void FlagOnly::
operator()(__attribute__((unused)) UInt node, Vector<bool> & flags,
__attribute__((unused)) Vector<Real> & primal,
__attribute__((unused)) const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
}
/* ---------------------------------------------------------------------- */
inline void FreeBoundary::
operator()(__attribute__((unused)) UInt node, Vector<bool> & flags,
__attribute__((unused)) Vector<Real> & primal,
__attribute__((unused)) const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = false;
}
/* ---------------------------------------------------------------------- */
inline void FixedValue::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
primal(this->axis) = value;
}
/* ---------------------------------------------------------------------- */
inline void IncrementValue::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
primal(this->axis) += value;
}
/* ---------------------------------------------------------------------- */
inline void Increment::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags.set(true);
primal += value;
}
} // end namespace Dirichlet
/* ------------------------------------------------------------------------ */
/* Neumann */
/* ------------------------------------------------------------------------ */
namespace Neumann {
/* ---------------------------------------------------------------------- */
inline void FreeBoundary::
operator()(__attribute__((unused)) const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused)) const Vector<Real> & coord,
__attribute__((unused)) const Vector<Real> & normals) const {
for (UInt i(0); i < dual.size(); ++i) {
dual(i) = 0.0;
}
}
/* ---------------------------------------------------------------------- */
inline void FromHigherDim::operator()(__attribute__((unused))
const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused))
const Vector<Real> & coord,
const Vector<Real> & normals) const {
dual.mul<false>(this->bc_data, normals);
}
/* ---------------------------------------------------------------------- */
inline void FromSameDim::
operator()(__attribute__((unused)) const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused)) const Vector<Real> & coord,
__attribute__((unused)) const Vector<Real> & normals) const {
dual = this->bc_data;
}
} // namespace Neumann
} // namespace BC
} // namespace akantu
#endif /* __AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_CC__ */
diff --git a/src/model/boundary_condition_python_functor.cc b/src/model/boundary_condition_python_functor.cc
index edc531d6f..d1c42d775 100644
--- a/src/model/boundary_condition_python_functor.cc
+++ b/src/model/boundary_condition_python_functor.cc
@@ -1,57 +1,57 @@
/**
* @file boundary_condition_python_functor.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Aug 31 2011
- * @date last modification: Fri Nov 13 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
* @brief Interface for BC::Functor written in python
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition_python_functor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace BC {
void PythonFunctorDirichlet::operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const {
this->callFunctor<void>("operator", node, flags, primal, coord);
}
void PythonFunctorNeumann::operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const {
this->callFunctor<void>("operator", quad_point, dual, coord, normals);
}
} // end namespace BC
} // akantu
diff --git a/src/model/boundary_condition_python_functor.hh b/src/model/boundary_condition_python_functor.hh
index da7e44410..2380f5052 100644
--- a/src/model/boundary_condition_python_functor.hh
+++ b/src/model/boundary_condition_python_functor.hh
@@ -1,116 +1,117 @@
/**
* @file boundary_condition_python_functor.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Fri Nov 13 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief interface for BC::Functor writen in python
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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 "boundary_condition_functor.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BOUNDARY_CONDITION_PYTHON_FUNCTOR_HH__
#define __AKANTU_BOUNDARY_CONDITION_PYTHON_FUNCTOR_HH__
/* -------------------------------------------------------------------------- */
#include "boundary_condition_functor.hh"
#include "python_functor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace BC {
class PythonFunctorDirichlet : public PythonFunctor, public Functor {
/* ------------------------------------------------------------------------
*/
/* Constructors/Destructors */
/* ------------------------------------------------------------------------
*/
public:
PythonFunctorDirichlet(PyObject * obj) : PythonFunctor(obj) {}
/* ------------------------------------------------------------------------
*/
/* Methods */
/* ------------------------------------------------------------------------
*/
public:
void operator()(UInt node, Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const;
/* ------------------------------------------------------------------------
*/
/* Class Members */
/* ------------------------------------------------------------------------
*/
public:
static const Type type = _dirichlet;
};
/* --------------------------------------------------------------------------
*/
class PythonFunctorNeumann : public PythonFunctor, public Functor {
/* ------------------------------------------------------------------------
*/
/* Constructors/Destructors */
/* ------------------------------------------------------------------------
*/
public:
PythonFunctorNeumann(PyObject * obj) : PythonFunctor(obj) {}
/* ------------------------------------------------------------------------
*/
/* Methods */
/* ------------------------------------------------------------------------
*/
public:
void operator()(const IntegrationPoint & quad_point, Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const;
/* ------------------------------------------------------------------------
*/
/* Class Members */
/* ------------------------------------------------------------------------
*/
public:
static const Type type = _neumann;
};
} // end namespace BC
} // akantu
#endif /* __AKANTU_BOUNDARY_CONDITION_PYTHON_FUNCTOR_HH__ */
diff --git a/src/model/boundary_condition_tmpl.hh b/src/model/boundary_condition_tmpl.hh
index bb4c58039..f45d2ac88 100644
--- a/src/model/boundary_condition_tmpl.hh
+++ b/src/model/boundary_condition_tmpl.hh
@@ -1,256 +1,256 @@
/**
* @file boundary_condition_tmpl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Fri Oct 16 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief implementation of the applyBC
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition.hh"
#include "element_group.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BOUNDARY_CONDITION_TMPL_HH__
#define __AKANTU_BOUNDARY_CONDITION_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename ModelType>
void BoundaryCondition<ModelType>::initBC(ModelType & model,
Array<Real> & primal,
Array<Real> & dual) {
this->model = &model;
this->primal = &primal;
this->dual = &dual;
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
void BoundaryCondition<ModelType>::initBC(ModelType & model,
Array<Real> & primal,
Array<Real> & primal_increment,
Array<Real> & dual) {
this->initBC(model, primal, dual);
this->primal_increment = &primal_increment;
}
/* -------------------------------------------------------------------------- */
/* Partial specialization for DIRICHLET functors */
template <typename ModelType>
template <typename FunctorType>
struct BoundaryCondition<ModelType>::TemplateFunctionWrapper<
FunctorType, BC::Functor::_dirichlet> {
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance) {
auto & model = bc_instance.getModel();
auto & primal = bc_instance.getPrimal();
const auto & coords = model.getMesh().getNodes();
auto & boundary_flags = model.getBlockedDOFs();
UInt dim = model.getMesh().getSpatialDimension();
auto primal_iter = primal.begin(primal.getNbComponent());
auto coords_iter = coords.begin(dim);
auto flags_iter = boundary_flags.begin(boundary_flags.getNbComponent());
for (auto n : group.getNodeGroup()) {
Vector<bool> flag(flags_iter[n]);
Vector<Real> primal(primal_iter[n]);
Vector<Real> coords(coords_iter[n]);
func(n, flag, primal, coords);
}
}
};
/* -------------------------------------------------------------------------- */
/* Partial specialization for NEUMANN functors */
template <typename ModelType>
template <typename FunctorType>
struct BoundaryCondition<ModelType>::TemplateFunctionWrapper<
FunctorType, BC::Functor::_neumann> {
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance) {
UInt dim = bc_instance.getModel().getSpatialDimension();
switch (dim) {
case 1: {
AKANTU_TO_IMPLEMENT();
break;
}
case 2:
case 3: {
applyBC(func, group, bc_instance, _not_ghost);
applyBC(func, group, bc_instance, _ghost);
break;
}
}
}
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance,
GhostType ghost_type) {
auto & model = bc_instance.getModel();
auto & dual = bc_instance.getDual();
const auto & mesh = model.getMesh();
const auto & nodes_coords = mesh.getNodes();
const auto & fem_boundary = model.getFEEngineBoundary();
UInt dim = model.getSpatialDimension();
UInt nb_degree_of_freedom = dual.getNbComponent();
IntegrationPoint quad_point;
quad_point.ghost_type = ghost_type;
// Loop over the boundary element types
for (auto && type : group.elementTypes(dim - 1, ghost_type)) {
const auto & element_ids = group.getElements(type, ghost_type);
UInt nb_quad_points =
fem_boundary.getNbIntegrationPoints(type, ghost_type);
UInt nb_elements = element_ids.size();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> * dual_before_integ = new Array<Real>(
nb_elements * nb_quad_points, nb_degree_of_freedom, 0.);
Array<Real> * quad_coords =
new Array<Real>(nb_elements * nb_quad_points, dim);
const auto & normals_on_quad =
fem_boundary.getNormalsOnIntegrationPoints(type, ghost_type);
fem_boundary.interpolateOnIntegrationPoints(
nodes_coords, *quad_coords, dim, type, ghost_type, element_ids);
auto normals_begin = normals_on_quad.begin(dim);
decltype(normals_begin) normals_iter;
auto quad_coords_iter = quad_coords->begin(dim);
auto dual_iter = dual_before_integ->begin(nb_degree_of_freedom);
quad_point.type = type;
for (auto el : element_ids) {
quad_point.element = el;
normals_iter = normals_begin + el * nb_quad_points;
for (auto && q : arange(nb_quad_points)) {
quad_point.num_point = q;
func(quad_point, *dual_iter, *quad_coords_iter, *normals_iter);
++dual_iter;
++quad_coords_iter;
++normals_iter;
}
}
delete quad_coords;
/* -------------------------------------------------------------------- */
// Initialization of iterators
auto dual_iter_mat = dual_before_integ->begin(nb_degree_of_freedom, 1);
auto shapes_iter_begin = fem_boundary.getShapes(type, ghost_type)
.begin(1, nb_nodes_per_element);
Array<Real> * dual_by_shapes =
new Array<Real>(nb_elements * nb_quad_points,
nb_degree_of_freedom * nb_nodes_per_element);
auto dual_by_shapes_iter =
dual_by_shapes->begin(nb_degree_of_freedom, nb_nodes_per_element);
/* -------------------------------------------------------------------- */
// Loop computing dual x shapes
for (auto el : element_ids) {
auto shapes_iter = shapes_iter_begin + el * nb_quad_points;
for (UInt q(0); q < nb_quad_points;
++q, ++dual_iter_mat, ++dual_by_shapes_iter, ++shapes_iter) {
dual_by_shapes_iter->template mul<false, false>(*dual_iter_mat,
*shapes_iter);
}
}
delete dual_before_integ;
Array<Real> * dual_by_shapes_integ = new Array<Real>(
nb_elements, nb_degree_of_freedom * nb_nodes_per_element);
fem_boundary.integrate(*dual_by_shapes, *dual_by_shapes_integ,
nb_degree_of_freedom * nb_nodes_per_element, type,
ghost_type, element_ids);
delete dual_by_shapes;
// assemble the result into force vector
model.getDOFManager().assembleElementalArrayLocalArray(
*dual_by_shapes_integ, dual, type, ghost_type, 1., element_ids);
delete dual_by_shapes_integ;
}
}
};
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void BoundaryCondition<ModelType>::applyBC(const FunctorType & func) {
auto bit = model->getMesh().getGroupManager().element_group_begin();
auto bend = model->getMesh().getGroupManager().element_group_end();
for (; bit != bend; ++bit)
applyBC(func, *bit);
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void
BoundaryCondition<ModelType>::applyBC(const FunctorType & func,
const std::string & group_name) {
try {
const ElementGroup & element_group =
model->getMesh().getElementGroup(group_name);
applyBC(func, element_group);
} catch (akantu::debug::Exception e) {
AKANTU_EXCEPTION("Error applying a boundary condition onto \""
<< group_name << "\"! [" << e.what() << "]");
}
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void
BoundaryCondition<ModelType>::applyBC(const FunctorType & func,
const ElementGroup & element_group) {
#if !defined(AKANTU_NDEBUG)
if (element_group.getDimension() != model->getSpatialDimension() - 1)
AKANTU_DEBUG_WARNING("The group "
<< element_group.getName()
<< " does not contain only boundaries elements");
#endif
TemplateFunctionWrapper<FunctorType>::applyBC(func, element_group, *this);
}
#endif /* __AKANTU_BOUNDARY_CONDITION_TMPL_HH__ */
} // namespace akantu
diff --git a/src/model/common/neighborhood_base.cc b/src/model/common/neighborhood_base.cc
index 1fbf3f5a4..aada85368 100644
--- a/src/model/common/neighborhood_base.cc
+++ b/src/model/common/neighborhood_base.cc
@@ -1,295 +1,295 @@
/**
* @file neighborhood_base.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Implementation of generic neighborhood base
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "grid_synchronizer.hh"
#include "mesh_accessor.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NeighborhoodBase::NeighborhoodBase(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), model(model), neighborhood_radius(0.),
spatial_grid(nullptr), is_creating_grid(false),
grid_synchronizer(nullptr), quad_coordinates(quad_coordinates),
spatial_dimension(this->model.getMesh().getSpatialDimension()) {
AKANTU_DEBUG_IN();
this->registerDataAccessor(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NeighborhoodBase::~NeighborhoodBase() = default;
/* -------------------------------------------------------------------------- */
// void NeighborhoodBase::createSynchronizerRegistry(
// DataAccessor<Element> * data_accessor) {
// this->synch_registry = new SynchronizerRegistry(*data_accessor);
// }
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::initNeighborhood() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Creating the grid");
this->createGrid();
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------- */
void NeighborhoodBase::createGrid() {
AKANTU_DEBUG_IN();
const Real safety_factor = 1.2; // for the cell grid spacing
Mesh & mesh = this->model.getMesh();
const auto & lower_bounds = mesh.getLocalLowerBounds();
const auto & upper_bounds = mesh.getLocalUpperBounds();
Vector<Real> center = 0.5 * (upper_bounds + lower_bounds);
Vector<Real> spacing(spatial_dimension,
this->neighborhood_radius * safety_factor);
spatial_grid = std::make_unique<SpatialGrid<IntegrationPoint>>(
spatial_dimension, spacing, center);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::updatePairList() {
AKANTU_DEBUG_IN();
//// loop over all quads -> all cells
for (auto && cell_id : *spatial_grid) {
AKANTU_DEBUG_INFO("Looping on next cell");
for (auto && q1 : spatial_grid->getCell(cell_id)) {
if (q1.ghost_type == _ghost)
break;
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
auto q1_coords = Vector<Real>(coords_type_1_it[q1.global_num]);
AKANTU_DEBUG_INFO("Current quadrature point in this cell: " << q1);
auto cell_id = spatial_grid->getCellID(q1_coords);
/// loop over all the neighboring cells of the current quad
for (auto && neighbor_cell : cell_id.neighbors()) {
// loop over the quadrature point in the current neighboring cell
for (auto && q2 : spatial_grid->getCell(neighbor_cell)) {
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
auto q2_coords = Vector<Real>(coords_type_2_it[q2.global_num]);
Real distance = q1_coords.distance(q2_coords);
if (distance <= this->neighborhood_radius + Math::getTolerance() &&
(q2.ghost_type == _ghost ||
(q2.ghost_type == _not_ghost &&
q1.global_num <= q2.global_num))) { // storing only half lists
pair_list[q2.ghost_type].push_back(std::make_pair(q1, q2));
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::savePairs(const std::string & filename) const {
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
std::ofstream pout;
pout.open(sstr.str().c_str());
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
const auto & q1 = pair.first;
const auto & q2 = pair.second;
pout << q1 << " " << q2 << " " << std::endl;
}
}
pout.close();
if (comm.getNbProc() != 1)
return;
Mesh mesh_out(spatial_dimension);
MeshAccessor mesh_accessor(mesh_out);
auto & connectivity = mesh_accessor.getConnectivity(_segment_2);
auto & tag = mesh_accessor.getData<UInt>("tag_1", _segment_2);
auto & nodes = mesh_accessor.getNodes();
std::map<IntegrationPoint, UInt> quad_to_nodes;
UInt node = 0;
IntegrationPoint q1, q2;
bool inserted;
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
std::tie(q1, q2) = pair;
auto add_node = [&](auto && q) {
std::tie(std::ignore, inserted) =
quad_to_nodes.insert(std::make_pair(q, node));
if (not inserted)
return;
auto coords_it = this->quad_coordinates(q.type, q.ghost_type)
.begin(spatial_dimension);
auto && coords = Vector<Real>(coords_it[q.global_num]);
nodes.push_back(coords);
++node;
};
add_node(q1);
add_node(q2);
}
}
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
std::tie(q1, q2) = pair;
UInt node1 = quad_to_nodes[q1];
UInt node2 = quad_to_nodes[q2];
connectivity.push_back(Vector<UInt>{node1, node2});
tag.push_back(node1 + 1);
if (node1 != node2) {
connectivity.push_back(Vector<UInt>{node2, node1});
tag.push_back(node2 + 1);
}
}
}
mesh_out.write(filename + ".msh");
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::saveNeighborCoords(const std::string & filename) const {
// this function is not optimized and only used for tests on small meshes
// @todo maybe optimize this function for better performance?
IntegrationPoint q2;
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
std::ofstream pout;
pout.open(sstr.str().c_str());
/// loop over all the quads and write the position of their neighbors
for (auto && cell_id : *spatial_grid) {
for (auto && q1 : spatial_grid->getCell(cell_id)) {
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
auto && q1_coords = Vector<Real>(coords_type_1_it[q1.global_num]);
pout << "#neighbors for quad " << q1.global_num << std::endl;
pout << q1_coords << std::endl;
for (auto && ghost_type2 : ghost_types) {
for (auto && pair : pair_list[ghost_type2]) {
if (q1 == pair.first && pair.second != q1) {
q2 = pair.second;
} else if (q1 == pair.second && pair.first != q1) {
q2 = pair.first;
} else {
continue;
}
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
auto && q2_coords = Vector<Real>(coords_type_2_it[q2.global_num]);
pout << q2_coords << std::endl;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = 0;
// Change the pairs in new global numbering
for (auto ghost_type2 : ghost_types) {
for (auto && pair : pair_list[ghost_type2]) {
auto cleanPoint = [&](auto && q) {
if (new_numbering.exists(q.type, q.ghost_type)) {
UInt q_new_el = new_numbering(q.type, q.ghost_type)(q.element);
AKANTU_DEBUG_ASSERT(q_new_el != UInt(-1),
"A local quadrature_point "
"as been removed instead of "
"just being renumbered");
q.element = q_new_el;
nb_quad = fem.getNbIntegrationPoints(q.type, q.ghost_type);
q.global_num = nb_quad * q.element + q.num_point;
}
};
cleanPoint(pair.first);
cleanPoint(pair.second);
}
}
this->grid_synchronizer->onElementsRemoved(element_list, new_numbering,
event);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/common/neighborhood_base.hh b/src/model/common/neighborhood_base.hh
index e0c51f496..a9dabe632 100644
--- a/src/model/common/neighborhood_base.hh
+++ b/src/model/common/neighborhood_base.hh
@@ -1,151 +1,151 @@
/**
* @file neighborhood_base.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Generic neighborhood of quadrature points
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NEIGHBORHOOD_BASE_HH__
#define __AKANTU_NEIGHBORHOOD_BASE_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_memory.hh"
#include "data_accessor.hh"
#include "integration_point.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
template <class T> class SpatialGrid;
class GridSynchronizer;
class RemovedElementsEvent;
} // namespace akantu
namespace akantu {
class NeighborhoodBase : protected Memory,
public DataAccessor<Element>,
public SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NeighborhoodBase(Model & model,
const ElementTypeMapArray<Real> & quad_coordinates,
const ID & id = "neighborhood",
const MemoryID & memory_id = 0);
~NeighborhoodBase() override;
using PairList = std::vector<std::pair<IntegrationPoint, IntegrationPoint>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// intialize the neighborhood
virtual void initNeighborhood();
// /// create a synchronizer registry
// void createSynchronizerRegistry(DataAccessor * data_accessor);
/// initialize the material computed parameter
inline void insertIntegrationPoint(const IntegrationPoint & quad,
const Vector<Real> & coords);
/// create the pairs of quadrature points
void updatePairList();
/// save the pairs of quadrature points in a file
void savePairs(const std::string & filename) const;
/// save the coordinates of all neighbors of a quad
void saveNeighborCoords(const std::string & filename) const;
/// create grid synchronizer and exchange ghost cells
virtual void createGridSynchronizer() = 0;
virtual void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) = 0;
/// inherited function from MeshEventHandler
virtual void
onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
protected:
/// create the grid
void createGrid();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
AKANTU_GET_MACRO(Model, model, const Model &);
/// return the object handling synchronizers
AKANTU_GET_MACRO(PairLists, pair_list, const PairList *);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the model to which the neighborhood belongs
Model & model;
/// Radius of impact: to determine if two quadrature points influence each
/// other
Real neighborhood_radius;
/**
* the pairs of quadrature points
* 0: not ghost to not ghost
* 1: not ghost to ghost
*/
PairList pair_list[2];
/// the regular grid to construct/update the pair lists
std::unique_ptr<SpatialGrid<IntegrationPoint>> spatial_grid;
bool is_creating_grid;
/// the grid synchronizer for parallel computations
std::unique_ptr<GridSynchronizer> grid_synchronizer;
/// the quadrature point positions
const ElementTypeMapArray<Real> & quad_coordinates;
/// the spatial dimension of the problem
const UInt spatial_dimension;
};
} // namespace akantu
#include "neighborhood_base_inline_impl.cc"
#endif /* __AKANTU_NEIGHBORHOOD_BASE_HH__ */
diff --git a/src/model/common/neighborhood_base_inline_impl.cc b/src/model/common/neighborhood_base_inline_impl.cc
index ebed56d3f..70de7429f 100644
--- a/src/model/common/neighborhood_base_inline_impl.cc
+++ b/src/model/common/neighborhood_base_inline_impl.cc
@@ -1,50 +1,50 @@
/**
* @file neighborhood_base_inline_impl.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Inline implementation of neighborhood base functions
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_grid_dynamic.hh"
#include "neighborhood_base.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_CC__
#define __AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_CC__
namespace akantu {
inline void
NeighborhoodBase::insertIntegrationPoint(const IntegrationPoint & quad,
const Vector<Real> & coords) {
this->spatial_grid->insert(quad, coords);
}
} // namespace akantu
#endif /* __AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_CC__ */
diff --git a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
index 6468159a4..bc55e366a 100644
--- a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
+++ b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
@@ -1,311 +1,311 @@
/**
* @file neighborhood_max_criterion.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Thu Oct 15 2015
- * @date last modification: Tue Nov 24 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of class NeighborhoodMaxCriterion
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_max_criterion.hh"
#include "grid_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NeighborhoodMaxCriterion::NeighborhoodMaxCriterion(
Model & model, const ElementTypeMapReal & quad_coordinates,
const ID & criterion_id, const ID & id, const MemoryID & memory_id)
: NeighborhoodBase(model, quad_coordinates, id, memory_id),
Parsable(ParserType::_non_local, id),
is_highest("is_highest", id, memory_id),
criterion(criterion_id, id, memory_id) {
AKANTU_DEBUG_IN();
this->registerParam("radius", neighborhood_radius, 100.,
_pat_parsable | _pat_readable, "Non local radius");
Mesh & mesh = this->model.getMesh();
/// allocate the element type map arrays for _not_ghosts: One entry per quad
GhostType ghost_type = _not_ghost;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last_type; ++it) {
UInt new_size = this->quad_coordinates(*it, ghost_type).size();
this->is_highest.alloc(new_size, 1, *it, ghost_type, true);
this->criterion.alloc(new_size, 1, *it, ghost_type, true);
}
/// criterion needs allocation also for ghost
ghost_type = _ghost;
it = mesh.firstType(spatial_dimension, ghost_type);
last_type = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last_type; ++it) {
UInt new_size = this->quad_coordinates(*it, ghost_type).size();
this->criterion.alloc(new_size, 1, *it, ghost_type, true);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NeighborhoodMaxCriterion::~NeighborhoodMaxCriterion() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::initNeighborhood() {
AKANTU_DEBUG_IN();
/// parse the input parameter
const Parser & parser = getStaticParser();
const ParserSection & section_neighborhood =
*(parser.getSubSections(ParserType::_neighborhood).first);
this->parseSection(section_neighborhood);
AKANTU_DEBUG_INFO("Creating the grid");
this->createGrid();
/// insert the non-ghost quads into the grid
this->insertAllQuads(_not_ghost);
/// store the number of current ghost elements for each type in the mesh
ElementTypeMap<UInt> nb_ghost_protected;
Mesh & mesh = this->model.getMesh();
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);
/// create the grid synchronizer
this->createGridSynchronizer();
/// insert the ghost quads into the grid
this->insertAllQuads(_ghost);
/// create the pair lists
this->updatePairList();
/// remove the unneccessary ghosts
this->cleanupExtraGhostElements(nb_ghost_protected);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::createGridSynchronizer() {
this->is_creating_grid = true;
std::set<SynchronizationTag> tags;
tags.insert(_gst_nh_criterion);
std::stringstream sstr;
sstr << getID() << ":grid_synchronizer";
this->grid_synchronizer = std::make_unique<GridSynchronizer>(
this->model.getMesh(), *spatial_grid, *this, tags, sstr.str(), 0, false);
this->is_creating_grid = false;
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::insertAllQuads(const GhostType & ghost_type) {
IntegrationPoint q;
q.ghost_type = ghost_type;
Mesh & mesh = this->model.getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last_type; ++it) {
UInt nb_element = mesh.getNbElement(*it, ghost_type);
UInt nb_quad =
this->model.getFEEngine().getNbIntegrationPoints(*it, ghost_type);
const Array<Real> & quads = this->quad_coordinates(*it, ghost_type);
q.type = *it;
auto quad = quads.begin(spatial_dimension);
for (UInt e = 0; e < nb_element; ++e) {
q.element = e;
for (UInt nq = 0; nq < nb_quad; ++nq) {
q.num_point = nq;
q.global_num = q.element * nb_quad + nq;
spatial_grid->insert(q, *quad);
++quad;
}
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::findMaxQuads(
std::vector<IntegrationPoint> & max_quads) {
AKANTU_DEBUG_IN();
/// clear the element type maps
this->is_highest.clear();
this->criterion.clear();
/// update the values of the criterion
this->model.updateDataForNonLocalCriterion(criterion);
/// start the exchange the value of the criterion on the ghost elements
this->model.asynchronousSynchronize(_gst_nh_criterion);
/// compare to not-ghost neighbors
checkNeighbors(_not_ghost);
/// finish the exchange
this->model.waitEndSynchronize(_gst_nh_criterion);
/// compare to ghost neighbors
checkNeighbors(_ghost);
/// extract the quads with highest criterion in their neighborhood
IntegrationPoint quad;
quad.ghost_type = _not_ghost;
Mesh & mesh = this->model.getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _not_ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _not_ghost);
for (; it != last_type; ++it) {
quad.type = *it;
Array<bool>::const_scalar_iterator is_highest_it =
is_highest(*it, _not_ghost).begin();
Array<bool>::const_scalar_iterator is_highest_end =
is_highest(*it, _not_ghost).end();
UInt nb_quadrature_points =
this->model.getFEEngine().getNbIntegrationPoints(*it, _not_ghost);
UInt q = 0;
/// loop over is_highest for the current element type
for (; is_highest_it != is_highest_end; ++is_highest_it, ++q) {
if (*is_highest_it) {
/// gauss point has the highest stress in his neighbourhood
quad.element = q / nb_quadrature_points;
quad.global_num = q;
quad.num_point = q % nb_quadrature_points;
max_quads.push_back(quad);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::checkNeighbors(const GhostType & ghost_type2) {
AKANTU_DEBUG_IN();
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
// Compute the weights
for (; first_pair != last_pair; ++first_pair) {
const IntegrationPoint & lq1 = first_pair->first;
const IntegrationPoint & lq2 = first_pair->second;
Array<bool> & has_highest_eq_stress_1 =
is_highest(lq1.type, lq1.ghost_type);
const Array<Real> & criterion_1 = this->criterion(lq1.type, lq1.ghost_type);
const Array<Real> & criterion_2 = this->criterion(lq2.type, lq2.ghost_type);
if (criterion_1(lq1.global_num) < criterion_2(lq2.global_num))
has_highest_eq_stress_1(lq1.global_num) = false;
else if (ghost_type2 != _ghost) {
Array<bool> & has_highest_eq_stress_2 =
is_highest(lq2.type, lq2.ghost_type);
has_highest_eq_stress_2(lq2.global_num) = false;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::cleanupExtraGhostElements(
const ElementTypeMap<UInt> & nb_ghost_protected) {
Mesh & mesh = this->model.getMesh();
/// create remove elements event
RemovedElementsEvent remove_elem(mesh);
/// create set of ghosts to keep
std::set<Element> relevant_ghost_elements;
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 IntegrationPoint & q2 = first_pair->second;
relevant_ghost_elements.insert(q2);
}
Array<Element> ghosts_to_erase(0);
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);
Element element;
element.ghost_type = _ghost;
auto end = relevant_ghost_elements.end();
for (; it != last_type; ++it) {
element.type = *it;
UInt nb_ghost_elem = 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);
Array<UInt> & new_numbering = remove_elem.getNewNumbering(*it, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
element.element = g;
if (element.element >= nb_ghost_elem_protected &&
relevant_ghost_elements.find(element) == end) {
ghosts_to_erase.push_back(element);
new_numbering(element.element) = UInt(-1);
}
}
/// renumber remaining ghosts
UInt ng = 0;
for (UInt g = 0; g < nb_ghost_elem; ++g) {
if (new_numbering(g) != UInt(-1)) {
new_numbering(g) = ng;
++ng;
}
}
}
mesh.sendEvent(remove_elem);
this->onElementsRemoved(ghosts_to_erase, remove_elem.getNewNumbering(),
remove_elem);
}
} // namespace akantu
diff --git a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
index 67b7f51c9..8ff079040 100644
--- a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
+++ b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
@@ -1,117 +1,117 @@
/**
* @file neighborhood_max_criterion.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Neighborhood to find a maximum value in a neighborhood
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__
#define __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class NeighborhoodMaxCriterion : public NeighborhoodBase, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NeighborhoodMaxCriterion(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & criterion_id,
const ID & id = "neighborhood_max_criterion",
const MemoryID & memory_id = 0);
~NeighborhoodMaxCriterion() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the neighborhood
void initNeighborhood() override;
/// create grid synchronizer and exchange ghost cells
void createGridSynchronizer() override;
/// find the quads which have the maximum criterion in their neighborhood
void findMaxQuads(std::vector<IntegrationPoint> & max_quads);
protected:
/// remove unneccessary ghost elements
void
cleanupExtraGhostElements(const ElementTypeMap<UInt> & nb_ghost_protected);
/// insert the quadrature points in the grid
void insertAllQuads(const GhostType & ghost_type);
/// compare criterion with neighbors
void checkNeighbors(const GhostType & ghost_type);
/* --------------------------------------------------------------------------
*/
/* DataAccessor inherited members */
/* --------------------------------------------------------------------------
*/
public:
virtual inline UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag);
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// a boolean to store the information if a quad has the max
/// criterion in the neighborhood
ElementTypeMapArray<bool> is_highest;
/// an element type map to store the flattened internal of the criterion
ElementTypeMapReal criterion;
};
} // akantu
#include "neighborhood_max_criterion_inline_impl.cc"
#endif /* __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__ */
diff --git a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.cc b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.cc
index bb2d331cb..a74051e21 100644
--- a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.cc
+++ b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.cc
@@ -1,81 +1,82 @@
/**
* @file neighborhood_max_criterion_inline_impl.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Implementation of inline functions for class NeighborhoodMaxCriterion
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model.hh"
#include "neighborhood_max_criterion.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_CC__
#define __AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt
NeighborhoodMaxCriterion::getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
UInt nb_quadrature_points = this->model.getNbIntegrationPoints(elements);
UInt size = 0;
if (tag == _gst_nh_criterion) {
size += sizeof(Real) * nb_quadrature_points;
}
return size;
}
/* -------------------------------------------------------------------------- */
inline void
NeighborhoodMaxCriterion::packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
if (tag == _gst_nh_criterion) {
this->packElementalDataHelper(criterion, buffer, elements, true,
this->model.getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
inline void
NeighborhoodMaxCriterion::unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
if (tag == _gst_nh_criterion) {
this->unpackElementalDataHelper(criterion, buffer, elements, true,
this->model.getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_CC__ */
diff --git a/src/model/common/non_local_toolbox/base_weight_function.hh b/src/model/common/non_local_toolbox/base_weight_function.hh
index 202b20073..94808505a 100644
--- a/src/model/common/non_local_toolbox/base_weight_function.hh
+++ b/src/model/common/non_local_toolbox/base_weight_function.hh
@@ -1,169 +1,169 @@
/**
* @file base_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Fri Dec 08 2017
*
* @brief Base weight function for non local materials
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "model.hh"
#include "non_local_manager.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BASE_WEIGHT_FUNCTION_HH__
#define __AKANTU_BASE_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Normal weight function */
/* -------------------------------------------------------------------------- */
class BaseWeightFunction : public Parsable, public DataAccessor<Element> {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
BaseWeightFunction(NonLocalManager & manager,
const std::string & type = "base")
: Parsable(ParserType::_weight_function, "weight_function:" + type),
manager(manager), type(type),
spatial_dimension(manager.getModel().getMesh().getSpatialDimension()) {
this->registerParam("update_rate", update_rate, UInt(1), _pat_parsmod,
"Update frequency");
}
~BaseWeightFunction() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
/// initialize the weight function
virtual inline void init();
/// update the internal parameters
virtual void updateInternals(){};
/* ------------------------------------------------------------------------ */
/// set the non-local radius
inline void setRadius(Real radius);
/* ------------------------------------------------------------------------ */
/// compute the weight for a given distance between two quadrature points
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2);
/// print function
void printself(std::ostream & stream, int indent = 0) const override {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "WeightFunction " << type << " [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
}
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
/// get the radius
Real getRadius() { return R; }
/// get the update rate
UInt getUpdateRate() { return update_rate; }
public:
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<Element> &,
const SynchronizationTag &) const override {
return 0;
}
inline void packData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) const override {}
inline void unpackData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) override {}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Type, type, const ID &);
protected:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// reference to the non-local manager
NonLocalManager & manager;
/// the non-local radius
Real R;
/// the non-local radius squared
Real R2;
/// the update rate
UInt update_rate;
/// name of the type of weight function
const std::string type;
/// the spatial dimension
UInt spatial_dimension;
};
inline std::ostream & operator<<(std::ostream & stream,
const BaseWeightFunction & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "base_weight_function_inline_impl.cc"
/* -------------------------------------------------------------------------- */
/* Include all other weight function types */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_DAMAGE_NON_LOCAL)
#include "damaged_weight_function.hh"
#include "remove_damaged_weight_function.hh"
#include "remove_damaged_with_damage_rate_weight_function.hh"
#include "stress_based_weight_function.hh"
#endif
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_BASE_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/common/non_local_toolbox/base_weight_function_inline_impl.cc b/src/model/common/non_local_toolbox/base_weight_function_inline_impl.cc
index 0c185e079..d80ccb2cf 100644
--- a/src/model/common/non_local_toolbox/base_weight_function_inline_impl.cc
+++ b/src/model/common/non_local_toolbox/base_weight_function_inline_impl.cc
@@ -1,70 +1,71 @@
/**
* @file base_weight_function_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
- * @date creation: Thu Feb 21 2013
- * @date last modification: Thu Oct 15 2015
+ * @date creation: Wed Sep 01 2010
+ * @date last modification: Wed Sep 27 2017
*
* @brief Implementation of inline function of base weight function
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_CC__
#define __AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void BaseWeightFunction::init() {
/// compute R^2 for a given non-local radius
this->R2 = this->R * this->R;
}
/* -------------------------------------------------------------------------- */
inline void BaseWeightFunction::setRadius(Real radius) {
/// set the non-local radius and update R^2 accordingly
this->R = radius;
this->R2 = this->R * this->R;
}
/* -------------------------------------------------------------------------- */
inline Real BaseWeightFunction::operator()(Real r, const IntegrationPoint &,
const IntegrationPoint &) {
/// initialize the weight
Real w = 0;
/// compute weight for given r
if (r <= this->R) {
Real alpha = (1. - r * r / this->R2);
w = alpha * alpha;
// *weight = 1 - sqrt(r / radius);
}
return w;
}
} // akantu
#endif /* __AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_CC__ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager.cc b/src/model/common/non_local_toolbox/non_local_manager.cc
index 386c3ee82..7fb9868df 100644
--- a/src/model/common/non_local_toolbox/non_local_manager.cc
+++ b/src/model/common/non_local_toolbox/non_local_manager.cc
@@ -1,639 +1,638 @@
/**
* @file non_local_manager.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Wed Dec 16 2015
+ * @date last modification: Tue Jan 16 2018
*
* @brief Implementation of non-local manager
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_local_manager.hh"
#include "grid_synchronizer.hh"
#include "model.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLocalManager::NonLocalManager(Model & model,
NonLocalManagerCallback & callback,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), Parsable(ParserType::_neighborhoods, id),
spatial_dimension(model.getMesh().getSpatialDimension()), model(model),
integration_points_positions("integration_points_positions", id,
memory_id),
volumes("volumes", id, memory_id), compute_stress_calls(0),
dummy_registry(nullptr), dummy_grid(nullptr) {
/// parse the neighborhood information from the input file
const Parser & parser = getStaticParser();
/// iterate over all the non-local sections and store them in a map
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
weight_sect = parser.getSubSections(ParserType::_non_local);
Parser::const_section_iterator it = weight_sect.first;
for (; it != weight_sect.second; ++it) {
const ParserSection & section = *it;
ID name = section.getName();
this->weight_function_types[name] = section;
}
this->callback = &callback;
}
/* -------------------------------------------------------------------------- */
NonLocalManager::~NonLocalManager() = default;
/* -------------------------------------------------------------------------- */
void NonLocalManager::initialize() {
volumes.initialize(this->model.getFEEngine(),
_spatial_dimension = spatial_dimension);
AKANTU_DEBUG_ASSERT(this->callback,
"A callback should be registered prior to this call");
this->callback->insertIntegrationPointsInNeighborhoods(_not_ghost);
auto & mesh = this->model.getMesh();
mesh.registerEventHandler(*this, _ehp_non_local_manager);
/// store the number of current ghost elements for each type in the mesh
// ElementTypeMap<UInt> nb_ghost_protected;
// for (auto type : mesh.elementTypes(spatial_dimension, _ghost))
// nb_ghost_protected(mesh.getNbElement(type, _ghost), type, _ghost);
/// exchange the missing ghosts for the non-local neighborhoods
this->createNeighborhoodSynchronizers();
/// insert the ghost quadrature points of the non-local materials into the
/// non-local neighborhoods
this->callback->insertIntegrationPointsInNeighborhoods(_ghost);
FEEngine & fee = this->model.getFEEngine();
this->updatePairLists();
/// cleanup the unneccessary ghost elements
this->cleanupExtraGhostElements(); // nb_ghost_protected);
this->callback->initializeNonLocal();
this->setJacobians(fee, _ek_regular);
this->initNonLocalVariables();
this->computeWeights();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::setJacobians(const FEEngine & fe_engine,
const ElementKind & kind) {
Mesh & mesh = this->model.getMesh();
for (auto ghost_type : ghost_types) {
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type, kind)) {
jacobians(type, ghost_type) =
&fe_engine.getIntegratorInterface().getJacobians(type, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::createNeighborhood(const ID & weight_func,
const ID & neighborhood_id) {
AKANTU_DEBUG_IN();
auto weight_func_it = this->weight_function_types.find(weight_func);
AKANTU_DEBUG_ASSERT(weight_func_it != weight_function_types.end(),
"No info found in the input file for the weight_function "
<< weight_func << " in the neighborhood "
<< neighborhood_id);
const ParserSection & section = weight_func_it->second;
const ID weight_func_type = section.getOption();
/// create new neighborhood for given ID
std::stringstream sstr;
sstr << id << ":neighborhood:" << neighborhood_id;
if (weight_func_type == "base_wf")
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<BaseWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
#if defined(AKANTU_DAMAGE_NON_LOCAL)
else if (weight_func_type == "remove_wf")
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<RemoveDamagedWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
else if (weight_func_type == "stress_wf")
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<StressBasedWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
else if (weight_func_type == "damage_wf")
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<DamagedWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
#endif
else
AKANTU_EXCEPTION("error in weight function type provided in material file");
neighborhoods[neighborhood_id]->parseSection(section);
neighborhoods[neighborhood_id]->initNeighborhood();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::createNeighborhoodSynchronizers() {
/// exchange all the neighborhood IDs, so that every proc knows how many
/// neighborhoods exist globally
/// First: Compute locally the maximum ID size
UInt max_id_size = 0;
UInt current_size = 0;
NeighborhoodMap::const_iterator it;
for (it = neighborhoods.begin(); it != neighborhoods.end(); ++it) {
current_size = it->first.size();
if (current_size > max_id_size)
max_id_size = current_size;
}
/// get the global maximum ID size on each proc
const Communicator & static_communicator = model.getMesh().getCommunicator();
static_communicator.allReduce(max_id_size, SynchronizerOperation::_max);
/// get the rank for this proc and the total nb proc
UInt prank = static_communicator.whoAmI();
UInt psize = static_communicator.getNbProc();
/// exchange the number of neighborhoods on each proc
Array<Int> nb_neighborhoods_per_proc(psize);
nb_neighborhoods_per_proc(prank) = neighborhoods.size();
static_communicator.allGather(nb_neighborhoods_per_proc);
/// compute the total number of neighborhoods
UInt nb_neighborhoods_global = std::accumulate(
nb_neighborhoods_per_proc.begin(), nb_neighborhoods_per_proc.end(), 0);
/// allocate an array of chars to store the names of all neighborhoods
Array<char> buffer(nb_neighborhoods_global, max_id_size);
/// starting index on this proc
UInt starting_index =
std::accumulate(nb_neighborhoods_per_proc.begin(),
nb_neighborhoods_per_proc.begin() + prank, 0);
it = neighborhoods.begin();
/// store the names of local neighborhoods in the buffer
for (UInt i = 0; i < neighborhoods.size(); ++i, ++it) {
UInt c = 0;
for (; c < it->first.size(); ++c)
buffer(i + starting_index, c) = it->first[c];
for (; c < max_id_size; ++c)
buffer(i + starting_index, c) = char(0);
}
/// store the nb of data to send in the all gather
Array<Int> buffer_size(nb_neighborhoods_per_proc);
buffer_size *= max_id_size;
/// exchange the names of all the neighborhoods with all procs
static_communicator.allGatherV(buffer, buffer_size);
for (UInt i = 0; i < nb_neighborhoods_global; ++i) {
std::stringstream neighborhood_id;
for (UInt c = 0; c < max_id_size; ++c) {
if (buffer(i, c) == char(0))
break;
neighborhood_id << buffer(i, c);
}
global_neighborhoods.insert(neighborhood_id.str());
}
/// this proc does not know all the neighborhoods -> create dummy
/// grid so that this proc can participate in the all gather for
/// detecting the overlap of neighborhoods this proc doesn't know
Vector<Real> grid_center(this->spatial_dimension,
std::numeric_limits<Real>::max());
Vector<Real> spacing(this->spatial_dimension, 0.);
dummy_grid = std::make_unique<SpatialGrid<IntegrationPoint>>(
this->spatial_dimension, spacing, grid_center);
for (auto & neighborhood_id : global_neighborhoods) {
it = neighborhoods.find(neighborhood_id);
if (it != neighborhoods.end()) {
it->second->createGridSynchronizer();
} else {
dummy_synchronizers[neighborhood_id] = std::make_unique<GridSynchronizer>(
this->model.getMesh(), *dummy_grid,
std::string(this->id + ":" + neighborhood_id + ":grid_synchronizer"),
this->memory_id, false);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) {
for (auto & neighborhood_id : global_neighborhoods) {
auto it = neighborhoods.find(neighborhood_id);
if (it != neighborhoods.end()) {
it->second->synchronize(data_accessor, tag);
} else {
auto synchronizer_it = dummy_synchronizers.find(neighborhood_id);
if (synchronizer_it == dummy_synchronizers.end())
continue;
synchronizer_it->second->synchronizeOnce(data_accessor, tag);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::averageInternals(const GhostType & ghost_type) {
/// update the weights of the weight function
if (ghost_type == _not_ghost)
this->computeWeights();
/// loop over all neighborhoods and compute the non-local variables
for (auto & neighborhood : neighborhoods) {
/// loop over all the non-local variables of the given neighborhood
for (auto & non_local_variable : non_local_variables) {
NonLocalVariable & non_local_var = *non_local_variable.second;
neighborhood.second->weightedAverageOnNeighbours(
non_local_var.local, non_local_var.non_local,
non_local_var.nb_component, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::computeWeights() {
AKANTU_DEBUG_IN();
this->updateWeightFunctionInternals();
this->volumes.clear();
for (const auto & global_neighborhood : global_neighborhoods) {
auto it = neighborhoods.find(global_neighborhood);
if (it != neighborhoods.end())
it->second->updateWeights();
else {
dummy_synchronizers[global_neighborhood]->synchronize(dummy_accessor,
_gst_mnl_weight);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::updatePairLists() {
AKANTU_DEBUG_IN();
integration_points_positions.initialize(
this->model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension);
/// compute the position of the quadrature points
this->model.getFEEngine().computeIntegrationPointsCoordinates(
integration_points_positions);
for (auto & pair : neighborhoods)
pair.second->updatePairList();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::registerNonLocalVariable(const ID & variable_name,
const ID & nl_variable_name,
UInt nb_component) {
AKANTU_DEBUG_IN();
auto non_local_variable_it = non_local_variables.find(variable_name);
if (non_local_variable_it == non_local_variables.end())
non_local_variables[nl_variable_name] = std::make_unique<NonLocalVariable>(
variable_name, nl_variable_name, this->id, nb_component);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementTypeMapReal &
NonLocalManager::registerWeightFunctionInternal(const ID & field_name) {
AKANTU_DEBUG_IN();
auto it = this->weight_function_internals.find(field_name);
if (it == weight_function_internals.end()) {
weight_function_internals[field_name] =
std::make_unique<ElementTypeMapReal>(field_name, this->id,
this->memory_id);
}
AKANTU_DEBUG_OUT();
return *(weight_function_internals[field_name]);
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::updateWeightFunctionInternals() {
for (auto & pair : this->weight_function_internals) {
auto & internals = *pair.second;
internals.clear();
for (auto ghost_type : ghost_types)
this->callback->updateLocalInternal(internals, ghost_type, _ek_regular);
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::initNonLocalVariables() {
/// loop over all the non-local variables
for (auto & pair : non_local_variables) {
auto & variable = *pair.second;
variable.non_local.initialize(this->model.getFEEngine(),
_nb_component = variable.nb_component,
_spatial_dimension = spatial_dimension);
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::computeAllNonLocalStresses() {
/// update the flattened version of the internals
for (auto & pair : non_local_variables) {
auto & variable = *pair.second;
variable.local.clear();
variable.non_local.clear();
for (auto ghost_type : ghost_types) {
this->callback->updateLocalInternal(variable.local, ghost_type,
_ek_regular);
}
}
this->volumes.clear();
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
neighborhood.asynchronousSynchronize(_gst_mnl_for_average);
}
this->averageInternals(_not_ghost);
AKANTU_DEBUG_INFO("Wait distant non local stresses");
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
neighborhood.waitEndSynchronize(_gst_mnl_for_average);
}
this->averageInternals(_ghost);
/// copy the results in the materials
for (auto & pair : non_local_variables) {
auto & variable = *pair.second;
for (auto ghost_type : ghost_types) {
this->callback->updateNonLocalInternal(variable.non_local, ghost_type,
_ek_regular);
}
}
this->callback->computeNonLocalStresses(_not_ghost);
++this->compute_stress_calls;
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::cleanupExtraGhostElements() {
// ElementTypeMap<UInt> & nb_ghost_protected) {
using ElementSet = std::set<Element>;
ElementSet relevant_ghost_elements;
/// loop over all the neighborhoods and get their protected ghosts
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
ElementSet to_keep_per_neighborhood;
neighborhood.cleanupExtraGhostElements(to_keep_per_neighborhood);
for (auto & element : to_keep_per_neighborhood)
relevant_ghost_elements.insert(element);
}
// /// remove all unneccessary ghosts from the mesh
// /// Create list of element to remove and new numbering for element to keep
// Mesh & mesh = this->model.getMesh();
// ElementSet ghost_to_erase;
// RemovedElementsEvent remove_elem(mesh);
// auto & new_numberings = remove_elem.getNewNumbering();
// Element element;
// element.ghost_type = _ghost;
// for (auto & type : mesh.elementTypes(spatial_dimension, _ghost)) {
// element.type = type;
// UInt nb_ghost_elem = mesh.getNbElement(type, _ghost);
// // UInt nb_ghost_elem_protected = 0;
// // try {
// // nb_ghost_elem_protected = nb_ghost_protected(type, _ghost);
// // } catch (...) {
// // }
// if (!new_numberings.exists(type, _ghost))
// new_numberings.alloc(nb_ghost_elem, 1, type, _ghost);
// else
// new_numberings(type, _ghost).resize(nb_ghost_elem);
// Array<UInt> & new_numbering = new_numberings(type, _ghost);
// for (UInt g = 0; g < nb_ghost_elem; ++g) {
// element.element = g;
// if (element.element >= nb_ghost_elem_protected &&
// relevant_ghost_elements.find(element) ==
// relevant_ghost_elements.end()) {
// remove_elem.getList().push_back(element);
// new_numbering(element.element) = UInt(-1);
// }
// }
// /// renumber remaining ghosts
// UInt ng = 0;
// for (UInt g = 0; g < nb_ghost_elem; ++g) {
// if (new_numbering(g) != UInt(-1)) {
// new_numbering(g) = ng;
// ++ng;
// }
// }
// }
// for (auto & type : mesh.elementTypes(spatial_dimension, _not_ghost)) {
// UInt nb_elem = mesh.getNbElement(type, _not_ghost);
// if (!new_numberings.exists(type, _not_ghost))
// new_numberings.alloc(nb_elem, 1, type, _not_ghost);
// Array<UInt> & new_numbering = new_numberings(type, _not_ghost);
// for (UInt e = 0; e < nb_elem; ++e) {
// new_numbering(e) = e;
// }
// }
// mesh.sendEvent(remove_elem);
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
FEEngine & fee = this->model.getFEEngine();
this->removeIntegrationPointsFromMap(
event.getNewNumbering(), spatial_dimension, integration_points_positions,
fee, _ek_regular);
this->removeIntegrationPointsFromMap(event.getNewNumbering(), 1, volumes, fee,
_ek_regular);
/// loop over all the neighborhoods and call onElementsRemoved
auto global_neighborhood_it = global_neighborhoods.begin();
NeighborhoodMap::iterator it;
for (; global_neighborhood_it != global_neighborhoods.end();
++global_neighborhood_it) {
it = neighborhoods.find(*global_neighborhood_it);
if (it != neighborhoods.end())
it->second->onElementsRemoved(element_list, new_numbering, event);
else
dummy_synchronizers[*global_neighborhood_it]->onElementsRemoved(
element_list, new_numbering, event);
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::onElementsAdded(const Array<Element> &,
const NewElementsEvent &) {
this->resizeElementTypeMap(1, volumes, model.getFEEngine());
this->resizeElementTypeMap(spatial_dimension, integration_points_positions,
model.getFEEngine());
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::resizeElementTypeMap(UInt nb_component,
ElementTypeMapReal & element_map,
const FEEngine & fee,
const ElementKind el_kind) {
Mesh & mesh = this->model.getMesh();
for (auto gt : ghost_types) {
for (auto type : mesh.elementTypes(spatial_dimension, gt, el_kind)) {
UInt nb_element = mesh.getNbElement(type, gt);
UInt nb_quads = fee.getNbIntegrationPoints(type, gt);
if (!element_map.exists(type, gt))
element_map.alloc(nb_element * nb_quads, nb_component, type, gt);
else
element_map(type, gt).resize(nb_element * nb_quads);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::removeIntegrationPointsFromMap(
const ElementTypeMapArray<UInt> & new_numbering, UInt nb_component,
ElementTypeMapReal & element_map, const FEEngine & fee,
const ElementKind el_kind) {
for (auto gt : ghost_types) {
for (auto type : new_numbering.elementTypes(_all_dimensions, gt, el_kind)) {
if (element_map.exists(type, gt)) {
const Array<UInt> & renumbering = new_numbering(type, gt);
Array<Real> & vect = element_map(type, gt);
UInt nb_quad_per_elem = fee.getNbIntegrationPoints(type, gt);
Array<Real> tmp(renumbering.size() * nb_quad_per_elem, nb_component);
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created or disappeared in "
<< vect.getID() << "(" << vect.size() << "!=" << tmp.size()
<< ") "
"!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
memcpy(tmp.storage() + new_i * nb_component * nb_quad_per_elem,
vect.storage() + i * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem * sizeof(Real));
++new_size;
}
}
tmp.resize(new_size * nb_quad_per_elem);
vect.copy(tmp);
}
}
}
}
/* -------------------------------------------------------------------------- */
UInt NonLocalManager::getNbData(const Array<Element> & elements,
const ID & id) const {
UInt size = 0;
UInt nb_quadrature_points = this->model.getNbIntegrationPoints(elements);
auto it = non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
size += it->second->nb_component * sizeof(Real) * nb_quadrature_points;
return size;
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & id) const {
auto it = non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
DataAccessor<Element>::packElementalDataHelper<Real>(
it->second->local, buffer, elements, true, this->model.getFEEngine());
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & id) const {
auto it = non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
DataAccessor<Element>::unpackElementalDataHelper<Real>(
it->second->local, buffer, elements, true, this->model.getFEEngine());
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/non_local_manager.hh b/src/model/common/non_local_toolbox/non_local_manager.hh
index cca5c52f1..775fb4982 100644
--- a/src/model/common/non_local_toolbox/non_local_manager.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager.hh
@@ -1,292 +1,292 @@
/**
* @file non_local_manager.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Classes that manages all the non-local neighborhoods
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
#include "data_accessor.hh"
#include "mesh_events.hh"
#include "non_local_manager_callback.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_MANAGER_HH__
#define __AKANTU_NON_LOCAL_MANAGER_HH__
namespace akantu {
class Model;
class NonLocalNeighborhoodBase;
class GridSynchronizer;
class SynchronizerRegistry;
class IntegrationPoint;
template <typename T> class SpatialGrid;
class FEEngine;
} // namespace akantu
namespace akantu {
class NonLocalManager : protected Memory,
public MeshEventHandler,
public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalManager(Model & model, NonLocalManagerCallback & callback,
const ID & id = "non_local_manager",
const MemoryID & memory_id = 0);
~NonLocalManager() override;
using NeighborhoodMap =
std::map<ID, std::unique_ptr<NonLocalNeighborhoodBase>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ----------------------------------------------------------------------- */
public:
/// register a new internal needed for the weight computations
ElementTypeMapReal & registerWeightFunctionInternal(const ID & field_name);
/// register a non-local variable
void registerNonLocalVariable(const ID & variable_name,
const ID & nl_variable_name, UInt nb_component);
/// register non-local neighborhood
inline void registerNeighborhood(const ID & neighborhood,
const ID & weight_func_id);
// void registerNonLocalManagerCallback(NonLocalManagerCallback & callback);
/// average the internals and compute the non-local stresses
virtual void computeAllNonLocalStresses();
/// initialize the non-local manager: compute pair lists and weights for all
/// neighborhoods
virtual void initialize();
/// synchronize once on a given tag using the neighborhoods synchronizer
void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag &);
protected:
/// create the grid synchronizers for each neighborhood
void createNeighborhoodSynchronizers();
/// compute the weights in each neighborhood for non-local averaging
void computeWeights();
/// compute the weights in each neighborhood for non-local averaging
void updatePairLists();
/// average the non-local variables
void averageInternals(const GhostType & ghost_type = _not_ghost);
/// update the flattened version of the weight function internals
void updateWeightFunctionInternals();
protected:
/// create a new neighborhood for a given domain ID
void createNeighborhood(const ID & weight_func, const ID & neighborhood);
/// set the values of the jacobians
void setJacobians(const FEEngine & fe_engine, const ElementKind & kind);
/// allocation of eelment type maps
// void initElementTypeMap(UInt nb_component,
// ElementTypeMapReal & element_map,
// const FEEngine & fe_engine,
// const ElementKind el_kind = _ek_regular);
/// resizing of element type maps
void resizeElementTypeMap(UInt nb_component, ElementTypeMapReal & element_map,
const FEEngine & fee,
const ElementKind el_kind = _ek_regular);
/// remove integration points from element type maps
void removeIntegrationPointsFromMap(
const ElementTypeMapArray<UInt> & new_numbering, UInt nb_component,
ElementTypeMapReal & element_map, const FEEngine & fee,
const ElementKind el_kind = _ek_regular);
/// allocate the non-local variables
void initNonLocalVariables();
/// cleanup unneccessary ghosts
void
cleanupExtraGhostElements(); // ElementTypeMap<UInt> & nb_ghost_protected);
/* ------------------------------------------------------------------------ */
/* DataAccessor kind of interface */
/* ------------------------------------------------------------------------ */
public:
/// get Nb data for synchronization in parallel
UInt getNbData(const Array<Element> & elements, const ID & id) const;
/// pack data for synchronization in parallel
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const ID & id) const;
/// unpack data for synchronization in parallel
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const ID & id) const;
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override {}
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override {}
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) override{};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
AKANTU_GET_MACRO(Model, model, const Model &);
AKANTU_GET_MACRO_NOT_CONST(Model, model, Model &);
AKANTU_GET_MACRO_NOT_CONST(Volumes, volumes, ElementTypeMapReal &)
AKANTU_GET_MACRO(NbStressCalls, compute_stress_calls, UInt);
/// return the fem object associated with a provided name
inline NonLocalNeighborhoodBase & getNeighborhood(const ID & name) const;
inline const Array<Real> & getJacobians(const ElementType & type,
const GhostType & ghost_type) {
return *jacobians(type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the spatial dimension
const UInt spatial_dimension;
protected:
/// the non-local neighborhoods present
NeighborhoodMap neighborhoods;
/// list of all the non-local materials in the model
// std::vector<ID> non_local_materials;
struct NonLocalVariable {
NonLocalVariable(const ID & variable_name, const ID & nl_variable_name,
const ID & id, UInt nb_component)
: local(variable_name, id, 0), non_local(nl_variable_name, id, 0),
nb_component(nb_component) {}
ElementTypeMapReal local;
ElementTypeMapReal non_local;
UInt nb_component;
};
/// the non-local variables associated to a certain neighborhood
std::map<ID, std::unique_ptr<NonLocalVariable>> non_local_variables;
/// reference to the model
Model & model;
/// jacobians for all the elements in the mesh
ElementTypeMap<const Array<Real> *> jacobians;
/// store the position of the quadrature points
ElementTypeMapReal integration_points_positions;
/// store the volume of each quadrature point for the non-local weight
/// normalization
ElementTypeMapReal volumes;
/// counter for computeStress calls
UInt compute_stress_calls;
/// map to store weight function types from input file
std::map<ID, ParserSection> weight_function_types;
/// map to store the internals needed by the weight functions
std::map<ID, std::unique_ptr<ElementTypeMapReal>> weight_function_internals;
/* --------------------------------------------------------------------------
*/
/// the following are members needed to make this processor participate in the
/// grid creation of neighborhoods he doesn't own as a member. For details see
/// createGridSynchronizers function
/// synchronizer registry for dummy grid synchronizers
std::unique_ptr<SynchronizerRegistry> dummy_registry;
/// map of dummy synchronizers
std::map<ID, std::unique_ptr<GridSynchronizer>> dummy_synchronizers;
/// dummy spatial grid
std::unique_ptr<SpatialGrid<IntegrationPoint>> dummy_grid;
/// create a set of all neighborhoods present in the simulation
std::set<ID> global_neighborhoods;
class DummyDataAccessor : public DataAccessor<Element> {
public:
inline UInt getNbData(const Array<Element> &,
const SynchronizationTag &) const override {
return 0;
};
inline void packData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) const override{};
inline void unpackData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) override{};
};
DummyDataAccessor dummy_accessor;
/* ------------------------------------------------------------------------ */
NonLocalManagerCallback * callback;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "non_local_manager_inline_impl.cc"
#endif /* __AKANTU_NON_LOCAL_MANAGER_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager_callback.hh b/src/model/common/non_local_toolbox/non_local_manager_callback.hh
index f29671b4d..b44a520e8 100644
--- a/src/model/common/non_local_toolbox/non_local_manager_callback.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager_callback.hh
@@ -1,66 +1,68 @@
/**
* @file non_local_manager_callback.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Sun Jul 09 2017
+ * @date creation: Fri Jul 21 2017
+ * @date last modification: Tue Sep 19 2017
*
- * @brief Callback functions for the non local manager
+ * @brief Callback functions for the non local manager
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH__
#define __AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH__
namespace akantu {
class NonLocalManager;
} // namespace akantu
namespace akantu {
class NonLocalManagerCallback {
public:
virtual void initializeNonLocal() {}
/* ------------------------------------------------------------------------ */
virtual void
insertIntegrationPointsInNeighborhoods(const GhostType & ghost_type) = 0;
virtual void computeNonLocalStresses(const GhostType & ghost_type) = 0;
/// update the values of the non local internal
virtual void updateLocalInternal(ElementTypeMapReal & internal_flat,
const GhostType & ghost_type,
const ElementKind & kind) = 0;
/// copy the results of the averaging in the materials
virtual void updateNonLocalInternal(ElementTypeMapReal & internal_flat,
const GhostType & ghost_type,
const ElementKind & kind) = 0;
};
} // namespace akantu
#endif /* __AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager_inline_impl.cc b/src/model/common/non_local_toolbox/non_local_manager_inline_impl.cc
index 8b63d0073..3649b1019 100644
--- a/src/model/common/non_local_toolbox/non_local_manager_inline_impl.cc
+++ b/src/model/common/non_local_toolbox/non_local_manager_inline_impl.cc
@@ -1,69 +1,68 @@
/**
* @file non_local_manager_inline_impl.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Mon Sep 11 2017
*
* @brief inline implementation of non-local manager functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_CC__
#define __AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::registerNeighborhood(const ID & neighborhood,
const ID & weight_func_id) {
/// check if neighborhood has already been created
auto it = neighborhoods.find(neighborhood);
if (it == neighborhoods.end()) {
this->createNeighborhood(weight_func_id, neighborhood);
}
}
/* -------------------------------------------------------------------------- */
inline NonLocalNeighborhoodBase &
NonLocalManager::getNeighborhood(const ID & name) const {
AKANTU_DEBUG_IN();
auto it = neighborhoods.find(name);
AKANTU_DEBUG_ASSERT(it != neighborhoods.end(),
"The neighborhood " << name << " is not registered");
AKANTU_DEBUG_OUT();
return *(it->second);
}
} // namespace akantu
#endif /* __AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_CC__ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood.hh b/src/model/common/non_local_toolbox/non_local_neighborhood.hh
index a847e9947..1dfd507e0 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood.hh
@@ -1,136 +1,135 @@
/**
* @file non_local_neighborhood.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Non-local neighborhood for non-local averaging based on
* weight function
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_HH__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_HH__
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
#include "non_local_neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class NonLocalManager;
class BaseWeightFunction;
} // namespace akantu
namespace akantu {
template <class WeightFunction = BaseWeightFunction>
class NonLocalNeighborhood : public NonLocalNeighborhoodBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalNeighborhood(NonLocalManager & manager,
const ElementTypeMapReal & quad_coordinates,
const ID & id = "neighborhood",
const MemoryID & memory_id = 0);
~NonLocalNeighborhood() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// compute the weights for non-local averaging
void computeWeights() override;
/// save the pair of weights in a file
void saveWeights(const std::string & filename) const override;
/// compute the non-local counter part for a given element type map
// compute the non-local counter part for a given element type map
void
weightedAverageOnNeighbours(const ElementTypeMapReal & to_accumulate,
ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom,
const GhostType & ghost_type2) const override;
/// update the weights based on the weight function
void updateWeights() override;
/// register a new non-local variable in the neighborhood
// void registerNonLocalVariable(const ID & id);
protected:
template <class Func>
inline void foreach_weight(const GhostType & ghost_type, Func && func);
template <class Func>
inline void foreach_weight(const GhostType & ghost_type, Func && func) const;
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(NonLocalManager, non_local_manager, const NonLocalManager &);
AKANTU_GET_MACRO_NOT_CONST(NonLocalManager, non_local_manager,
NonLocalManager &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Pointer to non-local manager class
NonLocalManager & non_local_manager;
/// the weights associated to the pairs
std::array<std::unique_ptr<Array<Real>>, 2> pair_weight;
/// weight function
std::unique_ptr<WeightFunction> weight_function;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Implementation of template functions */
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_inline_impl.cc"
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc b/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
index 81cf8934a..3e98bcc82 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
@@ -1,117 +1,117 @@
/**
* @file non_local_neighborhood_base.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Fri Dec 08 2017
*
* @brief Implementation of non-local neighborhood base
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_base.hh"
#include "grid_synchronizer.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLocalNeighborhoodBase::NonLocalNeighborhoodBase(
Model & model, const ElementTypeMapReal & quad_coordinates, const ID & id,
const MemoryID & memory_id)
: NeighborhoodBase(model, quad_coordinates, id, memory_id),
Parsable(ParserType::_non_local, id) {
AKANTU_DEBUG_IN();
this->registerParam("radius", neighborhood_radius, 100.,
_pat_parsable | _pat_readable, "Non local radius");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NonLocalNeighborhoodBase::~NonLocalNeighborhoodBase() = default;
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::createGridSynchronizer() {
this->is_creating_grid = true;
this->grid_synchronizer = std::make_unique<GridSynchronizer>(
this->model.getMesh(), *spatial_grid, *this,
std::set<SynchronizationTag>{_gst_mnl_weight, _gst_mnl_for_average},
std::string(getID() + ":grid_synchronizer"), this->memory_id, false);
this->is_creating_grid = false;
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::synchronize(
DataAccessor<Element> & data_accessor, const SynchronizationTag & tag) {
if (not grid_synchronizer)
return;
grid_synchronizer->synchronizeOnce(data_accessor, tag);
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::cleanupExtraGhostElements(
std::set<Element> & relevant_ghost_elements) {
for (auto && pair : pair_list[_ghost]) {
const auto & q2 = pair.second;
relevant_ghost_elements.insert(q2);
}
Array<Element> ghosts_to_erase(0);
auto & mesh = this->model.getMesh();
Element element;
element.ghost_type = _ghost;
auto end = relevant_ghost_elements.end();
for (auto & type : mesh.elementTypes(spatial_dimension, _ghost)) {
element.type = type;
UInt nb_ghost_elem = mesh.getNbElement(type, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
element.element = g;
if (relevant_ghost_elements.find(element) == end) {
ghosts_to_erase.push_back(element);
}
}
}
/// remove the unneccessary ghosts from the synchronizer
// this->grid_synchronizer->removeElements(ghosts_to_erase);
mesh.eraseElements(ghosts_to_erase);
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::registerNonLocalVariable(const ID & id) {
this->non_local_variables.insert(id);
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
index 3d6cfbe06..238705e74 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
@@ -1,128 +1,129 @@
/**
* @file non_local_neighborhood_base.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Non-local neighborhood base class
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__
namespace akantu {
class Model;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class NonLocalNeighborhoodBase : public NeighborhoodBase, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalNeighborhoodBase(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id = "non_local_neighborhood",
const MemoryID & memory_id = 0);
~NonLocalNeighborhoodBase() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create grid synchronizer and exchange ghost cells
void createGridSynchronizer() override;
void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) override;
/// compute weights, for instance needed for non-local damage computation
virtual void computeWeights(){};
// compute the non-local counter part for a given element type map
virtual void
weightedAverageOnNeighbours(const ElementTypeMapReal & to_accumulate,
ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom,
const GhostType & ghost_type2) const = 0;
/// update the weights for the non-local averaging
virtual void updateWeights() = 0;
/// update the weights for the non-local averaging
virtual void saveWeights(const std::string &) const { AKANTU_TO_IMPLEMENT(); }
/// register a new non-local variable in the neighborhood
virtual void registerNonLocalVariable(const ID & id);
/// clean up the unneccessary ghosts
void cleanupExtraGhostElements(std::set<Element> & relevant_ghost_elements);
protected:
/// create the grid
void createGrid();
/* --------------------------------------------------------------------------
*/
/* DataAccessor inherited members */
/* --------------------------------------------------------------------------
*/
public:
inline UInt getNbData(const Array<Element> &,
const SynchronizationTag &) const override {
return 0;
}
inline void packData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) const override {}
inline void unpackData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) override {}
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
AKANTU_GET_MACRO(NonLocalVariables, non_local_variables,
const std::set<ID> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// list of non-local variables associated to the neighborhood
std::set<ID> non_local_variables;
};
} // namespace akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc b/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc
index 389da6687..50e9cf512 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc
@@ -1,86 +1,87 @@
/**
* @file non_local_neighborhood_inline_impl.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 06 2015
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Thu Jul 06 2017
*
* @brief Implementation of inline functions of non-local neighborhood class
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_CC__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
inline UInt NonLocalNeighborhood<WeightFunction>::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
UInt size = 0;
if (tag == _gst_mnl_for_average) {
for (auto & variable_id : non_local_variables) {
size += this->non_local_manager.getNbData(elements, variable_id);
}
}
size += this->weight_function->getNbData(elements, tag);
return size;
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
inline void NonLocalNeighborhood<WeightFunction>::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_mnl_for_average) {
for (auto & variable_id : non_local_variables) {
this->non_local_manager.packData(buffer, elements, variable_id);
}
}
this->weight_function->packData(buffer, elements, tag);
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
inline void NonLocalNeighborhood<WeightFunction>::unpackData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == _gst_mnl_for_average) {
for (auto & variable_id : non_local_variables) {
this->non_local_manager.unpackData(buffer, elements, variable_id);
}
}
this->weight_function->unpackData(buffer, elements, tag);
}
} // namespace akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_CC__ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
index e6283a065..51ea76127 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
@@ -1,276 +1,276 @@
/**
* @file non_local_neighborhood_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 28 2015
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of class non-local neighborhood
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "non_local_manager.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
template <class Func>
inline void NonLocalNeighborhood<WeightFunction>::foreach_weight(
const GhostType & ghost_type, Func && func) {
auto weight_it =
pair_weight[ghost_type]->begin(pair_weight[ghost_type]->getNbComponent());
for (auto & pair : pair_list[ghost_type]) {
std::forward<decltype(func)>(func)(pair.first, pair.second, *weight_it);
++weight_it;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
template <class Func>
inline void NonLocalNeighborhood<WeightFunction>::foreach_weight(
const GhostType & ghost_type, Func && func) const {
auto weight_it =
pair_weight[ghost_type]->begin(pair_weight[ghost_type]->getNbComponent());
for (auto & pair : pair_list[ghost_type]) {
std::forward<decltype(func)>(func)(pair.first, pair.second, *weight_it);
++weight_it;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
NonLocalNeighborhood<WeightFunction>::NonLocalNeighborhood(
NonLocalManager & manager, const ElementTypeMapReal & quad_coordinates,
const ID & id, const MemoryID & memory_id)
: NonLocalNeighborhoodBase(manager.getModel(), quad_coordinates, id,
memory_id),
non_local_manager(manager) {
AKANTU_DEBUG_IN();
this->weight_function = std::make_unique<WeightFunction>(manager);
this->registerSubSection(ParserType::_weight_function, "weight_parameter",
*weight_function);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
NonLocalNeighborhood<WeightFunction>::~NonLocalNeighborhood() = default;
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::computeWeights() {
AKANTU_DEBUG_IN();
this->weight_function->setRadius(this->neighborhood_radius);
Vector<Real> q1_coord(this->spatial_dimension);
Vector<Real> q2_coord(this->spatial_dimension);
UInt nb_weights_per_pair = 2; /// w1: q1->q2, w2: q2->q1
/// get the elementtypemap for the neighborhood volume for each quadrature
/// point
ElementTypeMapReal & quadrature_points_volumes =
this->non_local_manager.getVolumes();
/// update the internals of the weight function if applicable (not
/// all the weight functions have internals and do noting in that
/// case)
weight_function->updateInternals();
for (auto ghost_type : ghost_types) {
/// allocate the array to store the weight, if it doesn't exist already
if (!(pair_weight[ghost_type])) {
pair_weight[ghost_type] =
std::make_unique<Array<Real>>(0, nb_weights_per_pair);
}
/// resize the array to the correct size
pair_weight[ghost_type]->resize(pair_list[ghost_type].size());
/// set entries to zero
pair_weight[ghost_type]->clear();
/// loop over all pairs in the current pair list array and their
/// corresponding weights
auto first_pair = pair_list[ghost_type].begin();
auto last_pair = pair_list[ghost_type].end();
auto weight_it = pair_weight[ghost_type]->begin(nb_weights_per_pair);
// Compute the weights
for (; first_pair != last_pair; ++first_pair, ++weight_it) {
Vector<Real> & weight = *weight_it;
const IntegrationPoint & q1 = first_pair->first;
const IntegrationPoint & q2 = first_pair->second;
/// get the coordinates for the given pair of quads
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(this->spatial_dimension);
q1_coord = coords_type_1_it[q1.global_num];
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(this->spatial_dimension);
q2_coord = coords_type_2_it[q2.global_num];
Array<Real> & quad_volumes_1 =
quadrature_points_volumes(q1.type, q1.ghost_type);
const Array<Real> & jacobians_2 =
this->non_local_manager.getJacobians(q2.type, q2.ghost_type);
const Real & q2_wJ = jacobians_2(q2.global_num);
/// compute distance between the two quadrature points
Real r = q1_coord.distance(q2_coord);
/// compute the weight for averaging on q1 based on the distance
Real w1 = this->weight_function->operator()(r, q1, q2);
weight(0) = q2_wJ * w1;
quad_volumes_1(q1.global_num) += weight(0);
if (q2.ghost_type != _ghost && q1.global_num != q2.global_num) {
const Array<Real> & jacobians_1 =
this->non_local_manager.getJacobians(q1.type, q1.ghost_type);
Array<Real> & quad_volumes_2 =
quadrature_points_volumes(q2.type, q2.ghost_type);
/// compute the weight for averaging on q2
const Real & q1_wJ = jacobians_1(q1.global_num);
Real w2 = this->weight_function->operator()(r, q2, q1);
weight(1) = q1_wJ * w2;
quad_volumes_2(q2.global_num) += weight(1);
} else
weight(1) = 0.;
}
}
/// normalize the weights
for (auto ghost_type : ghost_types) {
foreach_weight(ghost_type, [&](const auto & q1, const auto & q2,
auto & weight) {
auto & quad_volumes_1 = quadrature_points_volumes(q1.type, q1.ghost_type);
auto & quad_volumes_2 = quadrature_points_volumes(q2.type, q2.ghost_type);
Real q1_volume = quad_volumes_1(q1.global_num);
auto ghost_type2 = q2.ghost_type;
weight(0) *= 1. / q1_volume;
if (ghost_type2 != _ghost) {
Real q2_volume = quad_volumes_2(q2.global_num);
weight(1) *= 1. / q2_volume;
}
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::saveWeights(
const std::string & filename) const {
std::ofstream pout;
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
pout.open(sstr.str().c_str());
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
auto ghost_type = (GhostType)gt;
AKANTU_DEBUG_ASSERT((pair_weight[ghost_type]),
"the weights have not been computed yet");
Array<Real> & weights = *(pair_weight[ghost_type]);
auto weights_it = weights.begin(2);
for (UInt i = 0; i < weights.size(); ++i, ++weights_it)
pout << "w1: " << (*weights_it)(0) << " w2: " << (*weights_it)(1)
<< std::endl;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::weightedAverageOnNeighbours(
const ElementTypeMapReal & to_accumulate, ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom, const GhostType & ghost_type2) const {
auto it = non_local_variables.find(accumulated.getName());
// do averaging only for variables registered in the neighborhood
if (it == non_local_variables.end())
return;
foreach_weight(
ghost_type2,
[ghost_type2, nb_degree_of_freedom, &to_accumulate,
&accumulated](const auto & q1, const auto & q2, auto & weight) {
const Vector<Real> to_acc_1 =
to_accumulate(q1.type, q1.ghost_type)
.begin(nb_degree_of_freedom)[q1.global_num];
const Vector<Real> to_acc_2 =
to_accumulate(q2.type, q2.ghost_type)
.begin(nb_degree_of_freedom)[q2.global_num];
Vector<Real> acc_1 = accumulated(q1.type, q1.ghost_type)
.begin(nb_degree_of_freedom)[q1.global_num];
Vector<Real> acc_2 = accumulated(q2.type, q2.ghost_type)
.begin(nb_degree_of_freedom)[q2.global_num];
acc_1 += weight(0) * to_acc_2;
if (ghost_type2 != _ghost) {
acc_2 += weight(1) * to_acc_1;
}
});
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::updateWeights() {
// Update the weights for the non local variable averaging
if (this->weight_function->getUpdateRate() &&
(this->non_local_manager.getNbStressCalls() %
this->weight_function->getUpdateRate() ==
0)) {
SynchronizerRegistry::synchronize(_gst_mnl_weight);
this->computeWeights();
}
}
} // namespace akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL__ */
diff --git a/src/model/dof_manager.cc b/src/model/dof_manager.cc
index 7aaa2fccc..9f282345d 100644
--- a/src/model/dof_manager.cc
+++ b/src/model/dof_manager.cc
@@ -1,604 +1,605 @@
/**
* @file dof_manager.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 12 09:52:30 2015
+ * @date creation: Tue Aug 18 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the common parts of the DOFManagers
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
#include "non_linear_solver.hh"
#include "sparse_matrix.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id),
communicator(Communicator::getStaticCommunicator()) {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(Mesh & mesh, const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(&mesh), local_system_size(0),
pure_local_system_size(0), system_size(0),
communicator(mesh.getCommunicator()) {
this->mesh->registerEventHandler(*this, _ehp_dof_manager);
}
/* -------------------------------------------------------------------------- */
DOFManager::~DOFManager() = default;
/* -------------------------------------------------------------------------- */
// void DOFManager::getEquationsNumbers(const ID &, Array<UInt> &) {
// AKANTU_TO_IMPLEMENT();
// }
/* -------------------------------------------------------------------------- */
std::vector<ID> DOFManager::getDOFIDs() const {
std::vector<ID> keys;
for (const auto & dof_data : this->dofs)
keys.push_back(dof_data.first);
return keys;
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayLocalArray(
const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
const ElementType & type, const GhostType & ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_element;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
UInt * filter_it = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filter_it = filter_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
AKANTU_DEBUG_ASSERT(elementary_vect.size() == nb_element,
"The vector elementary_vect("
<< elementary_vect.getID()
<< ") has not the good size.");
const Array<UInt> & connectivity =
this->mesh->getConnectivity(type, ghost_type);
// Array<UInt>::const_vector_iterator conn_begin =
// connectivity.begin(nb_nodes_per_element);
// Array<UInt>::const_vector_iterator conn_it = conn_begin;
Array<Real>::const_matrix_iterator elem_it =
elementary_vect.begin(nb_degree_of_freedom, nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el, ++elem_it) {
UInt element = el;
if (filter_it != nullptr) {
// conn_it = conn_begin + *filter_it;
element = *filter_it;
}
// const Vector<UInt> & conn = *conn_it;
const Matrix<Real> & elemental_val = *elem_it;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt offset_node = connectivity(element, n) * nb_degree_of_freedom;
Vector<Real> assemble(array_assembeled.storage() + offset_node,
nb_degree_of_freedom);
Vector<Real> elem_val = elemental_val(n);
assemble.aXplusY(elem_val, scale_factor);
}
if (filter_it != nullptr)
++filter_it;
// else
// ++conn_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayToResidual(
const ID & dof_id, const Array<Real> & elementary_vect,
const ElementType & type, const GhostType & ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
nb_degree_of_freedom);
array_localy_assembeled.clear();
this->assembleElementalArrayLocalArray(
elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
filter_elements);
this->assembleToResidual(dof_id, array_localy_assembeled, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayToLumpedMatrix(
const ID & dof_id, const Array<Real> & elementary_vect,
const ID & lumped_mtx, const ElementType & type,
const GhostType & ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
nb_degree_of_freedom);
array_localy_assembeled.clear();
this->assembleElementalArrayLocalArray(
elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
filter_elements);
this->assembleToLumpedMatrix(dof_id, array_localy_assembeled, lumped_mtx, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleMatMulDOFsToResidual(const ID & A_id,
Real scale_factor) {
for (auto & pair : this->dofs) {
const auto & dof_id = pair.first;
auto & dof_data = *pair.second;
this->assembleMatMulVectToResidual(dof_id, A_id, *dof_data.dof,
scale_factor);
}
}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::DOFData(const ID & dof_id)
: support_type(_dst_generic), group_support("__mesh__"), dof(nullptr),
blocked_dofs(nullptr), increment(nullptr), previous(nullptr),
solution(0, 1, dof_id + ":solution"),
local_equation_number(0, 1, dof_id + ":local_equation_number") {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::~DOFData() = default;
/* -------------------------------------------------------------------------- */
DOFManager::DOFData & DOFManager::getNewDOFData(const ID & dof_id) {
auto it = this->dofs.find(dof_id);
if (it != this->dofs.end()) {
AKANTU_EXCEPTION("This dof array has already been registered");
}
std::unique_ptr<DOFData> dofs_storage = std::make_unique<DOFData>(dof_id);
this->dofs[dof_id] = std::move(dofs_storage);
return *dofs_storage;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsInternal(const ID & dof_id,
Array<Real> & dofs_array) {
DOFData & dofs_storage = this->getDOFData(dof_id);
dofs_storage.dof = &dofs_array;
UInt nb_local_dofs = 0;
UInt nb_pure_local = 0;
const DOFSupportType & support_type = dofs_storage.support_type;
switch (support_type) {
case _dst_nodal: {
UInt nb_nodes = 0;
const ID & group = dofs_storage.group_support;
NodeGroup * node_group = nullptr;
if (group == "__mesh__") {
nb_nodes = this->mesh->getNbNodes();
} else {
node_group = &this->mesh->getElementGroup(group).getNodeGroup();
nb_nodes = node_group->size();
}
nb_local_dofs = nb_nodes;
AKANTU_DEBUG_ASSERT(
dofs_array.size() == nb_local_dofs,
"The array of dof is too shot to be associated to nodes.");
for (UInt n = 0; n < nb_nodes; ++n) {
UInt node = n;
if (node_group)
node = node_group->getNodes()(n);
nb_pure_local += this->mesh->isLocalOrMasterNode(node) ? 1 : 0;
}
nb_pure_local *= dofs_array.getNbComponent();
nb_local_dofs *= dofs_array.getNbComponent();
break;
}
case _dst_generic: {
nb_local_dofs = nb_pure_local =
dofs_array.size() * dofs_array.getNbComponent();
break;
}
default: { AKANTU_EXCEPTION("This type of dofs is not handled yet."); }
}
this->pure_local_system_size += nb_pure_local;
this->local_system_size += nb_local_dofs;
communicator.allReduce(nb_pure_local, SynchronizerOperation::_sum);
this->system_size += nb_pure_local;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type) {
DOFData & dofs_storage = this->getNewDOFData(dof_id);
dofs_storage.support_type = support_type;
this->registerDOFsInternal(dof_id, dofs_array);
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & support_group) {
DOFData & dofs_storage = this->getNewDOFData(dof_id);
dofs_storage.support_type = _dst_nodal;
dofs_storage.group_support = support_group;
this->registerDOFsInternal(dof_id, dofs_array);
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsPrevious(const ID & dof_id, Array<Real> & array) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.previous != nullptr) {
AKANTU_EXCEPTION("The previous dofs array for "
<< dof_id << " has already been registered");
}
dof.previous = &array;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsIncrement(const ID & dof_id, Array<Real> & array) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.increment != nullptr) {
AKANTU_EXCEPTION("The dofs increment array for "
<< dof_id << " has already been registered");
}
dof.increment = &array;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsDerivative(const ID & dof_id, UInt order,
Array<Real> & dofs_derivative) {
DOFData & dof = this->getDOFData(dof_id);
std::vector<Array<Real> *> & derivatives = dof.dof_derivatives;
if (derivatives.size() < order) {
derivatives.resize(order, nullptr);
} else {
if (derivatives[order - 1] != nullptr) {
AKANTU_EXCEPTION("The dof derivatives of order "
<< order << " already been registered for this dof ("
<< dof_id << ")");
}
}
derivatives[order - 1] = &dofs_derivative;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerBlockedDOFs(const ID & dof_id,
Array<bool> & blocked_dofs) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.blocked_dofs != nullptr) {
AKANTU_EXCEPTION("The blocked dofs array for "
<< dof_id << " has already been registered");
}
dof.blocked_dofs = &blocked_dofs;
}
/* -------------------------------------------------------------------------- */
void DOFManager::splitSolutionPerDOFs() {
auto it = this->dofs.begin();
auto end = this->dofs.end();
for (; it != end; ++it) {
DOFData & dof_data = *it->second;
dof_data.solution.resize(dof_data.dof->size() *
dof_data.dof->getNbComponent());
this->getSolutionPerDOFs(it->first, dof_data.solution);
}
}
/* -------------------------------------------------------------------------- */
SparseMatrix &
DOFManager::registerSparseMatrix(const ID & matrix_id,
std::unique_ptr<SparseMatrix> & matrix) {
SparseMatricesMap::const_iterator it = this->matrices.find(matrix_id);
if (it != this->matrices.end()) {
AKANTU_EXCEPTION("The matrix " << matrix_id << " already exists in "
<< this->id);
}
SparseMatrix & ret = *matrix;
this->matrices[matrix_id] = std::move(matrix);
return ret;
}
/* -------------------------------------------------------------------------- */
/// Get an instance of a new SparseMatrix
Array<Real> & DOFManager::getNewLumpedMatrix(const ID & id) {
ID matrix_id = this->id + ":lumped_mtx:" + id;
LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
if (it != this->lumped_matrices.end()) {
AKANTU_EXCEPTION("The lumped matrix " << matrix_id << " already exists in "
<< this->id);
}
auto mtx =
std::make_unique<Array<Real>>(this->local_system_size, 1, matrix_id);
this->lumped_matrices[matrix_id] = std::move(mtx);
return *this->lumped_matrices[matrix_id];
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & DOFManager::registerNonLinearSolver(
const ID & non_linear_solver_id,
std::unique_ptr<NonLinearSolver> & non_linear_solver) {
NonLinearSolversMap::const_iterator it =
this->non_linear_solvers.find(non_linear_solver_id);
if (it != this->non_linear_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
<< " already exists in "
<< this->id);
}
NonLinearSolver & ret = *non_linear_solver;
this->non_linear_solvers[non_linear_solver_id] = std::move(non_linear_solver);
return ret;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManager::registerTimeStepSolver(
const ID & time_step_solver_id,
std::unique_ptr<TimeStepSolver> & time_step_solver) {
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
if (it != this->time_step_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
<< " already exists in "
<< this->id);
}
TimeStepSolver & ret = *time_step_solver;
this->time_step_solvers[time_step_solver_id] = std::move(time_step_solver);
return ret;
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManager::getMatrix(const ID & id) {
ID matrix_id = this->id + ":mtx:" + id;
SparseMatricesMap::const_iterator it = this->matrices.find(matrix_id);
if (it == this->matrices.end()) {
AKANTU_SILENT_EXCEPTION("The matrix " << matrix_id << " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasMatrix(const ID & id) const {
ID mtx_id = this->id + ":mtx:" + id;
auto it = this->matrices.find(mtx_id);
return it != this->matrices.end();
}
/* -------------------------------------------------------------------------- */
Array<Real> & DOFManager::getLumpedMatrix(const ID & id) {
ID matrix_id = this->id + ":lumped_mtx:" + id;
LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
if (it == this->lumped_matrices.end()) {
AKANTU_SILENT_EXCEPTION("The lumped matrix "
<< matrix_id << " does not exists in " << this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManager::getLumpedMatrix(const ID & id) const {
ID matrix_id = this->id + ":lumped_mtx:" + id;
auto it = this->lumped_matrices.find(matrix_id);
if (it == this->lumped_matrices.end()) {
AKANTU_SILENT_EXCEPTION("The lumped matrix "
<< matrix_id << " does not exists in " << this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasLumpedMatrix(const ID & id) const {
ID mtx_id = this->id + ":lumped_mtx:" + id;
auto it = this->lumped_matrices.find(mtx_id);
return it != this->lumped_matrices.end();
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & DOFManager::getNonLinearSolver(const ID & id) {
ID non_linear_solver_id = this->id + ":nls:" + id;
NonLinearSolversMap::const_iterator it =
this->non_linear_solvers.find(non_linear_solver_id);
if (it == this->non_linear_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
<< " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasNonLinearSolver(const ID & id) const {
ID solver_id = this->id + ":nls:" + id;
auto it = this->non_linear_solvers.find(solver_id);
return it != this->non_linear_solvers.end();
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManager::getTimeStepSolver(const ID & id) {
ID time_step_solver_id = this->id + ":tss:" + id;
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
if (it == this->time_step_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
<< " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasTimeStepSolver(const ID & solver_id) const {
ID time_step_solver_id = this->id + ":tss:" + solver_id;
auto it = this->time_step_solvers.find(time_step_solver_id);
return it != this->time_step_solvers.end();
}
/* -------------------------------------------------------------------------- */
void DOFManager::savePreviousDOFs(const ID & dofs_id) {
this->getPreviousDOFs(dofs_id).copy(this->getDOFs(dofs_id));
}
/* -------------------------------------------------------------------------- */
/* Mesh Events */
/* -------------------------------------------------------------------------- */
std::pair<UInt, UInt>
DOFManager::updateNodalDOFs(const ID & dof_id, const Array<UInt> & nodes_list) {
auto & dof_data = this->getDOFData(dof_id);
UInt nb_new_local_dofs = 0;
UInt nb_new_pure_local = 0;
nb_new_local_dofs = nodes_list.size();
for (const auto & node : nodes_list) {
nb_new_pure_local += this->mesh->isLocalOrMasterNode(node) ? 1 : 0;
}
const auto & dof_array = *dof_data.dof;
nb_new_pure_local *= dof_array.getNbComponent();
nb_new_local_dofs *= dof_array.getNbComponent();
this->pure_local_system_size += nb_new_pure_local;
this->local_system_size += nb_new_local_dofs;
UInt nb_new_global = nb_new_pure_local;
communicator.allReduce(nb_new_global, SynchronizerOperation::_sum);
this->system_size += nb_new_global;
return std::make_pair(nb_new_local_dofs, nb_new_pure_local);
}
/* -------------------------------------------------------------------------- */
void DOFManager::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent &) {
for (auto & pair : this->dofs) {
const auto & dof_id = pair.first;
auto & dof_data = this->getDOFData(dof_id);
if (dof_data.support_type != _dst_nodal)
continue;
const auto & group = dof_data.group_support;
if (group == "__mesh__") {
this->updateNodalDOFs(dof_id, nodes_list);
} else {
const auto & node_group =
this->mesh->getElementGroup(group).getNodeGroup();
Array<UInt> new_nodes_list;
for (const auto & node : nodes_list) {
if (node_group.find(node) != UInt(-1))
new_nodes_list.push_back(node);
}
this->updateNodalDOFs(dof_id, new_nodes_list);
}
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) {}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsAdded(const Array<Element> &,
const NewElementsEvent &) {}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) {}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsChanged(const Array<Element> &,
const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) {}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/dof_manager.hh b/src/model/dof_manager.hh
index 981501a3c..4539874d8 100644
--- a/src/model/dof_manager.hh
+++ b/src/model/dof_manager.hh
@@ -1,475 +1,476 @@
/**
* @file dof_manager.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Jul 22 11:43:43 2015
+ * @date creation: Tue Aug 18 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Class handling the different types of dofs
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_MANAGER_HH__
#define __AKANTU_DOF_MANAGER_HH__
namespace akantu {
class TermsToAssemble;
class NonLinearSolver;
class TimeStepSolver;
class SparseMatrix;
} // namespace akantu
namespace akantu {
class DOFManager : protected Memory, protected MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManager(const ID & id = "dof_manager", const MemoryID & memory_id = 0);
DOFManager(Mesh & mesh, const ID & id = "dof_manager",
const MemoryID & memory_id = 0);
~DOFManager() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/// common function to help registering dofs
void registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array);
public:
/// register an array of degree of freedom
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type);
/// the dof as an implied type of _dst_nodal and is defined only on a subset
/// of nodes
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & group_support);
/// register an array of previous values of the degree of freedom
virtual void registerDOFsPrevious(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of increment of degree of freedom
virtual void registerDOFsIncrement(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of derivatives for a particular dof array
virtual void registerDOFsDerivative(const ID & dof_id, UInt order,
Array<Real> & dofs_derivative);
/// register array representing the blocked degree of freedoms
virtual void registerBlockedDOFs(const ID & dof_id,
Array<bool> & blocked_dofs);
/// Assemble an array to the global residual array
virtual void assembleToResidual(const ID & dof_id,
const Array<Real> & array_to_assemble,
Real scale_factor = 1.) = 0;
/// Assemble an array to the global lumped matrix array
virtual void assembleToLumpedMatrix(const ID & dof_id,
const Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor = 1.) = 0;
/**
* Assemble elementary values to a local array of the size nb_nodes *
* nb_dof_per_node. The dof number is implicitly considered as
* conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayLocalArray(
const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
const ElementType & type, const GhostType & ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayToResidual(
const ID & dof_id, const Array<Real> & elementary_vect,
const ElementType & type, const GhostType & ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to a global array corresponding to a lumped
* matrix
*/
virtual void assembleElementalArrayToLumpedMatrix(
const ID & dof_id, const Array<Real> & elementary_vect,
const ID & lumped_mtx, const ElementType & type,
const GhostType & ghost_type, Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d. With 0 <
* n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
const Array<Real> & elementary_mat, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const MatrixType & elemental_matrix_type = _symmetric,
const Array<UInt> & filter_elements = empty_filter) = 0;
/// multiply a vector by a matrix and assemble the result to the residual
virtual void assembleMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) = 0;
/// multiply the dofs by a matrix and assemble the result to the residual
virtual void assembleMatMulDOFsToResidual(const ID & A_id,
Real scale_factor = 1);
/// multiply a vector by a lumped matrix and assemble the result to the
/// residual
virtual void assembleLumpedMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) = 0;
/// assemble coupling terms between to dofs
virtual void assemblePreassembledMatrix(const ID & dof_id_m,
const ID & dof_id_n,
const ID & matrix_id,
const TermsToAssemble & terms) = 0;
/// sets the residual to 0
virtual void clearResidual() = 0;
/// sets the matrix to 0
virtual void clearMatrix(const ID & mtx) = 0;
/// sets the lumped matrix to 0
virtual void clearLumpedMatrix(const ID & mtx) = 0;
/// splits the solution storage from a global view to the per dof storages
void splitSolutionPerDOFs();
/// extract a lumped matrix part corresponding to a given dof
virtual void getLumpedMatrixPerDOFs(const ID & dof_id, const ID & lumped_mtx,
Array<Real> & lumped) = 0;
protected:
/// minimum functionality to implement per derived version of the DOFManager
/// to allow the splitSolutionPerDOFs function to work
virtual void getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array) = 0;
protected:
/* ------------------------------------------------------------------------ */
/// register a matrix
SparseMatrix & registerSparseMatrix(const ID & matrix_id,
std::unique_ptr<SparseMatrix> & matrix);
/// register a non linear solver instantiated by a derived class
NonLinearSolver &
registerNonLinearSolver(const ID & non_linear_solver_id,
std::unique_ptr<NonLinearSolver> & non_linear_solver);
/// register a time step solver instantiated by a derived class
TimeStepSolver &
registerTimeStepSolver(const ID & time_step_solver_id,
std::unique_ptr<TimeStepSolver> & time_step_solver);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the equation numbers corresponding to a dof_id. This might be used to
/// access the matrix.
inline const Array<UInt> & getEquationsNumbers(const ID & dof_id) const;
/// Global number of dofs
AKANTU_GET_MACRO(SystemSize, this->system_size, UInt);
/// Local number of dofs
AKANTU_GET_MACRO(LocalSystemSize, this->local_system_size, UInt);
/// Retrieve all the registered DOFs
std::vector<ID> getDOFIDs() const;
/* ------------------------------------------------------------------------ */
/* DOFs and derivatives accessors */
/* ------------------------------------------------------------------------ */
/// Get a reference to the registered dof array for a given id
inline Array<Real> & getDOFs(const ID & dofs_id);
/// Get the support type of a given dof
inline DOFSupportType getSupportType(const ID & dofs_id) const;
/// are the dofs registered
inline bool hasDOFs(const ID & dofs_id) const;
/// Get a reference to the registered dof derivatives array for a given id
inline Array<Real> & getDOFsDerivatives(const ID & dofs_id, UInt order);
/// Does the dof has derivatives
inline bool hasDOFsDerivatives(const ID & dofs_id, UInt order) const;
/// Get a reference to the blocked dofs array registered for the given id
inline const Array<bool> & getBlockedDOFs(const ID & dofs_id) const;
/// Does the dof has a blocked array
inline bool hasBlockedDOFs(const ID & dofs_id) const;
/// Get a reference to the registered dof increment array for a given id
inline Array<Real> & getDOFsIncrement(const ID & dofs_id);
/// Does the dof has a increment array
inline bool hasDOFsIncrement(const ID & dofs_id) const;
/// Does the dof has a previous array
inline Array<Real> & getPreviousDOFs(const ID & dofs_id);
/// Get a reference to the registered dof array for previous step values a
/// given id
inline bool hasPreviousDOFs(const ID & dofs_id) const;
/// saves the values from dofs to previous dofs
virtual void savePreviousDOFs(const ID & dofs_id);
/// Get a reference to the solution array registered for the given id
inline const Array<Real> & getSolution(const ID & dofs_id) const;
/* ------------------------------------------------------------------------ */
/* Matrices accessors */
/* ------------------------------------------------------------------------ */
/// Get an instance of a new SparseMatrix
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) = 0;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) = 0;
/// Get the reference of an existing matrix
SparseMatrix & getMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasMatrix(const ID & matrix_id) const;
/// Get an instance of a new lumped matrix
virtual Array<Real> & getNewLumpedMatrix(const ID & matrix_id);
/// Get the lumped version of a given matrix
const Array<Real> & getLumpedMatrix(const ID & matrix_id) const;
/// Get the lumped version of a given matrix
Array<Real> & getLumpedMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasLumpedMatrix(const ID & matrix_id) const;
/* ------------------------------------------------------------------------ */
/* Non linear system solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a non linear solver
virtual NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & _non_linear_solver_type) = 0;
/// get instance of a non linear solver
virtual NonLinearSolver & getNonLinearSolver(const ID & nls_solver_id);
/// check if the given solver exists
bool hasNonLinearSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
/* Time-Step Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a time step solver
virtual TimeStepSolver &
getNewTimeStepSolver(const ID & time_step_solver_id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) = 0;
/// get instance of a time step solver
virtual TimeStepSolver & getTimeStepSolver(const ID & time_step_solver_id);
/// check if the given solver exists
bool hasTimeStepSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
const Mesh & getMesh() {
if (mesh) {
return *mesh;
} else {
AKANTU_EXCEPTION("No mesh registered in this dof manager");
}
}
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO(Communicator, communicator, const auto &);
AKANTU_GET_MACRO_NOT_CONST(Communicator, communicator, auto &);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler interface */
/* ------------------------------------------------------------------------ */
protected:
/// helper function for the DOFManager::onNodesAdded method
virtual std::pair<UInt, UInt> updateNodalDOFs(const ID & dof_id,
const Array<UInt> & nodes_list);
public:
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
/// function to implement to react on akantu::RemovedNodesEvent
void onNodesRemoved(const Array<UInt> & nodes_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) override;
/// function to implement to react on akantu::NewElementsEvent
void onElementsAdded(const Array<Element> & elements_list,
const NewElementsEvent & event) override;
/// function to implement to react on akantu::RemovedElementsEvent
void onElementsRemoved(const Array<Element> & elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
/// function to implement to react on akantu::ChangedElementsEvent
void onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) override;
protected:
struct DOFData;
inline DOFData & getDOFData(const ID & dof_id);
inline const DOFData & getDOFData(const ID & dof_id) const;
template <class _DOFData>
inline _DOFData & getDOFDataTyped(const ID & dof_id);
template <class _DOFData>
inline const _DOFData & getDOFDataTyped(const ID & dof_id) const;
virtual DOFData & getNewDOFData(const ID & dof_id);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// dof representations in the dof manager
struct DOFData {
DOFData() = delete;
explicit DOFData(const ID & dof_id);
virtual ~DOFData();
/// DOF support type (nodal, general) this is needed to determine how the
/// dof are shared among processors
DOFSupportType support_type;
ID group_support;
/// Degree of freedom array
Array<Real> * dof;
/// Blocked degree of freedoms array
Array<bool> * blocked_dofs;
/// Degree of freedoms increment
Array<Real> * increment;
/// Degree of freedoms at previous step
Array<Real> * previous;
/// Solution associated to the dof
Array<Real> solution;
/// local numbering equation numbers
Array<UInt> local_equation_number;
/* ---------------------------------------------------------------------- */
/* data for dynamic simulations */
/* ---------------------------------------------------------------------- */
/// Degree of freedom derivatives arrays
std::vector<Array<Real> *> dof_derivatives;
};
/// type to store dofs information
using DOFStorage = std::map<ID, std::unique_ptr<DOFData>>;
/// type to store all the matrices
using SparseMatricesMap = std::map<ID, std::unique_ptr<SparseMatrix>>;
/// type to store all the lumped matrices
using LumpedMatricesMap = std::map<ID, std::unique_ptr<Array<Real>>>;
/// type to store all the non linear solver
using NonLinearSolversMap = std::map<ID, std::unique_ptr<NonLinearSolver>>;
/// type to store all the time step solver
using TimeStepSolversMap = std::map<ID, std::unique_ptr<TimeStepSolver>>;
/// store a reference to the dof arrays
DOFStorage dofs;
/// list of sparse matrices that where created
SparseMatricesMap matrices;
/// list of lumped matrices
LumpedMatricesMap lumped_matrices;
/// non linear solvers storage
NonLinearSolversMap non_linear_solvers;
/// time step solvers storage
TimeStepSolversMap time_step_solvers;
/// reference to the underlying mesh
Mesh * mesh{nullptr};
/// Total number of degrees of freedom (size with the ghosts)
UInt local_system_size{0};
/// Number of purely local dofs (size without the ghosts)
UInt pure_local_system_size{0};
/// Total number of degrees of freedom
UInt system_size{0};
/// Communicator used for this manager, should be the same as in the mesh if a
/// mesh is registered
Communicator & communicator;
};
using DefaultDOFManagerFactory =
Factory<DOFManager, ID, const ID &, const MemoryID &>;
using DOFManagerFactory =
Factory<DOFManager, ID, Mesh &, const ID &, const MemoryID &>;
} // namespace akantu
#include "dof_manager_inline_impl.cc"
#endif /* __AKANTU_DOF_MANAGER_HH__ */
diff --git a/src/model/dof_manager_default.cc b/src/model/dof_manager_default.cc
index c4b511c60..6e917a7d9 100644
--- a/src/model/dof_manager_default.cc
+++ b/src/model/dof_manager_default.cc
@@ -1,921 +1,922 @@
/**
* @file dof_manager_default.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 11 16:21:01 2015
+ * @date creation: Tue Aug 18 2015
+ * @date last modification: Thu Feb 08 2018
*
* @brief Implementation of the default DOFManager
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "element_group.hh"
#include "node_synchronizer.hh"
#include "non_linear_solver_default.hh"
#include "sparse_matrix_aij.hh"
#include "terms_to_assemble.hh"
#include "time_step_solver_default.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <memory>
#include <numeric>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::addSymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & elementary_mat,
const Vector<UInt> & equation_numbers, UInt max_size) {
for (UInt i = 0; i < elementary_mat.rows(); ++i) {
UInt c_irn = equation_numbers(i);
if (c_irn < max_size) {
for (UInt j = i; j < elementary_mat.cols(); ++j) {
UInt c_jcn = equation_numbers(j);
if (c_jcn < max_size) {
matrix(c_irn, c_jcn) += elementary_mat(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::addUnsymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & elementary_mat,
const Vector<UInt> & equation_numbers, UInt max_size) {
for (UInt i = 0; i < elementary_mat.rows(); ++i) {
UInt c_irn = equation_numbers(i);
if (c_irn < max_size) {
for (UInt j = 0; j < elementary_mat.cols(); ++j) {
UInt c_jcn = equation_numbers(j);
if (c_jcn < max_size) {
if (c_jcn >= c_irn) {
matrix(c_irn, c_jcn) += elementary_mat(i, j);
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::addElementalMatrixToUnsymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & elementary_mat,
const Vector<UInt> & equation_numbers, UInt max_size) {
for (UInt i = 0; i < elementary_mat.rows(); ++i) {
UInt c_irn = equation_numbers(i);
if (c_irn < max_size) {
for (UInt j = 0; j < elementary_mat.cols(); ++j) {
UInt c_jcn = equation_numbers(j);
if (c_jcn < max_size) {
matrix(c_irn, c_jcn) += elementary_mat(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(const ID & id, const MemoryID & memory_id)
: DOFManager(id, memory_id), residual(0, 1, std::string(id + ":residual")),
global_residual(nullptr),
global_solution(0, 1, std::string(id + ":global_solution")),
global_blocked_dofs(0, 1, std::string(id + ":global_blocked_dofs")),
previous_global_blocked_dofs(
0, 1, std::string(id + ":previous_global_blocked_dofs")),
dofs_type(0, 1, std::string(id + ":dofs_type")),
data_cache(0, 1, std::string(id + ":data_cache_array")),
global_equation_number(0, 1, "global_equation_number"),
synchronizer(nullptr) {}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: DOFManager(mesh, id, memory_id),
residual(0, 1, std::string(id + ":residual")), global_residual(nullptr),
global_solution(0, 1, std::string(id + ":global_solution")),
global_blocked_dofs(0, 1, std::string(id + ":global_blocked_dofs")),
previous_global_blocked_dofs(
0, 1, std::string(id + ":previous_global_blocked_dofs")),
dofs_type(0, 1, std::string(id + ":dofs_type")),
data_cache(0, 1, std::string(id + ":data_cache_array")),
jacobian_release(0),
global_equation_number(0, 1, "global_equation_number"),
first_global_dof_id(0), synchronizer(nullptr) {
if (this->mesh->isDistributed())
this->synchronizer = std::make_unique<DOFSynchronizer>(
*this, this->id + ":dof_synchronizer", this->memory_id);
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::~DOFManagerDefault() = default;
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFManagerDefault::assembleToGlobalArray(
const ID & dof_id, const Array<T> & array_to_assemble,
Array<T> & global_array, T scale_factor) {
AKANTU_DEBUG_IN();
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
UInt nb_degree_of_freedoms =
array_to_assemble.size() * array_to_assemble.getNbComponent();
AKANTU_DEBUG_ASSERT(equation_number.size() == nb_degree_of_freedoms,
"The array to assemble does not have a correct size."
<< " (" << array_to_assemble.getID() << ")");
typename Array<T>::const_scalar_iterator arr_it =
array_to_assemble.begin_reinterpret(nb_degree_of_freedoms);
Array<UInt>::const_scalar_iterator equ_it = equation_number.begin();
for (UInt d = 0; d < nb_degree_of_freedoms; ++d, ++arr_it, ++equ_it) {
global_array(*equ_it) += scale_factor * (*arr_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFDataDefault::DOFDataDefault(const ID & dof_id)
: DOFData(dof_id), associated_nodes(0, 1, dof_id + "associated_nodes") {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData & DOFManagerDefault::getNewDOFData(const ID & dof_id) {
this->dofs[dof_id] = std::make_unique<DOFDataDefault>(dof_id);
return *this->dofs[dof_id];
}
/* -------------------------------------------------------------------------- */
class GlobalDOFInfoDataAccessor : public DataAccessor<UInt> {
public:
using size_type =
typename std::unordered_map<UInt, std::vector<UInt>>::size_type;
GlobalDOFInfoDataAccessor() = default;
void addDOFToNode(UInt node, UInt dof) { dofs_per_node[node].push_back(dof); }
UInt getNthDOFForNode(UInt nth_dof, UInt node) const {
auto it = dofs_per_node.find(node);
AKANTU_DEBUG_ASSERT(it != dofs_per_node.end(),
"Did not find the node " << node);
return it->second[nth_dof];
}
UInt getNbData(const Array<UInt> & nodes,
const SynchronizationTag & tag) const override {
if (tag == _gst_size) {
return nodes.size() * sizeof(size_type);
}
if (tag == _gst_update) {
UInt total_size = 0;
for (auto node : nodes) {
auto it = dofs_per_node.find(node);
if (it != dofs_per_node.end())
total_size += CommunicationBuffer::sizeInBuffer(it->second);
}
return total_size;
}
return 0;
}
void packData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) const override {
for (auto node : nodes) {
auto it = dofs_per_node.find(node);
if (tag == _gst_size) {
if (it != dofs_per_node.end()) {
buffer << it->second.size();
} else {
buffer << 0;
}
} else if (tag == _gst_update) {
if (it != dofs_per_node.end())
buffer << it->second;
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) override {
for (auto node : nodes) {
auto it = dofs_per_node.find(node);
if (tag == _gst_size) {
size_type size;
buffer >> size;
if (size != 0)
dofs_per_node[node].resize(size);
} else if (tag == _gst_update) {
if (it != dofs_per_node.end())
buffer >> it->second;
}
}
}
protected:
std::unordered_map<UInt, std::vector<UInt>> dofs_per_node;
};
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFsInternal(const ID & dof_id, UInt nb_dofs,
UInt nb_pure_local_dofs) {
// auto prank = this->communicator.whoAmI();
// auto psize = this->communicator.getNbProc();
// access the relevant data to update
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
const auto & support_type = dof_data.support_type;
const auto & group = dof_data.group_support;
if (support_type == _dst_nodal and group != "__mesh__") {
auto & support_nodes =
this->mesh->getElementGroup(group).getNodeGroup().getNodes();
this->updateDOFsData(
dof_data, nb_dofs, nb_pure_local_dofs,
[&support_nodes](UInt node) -> UInt { return support_nodes[node]; });
} else {
this->updateDOFsData(dof_data, nb_dofs, nb_pure_local_dofs,
[](UInt node) -> UInt { return node; });
}
// update the synchronizer if needed
if (this->synchronizer)
this->synchronizer->registerDOFs(dof_id);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFs(const ID & dof_id,
Array<Real> & dofs_array,
const DOFSupportType & support_type) {
// stores the current numbers of dofs
UInt nb_dofs_old = this->local_system_size;
UInt nb_pure_local_dofs_old = this->pure_local_system_size;
// update or create the dof_data
DOFManager::registerDOFs(dof_id, dofs_array, support_type);
UInt nb_dofs = this->local_system_size - nb_dofs_old;
UInt nb_pure_local_dofs =
this->pure_local_system_size - nb_pure_local_dofs_old;
this->registerDOFsInternal(dof_id, nb_dofs, nb_pure_local_dofs);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFs(const ID & dof_id,
Array<Real> & dofs_array,
const ID & group_support) {
// stores the current numbers of dofs
UInt nb_dofs_old = this->local_system_size;
UInt nb_pure_local_dofs_old = this->pure_local_system_size;
// update or create the dof_data
DOFManager::registerDOFs(dof_id, dofs_array, group_support);
UInt nb_dofs = this->local_system_size - nb_dofs_old;
UInt nb_pure_local_dofs =
this->pure_local_system_size - nb_pure_local_dofs_old;
this->registerDOFsInternal(dof_id, nb_dofs, nb_pure_local_dofs);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const MatrixType & matrix_type) {
ID matrix_id = this->id + ":mtx:" + id;
std::unique_ptr<SparseMatrix> sm =
std::make_unique<SparseMatrixAIJ>(*this, matrix_type, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const ID & matrix_to_copy_id) {
ID matrix_id = this->id + ":mtx:" + id;
SparseMatrixAIJ & sm_to_copy = this->getMatrix(matrix_to_copy_id);
std::unique_ptr<SparseMatrix> sm =
std::make_unique<SparseMatrixAIJ>(sm_to_copy, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ & DOFManagerDefault::getMatrix(const ID & id) {
SparseMatrix & matrix = DOFManager::getMatrix(id);
return dynamic_cast<SparseMatrixAIJ &>(matrix);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver &
DOFManagerDefault::getNewNonLinearSolver(const ID & id,
const NonLinearSolverType & type) {
ID non_linear_solver_id = this->id + ":nls:" + id;
std::unique_ptr<NonLinearSolver> nls;
switch (type) {
#if defined(AKANTU_IMPLICIT)
case _nls_newton_raphson:
case _nls_newton_raphson_modified: {
nls = std::make_unique<NonLinearSolverNewtonRaphson>(
*this, type, non_linear_solver_id, this->memory_id);
break;
}
case _nls_linear: {
nls = std::make_unique<NonLinearSolverLinear>(
*this, type, non_linear_solver_id, this->memory_id);
break;
}
#endif
case _nls_lumped: {
nls = std::make_unique<NonLinearSolverLumped>(
*this, type, non_linear_solver_id, this->memory_id);
break;
}
default:
AKANTU_EXCEPTION("The asked type of non linear solver is not supported by "
"this dof manager");
}
return this->registerNonLinearSolver(non_linear_solver_id, nls);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver &
DOFManagerDefault::getNewTimeStepSolver(const ID & id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) {
ID time_step_solver_id = this->id + ":tss:" + id;
std::unique_ptr<TimeStepSolver> tss = std::make_unique<TimeStepSolverDefault>(
*this, type, non_linear_solver, time_step_solver_id, this->memory_id);
return this->registerTimeStepSolver(time_step_solver_id, tss);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::clearResidual() {
this->residual.resize(this->local_system_size);
this->residual.clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::clearMatrix(const ID & mtx) {
this->getMatrix(mtx).clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::clearLumpedMatrix(const ID & mtx) {
this->getLumpedMatrix(mtx).clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::updateGlobalBlockedDofs() {
auto it = this->dofs.begin();
auto end = this->dofs.end();
this->previous_global_blocked_dofs.copy(this->global_blocked_dofs);
this->global_blocked_dofs.resize(this->local_system_size);
this->global_blocked_dofs.clear();
for (; it != end; ++it) {
if (!this->hasBlockedDOFs(it->first))
continue;
DOFData & dof_data = *it->second;
this->assembleToGlobalArray(it->first, *dof_data.blocked_dofs,
this->global_blocked_dofs, true);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFManagerDefault::getArrayPerDOFs(const ID & dof_id,
const Array<T> & global_array,
Array<T> & local_array) const {
AKANTU_DEBUG_IN();
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
UInt nb_degree_of_freedoms = equation_number.size();
local_array.resize(nb_degree_of_freedoms / local_array.getNbComponent());
auto loc_it = local_array.begin_reinterpret(nb_degree_of_freedoms);
auto equ_it = equation_number.begin();
for (UInt d = 0; d < nb_degree_of_freedoms; ++d, ++loc_it, ++equ_it) {
(*loc_it) = global_array(*equ_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void DOFManagerDefault::getEquationsNumbers(const ID & dof_id,
// Array<UInt> & equation_numbers) {
// AKANTU_DEBUG_IN();
// this->getArrayPerDOFs(dof_id, this->global_equation_number,
// equation_numbers); AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->global_solution, solution_array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::getLumpedMatrixPerDOFs(const ID & dof_id,
const ID & lumped_mtx,
Array<Real> & lumped) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->getLumpedMatrix(lumped_mtx), lumped);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleToResidual(
const ID & dof_id, const Array<Real> & array_to_assemble,
Real scale_factor) {
AKANTU_DEBUG_IN();
this->assembleToGlobalArray(dof_id, array_to_assemble, this->residual,
scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleToLumpedMatrix(
const ID & dof_id, const Array<Real> & array_to_assemble,
const ID & lumped_mtx, Real scale_factor) {
AKANTU_DEBUG_IN();
Array<Real> & lumped = this->getLumpedMatrix(lumped_mtx);
this->assembleToGlobalArray(dof_id, array_to_assemble, lumped, scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor) {
SparseMatrixAIJ & A = this->getMatrix(A_id);
// Array<Real> data_cache(this->local_system_size, 1, 0.);
this->data_cache.resize(this->local_system_size);
this->data_cache.clear();
this->assembleToGlobalArray(dof_id, x, data_cache, 1.);
A.matVecMul(data_cache, this->residual, scale_factor, 1.);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleLumpedMatMulVectToResidual(
const ID & dof_id, const ID & A_id, const Array<Real> & x,
Real scale_factor) {
const Array<Real> & A = this->getLumpedMatrix(A_id);
// Array<Real> data_cache(this->local_system_size, 1, 0.);
this->data_cache.resize(this->local_system_size);
this->data_cache.clear();
this->assembleToGlobalArray(dof_id, x, data_cache, scale_factor);
auto A_it = A.begin();
auto A_end = A.end();
auto x_it = data_cache.begin();
auto r_it = this->residual.begin();
for (; A_it != A_end; ++A_it, ++x_it, ++r_it) {
*r_it += *A_it * *x_it;
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id, const Array<Real> & elementary_mat,
const ElementType & type, const GhostType & ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
DOFData & dof_data = this->getDOFData(dof_id);
AKANTU_DEBUG_ASSERT(dof_data.support_type == _dst_nodal,
"This function applies only on Nodal dofs");
this->addToProfile(matrix_id, dof_id, type, ghost_type);
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
UInt nb_element;
UInt * filter_it = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filter_it = filter_elements.storage();
} else {
if (dof_data.group_support != "__mesh__") {
const Array<UInt> & group_elements =
this->mesh->getElementGroup(dof_data.group_support)
.getElements(type, ghost_type);
nb_element = group_elements.size();
filter_it = group_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
}
AKANTU_DEBUG_ASSERT(elementary_mat.size() == nb_element,
"The vector elementary_mat("
<< elementary_mat.getID()
<< ") has not the good size.");
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = dof_data.dof->getNbComponent();
const Array<UInt> & connectivity =
this->mesh->getConnectivity(type, ghost_type);
auto conn_begin = connectivity.begin(nb_nodes_per_element);
auto conn_it = conn_begin;
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom;
Vector<UInt> element_eq_nb(nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::const_matrix_iterator el_mat_it =
elementary_mat.begin(size_mat, size_mat);
for (UInt e = 0; e < nb_element; ++e, ++el_mat_it) {
if (filter_it)
conn_it = conn_begin + *filter_it;
this->extractElementEquationNumber(equation_number, *conn_it,
nb_degree_of_freedom, element_eq_nb);
std::transform(element_eq_nb.storage(),
element_eq_nb.storage() + element_eq_nb.size(),
element_eq_nb.storage(), [&](UInt & local) -> UInt {
return this->localToGlobalEquationNumber(local);
});
if (filter_it)
++filter_it;
else
++conn_it;
if (A.getMatrixType() == _symmetric)
if (elemental_matrix_type == _symmetric)
this->addSymmetricElementalMatrixToSymmetric(A, *el_mat_it,
element_eq_nb, A.size());
else
this->addUnsymmetricElementalMatrixToSymmetric(A, *el_mat_it,
element_eq_nb, A.size());
else
this->addElementalMatrixToUnsymmetric(A, *el_mat_it, element_eq_nb,
A.size());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assemblePreassembledMatrix(
const ID & dof_id_m, const ID & dof_id_n, const ID & matrix_id,
const TermsToAssemble & terms) {
const Array<UInt> & equation_number_m =
this->getLocalEquationNumbers(dof_id_m);
const Array<UInt> & equation_number_n =
this->getLocalEquationNumbers(dof_id_n);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
for (const auto & term : terms) {
UInt gi = this->localToGlobalEquationNumber(equation_number_m(term.i()));
UInt gj = this->localToGlobalEquationNumber(equation_number_n(term.j()));
A.add(gi, gj, term);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::addToProfile(const ID & matrix_id, const ID & dof_id,
const ElementType & type,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
const DOFData & dof_data = this->getDOFData(dof_id);
if (dof_data.support_type != _dst_nodal)
return;
auto mat_dof = std::make_pair(matrix_id, dof_id);
auto type_pair = std::make_pair(type, ghost_type);
auto prof_it = this->matrix_profiled_dofs.find(mat_dof);
if (prof_it != this->matrix_profiled_dofs.end() &&
std::find(prof_it->second.begin(), prof_it->second.end(), type_pair) !=
prof_it->second.end())
return;
UInt nb_degree_of_freedom_per_node = dof_data.dof->getNbComponent();
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
UInt size = A.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto & connectivity = this->mesh->getConnectivity(type, ghost_type);
auto cbegin = connectivity.begin(nb_nodes_per_element);
auto cit = cbegin;
UInt nb_elements = connectivity.size();
UInt * ge_it = nullptr;
if (dof_data.group_support != "__mesh__") {
const Array<UInt> & group_elements =
this->mesh->getElementGroup(dof_data.group_support)
.getElements(type, ghost_type);
ge_it = group_elements.storage();
nb_elements = group_elements.size();
}
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom_per_node;
Vector<UInt> element_eq_nb(size_mat);
for (UInt e = 0; e < nb_elements; ++e) {
if (ge_it)
cit = cbegin + *ge_it;
this->extractElementEquationNumber(
equation_number, *cit, nb_degree_of_freedom_per_node, element_eq_nb);
std::transform(element_eq_nb.storage(),
element_eq_nb.storage() + element_eq_nb.size(),
element_eq_nb.storage(), [&](UInt & local) -> UInt {
return this->localToGlobalEquationNumber(local);
});
if (ge_it)
++ge_it;
else
++cit;
for (UInt i = 0; i < size_mat; ++i) {
UInt c_irn = element_eq_nb(i);
if (c_irn < size) {
for (UInt j = 0; j < size_mat; ++j) {
UInt c_jcn = element_eq_nb(j);
if (c_jcn < size) {
A.add(c_irn, c_jcn);
}
}
}
}
}
this->matrix_profiled_dofs[mat_dof].push_back(type_pair);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::applyBoundary(const ID & matrix_id) {
SparseMatrixAIJ & J = this->getMatrix(matrix_id);
if (this->jacobian_release == J.getValueRelease()) {
auto are_equal =
std::equal(global_blocked_dofs.begin(), global_blocked_dofs.end(),
previous_global_blocked_dofs.begin());
if (not are_equal)
J.applyBoundary();
previous_global_blocked_dofs.copy(global_blocked_dofs);
} else {
J.applyBoundary();
}
this->jacobian_release = J.getValueRelease();
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManagerDefault::getGlobalResidual() {
if (this->synchronizer) {
if (not this->global_residual) {
this->global_residual =
std::make_unique<Array<Real>>(0, 1, "global_residual");
}
if (this->synchronizer->getCommunicator().whoAmI() == 0) {
this->global_residual->resize(this->system_size);
this->synchronizer->gather(this->residual, *this->global_residual);
} else {
this->synchronizer->gather(this->residual);
}
return *this->global_residual;
} else {
return this->residual;
}
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManagerDefault::getResidual() const {
return this->residual;
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::setGlobalSolution(const Array<Real> & solution) {
if (this->synchronizer) {
if (this->synchronizer->getCommunicator().whoAmI() == 0) {
this->synchronizer->scatter(this->global_solution, solution);
} else {
this->synchronizer->scatter(this->global_solution);
}
} else {
AKANTU_DEBUG_ASSERT(solution.size() == this->global_solution.size(),
"Sequential call to this function needs the solution "
"to be the same size as the global_solution");
this->global_solution.copy(solution);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) {
DOFManager::onNodesAdded(nodes_list, event);
if (this->synchronizer)
this->synchronizer->onNodesAdded(nodes_list);
}
/* -------------------------------------------------------------------------- */
std::pair<UInt, UInt>
DOFManagerDefault::updateNodalDOFs(const ID & dof_id,
const Array<UInt> & nodes_list) {
UInt nb_new_local_dofs, nb_new_pure_local;
std::tie(nb_new_local_dofs, nb_new_pure_local) =
DOFManager::updateNodalDOFs(dof_id, nodes_list);
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
updateDOFsData(dof_data, nb_new_local_dofs, nb_new_pure_local,
[&nodes_list](UInt pos) -> UInt { return nodes_list[pos]; });
return std::make_pair(nb_new_local_dofs, nb_new_pure_local);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::updateDOFsData(
DOFDataDefault & dof_data, UInt nb_new_local_dofs, UInt nb_new_pure_local,
const std::function<UInt(UInt)> & getNode) {
auto prank = this->communicator.whoAmI();
auto psize = this->communicator.getNbProc();
// access the relevant data to update
const auto & support_type = dof_data.support_type;
GlobalDOFInfoDataAccessor data_accessor;
// resize all relevant arrays
this->residual.resize(this->local_system_size);
this->dofs_type.resize(this->local_system_size);
this->global_solution.resize(this->local_system_size);
this->global_blocked_dofs.resize(this->local_system_size);
this->previous_global_blocked_dofs.resize(this->local_system_size);
this->global_equation_number.resize(this->local_system_size);
for (auto & lumped_matrix : lumped_matrices)
lumped_matrix.second->resize(this->local_system_size);
dof_data.local_equation_number.reserve(dof_data.local_equation_number.size() +
nb_new_local_dofs);
// determine the first local/global dof id to use
Array<UInt> nb_dofs_per_proc(psize);
nb_dofs_per_proc(prank) = nb_new_pure_local;
this->communicator.allGather(nb_dofs_per_proc);
this->first_global_dof_id += std::accumulate(
nb_dofs_per_proc.begin(), nb_dofs_per_proc.begin() + prank, 0);
UInt first_dof_id = this->local_system_size - nb_new_local_dofs;
if (support_type == _dst_nodal) {
dof_data.associated_nodes.reserve(dof_data.associated_nodes.size() +
nb_new_local_dofs);
}
// update per dof info
for (UInt d = 0; d < nb_new_local_dofs; ++d) {
UInt local_eq_num = first_dof_id + d;
dof_data.local_equation_number.push_back(local_eq_num);
bool is_local_dof = true;
// determine the dof type
switch (support_type) {
case _dst_nodal: {
UInt node = getNode(d / dof_data.dof->getNbComponent());
this->dofs_type(local_eq_num) = this->mesh->getNodeType(node);
dof_data.associated_nodes.push_back(node);
is_local_dof = this->mesh->isLocalOrMasterNode(node);
if (is_local_dof) {
data_accessor.addDOFToNode(node, first_global_dof_id);
}
break;
}
case _dst_generic: {
this->dofs_type(local_eq_num) = _nt_normal;
break;
}
default: { AKANTU_EXCEPTION("This type of dofs is not handled yet."); }
}
// update global id for local dofs
if (is_local_dof) {
this->global_equation_number(local_eq_num) = this->first_global_dof_id;
this->global_to_local_mapping[this->first_global_dof_id] = local_eq_num;
++this->first_global_dof_id;
} else {
this->global_equation_number(local_eq_num) = 0;
}
}
// synchronize the global numbering for slaves
if (support_type == _dst_nodal && this->synchronizer) {
auto nb_dofs_per_node = dof_data.dof->getNbComponent();
auto & node_synchronizer = this->mesh->getNodeSynchronizer();
node_synchronizer.synchronizeOnce(data_accessor, _gst_size);
node_synchronizer.synchronizeOnce(data_accessor, _gst_update);
std::vector<UInt> counters(nb_new_local_dofs / nb_dofs_per_node);
for (UInt d = 0; d < nb_new_local_dofs; ++d) {
UInt local_eq_num = first_dof_id + d;
if (not this->isSlaveDOF(local_eq_num))
continue;
UInt node = d / nb_dofs_per_node;
UInt dof_count = counters[node]++;
node = getNode(node);
UInt global_dof_id = data_accessor.getNthDOFForNode(dof_count, node);
this->global_equation_number(local_eq_num) = global_dof_id;
this->global_to_local_mapping[global_dof_id] = local_eq_num;
}
}
}
/* -------------------------------------------------------------------------- */
// register in factory
static bool default_dof_manager_is_registered[[gnu::unused]] =
DefaultDOFManagerFactory::getInstance().registerAllocator(
"default", [](const ID & id,
const MemoryID & mem_id) -> std::unique_ptr<DOFManager> {
return std::make_unique<DOFManagerDefault>(id, mem_id);
});
static bool dof_manager_is_registered[[gnu::unused]] =
DOFManagerFactory::getInstance().registerAllocator(
"default", [](Mesh & mesh, const ID & id,
const MemoryID & mem_id) -> std::unique_ptr<DOFManager> {
return std::make_unique<DOFManagerDefault>(mesh, id, mem_id);
});
} // namespace akantu
diff --git a/src/model/dof_manager_default.hh b/src/model/dof_manager_default.hh
index 8acd160f9..e8efa3b50 100644
--- a/src/model/dof_manager_default.hh
+++ b/src/model/dof_manager_default.hh
@@ -1,360 +1,361 @@
/**
* @file dof_manager_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 11 14:06:18 2015
+ * @date creation: Tue Aug 18 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Default implementation of the dof manager
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_MANAGER_DEFAULT_HH__
#define __AKANTU_DOF_MANAGER_DEFAULT_HH__
namespace akantu {
class SparseMatrixAIJ;
class NonLinearSolverDefault;
class TimeStepSolverDefault;
class DOFSynchronizer;
} // namespace akantu
namespace akantu {
class DOFManagerDefault : public DOFManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManagerDefault(const ID & id = "dof_manager_default",
const MemoryID & memory_id = 0);
DOFManagerDefault(Mesh & mesh, const ID & id = "dof_manager_default",
const MemoryID & memory_id = 0);
~DOFManagerDefault() override;
protected:
struct DOFDataDefault : public DOFData {
explicit DOFDataDefault(const ID & dof_id);
/// associated node for _dst_nodal dofs only
Array<UInt> associated_nodes;
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
void registerDOFsInternal(const ID & dof_id, UInt nb_dofs,
UInt nb_pure_local_dofs);
public:
/// register an array of degree of freedom
void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type) override;
/// the dof as an implied type of _dst_nodal and is defined only on a subset
/// of nodes
void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & group_support) override;
/// Assemble an array to the global residual array
void assembleToResidual(const ID & dof_id,
const Array<Real> & array_to_assemble,
Real scale_factor = 1.) override;
/// Assemble an array to the global lumped matrix array
void assembleToLumpedMatrix(const ID & dof_id,
const Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor = 1.) override;
/**
* Assemble elementary values to the global matrix. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
const Array<Real> & elementary_mat, const ElementType & type,
const GhostType & ghost_type, const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) override;
/// multiply a vector by a matrix and assemble the result to the residual
void assembleMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) override;
/// multiply a vector by a lumped matrix and assemble the result to the
/// residual
void assembleLumpedMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) override;
/// assemble coupling terms between to dofs
void assemblePreassembledMatrix(const ID & dof_id_m, const ID & dof_id_n,
const ID & matrix_id,
const TermsToAssemble & terms) override;
protected:
/// Assemble an array to the global residual array
template <typename T>
void assembleToGlobalArray(const ID & dof_id,
const Array<T> & array_to_assemble,
Array<T> & global_array, T scale_factor);
public:
/// clear the residual
void clearResidual() override;
/// sets the matrix to 0
void clearMatrix(const ID & mtx) override;
/// sets the lumped matrix to 0
void clearLumpedMatrix(const ID & mtx) override;
/// update the global dofs vector
virtual void updateGlobalBlockedDofs();
/// apply boundary conditions to jacobian matrix
virtual void applyBoundary(const ID & matrix_id = "J");
// void getEquationsNumbers(const ID & dof_id,
// Array<UInt> & equation_numbers) override;
protected:
/// Get local part of an array corresponding to a given dofdata
template <typename T>
void getArrayPerDOFs(const ID & dof_id, const Array<T> & global_array,
Array<T> & local_array) const;
/// Get the part of the solution corresponding to the dof_id
void getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array) override;
/// fill a Vector with the equation numbers corresponding to the given
/// connectivity
inline void extractElementEquationNumber(
const Array<UInt> & equation_numbers, const Vector<UInt> & connectivity,
UInt nb_degree_of_freedom, Vector<UInt> & local_equation_number);
public:
/// extract a lumped matrix part corresponding to a given dof
void getLumpedMatrixPerDOFs(const ID & dof_id, const ID & lumped_mtx,
Array<Real> & lumped) override;
private:
/// Add a symmetric matrices to a symmetric sparse matrix
void addSymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers, UInt max_size);
/// Add a unsymmetric matrices to a symmetric sparse matrix (i.e. cohesive
/// elements)
void addUnsymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers, UInt max_size);
/// Add a matrices to a unsymmetric sparse matrix
void addElementalMatrixToUnsymmetric(SparseMatrixAIJ & matrix,
const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers,
UInt max_size);
void addToProfile(const ID & matrix_id, const ID & dof_id,
const ElementType & type, const GhostType & ghost_type);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler interface */
/* ------------------------------------------------------------------------ */
protected:
std::pair<UInt, UInt>
updateNodalDOFs(const ID & dof_id, const Array<UInt> & nodes_list) override;
private:
void updateDOFsData(DOFDataDefault & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local,
const std::function<UInt(UInt)> & getNode);
public:
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get an instance of a new SparseMatrix
SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) override;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) override;
/// Get the reference of an existing matrix
SparseMatrixAIJ & getMatrix(const ID & matrix_id);
/* ------------------------------------------------------------------------ */
/* Non Linear Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a non linear solver
NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & _non_linear_solver_type) override;
/* ------------------------------------------------------------------------ */
/* Time-Step Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a time step solver
TimeStepSolver &
getNewTimeStepSolver(const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) override;
/* ------------------------------------------------------------------------ */
/// Get the solution array
AKANTU_GET_MACRO_NOT_CONST(GlobalSolution, global_solution, Array<Real> &);
/// Set the global solution array
void setGlobalSolution(const Array<Real> & solution);
/// Get the global residual array across processors (SMP call)
const Array<Real> & getGlobalResidual();
/// Get the residual array
const Array<Real> & getResidual() const;
/// Get the blocked dofs array
AKANTU_GET_MACRO(GlobalBlockedDOFs, global_blocked_dofs, const Array<bool> &);
/// Get the blocked dofs array
AKANTU_GET_MACRO(PreviousGlobalBlockedDOFs, previous_global_blocked_dofs,
const Array<bool> &);
/// Get the location type of a given dof
inline bool isLocalOrMasterDOF(UInt local_dof_num);
/// Answer to the question is a dof a slave dof ?
inline bool isSlaveDOF(UInt local_dof_num);
/// get the equation numbers (in local numbering) corresponding to a dof ID
inline const Array<UInt> & getLocalEquationNumbers(const ID & dof_id) const;
/// tells if the dof manager knows about a global dof
bool hasGlobalEquationNumber(UInt global) const;
/// return the local index of the global equation number
inline UInt globalToLocalEquationNumber(UInt global) const;
/// converts local equation numbers to global equation numbers;
inline UInt localToGlobalEquationNumber(UInt local) const;
/// get the array of dof types (use only if you know what you do...)
inline Int getDOFType(UInt local_id) const;
/// get the array of dof types (use only if you know what you do...)
inline const Array<UInt> & getDOFsAssociatedNodes(const ID & dof_id) const;
/// access the internal dof_synchronizer
AKANTU_GET_MACRO_NOT_CONST(Synchronizer, *synchronizer, DOFSynchronizer &);
/// access the internal dof_synchronizer
bool hasSynchronizer() const { return synchronizer != nullptr; }
protected:
DOFData & getNewDOFData(const ID & dof_id) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// using AIJMatrixMap = std::map<ID, std::unique_ptr<SparseMatrixAIJ>>;
// using DefaultNonLinearSolversMap =
// std::map<ID, std::unique_ptr<NonLinearSolverDefault>>;
// using DefaultTimeStepSolversMap =
// std::map<ID, std::unique_ptr<TimeStepSolverDefault>>;
using DOFToMatrixProfile =
std::map<std::pair<ID, ID>,
std::vector<std::pair<ElementType, GhostType>>>;
/// contains the the dofs that where added to the profile of a given matrix.
DOFToMatrixProfile matrix_profiled_dofs;
/// rhs to the system of equation corresponding to the residual linked to the
/// different dofs
Array<Real> residual;
/// rhs used only on root proc in case of parallel computing, this is the full
/// gathered rhs array
std::unique_ptr<Array<Real>> global_residual;
/// solution of the system of equation corresponding to the different dofs
Array<Real> global_solution;
/// blocked degree of freedom in the system equation corresponding to the
/// different dofs
Array<bool> global_blocked_dofs;
/// blocked degree of freedom in the system equation corresponding to the
/// different dofs
Array<bool> previous_global_blocked_dofs;
/// define the dofs type, local, shared, ghost
Array<Int> dofs_type;
/// Map of the different matrices stored in the dof manager
// AIJMatrixMap aij_matrices;
/// Map of the different time step solvers stored with there real type
// DefaultTimeStepSolversMap default_time_step_solver_map;
/// Memory cache, this is an array to keep the temporary memory needed for
/// some operations, it is meant to be resized or cleared when needed
Array<Real> data_cache;
/// Release at last apply boundary on jacobian
UInt jacobian_release{0};
/// equation number in global numbering
Array<UInt> global_equation_number;
using equation_numbers_map = std::unordered_map<UInt, UInt>;
/// dual information of global_equation_number
equation_numbers_map global_to_local_mapping;
/// accumulator to know what would be the next global id to use
UInt first_global_dof_id{0};
/// synchronizer to maintain coherency in dof fields
std::unique_ptr<DOFSynchronizer> synchronizer;
};
} // namespace akantu
#include "dof_manager_default_inline_impl.cc"
#endif /* __AKANTU_DOF_MANAGER_DEFAULT_HH__ */
diff --git a/src/model/dof_manager_default_inline_impl.cc b/src/model/dof_manager_default_inline_impl.cc
index 1dc37020f..26b764a7c 100644
--- a/src/model/dof_manager_default_inline_impl.cc
+++ b/src/model/dof_manager_default_inline_impl.cc
@@ -1,104 +1,105 @@
/**
* @file dof_manager_default_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 12 10:57:47 2015
+ * @date creation: Tue Aug 18 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the DOFManagerDefault inline functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_CC__
#define __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline bool DOFManagerDefault::isLocalOrMasterDOF(UInt dof_num) {
Int dof_type = this->dofs_type(dof_num);
return (dof_type == Int(_nt_normal)) || (dof_type == Int(_nt_master));
}
/* -------------------------------------------------------------------------- */
inline bool DOFManagerDefault::isSlaveDOF(UInt dof_num) {
Int dof_type = this->dofs_type(dof_num);
return (dof_type >= 0);
}
/* -------------------------------------------------------------------------- */
inline const Array<UInt> &
DOFManagerDefault::getLocalEquationNumbers(const ID & dof_id) const {
return this->getDOFData(dof_id).local_equation_number;
}
inline const Array<UInt> &
DOFManagerDefault::getDOFsAssociatedNodes(const ID & dof_id) const {
const auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
return dof_data.associated_nodes;
}
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::extractElementEquationNumber(
const Array<UInt> & equation_numbers, const Vector<UInt> & connectivity,
UInt nb_degree_of_freedom, Vector<UInt> & element_equation_number) {
for (UInt i = 0, ld = 0; i < connectivity.size(); ++i) {
UInt n = connectivity(i);
for (UInt d = 0; d < nb_degree_of_freedom; ++d, ++ld) {
element_equation_number(ld) =
equation_numbers(n * nb_degree_of_freedom + d);
}
}
}
/* -------------------------------------------------------------------------- */
inline UInt DOFManagerDefault::localToGlobalEquationNumber(UInt local) const {
return this->global_equation_number(local);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManagerDefault::hasGlobalEquationNumber(UInt global) const {
auto it = this->global_to_local_mapping.find(global);
return (it != this->global_to_local_mapping.end());
}
/* -------------------------------------------------------------------------- */
inline UInt DOFManagerDefault::globalToLocalEquationNumber(UInt global) const {
auto it = this->global_to_local_mapping.find(global);
AKANTU_DEBUG_ASSERT(it != this->global_to_local_mapping.end(),
"This global equation number "
<< global << " does not exists in " << this->id);
return it->second;
}
/* -------------------------------------------------------------------------- */
inline Int DOFManagerDefault::getDOFType(UInt local_id) const {
return this->dofs_type(local_id);
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_CC_ */
diff --git a/src/model/dof_manager_inline_impl.cc b/src/model/dof_manager_inline_impl.cc
index 0be0ecd85..71ebf49fd 100644
--- a/src/model/dof_manager_inline_impl.cc
+++ b/src/model/dof_manager_inline_impl.cc
@@ -1,153 +1,154 @@
/**
* @file dof_manager_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 12 11:07:01 2015
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Wed Jan 31 2018
*
- * @brief
+ * @brief inline functions of the dof manager
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_MANAGER_INLINE_IMPL_CC__
#define __AKANTU_DOF_MANAGER_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFs(const ID & dof_id) const {
auto it = this->dofs.find(dof_id);
return it != this->dofs.end();
}
/* -------------------------------------------------------------------------- */
inline DOFManager::DOFData & DOFManager::getDOFData(const ID & dof_id) {
auto it = this->dofs.find(dof_id);
if (it == this->dofs.end()) {
AKANTU_EXCEPTION("The dof " << dof_id << " does not exists in "
<< this->id);
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
const DOFManager::DOFData & DOFManager::getDOFData(const ID & dof_id) const {
auto it = this->dofs.find(dof_id);
if (it == this->dofs.end()) {
AKANTU_EXCEPTION("The dof " << dof_id << " does not exists in "
<< this->id);
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
const Array<UInt> & DOFManager::getEquationsNumbers(const ID & dof_id) const {
return getDOFData(dof_id).local_equation_number;
}
/* -------------------------------------------------------------------------- */
template <class _DOFData>
inline _DOFData & DOFManager::getDOFDataTyped(const ID & dof_id) {
return dynamic_cast<_DOFData &>(this->getDOFData(dof_id));
}
/* -------------------------------------------------------------------------- */
template <class _DOFData>
inline const _DOFData & DOFManager::getDOFDataTyped(const ID & dof_id) const {
return dynamic_cast<const _DOFData &>(this->getDOFData(dof_id));
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFs(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).dof);
}
/* -------------------------------------------------------------------------- */
inline DOFSupportType DOFManager::getSupportType(const ID & dofs_id) const {
return this->getDOFData(dofs_id).support_type;
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getPreviousDOFs(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).previous);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasPreviousDOFs(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).previous != nullptr);
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFsIncrement(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).increment);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFsIncrement(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).increment != nullptr);
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFsDerivatives(const ID & dofs_id,
UInt order) {
std::vector<Array<Real> *> & derivatives =
this->getDOFData(dofs_id).dof_derivatives;
if ((order > derivatives.size()) || (derivatives[order - 1] == nullptr))
AKANTU_EXCEPTION("No derivatives of order " << order << " present in "
<< this->id << " for dof "
<< dofs_id);
return *derivatives[order - 1];
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFsDerivatives(const ID & dofs_id,
UInt order) const {
const std::vector<Array<Real> *> & derivatives =
this->getDOFData(dofs_id).dof_derivatives;
return ((order < derivatives.size()) && (derivatives[order - 1] != nullptr));
}
/* -------------------------------------------------------------------------- */
inline const Array<Real> & DOFManager::getSolution(const ID & dofs_id) const {
return this->getDOFData(dofs_id).solution;
}
/* -------------------------------------------------------------------------- */
inline const Array<bool> &
DOFManager::getBlockedDOFs(const ID & dofs_id) const {
return *(this->getDOFData(dofs_id).blocked_dofs);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasBlockedDOFs(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).blocked_dofs != nullptr);
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_DOF_MANAGER_INLINE_IMPL_CC__ */
diff --git a/src/model/dof_manager_petsc.cc b/src/model/dof_manager_petsc.cc
index 0c168640d..2f8f332d4 100644
--- a/src/model/dof_manager_petsc.cc
+++ b/src/model/dof_manager_petsc.cc
@@ -1,395 +1,396 @@
/**
* @file dof_manager_petsc.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Oct 5 21:19:58 2015
+ * @date creation: Wed Oct 07 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief DOFManaterPETSc is the PETSc implementation of the DOFManager
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_petsc.hh"
#include "cppargparse.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_type_wrapper.hh"
#include "static_communicator.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <petscsys.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
#if not defined(PETSC_CLANGUAGE_CXX)
/// small hack to use the c binding of petsc when the cxx binding does notation
/// exists
int aka_PETScError(int ierr) {
CHKERRQ(ierr);
return 0;
}
#endif
UInt DOFManagerPETSc::petsc_dof_manager_instances = 0;
/// Error handler to make PETSc errors caught by Akantu
#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_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_ERROR("An error occured in PETSc in file \""
<< file << ":" << line << "\" - PetscErrorCode " << number
<< " - \"" << message << "\"");
}
#endif
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFManagerPETSc(const ID & id, const MemoryID & memory_id)
: DOFManager(id, memory_id) {
// check if the akantu types and PETSc one are consistant
#if __cplusplus > 199711L
static_assert(sizeof(Int) == sizeof(PetscInt),
"The integer type of Akantu does not match the one from PETSc");
static_assert(sizeof(Real) == sizeof(PetscReal),
"The integer type of Akantu does not match the one from PETSc");
#else
AKANTU_DEBUG_ASSERT(
sizeof(Int) == sizeof(PetscInt),
"The integer type of Akantu does not match the one from PETSc");
AKANTU_DEBUG_ASSERT(
sizeof(Real) == sizeof(PetscReal),
"The integer type of Akantu does not match the one from PETSc");
#endif
if (this->petsc_dof_manager_instances == 0) {
#if defined(AKANTU_USE_MPI)
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
const StaticCommunicatorMPI & mpi_st_comm =
dynamic_cast<const StaticCommunicatorMPI &>(
comm.getRealStaticCommunicator());
this->mpi_communicator =
mpi_st_comm.getMPITypeWrapper().getMPICommunicator();
#else
this->mpi_communicator = PETSC_COMM_SELF;
#endif
cppargparse::ArgumentParser & argparser = getStaticArgumentParser();
int & argc = argparser.getArgC();
char **& argv = argparser.getArgV();
PetscErrorCode petsc_error = PetscInitialize(&argc, &argv, NULL, NULL);
if (petsc_error != 0) {
AKANTU_ERROR("An error occured while initializing Petsc (PetscErrorCode "
<< petsc_error << ")");
}
PetscPushErrorHandler(PETScErrorHandler, NULL);
this->petsc_dof_manager_instances++;
}
VecCreate(PETSC_COMM_WORLD, &this->residual);
VecCreate(PETSC_COMM_WORLD, &this->solution);
}
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::~DOFManagerPETSc() {
PetscErrorCode ierr;
ierr = VecDestroy(&(this->residual));
CHKERRXX(ierr);
ierr = VecDestroy(&(this->solution));
CHKERRXX(ierr);
this->petsc_dof_manager_instances--;
if (this->petsc_dof_manager_instances == 0) {
PetscFinalize();
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
DOFSupportType & support_type) {
DOFManager::registerDOFs(dof_id, dofs_array, support_type);
PetscErrorCode ierr;
PetscInt current_size;
ierr = VecGetSize(this->residual, ¤t_size);
CHKERRXX(ierr);
if (current_size == 0) { // first time vector is set
PetscInt local_size = this->pure_local_system_size;
ierr = VecSetSizes(this->residual, local_size, PETSC_DECIDE);
CHKERRXX(ierr);
ierr = VecSetFromOptions(this->residual);
CHKERRXX(ierr);
#ifndef AKANTU_NDEBUG
PetscInt global_size;
ierr = VecGetSize(this->residual, &global_size);
CHKERRXX(ierr);
AKANTU_DEBUG_ASSERT(this->system_size == UInt(global_size),
"The local value of the system size does not match the "
"one determined by PETSc");
#endif
PetscInt start_dof, end_dof;
VecGetOwnershipRange(this->residual, &start_dof, &end_dof);
PetscInt * global_indices = new PetscInt[local_size];
global_indices[0] = start_dof;
for (PetscInt d = 0; d < local_size; d++)
global_indices[d + 1] = global_indices[d] + 1;
// To be change if we switch to a block definition
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
ISLocalToGlobalMappingCreate(this->communicator, 1, local_size,
global_indices, PETSC_COPY_VALUES,
&this->is_ltog);
#else
ISLocalToGlobalMappingCreate(this->communicator, local_size, global_indices,
PETSC_COPY_VALUES, &this->is_ltog);
#endif
VecSetLocalToGlobalMapping(this->residual, this->is_ltog);
delete[] global_indices;
ierr = VecDuplicate(this->residual, &this->solution);
CHKERRXX(ierr);
} else { // this is an update of the object already created
AKANTU_TO_IMPLEMENT();
}
/// set the solution to zero
// ierr = VecZeroEntries(this->solution);
// CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
/**
* 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 SparseMatrixPETSc::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];
// 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;
// /**
// * 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_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();
// }
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/dof_manager_petsc.hh b/src/model/dof_manager_petsc.hh
index e994d5c73..8e199a964 100644
--- a/src/model/dof_manager_petsc.hh
+++ b/src/model/dof_manager_petsc.hh
@@ -1,173 +1,174 @@
/**
* @file dof_manager_petsc.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 11 14:06:18 2015
+ * @date creation: Tue Aug 18 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief PETSc implementation of the dof manager
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
#include <petscis.h>
#include <petscvec.h>
/* -------------------------------------------------------------------------- */
#if not defined(PETSC_CLANGUAGE_CXX)
extern int aka_PETScError(int ierr);
#define CHKERRXX(x) \
do { \
int error = aka_PETScError(x); \
if (error != 0) { \
AKANTU_EXCEPTION("Error in PETSC"); \
} \
} while (0)
#endif
#ifndef __AKANTU_DOF_MANAGER_PETSC_HH__
#define __AKANTU_DOF_MANAGER_PETSC_HH__
namespace akantu {
class SparseMatrixPETSc;
class DOFManagerPETSc : public DOFManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManagerPETSc(const ID & id = "dof_manager_petsc",
const MemoryID & memory_id = 0);
DOFManagerPETSc(Mesh & mesh, const ID & id = "dof_manager_petsc",
const MemoryID & memory_id = 0);
virtual ~DOFManagerPETSc();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register an array of degree of freedom
void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
DOFSupportType & support_type);
/// Assemble an array to the global residual array
virtual void assembleToResidual(const ID & dof_id,
const Array<Real> & array_to_assemble,
Real scale_factor = 1.);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayResidual(
const ID & dof_id, const Array<Real> & array_to_assemble,
const ElementType & type, const GhostType & ghost_type,
Real scale_factor = 1.);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
const Array<Real> & elementary_mat, const ElementType & type,
const GhostType & ghost_type, const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements);
protected:
/// Get the part of the solution corresponding to the dof_id
virtual void getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array);
private:
/// Add a symmetric matrices to a symmetric sparse matrix
inline void addSymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers, UInt max_size);
/// Add a unsymmetric matrices to a symmetric sparse matrix (i.e. cohesive
/// elements)
inline void addUnsymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers, UInt max_size);
/// Add a matrices to a unsymmetric sparse matrix
inline void addElementalMatrixToUnsymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers, UInt max_size);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get an instance of a new SparseMatrix
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type);
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id);
/// Get the reference of an existing matrix
SparseMatrixPETSc & getMatrix(const ID & matrix_id);
/// Get the solution array
AKANTU_GET_MACRO_NOT_CONST(GlobalSolution, this->solution, Vec &);
/// Get the residual array
AKANTU_GET_MACRO_NOT_CONST(Residual, this->residual, Vec &);
/// Get the blocked dofs array
// AKANTU_GET_MACRO(BlockedDOFs, blocked_dofs, const Array<bool> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
typedef std::map<ID, SparseMatrixPETSc *> PETScMatrixMap;
/// list of matrices registered to the dof manager
PETScMatrixMap petsc_matrices;
/// PETSc version of the solution
Vec solution;
/// PETSc version of the residual
Vec residual;
/// PETSc local to global mapping of dofs
ISLocalToGlobalMapping is_ltog;
/// Communicator associated to PETSc
MPI_Comm mpi_communicator;
/// Static handler for petsc to know if it was initialized or not
static UInt petsc_dof_manager_instances;
};
} // akantu
#endif /* __AKANTU_DOF_MANAGER_PETSC_HH__ */
diff --git a/src/model/heat_transfer/heat_transfer_model.cc b/src/model/heat_transfer/heat_transfer_model.cc
index 031214f49..4cd6ef3ad 100644
--- a/src/model/heat_transfer/heat_transfer_model.cc
+++ b/src/model/heat_transfer/heat_transfer_model.cc
@@ -1,958 +1,958 @@
/**
* @file heat_transfer_model.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Rui Wang <rui.wang@epfl.ch>
*
* @date creation: Sun May 01 2011
- * @date last modification: Mon Nov 30 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of HeatTransferModel class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model.hh"
#include "dumpable_inline_impl.hh"
#include "element_synchronizer.hh"
#include "fe_engine_template.hh"
#include "generalized_trapezoidal.hh"
#include "group_manager_inline_impl.cc"
#include "integrator_gauss.hh"
#include "mesh.hh"
#include "parser.hh"
#include "shape_lagrange.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_element_partition.hh"
#include "dumper_elemental_field.hh"
#include "dumper_internal_material_field.hh"
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace heat_transfer {
namespace details {
class ComputeRhoFunctor {
public:
ComputeRhoFunctor(const HeatTransferModel & model) : model(model){};
void operator()(Matrix<Real> & rho, const Element &) const {
rho.set(model.getCapacity());
}
private:
const HeatTransferModel & model;
};
}
}
/* -------------------------------------------------------------------------- */
HeatTransferModel::HeatTransferModel(Mesh & mesh, UInt dim, const ID & id,
const MemoryID & memory_id)
: Model(mesh, ModelType::_heat_transfer_model, dim, id, memory_id),
temperature_gradient("temperature_gradient", id),
temperature_on_qpoints("temperature_on_qpoints", id),
conductivity_on_qpoints("conductivity_on_qpoints", id),
k_gradt_on_qpoints("k_gradt_on_qpoints", id) {
AKANTU_DEBUG_IN();
conductivity = Matrix<Real>(this->spatial_dimension, this->spatial_dimension);
this->initDOFManager();
this->registerDataAccessor(*this);
if (this->mesh.isDistributed()) {
auto & synchronizer = this->mesh.getElementSynchronizer();
this->registerSynchronizer(synchronizer, _gst_htm_capacity);
this->registerSynchronizer(synchronizer, _gst_htm_temperature);
this->registerSynchronizer(synchronizer, _gst_htm_gradient_temperature);
}
registerFEEngineObject<FEEngineType>(id + ":fem", mesh, spatial_dimension);
#ifdef AKANTU_USE_IOHELPER
this->mesh.registerDumper<DumperParaview>("heat_transfer", id, true);
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
#endif
this->registerParam("conductivity", conductivity, _pat_parsmod);
this->registerParam("conductivity_variation", conductivity_variation, 0.,
_pat_parsmod);
this->registerParam("temperature_reference", T_ref, 0., _pat_parsmod);
this->registerParam("capacity", capacity, _pat_parsmod);
this->registerParam("density", density, _pat_parsmod);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initModel() {
auto & fem = this->getFEEngine();
fem.initShapeFunctions(_not_ghost);
fem.initShapeFunctions(_ghost);
temperature_on_qpoints.initialize(fem, _nb_component = 1);
temperature_gradient.initialize(fem, _nb_component = spatial_dimension);
conductivity_on_qpoints.initialize(
fem, _nb_component = spatial_dimension * spatial_dimension);
k_gradt_on_qpoints.initialize(fem, _nb_component = spatial_dimension);
}
/* -------------------------------------------------------------------------- */
FEEngine & HeatTransferModel::getFEEngineBoundary(const ID & name) {
return dynamic_cast<FEEngine &>(getFEEngineClassBoundary<FEEngineType>(name));
}
/* -------------------------------------------------------------------------- */
template <typename T>
void HeatTransferModel::allocNodalField(Array<T> *& array, const ID & name) {
if (array == nullptr) {
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_disp;
sstr_disp << id << ":" << name;
array = &(alloc<T>(sstr_disp.str(), nb_nodes, 1, T()));
}
}
/* -------------------------------------------------------------------------- */
HeatTransferModel::~HeatTransferModel() = default;
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacityLumped(const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<FEEngineType>();
heat_transfer::details::ComputeRhoFunctor compute_rho(*this);
for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {
fem.assembleFieldLumped(compute_rho, "M", "temperature",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MatrixType HeatTransferModel::getMatrixType(const ID & matrix_id) {
if (matrix_id == "K" or matrix_id == "M") {
return _symmetric;
}
return _mt_not_defined;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleConductivityMatrix();
} else if (matrix_id == "M") {
this->assembleCapacity();
} else {
AKANTU_TO_IMPLEMENT();
}
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleLumpedMatrix(const ID & matrix_id) {
if (matrix_id == "M") {
this->assembleCapacityLumped();
} else {
AKANTU_TO_IMPLEMENT();
}
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleResidual() {
AKANTU_DEBUG_IN();
this->assembleInternalHeatRate();
this->getDOFManager().assembleToResidual("temperature",
*this->external_heat_rate, 1);
this->getDOFManager().assembleToResidual("temperature",
*this->internal_heat_rate, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::predictor() { ++temperature_release; }
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacityLumped() {
AKANTU_DEBUG_IN();
if (!this->getDOFManager().hasLumpedMatrix("M")) {
this->getDOFManager().getNewLumpedMatrix("M");
}
this->getDOFManager().clearLumpedMatrix("M");
assembleCapacityLumped(_not_ghost);
assembleCapacityLumped(_ghost);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType) {
DOFManager & dof_manager = this->getDOFManager();
this->allocNodalField(this->temperature, "temperature");
this->allocNodalField(this->external_heat_rate, "external_heat_rate");
this->allocNodalField(this->internal_heat_rate, "internal_heat_rate");
this->allocNodalField(this->blocked_dofs, "blocked_dofs");
if (!dof_manager.hasDOFs("temperature")) {
dof_manager.registerDOFs("temperature", *this->temperature, _dst_nodal);
dof_manager.registerBlockedDOFs("temperature", *this->blocked_dofs);
}
if (time_step_solver_type == _tsst_dynamic ||
time_step_solver_type == _tsst_dynamic_lumped) {
this->allocNodalField(this->temperature_rate, "temperature_rate");
if (!dof_manager.hasDOFsDerivatives("temperature", 1)) {
dof_manager.registerDOFsDerivative("temperature", 1,
*this->temperature_rate);
}
}
}
/* -------------------------------------------------------------------------- */
std::tuple<ID, TimeStepSolverType>
HeatTransferModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _explicit_lumped_mass: {
return std::make_tuple("explicit_lumped", _tsst_dynamic_lumped);
}
case _static: {
return std::make_tuple("static", _tsst_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", _tsst_dynamic);
}
default:
return std::make_tuple("unknown", _tsst_not_defined);
}
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions HeatTransferModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case _tsst_dynamic_lumped: {
options.non_linear_solver_type = _nls_lumped;
options.integration_scheme_type["temperature"] = _ist_forward_euler;
options.solution_type["temperature"] = IntegrationScheme::_temperature_rate;
break;
}
case _tsst_static: {
options.non_linear_solver_type = _nls_newton_raphson;
options.integration_scheme_type["temperature"] = _ist_pseudo_time;
options.solution_type["temperature"] = IntegrationScheme::_not_defined;
break;
}
case _tsst_dynamic: {
if (this->method == _explicit_consistent_mass) {
options.non_linear_solver_type = _nls_newton_raphson;
options.integration_scheme_type["temperature"] = _ist_forward_euler;
options.solution_type["temperature"] =
IntegrationScheme::_temperature_rate;
} else {
options.non_linear_solver_type = _nls_newton_raphson;
options.integration_scheme_type["temperature"] = _ist_trapezoidal_rule_1;
options.solution_type["temperature"] = IntegrationScheme::_temperature;
}
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleConductivityMatrix() {
AKANTU_DEBUG_IN();
this->computeConductivityOnQuadPoints(_not_ghost);
if (conductivity_release[_not_ghost] == conductivity_matrix_release)
return;
if (!this->getDOFManager().hasMatrix("K")) {
this->getDOFManager().getNewMatrix("K", getMatrixType("K"));
}
this->getDOFManager().clearMatrix("K");
switch (mesh.getSpatialDimension()) {
case 1:
this->assembleConductivityMatrix<1>(_not_ghost);
break;
case 2:
this->assembleConductivityMatrix<2>(_not_ghost);
break;
case 3:
this->assembleConductivityMatrix<3>(_not_ghost);
break;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void HeatTransferModel::assembleConductivityMatrix(
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = this->getFEEngine();
for (auto && type : mesh.elementTypes(spatial_dimension, ghost_type)) {
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
auto bt_d_b = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points,
nb_nodes_per_element * nb_nodes_per_element, "B^t*D*B");
fem.computeBtDB(conductivity_on_qpoints(type, ghost_type), *bt_d_b, 2, type,
ghost_type);
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto K_e = std::make_unique<Array<Real>>(
nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_e");
fem.integrate(*bt_d_b, *K_e, nb_nodes_per_element * nb_nodes_per_element,
type, ghost_type);
this->getDOFManager().assembleElementalMatricesToMatrix(
"K", "temperature", *K_e, type, ghost_type, _symmetric);
}
conductivity_matrix_release = conductivity_release[ghost_type];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeConductivityOnQuadPoints(
const GhostType & ghost_type) {
// if already computed once check if need to compute
if (not initial_conductivity[ghost_type]) {
// if temperature did not change, condictivity will not vary
if (temperature_release == conductivity_release[ghost_type])
return;
// if conductivity_variation is 0 no need to recompute
if (conductivity_variation == 0.)
return;
}
for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {
auto & temperature_interpolated = temperature_on_qpoints(type, ghost_type);
// compute the temperature on quadrature points
this->getFEEngine().interpolateOnIntegrationPoints(
*temperature, temperature_interpolated, 1, type, ghost_type);
auto & cond = conductivity_on_qpoints(type, ghost_type);
for (auto && tuple :
zip(make_view(cond, spatial_dimension, spatial_dimension),
temperature_interpolated)) {
auto & C = std::get<0>(tuple);
auto & T = std::get<1>(tuple);
C = conductivity;
Matrix<Real> variation(spatial_dimension, spatial_dimension,
conductivity_variation * (T - T_ref));
// @TODO: Guillaume are you sure ? why due you compute variation then ?
C += conductivity_variation;
}
}
conductivity_release[ghost_type] = temperature_release;
initial_conductivity[ghost_type] = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeKgradT(const GhostType & ghost_type) {
computeConductivityOnQuadPoints(ghost_type);
for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {
auto & gradient = temperature_gradient(type, ghost_type);
this->getFEEngine().gradientOnIntegrationPoints(*temperature, gradient, 1,
type, ghost_type);
for (auto && values :
zip(make_view(conductivity_on_qpoints(type, ghost_type),
spatial_dimension, spatial_dimension),
make_view(gradient, spatial_dimension),
make_view(k_gradt_on_qpoints(type, ghost_type),
spatial_dimension))) {
const auto & C = std::get<0>(values);
const auto & BT = std::get<1>(values);
auto & k_BT = std::get<2>(values);
k_BT.mul<false>(C, BT);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleInternalHeatRate() {
AKANTU_DEBUG_IN();
this->internal_heat_rate->clear();
this->synchronize(_gst_htm_temperature);
auto & fem = this->getFEEngine();
for (auto ghost_type : ghost_types) {
// compute k \grad T
computeKgradT(ghost_type);
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type)) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto & k_gradt_on_qpoints_vect = k_gradt_on_qpoints(type, ghost_type);
UInt nb_quad_points = k_gradt_on_qpoints_vect.size();
Array<Real> bt_k_gT(nb_quad_points, nb_nodes_per_element);
fem.computeBtD(k_gradt_on_qpoints_vect, bt_k_gT, type, ghost_type);
UInt nb_elements = mesh.getNbElement(type, ghost_type);
Array<Real> int_bt_k_gT(nb_elements, nb_nodes_per_element);
fem.integrate(bt_k_gT, int_bt_k_gT, nb_nodes_per_element, type,
ghost_type);
this->getDOFManager().assembleElementalArrayLocalArray(
int_bt_k_gT, *this->internal_heat_rate, type, ghost_type, -1);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real el_size;
Real min_el_size = std::numeric_limits<Real>::max();
Real conductivitymax = conductivity(0, 0);
// get the biggest parameter from k11 until k33//
for (UInt i = 0; i < spatial_dimension; i++)
for (UInt j = 0; j < spatial_dimension; j++)
conductivitymax = std::max(conductivity(i, j), conductivitymax);
for (auto & type : mesh.elementTypes(spatial_dimension, _not_ghost)) {
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> coord(0, nb_nodes_per_element * spatial_dimension);
FEEngine::extractNodalToElementField(mesh, mesh.getNodes(), coord, type,
_not_ghost);
auto el_coord = coord.begin(spatial_dimension, nb_nodes_per_element);
UInt nb_element = mesh.getNbElement(type);
for (UInt el = 0; el < nb_element; ++el, ++el_coord) {
el_size = getFEEngine().getElementInradius(*el_coord, type);
min_el_size = std::min(min_el_size, el_size);
}
AKANTU_DEBUG_INFO("The minimum element size : "
<< min_el_size
<< " and the max conductivity is : " << conductivitymax);
}
Real min_dt =
2 * min_el_size * min_el_size * density * capacity / conductivitymax;
mesh.getCommunicator().allReduce(min_dt, SynchronizerOperation::_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::readMaterials() {
auto sect = this->getParserSection();
if (not std::get<1>(sect)) {
const auto & section = std::get<0>(sect);
this->parseSection(section);
}
conductivity_on_qpoints.set(conductivity);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initFullImpl(const ModelOptions & options) {
Model::initFullImpl(options);
readMaterials();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacity() {
AKANTU_DEBUG_IN();
auto ghost_type = _not_ghost;
auto & fem = getFEEngineClass<FEEngineType>();
heat_transfer::details::ComputeRhoFunctor rho_functor(*this);
for (auto && type : mesh.elementTypes(spatial_dimension, ghost_type)) {
fem.assembleFieldMatrix(rho_functor, "M", "temperature",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeRho(Array<Real> & rho, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->getFEEngine();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
rho.resize(nb_element * nb_quadrature_points);
rho.set(this->capacity);
// Real * rho_1_val = rho.storage();
// /// compute @f$ rho @f$ for each nodes of each element
// for (UInt el = 0; el < nb_element; ++el) {
// for (UInt n = 0; n < nb_quadrature_points; ++n) {
// *rho_1_val++ = this->capacity;
// }
// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::computeThermalEnergyByNode() {
AKANTU_DEBUG_IN();
Real ethermal = 0.;
for (auto && pair : enumerate(make_view(
*internal_heat_rate, internal_heat_rate->getNbComponent()))) {
auto n = std::get<0>(pair);
auto & heat_rate = std::get<1>(pair);
Real heat = 0.;
bool is_local_node = mesh.isLocalOrMasterNode(n);
bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
bool count_node = is_local_node && is_not_pbc_slave_node;
for (UInt i = 0; i < heat_rate.size(); ++i) {
if (count_node)
heat += heat_rate[i] * time_step;
}
ethermal += heat;
}
mesh.getCommunicator().allReduce(ethermal, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return ethermal;
}
/* -------------------------------------------------------------------------- */
template <class iterator>
void HeatTransferModel::getThermalEnergy(
iterator Eth, Array<Real>::const_iterator<Real> T_it,
Array<Real>::const_iterator<Real> T_end) const {
for (; T_it != T_end; ++T_it, ++Eth) {
*Eth = capacity * density * *T_it;
}
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getThermalEnergy(const ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
Vector<Real> Eth_on_quarature_points(nb_quadrature_points);
auto T_it = this->temperature_on_qpoints(type).begin();
T_it += index * nb_quadrature_points;
auto T_end = T_it + nb_quadrature_points;
getThermalEnergy(Eth_on_quarature_points.storage(), T_it, T_end);
return getFEEngine().integrate(Eth_on_quarature_points, type, index);
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getThermalEnergy() {
Real Eth = 0;
auto & fem = getFEEngine();
for (auto && type : mesh.elementTypes(spatial_dimension)) {
auto nb_element = mesh.getNbElement(type, _not_ghost);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type, _not_ghost);
Array<Real> Eth_per_quad(nb_element * nb_quadrature_points, 1);
auto & temperature_interpolated = temperature_on_qpoints(type);
// compute the temperature on quadrature points
this->getFEEngine().interpolateOnIntegrationPoints(
*temperature, temperature_interpolated, 1, type);
auto T_it = temperature_interpolated.begin();
auto T_end = temperature_interpolated.end();
getThermalEnergy(Eth_per_quad.begin(), T_it, T_end);
Eth += fem.integrate(Eth_per_quad, type);
}
return Eth;
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getEnergy(const std::string & id) {
AKANTU_DEBUG_IN();
Real energy = 0;
if (id == "thermal")
energy = getThermalEnergy();
// reduction sum over all processors
mesh.getCommunicator().allReduce(energy, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getEnergy(const std::string & id,
const ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
Real energy = 0.;
if (id == "thermal")
energy = getThermalEnergy(type, index);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
dumper::Field * HeatTransferModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs;
dumper::Field * field = nullptr;
field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createNodalFieldReal(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["temperature"] = temperature;
real_nodal_fields["temperature_rate"] = temperature_rate;
real_nodal_fields["external_heat_rate"] = external_heat_rate;
real_nodal_fields["internal_heat_rate"] = internal_heat_rate;
real_nodal_fields["capacity_lumped"] = capacity_lumped;
real_nodal_fields["increment"] = increment;
dumper::Field * field =
mesh.createNodalField(real_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createElementalField(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag,
__attribute__((unused)) const UInt & spatial_dimension,
const ElementKind & element_kind) {
dumper::Field * field = nullptr;
if (field_name == "partitions")
field = mesh.createElementalField<UInt, dumper::ElementPartitionField>(
mesh.getConnectivities(), group_name, this->spatial_dimension,
element_kind);
else if (field_name == "temperature_gradient") {
ElementTypeMap<UInt> nb_data_per_elem =
this->mesh.getNbDataPerElem(temperature_gradient, element_kind);
field = mesh.createElementalField<Real, dumper::InternalMaterialField>(
temperature_gradient, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
} else if (field_name == "conductivity") {
ElementTypeMap<UInt> nb_data_per_elem =
this->mesh.getNbDataPerElem(conductivity_on_qpoints, element_kind);
field = mesh.createElementalField<Real, dumper::InternalMaterialField>(
conductivity_on_qpoints, group_name, this->spatial_dimension,
element_kind, nb_data_per_elem);
}
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createElementalField(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag,
__attribute__((unused)) const ElementKind & element_kind) {
return nullptr;
}
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createNodalFieldBool(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return nullptr;
}
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createNodalFieldReal(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return nullptr;
}
#endif
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump(const std::string & dumper_name) {
mesh.dump(dumper_name);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump(const std::string & dumper_name, UInt step) {
mesh.dump(dumper_name, step);
}
/* ------------------------------------------------------------------------- */
void HeatTransferModel::dump(const std::string & dumper_name, Real time,
UInt step) {
mesh.dump(dumper_name, time, step);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump() { mesh.dump(); }
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump(UInt step) { mesh.dump(step); }
/* -------------------------------------------------------------------------- */
void HeatTransferModel::dump(Real time, UInt step) { mesh.dump(time, step); }
/* -------------------------------------------------------------------------- */
inline UInt HeatTransferModel::getNbData(const Array<UInt> & indexes,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes = indexes.size();
switch (tag) {
case _gst_htm_capacity:
case _gst_htm_temperature: {
size += nb_nodes * sizeof(Real);
break;
}
default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::packData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
for (auto index : indexes) {
switch (tag) {
case _gst_htm_capacity:
buffer << (*capacity_lumped)(index);
break;
case _gst_htm_temperature: {
buffer << (*temperature)(index);
break;
}
default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::unpackData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
for (auto index : indexes) {
switch (tag) {
case _gst_htm_capacity: {
buffer >> (*capacity_lumped)(index);
break;
}
case _gst_htm_temperature: {
buffer >> (*temperature)(index);
break;
}
default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline UInt HeatTransferModel::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes_per_element = 0;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
const Element & el = *it;
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
switch (tag) {
case _gst_htm_capacity: {
size += nb_nodes_per_element * sizeof(Real); // capacity vector
break;
}
case _gst_htm_temperature: {
size += nb_nodes_per_element * sizeof(Real); // temperature
break;
}
case _gst_htm_gradient_temperature: {
// temperature gradient
size += getNbIntegrationPoints(elements) * spatial_dimension * sizeof(Real);
size += nb_nodes_per_element * sizeof(Real); // nodal temperatures
break;
}
default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
switch (tag) {
case _gst_htm_capacity: {
packNodalDataHelper(*capacity_lumped, buffer, elements, mesh);
break;
}
case _gst_htm_temperature: {
packNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
case _gst_htm_gradient_temperature: {
packElementalDataHelper(temperature_gradient, buffer, elements, true,
getFEEngine());
packNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
}
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
switch (tag) {
case _gst_htm_capacity: {
unpackNodalDataHelper(*capacity_lumped, buffer, elements, mesh);
break;
}
case _gst_htm_temperature: {
unpackNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
case _gst_htm_gradient_temperature: {
unpackElementalDataHelper(temperature_gradient, buffer, elements, true,
getFEEngine());
unpackNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
}
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/heat_transfer/heat_transfer_model.hh b/src/model/heat_transfer/heat_transfer_model.hh
index 723f6bf2b..1e50f36df 100644
--- a/src/model/heat_transfer/heat_transfer_model.hh
+++ b/src/model/heat_transfer/heat_transfer_model.hh
@@ -1,337 +1,337 @@
/**
* @file heat_transfer_model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Rui Wang <rui.wang@epfl.ch>
*
* @date creation: Sun May 01 2011
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Mon Feb 05 2018
*
* @brief Model of Heat Transfer
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <array>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_HEAT_TRANSFER_MODEL_HH__
#define __AKANTU_HEAT_TRANSFER_MODEL_HH__
namespace akantu {
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
}
namespace akantu {
class HeatTransferModel : public Model,
public DataAccessor<Element>,
public DataAccessor<UInt> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using FEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
HeatTransferModel(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "heat_transfer_model",
const MemoryID & memory_id = 0);
virtual ~HeatTransferModel();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// generic function to initialize everything ready for explicit dynamics
void initFullImpl(const ModelOptions & options) override;
/// read one material file to instantiate all the materials
void readMaterials();
/// allocate all vectors
void initSolver(TimeStepSolverType, NonLinearSolverType) override;
/// initialize the model
void initModel() override;
void predictor() override;
/// compute the heat flux
void assembleResidual() override;
/// get the type of matrix needed
MatrixType getMatrixType(const ID &) override;
/// callback to assemble a Matrix
void assembleMatrix(const ID &) override;
/// callback to assemble a lumped Matrix
void assembleLumpedMatrix(const ID &) override;
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const;
/* ------------------------------------------------------------------------ */
/* Methods for explicit */
/* ------------------------------------------------------------------------ */
public:
/// compute and get the stable time step
Real getStableTimeStep();
/// compute the internal heat flux
void assembleInternalHeatRate();
/// calculate the lumped capacity vector for heat transfer problem
void assembleCapacityLumped();
/* ------------------------------------------------------------------------ */
/* Methods for static */
/* ------------------------------------------------------------------------ */
public:
/// assemble the conductivity matrix
void assembleConductivityMatrix();
/// assemble the conductivity matrix
void assembleCapacity();
/// compute the capacity on quadrature points
void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);
private:
/// calculate the lumped capacity vector for heat transfer problem (w
/// ghost type)
void assembleCapacityLumped(const GhostType & ghost_type);
/// assemble the conductivity matrix (w/ ghost type)
template <UInt dim>
void assembleConductivityMatrix(const GhostType & ghost_type);
/// compute the conductivity tensor for each quadrature point in an array
void computeConductivityOnQuadPoints(const GhostType & ghost_type);
/// compute vector k \grad T for each quadrature point
void computeKgradT(const GhostType & ghost_type);
/// compute the thermal energy
Real computeThermalEnergyByNode();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
inline UInt getNbData(const Array<UInt> & indexes,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
dumper::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
dumper::Field * createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
dumper::Field * createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
const UInt & spatial_dimension,
const ElementKind & kind) override;
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);
void dump() override;
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Density, density, Real);
AKANTU_GET_MACRO(Capacity, capacity, Real);
/// get 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);
/// get the assembled heat flux
AKANTU_GET_MACRO(InternalHeatRate, *internal_heat_rate, Array<Real> &);
/// get the lumped capacity
AKANTU_GET_MACRO(CapacityLumped, *capacity_lumped, Array<Real> &);
/// get the boundary vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool> &);
/// get the external heat rate vector
AKANTU_GET_MACRO(ExternalHeatRate, *external_heat_rate, Array<Real> &);
/// get the temperature gradient
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(TemperatureGradient,
temperature_gradient, Real);
/// get the conductivity on q points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ConductivityOnQpoints,
conductivity_on_qpoints, Real);
/// get the conductivity on q points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(TemperatureOnQpoints,
temperature_on_qpoints, Real);
/// internal variables
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(KgradT, k_gradt_on_qpoints, Real);
/// get the temperature
AKANTU_GET_MACRO(Temperature, *temperature, Array<Real> &);
/// get the temperature derivative
AKANTU_GET_MACRO(TemperatureRate, *temperature_rate, Array<Real> &);
/// get the energy denominated by thermal
Real getEnergy(const std::string & energy_id, const ElementType & type,
UInt index);
/// get the energy denominated by thermal
Real getEnergy(const std::string & energy_id);
/// get the thermal energy for a given element
Real getThermalEnergy(const ElementType & type, UInt index);
/// get the thermal energy for a given element
Real getThermalEnergy();
protected:
/* ------------------------------------------------------------------------ */
FEEngine & getFEEngineBoundary(const ID & name = "") override;
/* ----------------------------------------------------------------------- */
template <class iterator>
void getThermalEnergy(iterator Eth, Array<Real>::const_iterator<Real> T_it,
Array<Real>::const_iterator<Real> T_end) const;
template <typename T>
void allocNodalField(Array<T> *& array, const ID & name);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// number of iterations
UInt n_iter;
/// time step
Real time_step;
/// temperatures array
Array<Real> * temperature{nullptr};
/// temperatures derivatives array
Array<Real> * temperature_rate{nullptr};
/// increment array (@f$\delta \dot T@f$ or @f$\delta T@f$)
Array<Real> * increment{nullptr};
/// the density
Real density;
/// the speed of the changing temperature
ElementTypeMapArray<Real> temperature_gradient;
/// temperature field on quadrature points
ElementTypeMapArray<Real> temperature_on_qpoints;
/// conductivity tensor on quadrature points
ElementTypeMapArray<Real> conductivity_on_qpoints;
/// vector k \grad T on quad points
ElementTypeMapArray<Real> k_gradt_on_qpoints;
/// external flux vector
Array<Real> * external_heat_rate{nullptr};
/// residuals array
Array<Real> * internal_heat_rate{nullptr};
// lumped vector
Array<Real> * capacity_lumped{nullptr};
/// boundary vector
Array<bool> * blocked_dofs{nullptr};
// realtime
Real time;
/// capacity
Real capacity;
// conductivity matrix
Matrix<Real> conductivity;
// linear variation of the conductivity (for temperature dependent
// conductivity)
Real conductivity_variation;
// reference temperature for the interpretation of temperature variation
Real T_ref;
// the biggest parameter of conductivity matrix
Real conductivitymax;
UInt temperature_release{0};
UInt conductivity_matrix_release{0};
std::unordered_map<GhostType, bool> initial_conductivity{{_not_ghost, true},
{_ghost, true}};
std::unordered_map<GhostType, UInt> conductivity_release{{_not_ghost, 0},
{_ghost, 0}};
};
} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model_inline_impl.cc"
#endif /* __AKANTU_HEAT_TRANSFER_MODEL_HH__ */
diff --git a/src/model/heat_transfer/heat_transfer_model_inline_impl.cc b/src/model/heat_transfer/heat_transfer_model_inline_impl.cc
index 9eca9dd79..1f10eb039 100644
--- a/src/model/heat_transfer/heat_transfer_model_inline_impl.cc
+++ b/src/model/heat_transfer/heat_transfer_model_inline_impl.cc
@@ -1,42 +1,42 @@
/**
* @file heat_transfer_model_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Aug 20 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the inline functions of the HeatTransferModel class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef __AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_CC__
#define __AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_CC__ */
diff --git a/src/model/integration_scheme/generalized_trapezoidal.cc b/src/model/integration_scheme/generalized_trapezoidal.cc
index 9dc57650c..91d937d32 100644
--- a/src/model/integration_scheme/generalized_trapezoidal.cc
+++ b/src/model/integration_scheme/generalized_trapezoidal.cc
@@ -1,193 +1,193 @@
/**
* @file generalized_trapezoidal.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Jul 04 2011
- * @date last modification: Thu Jun 05 2014
+ * @date creation: Fri Oct 23 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief implementation of inline functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "generalized_trapezoidal.hh"
#include "aka_array.hh"
#include "dof_manager.hh"
#include "mesh.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
GeneralizedTrapezoidal::GeneralizedTrapezoidal(DOFManager & dof_manager,
const ID & dof_id, Real alpha)
: IntegrationScheme1stOrder(dof_manager, dof_id), alpha(alpha) {
this->registerParam("alpha", this->alpha, alpha, _pat_parsmod,
"The alpha parameter");
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::predictor(Real delta_t, Array<Real> & u,
Array<Real> & u_dot,
const Array<bool> & blocked_dofs) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt d = 0; d < nb_degree_of_freedom; d++) {
if (!(*blocked_dofs_val)) {
*u_val += (1. - alpha) * delta_t * *u_dot_val;
}
u_val++;
u_dot_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
switch (type) {
case _temperature:
this->allCorrector<_temperature>(delta_t, u, u_dot, blocked_dofs, delta);
break;
case _temperature_rate:
this->allCorrector<_temperature_rate>(delta_t, u, u_dot, blocked_dofs,
delta);
break;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real GeneralizedTrapezoidal::getTemperatureCoefficient(
const SolutionType & type, Real delta_t) const {
switch (type) {
case _temperature:
return 1.;
case _temperature_rate:
return alpha * delta_t;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real GeneralizedTrapezoidal::getTemperatureRateCoefficient(
const SolutionType & type, Real delta_t) const {
switch (type) {
case _temperature:
return 1. / (alpha * delta_t);
case _temperature_rate:
return 1.;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
template <IntegrationScheme::SolutionType type>
void GeneralizedTrapezoidal::allCorrector(Real delta_t, Array<Real> & u,
Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real e = getTemperatureCoefficient(type, delta_t);
Real d = getTemperatureRateCoefficient(type, delta_t);
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * delta_val = delta.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt dof = 0; dof < nb_degree_of_freedom; dof++) {
if (!(*blocked_dofs_val)) {
*u_val += e * *delta_val;
*u_dot_val += d * *delta_val;
}
u_val++;
u_dot_val++;
delta_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::assembleJacobian(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & M = this->dof_manager.getMatrix("M");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
bool does_j_need_update = false;
does_j_need_update |= M.getRelease() != m_release;
does_j_need_update |= K.getRelease() != k_release;
if (!does_j_need_update) {
AKANTU_DEBUG_OUT();
return;
}
J.clear();
Real c = this->getTemperatureRateCoefficient(type, delta_t);
Real e = this->getTemperatureCoefficient(type, delta_t);
J.add(M, e);
J.add(K, c);
m_release = M.getRelease();
k_release = K.getRelease();
AKANTU_DEBUG_OUT();
}
} // akantu
diff --git a/src/model/integration_scheme/generalized_trapezoidal.hh b/src/model/integration_scheme/generalized_trapezoidal.hh
index b984d5590..5ad22cdaf 100644
--- a/src/model/integration_scheme/generalized_trapezoidal.hh
+++ b/src/model/integration_scheme/generalized_trapezoidal.hh
@@ -1,166 +1,165 @@
/**
* @file generalized_trapezoidal.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 04 2011
- * @date last modification: Fri Oct 23 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Generalized Trapezoidal Method. This implementation is taken from
* Méthodes numériques en mécanique des solides by Alain Curnier \note{ISBN:
* 2-88074-247-1}
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GENERALIZED_TRAPEZOIDAL_HH__
#define __AKANTU_GENERALIZED_TRAPEZOIDAL_HH__
#include "integration_scheme_1st_order.hh"
namespace akantu {
/**
* The two differentiate equation (thermal and kinematic) are :
* @f{eqnarray*}{
* C\dot{u}_{n+1} + Ku_{n+1} = q_{n+1}\\
* u_{n+1} = u_{n} + (1-\alpha) \Delta t \dot{u}_{n} + \alpha \Delta t
*\dot{u}_{n+1}
* @f}
*
* To solve it :
* Predictor :
* @f{eqnarray*}{
* u^0_{n+1} &=& u_{n} + (1-\alpha) \Delta t v_{n} \\
* \dot{u}^0_{n+1} &=& \dot{u}_{n}
* @f}
*
* Solve :
* @f[ (a C + b K^i_{n+1}) w = q_{n+1} - f^i_{n+1} - C \dot{u}^i_{n+1} @f]
*
* Corrector :
* @f{eqnarray*}{
* \dot{u}^{i+1}_{n+1} &=& \dot{u}^{i}_{n+1} + a w \\
* u^{i+1}_{n+1} &=& u^{i}_{n+1} + b w
* @f}
*
* a and b depends on the resolution method : temperature (u) or temperature
*rate (@f$\dot{u}@f$)
*
* For temperature : @f$ w = \delta u, a = 1 / (\alpha \Delta t) , b = 1 @f$ @n
* For temperature rate : @f$ w = \delta \dot{u}, a = 1, b = \alpha \Delta t @f$
*/
class GeneralizedTrapezoidal : public IntegrationScheme1stOrder {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GeneralizedTrapezoidal(DOFManager & dof_manager, const ID & dof_id,
Real alpha = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs) const override;
void corrector(const SolutionType & type, Real delta_t, Array<Real> & u,
Array<Real> & u_dot, const Array<bool> & blocked_dofs,
const Array<Real> & delta) const override;
void assembleJacobian(const SolutionType & type, Real time_step) override;
public:
/// the coeffichent @f{b@f} in the description
Real getTemperatureCoefficient(const SolutionType & type,
Real delta_t) const override;
/// the coeffichent @f{a@f} in the description
Real getTemperatureRateCoefficient(const SolutionType & type,
Real delta_t) const override;
private:
template <SolutionType type>
void allCorrector(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Alpha, alpha, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the @f$\alpha@f$ parameter
Real alpha;
/// last release of M matrix
UInt m_release;
/// last release of K matrix
UInt k_release;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/**
* Forward Euler (explicit) -> condition on delta_t
*/
class ForwardEuler : public GeneralizedTrapezoidal {
public:
ForwardEuler(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, 0.){};
std::vector<std::string> getNeededMatrixList() override { return {"M"}; }
};
/**
* Trapezoidal rule (implicit), midpoint rule or Crank-Nicolson
*/
class TrapezoidalRule1 : public GeneralizedTrapezoidal {
public:
TrapezoidalRule1(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, .5){};
};
/**
* Backward Euler (implicit)
*/
class BackwardEuler : public GeneralizedTrapezoidal {
public:
BackwardEuler(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, 1.){};
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_GENERALIZED_TRAPEZOIDAL_HH__ */
diff --git a/src/model/integration_scheme/integration_scheme.cc b/src/model/integration_scheme/integration_scheme.cc
index dc28ebb5e..68073a71d 100644
--- a/src/model/integration_scheme/integration_scheme.cc
+++ b/src/model/integration_scheme/integration_scheme.cc
@@ -1,66 +1,67 @@
/**
* @file integration_scheme.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Oct 23 15:33:36 2015
+ * @date creation: Tue Aug 18 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Common interface to all interface schemes
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme.hh"
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
IntegrationScheme::IntegrationScheme(DOFManager & dof_manager,
const ID & dof_id, UInt order)
: Parsable(ParserType::_integration_scheme, dof_id),
dof_manager(dof_manager), dof_id(dof_id), order(order) {}
/* -------------------------------------------------------------------------- */
/// standard input stream operator for SolutionType
std::istream & operator>>(std::istream & stream,
IntegrationScheme::SolutionType & type) {
std::string str;
stream >> str;
if (str == "displacement")
type = IntegrationScheme::_displacement;
else if (str == "temperature")
type = IntegrationScheme::_temperature;
else if (str == "velocity")
type = IntegrationScheme::_velocity;
else if (str == "temperature_rate")
type = IntegrationScheme::_temperature_rate;
else if (str == "acceleration")
type = IntegrationScheme::_acceleration;
else {
stream.setstate(std::ios::failbit);
}
return stream;
}
} // akantu
diff --git a/src/model/integration_scheme/integration_scheme.hh b/src/model/integration_scheme/integration_scheme.hh
index 024313073..ccf850bf8 100644
--- a/src/model/integration_scheme/integration_scheme.hh
+++ b/src/model/integration_scheme/integration_scheme.hh
@@ -1,111 +1,111 @@
-
/**
* @file integration_scheme.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Sep 28 10:43:18 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
* @brief This class is just a base class for the integration schemes
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTEGRATION_SCHEME_HH__
#define __AKANTU_INTEGRATION_SCHEME_HH__
namespace akantu {
class DOFManager;
}
namespace akantu {
class IntegrationScheme : public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
enum SolutionType {
_not_defined = -1,
_displacement = 0,
_temperature = 0,
_velocity = 1,
_temperature_rate = 1,
_acceleration = 2,
};
IntegrationScheme(DOFManager & dof_manager, const ID & dof_id, UInt order);
~IntegrationScheme() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// generic interface of a predictor
virtual void predictor(Real delta_t) = 0;
/// generic interface of a corrector
virtual void corrector(const SolutionType & type, Real delta_t) = 0;
/// assemble the jacobian matrix
virtual void assembleJacobian(const SolutionType & type, Real delta_t) = 0;
/// assemble the residual
virtual void assembleResidual(bool is_lumped) = 0;
/// returns a list of needed matrices
virtual std::vector<std::string> getNeededMatrixList() = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the order of the integration scheme
UInt getOrder() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// The underlying DOFManager
DOFManager & dof_manager;
/// The id of the dof treated by this integration scheme.
ID dof_id;
/// The order of the integrator
UInt order;
};
/* -------------------------------------------------------------------------- */
// std::ostream & operator<<(std::ostream & stream,
// const IntegrationScheme::SolutionType & type);
std::istream & operator>>(std::istream & stream,
IntegrationScheme::SolutionType & type);
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_INTEGRATION_SCHEME_HH__ */
diff --git a/src/model/integration_scheme/integration_scheme_1st_order.cc b/src/model/integration_scheme/integration_scheme_1st_order.cc
index e9701c486..af6e9d8e0 100644
--- a/src/model/integration_scheme/integration_scheme_1st_order.cc
+++ b/src/model/integration_scheme/integration_scheme_1st_order.cc
@@ -1,95 +1,96 @@
/**
* @file integration_scheme_1st_order.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Oct 23 12:31:32 2015
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the common functions for 1st order time
- *integrations
+ * integrations
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme_1st_order.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
std::vector<std::string> IntegrationScheme1stOrder::getNeededMatrixList() {
return {"K", "M"};
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::predictor(Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->predictor(delta_t, u, u_dot, blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::corrector(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
const Array<Real> & solution = this->dof_manager.getSolution(this->dof_id);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->corrector(type, delta_t, u, u_dot, blocked_dofs, solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::assembleResidual(bool is_lumped) {
AKANTU_DEBUG_IN();
const Array<Real> & first_derivative =
dof_manager.getDOFsDerivatives(this->dof_id, 1);
if (not is_lumped) {
if (this->dof_manager.hasMatrix("M"))
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "M",
first_derivative, -1);
} else {
if (this->dof_manager.hasLumpedMatrix("M"))
this->dof_manager.assembleLumpedMatMulVectToResidual(
this->dof_id, "M", first_derivative, -1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/integration_scheme/integration_scheme_1st_order.hh b/src/model/integration_scheme/integration_scheme_1st_order.hh
index d15ec19df..1f77217b6 100644
--- a/src/model/integration_scheme/integration_scheme_1st_order.hh
+++ b/src/model/integration_scheme/integration_scheme_1st_order.hh
@@ -1,95 +1,94 @@
/**
* @file integration_scheme_1st_order.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Oct 23 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Interface of the time integrator of first order
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH__
#define __AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH__
namespace akantu {
class IntegrationScheme1stOrder : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationScheme1stOrder(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 1){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
/// assemble the residual
void assembleResidual(bool is_lumped) override;
protected:
/// generic interface of a predictor of 1st order
virtual void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & boundary) const = 0;
/// generic interface of a corrector of 1st order
virtual void corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & boundary,
const Array<Real> & delta) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
virtual Real getTemperatureCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getTemperatureRateCoefficient(const SolutionType & type,
Real delta_t) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // akantu
#include "generalized_trapezoidal.hh"
#endif /* __AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH__ */
diff --git a/src/model/integration_scheme/integration_scheme_2nd_order.cc b/src/model/integration_scheme/integration_scheme_2nd_order.cc
index e308331dc..ee1dd2a39 100644
--- a/src/model/integration_scheme/integration_scheme_2nd_order.cc
+++ b/src/model/integration_scheme/integration_scheme_2nd_order.cc
@@ -1,105 +1,106 @@
/**
* @file integration_scheme_2nd_order.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Oct 20 10:41:12 2015
+ * @date creation: Fri Oct 23 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the common part of 2nd order integration schemes
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme_2nd_order.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
std::vector<std::string> IntegrationScheme2ndOrder::getNeededMatrixList() {
return {"K", "M", "C"};
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme2ndOrder::predictor(Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
Array<Real> & u_dot_dot =
this->dof_manager.getDOFsDerivatives(this->dof_id, 2);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->predictor(delta_t, u, u_dot, u_dot_dot, blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme2ndOrder::corrector(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
Array<Real> & u_dot_dot =
this->dof_manager.getDOFsDerivatives(this->dof_id, 2);
const Array<Real> & solution = this->dof_manager.getSolution(this->dof_id);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->corrector(type, delta_t, u, u_dot, u_dot_dot, blocked_dofs, solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme2ndOrder::assembleResidual(bool is_lumped) {
AKANTU_DEBUG_IN();
if (this->dof_manager.hasMatrix("C")) {
const Array<Real> & first_derivative =
this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "C",
first_derivative, -1);
}
const Array<Real> & second_derivative =
this->dof_manager.getDOFsDerivatives(this->dof_id, 2);
if (not is_lumped) {
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "M",
second_derivative, -1);
} else {
this->dof_manager.assembleLumpedMatMulVectToResidual(this->dof_id, "M",
second_derivative, -1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/integration_scheme/integration_scheme_2nd_order.hh b/src/model/integration_scheme/integration_scheme_2nd_order.hh
index d60ee5777..d171a2e8b 100644
--- a/src/model/integration_scheme/integration_scheme_2nd_order.hh
+++ b/src/model/integration_scheme/integration_scheme_2nd_order.hh
@@ -1,108 +1,107 @@
/**
* @file integration_scheme_2nd_order.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Oct 23 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Interface of the integrator of second order
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__
#define __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__
namespace akantu {
class SparseMatrix;
}
namespace akantu {
class IntegrationScheme2ndOrder : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationScheme2ndOrder(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 2){};
~IntegrationScheme2ndOrder() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
void assembleResidual(bool is_lumped) override;
protected:
/// generic interface of a predictor of 2nd order
virtual void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const = 0;
/// generic interface of a corrector of 2nd order
virtual void corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
virtual Real getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getVelocityCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // akantu
#include "newmark-beta.hh"
#endif /* __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__ */
diff --git a/src/model/integration_scheme/newmark-beta.cc b/src/model/integration_scheme/newmark-beta.cc
index be0d3cdeb..0831da765 100644
--- a/src/model/integration_scheme/newmark-beta.cc
+++ b/src/model/integration_scheme/newmark-beta.cc
@@ -1,260 +1,260 @@
/**
* @file newmark-beta.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Tue Oct 05 2010
- * @date last modification: Thu Jun 05 2014
+ * @date creation: Fri Oct 23 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief implementation of the newmark-@f$\beta@f$ integration scheme. This
* implementation is taken from Méthodes numériques en mécanique des solides by
* Alain Curnier \note{ISBN: 2-88074-247-1}
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "newmark-beta.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NewmarkBeta::NewmarkBeta(DOFManager & dof_manager, const ID & dof_id,
Real alpha, Real beta)
: IntegrationScheme2ndOrder(dof_manager, dof_id), beta(beta), alpha(alpha),
k(0.), h(0.), m_release(0), k_release(0), c_release(0) {
this->registerParam("alpha", this->alpha, alpha, _pat_parsmod,
"The alpha parameter");
this->registerParam("beta", this->beta, beta, _pat_parsmod,
"The beta parameter");
}
/* -------------------------------------------------------------------------- */
/*
* @f$ \tilde{u_{n+1}} = u_{n} + \Delta t \dot{u}_n + \frac{\Delta t^2}{2}
* \ddot{u}_n @f$
* @f$ \tilde{\dot{u}_{n+1}} = \dot{u}_{n} + \Delta t \ddot{u}_{n} @f$
* @f$ \tilde{\ddot{u}_{n}} = \ddot{u}_{n} @f$
*/
void NewmarkBeta::predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * u_dot_dot_val = u_dot_dot.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt d = 0; d < nb_degree_of_freedom; d++) {
if (!(*blocked_dofs_val)) {
Real dt_a_n = delta_t * *u_dot_dot_val;
*u_val += (1 - k * alpha) * delta_t * *u_dot_val +
(.5 - h * alpha * beta) * delta_t * dt_a_n;
*u_dot_val = (1 - k) * *u_dot_val + (1 - h * beta) * dt_a_n;
*u_dot_dot_val = (1 - h) * *u_dot_dot_val;
}
u_val++;
u_dot_val++;
u_dot_dot_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NewmarkBeta::corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
switch (type) {
case _acceleration: {
this->allCorrector<_acceleration>(delta_t, u, u_dot, u_dot_dot,
blocked_dofs, delta);
break;
}
case _velocity: {
this->allCorrector<_velocity>(delta_t, u, u_dot, u_dot_dot, blocked_dofs,
delta);
break;
}
case _displacement: {
this->allCorrector<_displacement>(delta_t, u, u_dot, u_dot_dot,
blocked_dofs, delta);
break;
}
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return 1.;
case _velocity:
return 1. / (beta * delta_t);
case _displacement:
return 1. / (alpha * beta * delta_t * delta_t);
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getVelocityCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return beta * delta_t;
case _velocity:
return 1.;
case _displacement:
return 1. / (alpha * delta_t);
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return alpha * beta * delta_t * delta_t;
case _velocity:
return alpha * delta_t;
case _displacement:
return 1.;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
template <IntegrationScheme::SolutionType type>
void NewmarkBeta::allCorrector(Real delta_t, Array<Real> & u,
Array<Real> & u_dot, Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real c = getAccelerationCoefficient(type, delta_t);
Real d = getVelocityCoefficient(type, delta_t);
Real e = getDisplacementCoefficient(type, delta_t);
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * u_dot_dot_val = u_dot_dot.storage();
Real * delta_val = delta.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt dof = 0; dof < nb_degree_of_freedom; dof++) {
if (!(*blocked_dofs_val)) {
*u_val += e * *delta_val;
*u_dot_val += d * *delta_val;
*u_dot_dot_val += c * *delta_val;
}
u_val++;
u_dot_val++;
u_dot_dot_val++;
delta_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NewmarkBeta::assembleJacobian(const SolutionType & type, Real delta_t) {
AKANTU_DEBUG_IN();
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & M = this->dof_manager.getMatrix("M");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
bool does_j_need_update = false;
does_j_need_update |= M.getRelease() != m_release;
does_j_need_update |= K.getRelease() != k_release;
if (this->dof_manager.hasMatrix("C")) {
const SparseMatrix & C = this->dof_manager.getMatrix("C");
does_j_need_update |= C.getRelease() != c_release;
}
if (!does_j_need_update) {
AKANTU_DEBUG_OUT();
return;
}
J.clear();
Real c = this->getAccelerationCoefficient(type, delta_t);
Real e = this->getDisplacementCoefficient(type, delta_t);
if (!(e == 0.)) { // in explicit this coefficient is exactly 0.
J.add(K, e);
}
J.add(M, c);
m_release = M.getRelease();
k_release = K.getRelease();
if (this->dof_manager.hasMatrix("C")) {
Real d = this->getVelocityCoefficient(type, delta_t);
const SparseMatrix & C = this->dof_manager.getMatrix("C");
J.add(C, d);
c_release = C.getRelease();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/integration_scheme/newmark-beta.hh b/src/model/integration_scheme/newmark-beta.hh
index 7373c56a9..d3742a76d 100644
--- a/src/model/integration_scheme/newmark-beta.hh
+++ b/src/model/integration_scheme/newmark-beta.hh
@@ -1,196 +1,195 @@
/**
* @file newmark-beta.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 05 2010
- * @date last modification: Fri Oct 23 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief implementation of the newmark-@f$\beta@f$ integration scheme. This
* implementation is taken from Méthodes numériques en mécanique des solides by
* Alain Curnier \note{ISBN: 2-88074-247-1}
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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_NEWMARK_BETA_HH__
#define __AKANTU_NEWMARK_BETA_HH__
/* -------------------------------------------------------------------------- */
#include "integration_scheme_2nd_order.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* The three differentiate equations (dynamic and cinematic) are :
* @f{eqnarray*}{
* M \ddot{u}_{n+1} + C \dot{u}_{n+1} + K u_{n+1} &=& q_{n+1} \\
* u_{n+1} &=& u_{n} + (1 - \alpha) \Delta t \dot{u}_{n} + \alpha \Delta t
*\dot{u}_{n+1} + (1/2 - \alpha) \Delta t^2 \ddot{u}_n \\
* \dot{u}_{n+1} &=& \dot{u}_{n} + (1 - \beta) \Delta t \ddot{u}_{n} + \beta
*\Delta t \ddot{u}_{n+1}
* @f}
*
* Predictor:
* @f{eqnarray*}{
* u^{0}_{n+1} &=& u_{n} + \Delta t \dot{u}_n + \frac{\Delta t^2}{2}
*\ddot{u}_n \\
* \dot{u}^{0}_{n+1} &=& \dot{u}_{n} + \Delta t \ddot{u}_{n} \\
* \ddot{u}^{0}_{n+1} &=& \ddot{u}_{n}
* @f}
*
* Solve :
* @f[ (c M + d C + e K^i_{n+1}) w = = q_{n+1} - f^i_{n+1} - C \dot{u}^i_{n+1}
*- M \ddot{u}^i_{n+1} @f]
*
* Corrector :
* @f{eqnarray*}{
* \ddot{u}^{i+1}_{n+1} &=& \ddot{u}^{i}_{n+1} + c w \\
* \dot{u}^{i+1}_{n+1} &=& \dot{u}^{i}_{n+1} + d w \\
* u^{i+1}_{n+1} &=& u^{i}_{n+1} + e w
* @f}
*
* c, d and e are parameters depending on the method used to solve the equations
*@n
* For acceleration : @f$ w = \delta \ddot{u}, e = \alpha \beta \Delta t^2, d =
*\beta \Delta t, c = 1 @f$ @n
* For velocity : @f$ w = \delta \dot{u}, e = 1/\beta \Delta t, d =
*1, c = \alpha \Delta t @f$ @n
* For displacement : @f$ w = \delta u, e = 1, d =
*1/\alpha \Delta t, c = 1/\alpha \beta \Delta t^2 @f$
*/
class NewmarkBeta : public IntegrationScheme2ndOrder {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NewmarkBeta(DOFManager & dof_manager, const ID & dof_id, Real alpha = 0.,
Real beta = 0.);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const override;
void corrector(const SolutionType & type, Real delta_t, Array<Real> & u,
Array<Real> & u_dot, Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const override;
void assembleJacobian(const SolutionType & type, Real delta_t) override;
public:
Real getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const override;
Real getVelocityCoefficient(const SolutionType & type,
Real delta_t) const override;
Real getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const override;
private:
template <SolutionType type>
void allCorrector(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot, const Array<bool> & blocked_dofs,
const Array<Real> & delta) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Beta, beta, Real);
AKANTU_GET_MACRO(Alpha, alpha, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the @f$\beta@f$ parameter
Real beta;
/// the @f$\alpha@f$ parameter
Real alpha;
Real k;
Real h;
/// last release of M matrix
UInt m_release;
/// last release of K matrix
UInt k_release;
/// last release of C matrix
UInt c_release;
};
/**
* central difference method (explicit)
* undamped stability condition :
* @f$ \Delta t = \alpha \Delta t_{crit} = \frac{2}{\omega_{max}} \leq \min_{e}
*\frac{l_e}{c_e}
*
*/
class CentralDifference : public NewmarkBeta {
public:
CentralDifference(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 0., 1. / 2.){};
std::vector<std::string> getNeededMatrixList() override { return {"M", "C"}; }
};
//#include "integration_scheme/central_difference.hh"
/// undamped trapezoidal rule (implicit)
class TrapezoidalRule2 : public NewmarkBeta {
public:
TrapezoidalRule2(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 2., 1. / 2.){};
};
/// Fox-Goodwin rule (implicit)
class FoxGoodwin : public NewmarkBeta {
public:
FoxGoodwin(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 6., 1. / 2.){};
};
/// Linear acceleration (implicit)
class LinearAceleration : public NewmarkBeta {
public:
LinearAceleration(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 3., 1. / 2.){};
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_NEWMARK_BETA_HH__ */
diff --git a/src/model/integration_scheme/pseudo_time.cc b/src/model/integration_scheme/pseudo_time.cc
index 6b350562d..1ca15129b 100644
--- a/src/model/integration_scheme/pseudo_time.cc
+++ b/src/model/integration_scheme/pseudo_time.cc
@@ -1,81 +1,82 @@
/**
* @file pseudo_time.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Feb 17 09:49:10 2016
+ * @date creation: Fri Feb 19 2016
+ * @date last modification: Wed Jan 31 2018
*
* @brief Implementation of a really simple integration scheme
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "pseudo_time.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
PseudoTime::PseudoTime(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 0), k_release(0) {}
/* -------------------------------------------------------------------------- */
std::vector<std::string> PseudoTime::getNeededMatrixList() { return {"K"}; }
/* -------------------------------------------------------------------------- */
void PseudoTime::predictor(Real) {}
/* -------------------------------------------------------------------------- */
void PseudoTime::corrector(const SolutionType &, Real) {
auto & us = this->dof_manager.getDOFs(this->dof_id);
const auto & deltas = this->dof_manager.getSolution(this->dof_id);
const auto & blocked_dofs = this->dof_manager.getBlockedDOFs(this->dof_id);
for (auto && tuple : zip(make_view(us), deltas, make_view(blocked_dofs))) {
auto & u = std::get<0>(tuple);
const auto & delta = std::get<1>(tuple);
const auto & bld = std::get<2>(tuple);
if (not bld)
u += delta;
}
}
/* -------------------------------------------------------------------------- */
void PseudoTime::assembleJacobian(const SolutionType &, Real) {
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
if (K.getRelease() == k_release)
return;
J.clear();
J.add(K);
k_release = K.getRelease();
}
/* -------------------------------------------------------------------------- */
void PseudoTime::assembleResidual(bool) {}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/integration_scheme/pseudo_time.hh b/src/model/integration_scheme/pseudo_time.hh
index 8950f86b1..a93e66986 100644
--- a/src/model/integration_scheme/pseudo_time.hh
+++ b/src/model/integration_scheme/pseudo_time.hh
@@ -1,72 +1,73 @@
/**
* @file pseudo_time.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Feb 17 09:46:05 2016
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
* @brief Pseudo time integration scheme
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PSEUDO_TIME_HH__
#define __AKANTU_PSEUDO_TIME_HH__
namespace akantu {
class PseudoTime : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PseudoTime(DOFManager & dof_manager, const ID & dof_id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
/// assemble the jacobian matrix
void assembleJacobian(const SolutionType & type, Real delta_t) override;
/// assemble the residual
void assembleResidual(bool is_lumped) override;
protected:
/// last release of K matrix
UInt k_release;
};
} // namespace akantu
#endif /* __AKANTU_PSEUDO_TIME_HH__ */
diff --git a/src/model/model.cc b/src/model/model.cc
index 959a2fba5..9a4a9577a 100644
--- a/src/model/model.cc
+++ b/src/model/model.cc
@@ -1,369 +1,369 @@
/**
* @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: Thu Nov 19 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief implementation of model common parts
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "model.hh"
#include "communicator.hh"
#include "data_accessor.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Model::Model(Mesh & mesh, const ModelType & type, UInt dim, const ID & id,
const MemoryID & memory_id)
: Memory(id, memory_id), ModelSolver(mesh, type, id, memory_id), mesh(mesh),
spatial_dimension(dim == _all_dimensions ? mesh.getSpatialDimension()
: dim),
is_pbc_slave_node(0, 1, "is_pbc_slave_node"), parser(getStaticParser()) {
AKANTU_DEBUG_IN();
this->mesh.registerEventHandler(*this, _ehp_model);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Model::~Model() = default;
/* -------------------------------------------------------------------------- */
// void Model::setParser(Parser & parser) { this->parser = &parser; }
/* -------------------------------------------------------------------------- */
void Model::initFullImpl(const ModelOptions & options) {
AKANTU_DEBUG_IN();
method = options.analysis_method;
if (!this->hasDefaultSolver()) {
this->initNewSolver(this->method);
}
initModel();
initFEEngineBoundary();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Model::initNewSolver(const AnalysisMethod & method) {
ID solver_name;
TimeStepSolverType tss_type;
std::tie(solver_name, tss_type) = this->getDefaultSolverID(method);
if (not this->hasSolver(solver_name)) {
ModelSolverOptions options = this->getDefaultSolverOptions(tss_type);
this->getNewSolver(solver_name, tss_type, options.non_linear_solver_type);
for (auto && is_type : options.integration_scheme_type) {
if (!this->hasIntegrationScheme(solver_name, is_type.first)) {
this->setIntegrationScheme(solver_name, is_type.first, is_type.second,
options.solution_type[is_type.first]);
}
}
}
this->method = method;
this->setDefaultSolver(solver_name);
}
/* -------------------------------------------------------------------------- */
void Model::initPBC() {
auto it = pbc_pair.begin();
auto end = pbc_pair.end();
is_pbc_slave_node.resize(mesh.getNbNodes());
#ifndef AKANTU_NDEBUG
auto coord_it = mesh.getNodes().begin(this->spatial_dimension);
#endif
while (it != end) {
UInt i1 = (*it).first;
is_pbc_slave_node(i1) = true;
#ifndef AKANTU_NDEBUG
UInt i2 = (*it).second;
UInt slave = mesh.isDistributed() ? mesh.getGlobalNodesIds()(i1) : i1;
UInt master = mesh.isDistributed() ? mesh.getGlobalNodesIds()(i2) : i2;
AKANTU_DEBUG_INFO("pairing " << slave << " (" << Vector<Real>(coord_it[i1])
<< ") with " << master << " ("
<< Vector<Real>(coord_it[i2]) << ")");
#endif
++it;
}
}
/* -------------------------------------------------------------------------- */
void Model::initFEEngineBoundary() {
FEEngine & fem_boundary = getFEEngineBoundary();
fem_boundary.initShapeFunctions(_not_ghost);
fem_boundary.initShapeFunctions(_ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_not_ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_ghost);
}
/* -------------------------------------------------------------------------- */
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() {
auto bit = mesh.element_group_begin();
auto bend = mesh.element_group_end();
for (; bit != bend; ++bit) {
bit->second->dump();
}
}
/* -------------------------------------------------------------------------- */
void Model::setGroupDirectory(const std::string & directory) {
auto bit = mesh.element_group_begin();
auto 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,
true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldVector(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->addDumpGroupFieldVectorToDumper(group.getDefaultDumperName(), field_id,
group_name);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
_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) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
this->spatial_dimension, element_kind,
padding_flag);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
UInt spatial_dimension,
const ElementKind & element_kind,
bool padding_flag) {
#ifdef AKANTU_USE_IOHELPER
dumper::Field * field = nullptr;
if (!field)
field = this->createNodalFieldReal(field_id, group_name, padding_flag);
if (!field)
field = this->createNodalFieldUInt(field_id, group_name, padding_flag);
if (!field)
field = this->createNodalFieldBool(field_id, group_name, padding_flag);
if (!field)
field = this->createElementalField(field_id, group_name, padding_flag,
spatial_dimension, element_kind);
if (!field)
field = this->mesh.createFieldFromAttachedData<UInt>(field_id, group_name,
element_kind);
if (!field)
field = this->mesh.createFieldFromAttachedData<Real>(field_id, group_name,
element_kind);
#ifndef AKANTU_NDEBUG
if (!field) {
AKANTU_DEBUG_WARNING("No field could be found based on name: " << field_id);
}
#endif
if (field) {
DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name, group_name);
this->addDumpGroupFieldToDumper(field_id, field, dumper);
}
#endif
}
/* -------------------------------------------------------------------------- */
void Model::dump() { 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);
}
/* -------------------------------------------------------------------------- */
void Model::setTextModeToDumper() { mesh.setTextModeToDumper(); }
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/model.hh b/src/model/model.hh
index af1032fae..b162476fd 100644
--- a/src/model/model.hh
+++ b/src/model/model.hh
@@ -1,376 +1,376 @@
/**
* @file model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Oct 16 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Interface of a model
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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_named_argument.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "model_options.hh"
#include "model_solver.hh"
/* -------------------------------------------------------------------------- */
#include <typeindex>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MODEL_HH__
#define __AKANTU_MODEL_HH__
namespace akantu {
class SynchronizerRegistry;
class Parser;
class DumperIOHelper;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model : public Memory, public ModelSolver, public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Model(Mesh & mesh, const ModelType & type,
UInt spatial_dimension = _all_dimensions, const ID & id = "model",
const MemoryID & memory_id = 0);
~Model() override;
using FEEngineMap = std::map<std::string, std::unique_ptr<FEEngine>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
virtual void initFullImpl(const ModelOptions & options);
public:
#ifndef SWIG
template <typename... pack>
std::enable_if_t<are_named_argument<pack...>::value>
initFull(pack &&... _pack) {
switch (this->model_type) {
#ifdef AKANTU_SOLID_MECHANICS
case ModelType::_solid_mechanics_model:
this->initFullImpl(SolidMechanicsModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_COHESIVE_ELEMENT
case ModelType::_solid_mechanics_model_cohesive:
this->initFullImpl(SolidMechanicsModelCohesiveOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_HEAT_TRANSFER
case ModelType::_heat_transfer_model:
this->initFullImpl(HeatTransferModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_EMBEDDED
case ModelType::_embedded_model:
this->initFullImpl(EmbeddedInterfaceModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
default:
this->initFullImpl(ModelOptions{use_named_args,
std::forward<decltype(_pack)>(_pack)...});
}
}
template <typename... pack>
std::enable_if_t<not are_named_argument<pack...>::value>
initFull(pack &&... _pack) {
this->initFullImpl(std::forward<decltype(_pack)>(_pack)...);
}
#endif
/// initialize a new solver if needed
void initNewSolver(const AnalysisMethod & method);
protected:
/// get some default values for derived classes
virtual std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) = 0;
virtual void initModel() = 0;
virtual void initFEEngineBoundary();
// /// 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
void printself(std::ostream &, int = 0) const override{};
// /// initialize the model for PBC
// void setPBC(UInt x, UInt y, UInt z);
// void setPBC(SurfacePairList & surface_pairs);
public:
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);
/* ------------------------------------------------------------------------ */
/* Function for non local capabilities */
/* ------------------------------------------------------------------------ */
virtual void updateDataForNonLocalCriterion(__attribute__((unused))
ElementTypeMapReal & criterion) {
AKANTU_TO_IMPLEMENT();
}
protected:
template <typename T>
void allocNodalField(Array<T> *& array, UInt nb_component, const ID & 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 &)
/// 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) const {
throw;
return false; /* TODO repair PBC*/
}
/// returns the array of pbc slave nodes (boolean information)
AKANTU_GET_MACRO(IsPBCSlaveNode, is_pbc_slave_node, const Array<bool> &)
/// Get the type of analysis method used
AKANTU_GET_MACRO(AnalysisMethod, method, AnalysisMethod);
/* ------------------------------------------------------------------------ */
/* Pack and unpack helper functions */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbIntegrationPoints(const Array<Element> & elements,
const ID & fem_id = ID()) const;
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
void setTextModeToDumper();
virtual void addDumpGroupFieldToDumper(const std::string & field_id,
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 addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
UInt spatial_dimension,
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(__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return nullptr;
}
virtual dumper::Field *
createNodalFieldUInt(__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return nullptr;
}
virtual dumper::Field *
createNodalFieldBool(__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return nullptr;
}
virtual dumper::Field *
createElementalField(__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag,
__attribute__((unused)) const UInt & spatial_dimension,
__attribute__((unused)) const ElementKind & kind) {
return nullptr;
}
void setDirectory(const std::string & directory);
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory);
virtual void dump();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
friend std::ostream & operator<<(std::ostream &, const Model &);
/// analysis method check the list in akantu::AnalysisMethod
AnalysisMethod method;
/// Mesh
Mesh & mesh;
/// Spatial dimension of the problem
UInt spatial_dimension;
/// the main fem object present in all models
FEEngineMap fems;
/// the fem object present in all models for boundaries
FEEngineMap fems_boundary;
/// default fem object
std::string default_fem;
/// 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;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Model & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "model_inline_impl.cc"
#endif /* __AKANTU_MODEL_HH__ */
diff --git a/src/model/model_inline_impl.cc b/src/model/model_inline_impl.cc
index c57bbf7ed..c786190ed 100644
--- a/src/model/model_inline_impl.cc
+++ b/src/model/model_inline_impl.cc
@@ -1,217 +1,216 @@
/**
* @file model_inline_impl.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: Wed Aug 25 2010
- * @date last modification: Wed Nov 11 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief inline implementation of the model class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MODEL_INLINE_IMPL_CC__
#define __AKANTU_MODEL_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline FEEngineClass & Model::getFEEngineClassBoundary(std::string name) {
AKANTU_DEBUG_IN();
if (name == "")
name = default_fem;
FEEngineMap::const_iterator it_boun = fems_boundary.find(name);
if (it_boun == fems_boundary.end()) {
AKANTU_DEBUG_INFO("Creating FEEngine boundary " << name);
FEEngineMap::const_iterator it = fems.find(name);
AKANTU_DEBUG_ASSERT(it != fems.end(),
"The FEEngine " << name << " is not registered");
UInt spatial_dimension = it->second->getElementDimension();
std::stringstream sstr;
sstr << id << ":fem_boundary:" << name;
fems_boundary[name] = std::make_unique<FEEngineClass>(
it->second->getMesh(), spatial_dimension - 1, sstr.str(), memory_id);
}
AKANTU_DEBUG_OUT();
return dynamic_cast<FEEngineClass &>(*fems_boundary[name]);
}
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline FEEngineClass & Model::getFEEngineClass(std::string name) const {
AKANTU_DEBUG_IN();
if (name == "")
name = default_fem;
auto it = fems.find(name);
AKANTU_DEBUG_ASSERT(it != fems.end(),
"The FEEngine " << name << " is not registered");
AKANTU_DEBUG_OUT();
return dynamic_cast<FEEngineClass &>(*(it->second));
}
/* -------------------------------------------------------------------------- */
inline void Model::unRegisterFEEngineObject(const std::string & name) {
auto it = fems.find(name);
AKANTU_DEBUG_ASSERT(it != fems.end(),
"FEEngine object with name " << name << " was not found");
fems.erase(it);
if (!fems.empty())
default_fem = (*fems.begin()).first;
}
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline void Model::registerFEEngineObject(const std::string & name, Mesh & mesh,
UInt spatial_dimension) {
if (fems.size() == 0)
default_fem = name;
#ifndef AKANTU_NDEBUG
auto it = fems.find(name);
AKANTU_DEBUG_ASSERT(it == fems.end(),
"FEEngine object with name " << name
<< " was already created");
#endif
std::stringstream sstr;
sstr << id << ":fem:" << name << memory_id;
fems[name] = std::make_unique<FEEngineClass>(mesh, spatial_dimension,
sstr.str(), memory_id);
}
/* -------------------------------------------------------------------------- */
inline FEEngine & Model::getFEEngine(const ID & name) const {
AKANTU_DEBUG_IN();
ID tmp_name = name;
if (name == "")
tmp_name = default_fem;
auto it = fems.find(tmp_name);
AKANTU_DEBUG_ASSERT(it != fems.end(),
"The FEEngine " << tmp_name << " is not registered");
AKANTU_DEBUG_OUT();
return *(it->second);
}
/* -------------------------------------------------------------------------- */
inline FEEngine & Model::getFEEngineBoundary(const ID & name) {
AKANTU_DEBUG_IN();
ID tmp_name = name;
if (name == "")
tmp_name = default_fem;
FEEngineMap::const_iterator it = fems_boundary.find(tmp_name);
AKANTU_DEBUG_ASSERT(it != fems_boundary.end(),
"The FEEngine boundary " << tmp_name
<< " is not registered");
AKANTU_DEBUG_ASSERT(it->second != nullptr,
"The FEEngine boundary " << tmp_name
<< " was not created");
AKANTU_DEBUG_OUT();
return *(it->second);
}
// /* --------------------------------------------------------------------------
// */
// /// @todo : should merge with a single function which handles local and
// global
// inline void Model::changeLocalEquationNumberForPBC(std::map<UInt,UInt> &
// pbc_pair,
// UInt dimension){
// for (std::map<UInt,UInt>::iterator it = pbc_pair.begin();
// it != pbc_pair.end();++it) {
// Int node_master = (*it).second;
// Int node_slave = (*it).first;
// for (UInt i = 0; i < dimension; ++i) {
// (*dof_synchronizer->getLocalDOFEquationNumbersPointer())
// (node_slave*dimension+i) = dimension*node_master+i;
// (*dof_synchronizer->getGlobalDOFEquationNumbersPointer())
// (node_slave*dimension+i) = dimension*node_master+i;
// }
// }
// }
// /* --------------------------------------------------------------------------
// */
// inline bool Model::isPBCSlaveNode(const UInt node) const {
// // if no pbc is defined, is_pbc_slave_node is of size zero
// if (is_pbc_slave_node.size() == 0)
// return false;
// else
// return is_pbc_slave_node(node);
// }
/* -------------------------------------------------------------------------- */
template <typename T>
void Model::allocNodalField(Array<T> *& array, UInt nb_component,
const ID & name) {
if (array == nullptr) {
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_disp;
sstr_disp << id << ":" << name;
array = &(alloc<T>(sstr_disp.str(), nb_nodes, nb_component, T()));
}
}
/* -------------------------------------------------------------------------- */
inline UInt Model::getNbIntegrationPoints(const Array<Element> & elements,
const ID & fem_id) const {
UInt nb_quad = 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_quad +=
getFEEngine(fem_id).getNbIntegrationPoints(el.type, el.ghost_type);
}
return nb_quad;
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_MODEL_INLINE_IMPL_CC__ */
diff --git a/src/model/model_options.hh b/src/model/model_options.hh
index c431d6931..7e2e0a15c 100644
--- a/src/model/model_options.hh
+++ b/src/model/model_options.hh
@@ -1,137 +1,139 @@
/**
* @file model_options.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Mon Dec 04 2017
+ * @date creation: Mon Dec 04 2017
+ * @date last modification: Wed Jan 31 2018
*
- * @brief A Documented file.
+ * @brief A Documented file.
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_named_argument.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MODEL_OPTIONS_HH__
#define __AKANTU_MODEL_OPTIONS_HH__
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(analysis_method);
}
struct ModelOptions {
explicit ModelOptions(AnalysisMethod analysis_method = _static)
: analysis_method(analysis_method) {}
template <typename... pack>
ModelOptions(use_named_args_t, pack &&... _pack)
: ModelOptions(OPTIONAL_NAMED_ARG(analysis_method, _static)) {}
virtual ~ModelOptions() = default;
AnalysisMethod analysis_method;
};
#ifdef AKANTU_SOLID_MECHANICS
/* -------------------------------------------------------------------------- */
struct SolidMechanicsModelOptions : public ModelOptions {
explicit SolidMechanicsModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass)
: ModelOptions(analysis_method) {}
template <typename... pack>
SolidMechanicsModelOptions(use_named_args_t, pack &&... _pack)
: SolidMechanicsModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass)) {}
};
#endif
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_COHESIVE_ELEMENT
namespace {
DECLARE_NAMED_ARGUMENT(is_extrinsic);
}
/* -------------------------------------------------------------------------- */
struct SolidMechanicsModelCohesiveOptions : public SolidMechanicsModelOptions {
SolidMechanicsModelCohesiveOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass,
bool extrinsic = false)
: SolidMechanicsModelOptions(analysis_method), extrinsic(extrinsic) {}
template <typename... pack>
SolidMechanicsModelCohesiveOptions(use_named_args_t, pack &&... _pack)
: SolidMechanicsModelCohesiveOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass),
OPTIONAL_NAMED_ARG(is_extrinsic, false)) {}
bool extrinsic{false};
};
#endif
#ifdef AKANTU_HEAT_TRANSFER
/* -------------------------------------------------------------------------- */
struct HeatTransferModelOptions : public ModelOptions {
explicit HeatTransferModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass)
: ModelOptions(analysis_method) {}
template <typename... pack>
HeatTransferModelOptions(use_named_args_t, pack &&... _pack)
: HeatTransferModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass)) {}
};
#endif
#ifdef AKANTU_EMBEDDED
namespace {
DECLARE_NAMED_ARGUMENT(init_intersections);
}
/* -------------------------------------------------------------------------- */
struct EmbeddedInterfaceModelOptions : SolidMechanicsModelOptions {
/**
* @brief Constructor for EmbeddedInterfaceModelOptions
* @param analysis_method see SolidMechanicsModelOptions
* @param init_intersections compute intersections
*/
EmbeddedInterfaceModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass,
bool init_intersections = true)
: SolidMechanicsModelOptions(analysis_method),
has_intersections(init_intersections) {}
template <typename... pack>
EmbeddedInterfaceModelOptions(use_named_args_t, pack &&... _pack)
: EmbeddedInterfaceModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass),
OPTIONAL_NAMED_ARG(init_intersections, true)) {}
/// Should consider reinforcements
bool has_intersections;
};
#endif
} // akantu
#endif /* __AKANTU_MODEL_OPTIONS_HH__ */
diff --git a/src/model/model_solver.cc b/src/model/model_solver.cc
index 78e97c629..1891e7fd3 100644
--- a/src/model/model_solver.cc
+++ b/src/model/model_solver.cc
@@ -1,364 +1,365 @@
/**
* @file model_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 12 13:31:56 2015
+ * @date creation: Tue Aug 18 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Implementation of ModelSolver
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model_solver.hh"
#include "dof_manager.hh"
#include "dof_manager_default.hh"
#include "mesh.hh"
#include "non_linear_solver.hh"
#include "time_step_solver.hh"
#if defined(AKANTU_USE_PETSC)
#include "dof_manager_petsc.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> static T getOptionToType(const std::string & opt_str) {
std::stringstream sstr(opt_str);
T opt;
sstr >> opt;
return opt;
}
/* -------------------------------------------------------------------------- */
ModelSolver::ModelSolver(Mesh & mesh, const ModelType & type, const ID & id,
UInt memory_id)
: Parsable(ParserType::_model, id), SolverCallback(), model_type(type),
parent_id(id), parent_memory_id(memory_id), mesh(mesh),
dof_manager(nullptr), default_solver_id("") {}
/* -------------------------------------------------------------------------- */
ModelSolver::~ModelSolver() = default;
/* -------------------------------------------------------------------------- */
std::tuple<ParserSection, bool> ModelSolver::getParserSection() {
auto sub_sections = getStaticParser().getSubSections(ParserType::_model);
auto it = std::find_if(
sub_sections.begin(), sub_sections.end(), [&](auto && section) {
ModelType type = getOptionToType<ModelType>(section.getName());
// default id should be the model type if not defined
std::string name = section.getParameter("name", this->parent_id);
return type == model_type and name == this->parent_id;
});
if (it == sub_sections.end())
return std::make_tuple(ParserSection(), true);
return std::make_tuple(*it, false);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::initDOFManager() {
// default without external solver activated at compilation same as mumps that
// is the historical solver but with only the lumped solver
ID solver_type = "default";
#if defined(AKANTU_USE_MUMPS)
solver_type = "default";
#elif defined(AKANTU_USE_PETSC)
solver_type = "petsc";
#endif
ParserSection section;
bool is_empty;
std::tie(section, is_empty) = this->getParserSection();
if (not is_empty) {
solver_type = section.getOption(solver_type);
this->initDOFManager(section, solver_type);
} else {
this->initDOFManager(solver_type);
}
}
/* -------------------------------------------------------------------------- */
void ModelSolver::initDOFManager(const ID & solver_type) {
try {
this->dof_manager = DOFManagerFactory::getInstance().allocate(
solver_type, mesh, this->parent_id + ":dof_manager" + solver_type,
this->parent_memory_id);
} catch (...) {
AKANTU_EXCEPTION(
"To use the solver "
<< solver_type
<< " you will have to code it. This is an unknown solver type.");
}
this->setDOFManager(*this->dof_manager);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::initDOFManager(const ParserSection & section,
const ID & solver_type) {
this->initDOFManager(solver_type);
auto sub_sections = section.getSubSections(ParserType::_time_step_solver);
// parsing the time step solvers
for (auto && section : sub_sections) {
ID type = section.getName();
ID solver_id = section.getParameter("name", type);
auto tss_type = getOptionToType<TimeStepSolverType>(type);
auto tss_options = this->getDefaultSolverOptions(tss_type);
auto sub_solvers_sect =
section.getSubSections(ParserType::_non_linear_solver);
auto nb_non_linear_solver_section =
section.getNbSubSections(ParserType::_non_linear_solver);
auto nls_type = tss_options.non_linear_solver_type;
if (nb_non_linear_solver_section == 1) {
auto && nls_section = *(sub_solvers_sect.first);
nls_type = getOptionToType<NonLinearSolverType>(nls_section.getName());
} else if (nb_non_linear_solver_section > 0) {
AKANTU_EXCEPTION("More than one non linear solver are provided for the "
"time step solver "
<< solver_id);
}
this->getNewSolver(solver_id, tss_type, nls_type);
if (nb_non_linear_solver_section == 1) {
const auto & nls_section = *(sub_solvers_sect.first);
this->dof_manager->getNonLinearSolver(solver_id).parseSection(
nls_section);
}
auto sub_integrator_sections =
section.getSubSections(ParserType::_integration_scheme);
for (auto && is_section : sub_integrator_sections) {
const auto & dof_type_str = is_section.getName();
ID dof_id;
try {
ID tmp = is_section.getParameter("name");
dof_id = tmp;
} catch (...) {
AKANTU_EXCEPTION("No degree of freedom name specified for the "
"integration scheme of type "
<< dof_type_str);
}
auto it_type = getOptionToType<IntegrationSchemeType>(dof_type_str);
IntegrationScheme::SolutionType s_type = is_section.getParameter(
"solution_type", tss_options.solution_type[dof_id]);
this->setIntegrationScheme(solver_id, dof_id, it_type, s_type);
}
for (auto & is_type : tss_options.integration_scheme_type) {
if (!this->hasIntegrationScheme(solver_id, is_type.first)) {
this->setIntegrationScheme(solver_id, is_type.first, is_type.second,
tss_options.solution_type[is_type.first]);
}
}
}
if (section.hasParameter("default_solver")) {
ID default_solver = section.getParameter("default_solver");
if (this->hasSolver(default_solver)) {
this->setDefaultSolver(default_solver);
} else
AKANTU_EXCEPTION(
"The solver \""
<< default_solver
<< "\" was not created, it cannot be set as default solver");
}
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & ModelSolver::getSolver(const ID & solver_id) {
ID tmp_solver_id = solver_id;
if (tmp_solver_id == "")
tmp_solver_id = this->default_solver_id;
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(tmp_solver_id);
return tss;
}
/* -------------------------------------------------------------------------- */
const TimeStepSolver & ModelSolver::getSolver(const ID & solver_id) const {
ID tmp_solver_id = solver_id;
if (solver_id == "")
tmp_solver_id = this->default_solver_id;
const TimeStepSolver & tss =
this->dof_manager->getTimeStepSolver(tmp_solver_id);
return tss;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & ModelSolver::getTimeStepSolver(const ID & solver_id) {
return this->getSolver(solver_id);
}
/* -------------------------------------------------------------------------- */
const TimeStepSolver &
ModelSolver::getTimeStepSolver(const ID & solver_id) const {
return this->getSolver(solver_id);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & ModelSolver::getNonLinearSolver(const ID & solver_id) {
return this->getSolver(solver_id).getNonLinearSolver();
}
/* -------------------------------------------------------------------------- */
const NonLinearSolver &
ModelSolver::getNonLinearSolver(const ID & solver_id) const {
return this->getSolver(solver_id).getNonLinearSolver();
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasSolver(const ID & solver_id) const {
ID tmp_solver_id = solver_id;
if (solver_id == "")
tmp_solver_id = this->default_solver_id;
if (not this->dof_manager) {
AKANTU_EXCEPTION("No DOF manager was initialized");
}
return this->dof_manager->hasTimeStepSolver(tmp_solver_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setDefaultSolver(const ID & solver_id) {
AKANTU_DEBUG_ASSERT(
this->hasSolver(solver_id),
"Cannot set the default solver to a solver that does not exists");
this->default_solver_id = solver_id;
}
/* -------------------------------------------------------------------------- */
void ModelSolver::solveStep(const ID & solver_id) {
AKANTU_DEBUG_IN();
TimeStepSolver & tss = this->getSolver(solver_id);
// make one non linear solve
tss.solveStep(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ModelSolver::getNewSolver(const ID & solver_id,
TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) {
if (this->default_solver_id == "") {
this->default_solver_id = solver_id;
}
if (non_linear_solver_type == _nls_auto) {
switch (time_step_solver_type) {
case _tsst_dynamic:
case _tsst_static:
non_linear_solver_type = _nls_newton_raphson;
break;
case _tsst_dynamic_lumped:
non_linear_solver_type = _nls_lumped;
break;
case _tsst_not_defined:
AKANTU_EXCEPTION(time_step_solver_type
<< " is not a valid time step solver type");
break;
}
}
this->initSolver(time_step_solver_type, non_linear_solver_type);
NonLinearSolver & nls = this->dof_manager->getNewNonLinearSolver(
solver_id, non_linear_solver_type);
this->dof_manager->getNewTimeStepSolver(solver_id, time_step_solver_type,
nls);
}
/* -------------------------------------------------------------------------- */
Real ModelSolver::getTimeStep(const ID & solver_id) const {
const TimeStepSolver & tss = this->getSolver(solver_id);
return tss.getTimeStep();
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setTimeStep(Real time_step, const ID & solver_id) {
TimeStepSolver & tss = this->getSolver(solver_id);
return tss.setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setIntegrationScheme(
const ID & solver_id, const ID & dof_id,
const IntegrationSchemeType & integration_scheme_type,
IntegrationScheme::SolutionType solution_type) {
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(solver_id);
tss.setIntegrationScheme(dof_id, integration_scheme_type, solution_type);
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasDefaultSolver() const {
return (this->default_solver_id != "");
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasIntegrationScheme(const ID & solver_id,
const ID & dof_id) const {
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(solver_id);
return tss.hasIntegrationScheme(dof_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::predictor() {}
/* -------------------------------------------------------------------------- */
void ModelSolver::corrector() {}
/* -------------------------------------------------------------------------- */
TimeStepSolverType ModelSolver::getDefaultSolverType() const {
return _tsst_dynamic_lumped;
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions
ModelSolver::getDefaultSolverOptions(__attribute__((unused))
const TimeStepSolverType & type) const {
ModelSolverOptions options;
options.non_linear_solver_type = _nls_auto;
return options;
}
} // namespace akantu
diff --git a/src/model/model_solver.hh b/src/model/model_solver.hh
index 4c6179ad9..7b2c61c21 100644
--- a/src/model/model_solver.hh
+++ b/src/model/model_solver.hh
@@ -1,193 +1,194 @@
/**
* @file model_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Jul 22 10:53:10 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
* @brief Class regrouping the common solve interface to the different models
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "integration_scheme.hh"
#include "parsable.hh"
#include "solver_callback.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MODEL_SOLVER_HH__
#define __AKANTU_MODEL_SOLVER_HH__
namespace akantu {
class Mesh;
class DOFManager;
class TimeStepSolver;
class NonLinearSolver;
struct ModelSolverOptions;
}
namespace akantu {
class ModelSolver : public Parsable,
public SolverCallback,
public SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ModelSolver(Mesh & mesh, const ModelType & type, const ID & id,
UInt memory_id);
~ModelSolver() override;
/// initialize the dof manager based on solver type passed in the input file
void initDOFManager();
/// initialize the dof manager based on the used chosen solver type
void initDOFManager(const ID & solver_type);
protected:
/// initialize the dof manager based on the used chosen solver type
void initDOFManager(const ParserSection & section, const ID & solver_type);
/// Callback for the model to instantiate the matricees when needed
virtual void initSolver(TimeStepSolverType /*time_step_solver_type*/,
NonLinearSolverType /*non_linear_solver_type*/) {}
/// get the section in the input file (if it exsits) corresponding to this
/// model
std::tuple<ParserSection, bool> getParserSection();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solve a step using a given pre instantiated time step solver and
/// nondynamic linear solver
virtual void solveStep(const ID & solver_id = "");
/// Initialize a time solver that can be used afterwards with its id
void getNewSolver(const ID & solver_id,
TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type = _nls_auto);
/// set an integration scheme for a given dof and a given solver
void
setIntegrationScheme(const ID & solver_id, const ID & dof_id,
const IntegrationSchemeType & integration_scheme_type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
/// set an externally instantiated integration scheme
void setIntegrationScheme(const ID & solver_id, const ID & dof_id,
IntegrationScheme & integration_scheme,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
/* ------------------------------------------------------------------------ */
/* SolverCallback interface */
/* ------------------------------------------------------------------------ */
public:
/// Predictor interface for the callback
void predictor() override;
/// Corrector interface for the callback
void corrector() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Default time step solver to instantiate for this model
virtual TimeStepSolverType getDefaultSolverType() const;
/// Default configurations for a given time step solver
virtual ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const;
/// get access to the internal dof manager
DOFManager & getDOFManager() { return *this->dof_manager; }
/// get the time step of a given solver
Real getTimeStep(const ID & solver_id = "") const;
/// set the time step of a given solver
virtual void setTimeStep(Real time_step, const ID & solver_id = "");
/// set the parameter 'param' of the solver 'solver_id'
// template <typename T>
// void set(const ID & param, const T & value, const ID & solver_id = "");
/// get the parameter 'param' of the solver 'solver_id'
// const Parameter & get(const ID & param, const ID & solver_id = "") const;
/// answer to the question "does the solver exists ?"
bool hasSolver(const ID & solver_id) const;
/// changes the current default solver
void setDefaultSolver(const ID & solver_id);
/// is a default solver defined
bool hasDefaultSolver() const;
/// is an integration scheme set for a given solver and a given dof
bool hasIntegrationScheme(const ID & solver_id, const ID & dof_id) const;
TimeStepSolver & getTimeStepSolver(const ID & solver_id = "");
NonLinearSolver & getNonLinearSolver(const ID & solver_id = "");
const TimeStepSolver & getTimeStepSolver(const ID & solver_id = "") const;
const NonLinearSolver & getNonLinearSolver(const ID & solver_id = "") const;
private:
TimeStepSolver & getSolver(const ID & solver_id);
const TimeStepSolver & getSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ModelType model_type;
private:
ID parent_id;
UInt parent_memory_id;
/// Underlying mesh
Mesh & mesh;
/// Underlying dof_manager (the brain...)
std::unique_ptr<DOFManager> dof_manager;
/// Default time step solver to use
ID default_solver_id;
};
struct ModelSolverOptions {
NonLinearSolverType non_linear_solver_type;
std::map<ID, IntegrationSchemeType> integration_scheme_type;
std::map<ID, IntegrationScheme::SolutionType> solution_type;
};
} // akantu
#endif /* __AKANTU_MODEL_SOLVER_HH__ */
diff --git a/src/model/non_linear_solver.cc b/src/model/non_linear_solver.cc
index a6333d41e..0fcf58024 100644
--- a/src/model/non_linear_solver.cc
+++ b/src/model/non_linear_solver.cc
@@ -1,78 +1,79 @@
/**
* @file non_linear_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Oct 13 15:34:43 2015
+ * @date creation: Tue Jul 20 2010
+ * @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the base class NonLinearSolver
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "dof_manager.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolver::NonLinearSolver(
DOFManager & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: Memory(id, memory_id), Parsable(ParserType::_non_linear_solver, id),
_dof_manager(dof_manager),
non_linear_solver_type(non_linear_solver_type) {
this->registerParam("type", this->non_linear_solver_type, _pat_parsable,
"Non linear solver type");
}
/* -------------------------------------------------------------------------- */
NonLinearSolver::~NonLinearSolver() = default;
/* -------------------------------------------------------------------------- */
void NonLinearSolver::checkIfTypeIsSupported() {
if (this->supported_type.find(this->non_linear_solver_type) ==
this->supported_type.end()) {
AKANTU_EXCEPTION("The resolution method "
<< this->non_linear_solver_type
<< " is not implemented in the non linear solver "
<< this->id << "!");
}
}
/* -------------------------------------------------------------------------- */
void NonLinearSolver::assembleResidual(SolverCallback & solver_callback) {
if (solver_callback.canSplitResidual() and
non_linear_solver_type == _nls_linear) {
this->_dof_manager.clearResidual();
solver_callback.assembleResidual("external");
this->_dof_manager.assembleMatMulDOFsToResidual("K", -1.);
solver_callback.assembleResidual("inertial");
} else {
solver_callback.assembleResidual();
}
}
} // akantu
diff --git a/src/model/non_linear_solver.hh b/src/model/non_linear_solver.hh
index 2cea85168..ef6d5a624 100644
--- a/src/model/non_linear_solver.hh
+++ b/src/model/non_linear_solver.hh
@@ -1,98 +1,99 @@
/**
* @file non_linear_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Aug 24 23:48:41 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Feb 21 2018
*
* @brief Non linear solver interface
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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 "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_HH__
#define __AKANTU_NON_LINEAR_SOLVER_HH__
namespace akantu {
class DOFManager;
class SolverCallback;
}
namespace akantu {
class NonLinearSolver : private Memory, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolver(DOFManager & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver", UInt memory_id = 0);
~NonLinearSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solve the system described by the jacobian matrix, and rhs contained in
/// the dof manager
virtual void solve(SolverCallback & callback) = 0;
protected:
void checkIfTypeIsSupported();
void assembleResidual(SolverCallback & callback);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
DOFManager & _dof_manager;
/// type of non linear solver
NonLinearSolverType non_linear_solver_type;
/// list of supported non linear solver types
std::set<NonLinearSolverType> supported_type;
};
namespace debug {
class NLSNotConvergedException : public Exception {
public:
NLSNotConvergedException(Real threshold, UInt niter, Real error)
: Exception("The non linear solver did not converge."),
threshold(threshold), niter(niter), error(error) {}
Real threshold;
UInt niter;
Real error;
};
}
} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_HH__ */
diff --git a/src/model/non_linear_solver_callback.hh b/src/model/non_linear_solver_callback.hh
index 43895ca8e..45fe7cddd 100644
--- a/src/model/non_linear_solver_callback.hh
+++ b/src/model/non_linear_solver_callback.hh
@@ -1,60 +1,61 @@
/**
* @file non_linear_solver_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Sep 28 18:48:21 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Tue Feb 20 2018
*
* @brief Interface to implement for the non linear solver to work
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_CALLBACK_HH__
#define __AKANTU_NON_LINEAR_SOLVER_CALLBACK_HH__
namespace akantu {
class NonLinearSolverCallback {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// callback to assemble the Jacobian Matrix
virtual void assembleJacobian() { AKANTU_TO_IMPLEMENT(); }
/// callback to assemble the residual (rhs)
virtual void assembleResidual() { AKANTU_TO_IMPLEMENT(); }
/* ------------------------------------------------------------------------ */
/* Dynamic simulations part */
/* ------------------------------------------------------------------------ */
/// callback for the predictor (in case of dynamic simulation)
virtual void predictor() { AKANTU_TO_IMPLEMENT(); }
/// callback for the corrector (in case of dynamic simulation)
virtual void corrector() { AKANTU_TO_IMPLEMENT(); }
};
} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_CALLBACK_HH__ */
diff --git a/src/model/non_linear_solver_default.hh b/src/model/non_linear_solver_default.hh
index 3f7dad3e2..7cc1f2b53 100644
--- a/src/model/non_linear_solver_default.hh
+++ b/src/model/non_linear_solver_default.hh
@@ -1,44 +1,45 @@
/**
* @file non_linear_solver_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Feb 16 10:37:01 2016
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
* @brief Include for the default non linear solvers
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH__
#define __AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH__
#if defined(AKANTU_IMPLICIT)
#include "non_linear_solver_linear.hh"
#include "non_linear_solver_newton_raphson.hh"
#endif
#include "non_linear_solver_lumped.hh"
#endif /* __AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH__ */
diff --git a/src/model/non_linear_solver_linear.cc b/src/model/non_linear_solver_linear.cc
index 4a5704d52..6530cc27d 100644
--- a/src/model/non_linear_solver_linear.cc
+++ b/src/model/non_linear_solver_linear.cc
@@ -1,73 +1,74 @@
/**
* @file non_linear_solver_linear.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 25 00:57:00 2015
+ * @date creation: Tue Jul 20 2010
+ * @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the default NonLinearSolver
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_linear.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverLinear::NonLinearSolverLinear(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id, memory_id),
dof_manager(dof_manager),
solver(dof_manager, "J", id + ":sparse_solver", memory_id) {
this->supported_type.insert(_nls_linear);
this->checkIfTypeIsSupported();
}
/* -------------------------------------------------------------------------- */
NonLinearSolverLinear::~NonLinearSolverLinear() = default;
/* ------------------------------------------------------------------------ */
void NonLinearSolverLinear::solve(SolverCallback & solver_callback) {
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
solver_callback.assembleMatrix("J");
// Residual computed after J to allow the model to use K to compute the
// residual
this->assembleResidual(solver_callback);
this->solver.solve();
solver_callback.corrector();
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/non_linear_solver_linear.hh b/src/model/non_linear_solver_linear.hh
index d402ec16e..155fb8246 100644
--- a/src/model/non_linear_solver_linear.hh
+++ b/src/model/non_linear_solver_linear.hh
@@ -1,78 +1,80 @@
/**
* @file non_linear_solver_linear.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 25 00:48:07 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
- * @brief Default implementation of NonLinearSolver, in case no external library
+ * @brief Default implementation of NonLinearSolver, in case no external
+ * library
* is there to do the job
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__
#define __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class NonLinearSolverLinear : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverLinear(DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_linear",
UInt memory_id = 0);
~NonLinearSolverLinear() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
void solve(SolverCallback & solver_callback) override;
AKANTU_GET_MACRO_NOT_CONST(Solver, solver, SparseSolverMumps &);
AKANTU_GET_MACRO(Solver, solver, const SparseSolverMumps &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
DOFManagerDefault & dof_manager;
/// Sparse solver used for the linear solves
SparseSolverMumps solver;
};
} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__ */
diff --git a/src/model/non_linear_solver_lumped.cc b/src/model/non_linear_solver_lumped.cc
index 1b0f70487..69e3e3a0f 100644
--- a/src/model/non_linear_solver_lumped.cc
+++ b/src/model/non_linear_solver_lumped.cc
@@ -1,102 +1,103 @@
/**
* @file non_linear_solver_lumped.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 25 00:57:00 2015
+ * @date creation: Tue Feb 16 2016
+ * @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the default NonLinearSolver
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_lumped.hh"
#include "communicator.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverLumped::NonLinearSolverLumped(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id, memory_id),
dof_manager(dof_manager) {
this->supported_type.insert(_nls_lumped);
this->checkIfTypeIsSupported();
this->registerParam("b_a2x", this->alpha, 1., _pat_parsmod,
"Conversion coefficient between x and A^{-1} b");
}
/* -------------------------------------------------------------------------- */
NonLinearSolverLumped::~NonLinearSolverLumped() = default;
/* ------------------------------------------------------------------------ */
void NonLinearSolverLumped::solve(SolverCallback & solver_callback) {
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
auto & x = this->dof_manager.getGlobalSolution();
const auto & b = this->dof_manager.getResidual();
x.resize(b.size());
this->dof_manager.updateGlobalBlockedDofs();
const Array<bool> & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
solver_callback.assembleResidual();
const auto & A = this->dof_manager.getLumpedMatrix("M");
// alpha is the conversion factor from from force/mass to acceleration needed
// in model coupled with atomistic \todo find a way to define alpha per dof
// type
this->solveLumped(A, x, b, blocked_dofs, alpha);
this->dof_manager.splitSolutionPerDOFs();
solver_callback.corrector();
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverLumped::solveLumped(const Array<Real> & A, Array<Real> & x,
const Array<Real> & b,
const Array<bool> & blocked_dofs,
Real alpha) {
auto A_it = A.begin();
auto x_it = x.begin();
auto x_end = x.end();
auto b_it = b.begin();
auto blocked_it = blocked_dofs.begin();
for (; x_it != x_end; ++x_it, ++b_it, ++A_it, ++blocked_it) {
if (!(*blocked_it)) {
*x_it = alpha * (*b_it / *A_it);
}
}
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/non_linear_solver_lumped.hh b/src/model/non_linear_solver_lumped.hh
index b27623579..8241391b0 100644
--- a/src/model/non_linear_solver_lumped.hh
+++ b/src/model/non_linear_solver_lumped.hh
@@ -1,79 +1,81 @@
/**
* @file non_linear_solver_lumped.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 25 00:48:07 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
- * @brief Default implementation of NonLinearSolver, in case no external library
+ * @brief Default implementation of NonLinearSolver, in case no external
+ * library
* is there to do the job
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__
#define __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class NonLinearSolverLumped : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverLumped(DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_lumped",
UInt memory_id = 0);
~NonLinearSolverLumped() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
void solve(SolverCallback & solver_callback) override;
static void solveLumped(const Array<Real> & A, Array<Real> & x,
const Array<Real> & b,
const Array<bool> & blocked_dofs, Real alpha);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// Coefficient to apply between x and A^{-1} b
Real alpha;
};
} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__ */
diff --git a/src/model/non_linear_solver_newton_raphson.cc b/src/model/non_linear_solver_newton_raphson.cc
index 540ac8dd0..67618fff6 100644
--- a/src/model/non_linear_solver_newton_raphson.cc
+++ b/src/model/non_linear_solver_newton_raphson.cc
@@ -1,191 +1,192 @@
/**
* @file non_linear_solver_newton_raphson.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 25 00:57:00 2015
+ * @date creation: Tue Sep 15 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the default NonLinearSolver
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_newton_raphson.hh"
#include "communicator.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverNewtonRaphson::NonLinearSolverNewtonRaphson(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id, memory_id),
dof_manager(dof_manager),
solver(std::make_unique<SparseSolverMumps>(
dof_manager, "J", id + ":sparse_solver", memory_id)) {
this->supported_type.insert(_nls_newton_raphson_modified);
this->supported_type.insert(_nls_newton_raphson);
this->supported_type.insert(_nls_linear);
this->checkIfTypeIsSupported();
this->registerParam("threshold", convergence_criteria, 1e-10, _pat_parsmod,
"Threshold to consider results as converged");
this->registerParam("convergence_type", convergence_criteria_type,
_scc_solution, _pat_parsmod,
"Type of convergence criteria");
this->registerParam("max_iterations", max_iterations, 10, _pat_parsmod,
"Max number of iterations");
this->registerParam("error", error, _pat_readable, "Last reached error");
this->registerParam("nb_iterations", n_iter, _pat_readable,
"Last reached number of iterations");
this->registerParam("converged", converged, _pat_readable,
"Did last solve converged");
this->registerParam("force_linear_recompute", force_linear_recompute, true,
_pat_modifiable,
"Force reassembly of the jacobian matrix");
}
/* -------------------------------------------------------------------------- */
NonLinearSolverNewtonRaphson::~NonLinearSolverNewtonRaphson() = default;
/* ------------------------------------------------------------------------ */
void NonLinearSolverNewtonRaphson::solve(SolverCallback & solver_callback) {
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
if (non_linear_solver_type == _nls_linear and
solver_callback.canSplitResidual())
solver_callback.assembleMatrix("K");
this->assembleResidual(solver_callback);
if (this->non_linear_solver_type == _nls_newton_raphson_modified ||
(this->non_linear_solver_type == _nls_linear &&
this->force_linear_recompute)) {
solver_callback.assembleMatrix("J");
this->force_linear_recompute = false;
}
this->n_iter = 0;
this->converged = false;
if (this->convergence_criteria_type == _scc_residual) {
this->converged = this->testConvergence(this->dof_manager.getResidual());
if (this->converged)
return;
}
do {
if (this->non_linear_solver_type == _nls_newton_raphson)
solver_callback.assembleMatrix("J");
this->solver->solve();
solver_callback.corrector();
// EventManager::sendEvent(NonLinearSolver::AfterSparseSolve(method));
if (this->convergence_criteria_type == _scc_residual) {
this->assembleResidual(solver_callback);
this->converged = this->testConvergence(this->dof_manager.getResidual());
} else {
this->converged =
this->testConvergence(this->dof_manager.getGlobalSolution());
}
if (this->convergence_criteria_type == _scc_solution and
not this->converged)
this->assembleResidual(solver_callback);
// this->dump();
this->n_iter++;
AKANTU_DEBUG_INFO(
"[" << this->convergence_criteria_type << "] Convergence iteration "
<< std::setw(std::log10(this->max_iterations)) << this->n_iter
<< ": error " << this->error << (this->converged ? " < " : " > ")
<< this->convergence_criteria);
} while (not this->converged and this->n_iter < this->max_iterations);
// this makes sure that you have correct strains and stresses after the
// solveStep function (e.g., for dumping)
if (this->convergence_criteria_type == _scc_solution)
this->assembleResidual(solver_callback);
if (this->converged) {
// this->sendEvent(NonLinearSolver::ConvergedEvent(method));
} else if (this->n_iter == this->max_iterations) {
AKANTU_CUSTOM_EXCEPTION(debug::NLSNotConvergedException(
this->convergence_criteria, this->n_iter, this->error));
AKANTU_DEBUG_WARNING("[" << this->convergence_criteria_type
<< "] Convergence not reached after "
<< std::setw(std::log10(this->max_iterations))
<< this->n_iter << " iteration"
<< (this->n_iter == 1 ? "" : "s") << "!");
}
return;
}
/* -------------------------------------------------------------------------- */
bool NonLinearSolverNewtonRaphson::testConvergence(const Array<Real> & array) {
AKANTU_DEBUG_IN();
const Array<bool> & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
UInt nb_degree_of_freedoms = array.size();
auto arr_it = array.begin();
auto bld_it = blocked_dofs.begin();
Real norm = 0.;
for (UInt n = 0; n < nb_degree_of_freedoms; ++n, ++arr_it, ++bld_it) {
bool is_local_node = this->dof_manager.isLocalOrMasterDOF(n);
if ((!*bld_it) && is_local_node) {
norm += *arr_it * *arr_it;
}
}
dof_manager.getCommunicator().allReduce(norm, SynchronizerOperation::_sum);
norm = std::sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm),
"Something went wrong in the solve phase");
this->error = norm;
return (error < this->convergence_criteria);
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/non_linear_solver_newton_raphson.hh b/src/model/non_linear_solver_newton_raphson.hh
index aff6ee6b8..f55719533 100644
--- a/src/model/non_linear_solver_newton_raphson.hh
+++ b/src/model/non_linear_solver_newton_raphson.hh
@@ -1,104 +1,106 @@
/**
* @file non_linear_solver_newton_raphson.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 25 00:48:07 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
- * @brief Default implementation of NonLinearSolver, in case no external library
+ * @brief Default implementation of NonLinearSolver, in case no external
+ * library
* is there to do the job
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH__
#define __AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH__
namespace akantu {
class DOFManagerDefault;
class SparseSolverMumps;
}
namespace akantu {
class NonLinearSolverNewtonRaphson : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverNewtonRaphson(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_newton_raphson", UInt memory_id = 0);
~NonLinearSolverNewtonRaphson() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
void solve(SolverCallback & solver_callback) override;
AKANTU_GET_MACRO_NOT_CONST(Solver, *solver, SparseSolverMumps &);
AKANTU_GET_MACRO(Solver, *solver, const SparseSolverMumps &);
protected:
/// test the convergence compare norm of array to convergence_criteria
bool testConvergence(const Array<Real> & array);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// Sparse solver used for the linear solves
std::unique_ptr<SparseSolverMumps> solver;
/// Type of convergence criteria
SolveConvergenceCriteria convergence_criteria_type;
/// convergence threshold
Real convergence_criteria;
/// Max number of iterations
int max_iterations;
/// Number of iterations at last solve call
int n_iter{0};
/// Convergence error at last solve call
Real error{0.};
/// Did the last call to solve reached convergence
bool converged{false};
/// Force a re-computation of the jacobian matrix
bool force_linear_recompute{true};
};
} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH__ */
diff --git a/src/model/solid_mechanics/material.cc b/src/model/solid_mechanics/material.cc
index d266c906c..638092d44 100644
--- a/src/model/solid_mechanics/material.cc
+++ b/src/model/solid_mechanics/material.cc
@@ -1,1377 +1,1377 @@
/**
* @file material.cc
*
+ * @author Guillaume Anciaux <guillaume.anciaux@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>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
- * @date last modification: Tue Nov 24 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the common part of the material class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Material::Material(SolidMechanicsModel & model, const ID & id)
: Memory(id, model.getMemoryID()), Parsable(ParserType::_material, id),
is_init(false), fem(model.getFEEngine()), finite_deformation(false),
name(""), model(model),
spatial_dimension(this->model.getSpatialDimension()),
element_filter("element_filter", id, this->memory_id),
stress("stress", *this), eigengradu("eigen_grad_u", *this),
gradu("grad_u", *this), green_strain("green_strain", *this),
piola_kirchhoff_2("piola_kirchhoff_2", *this),
potential_energy("potential_energy", *this), 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
element_filter.initialize(model.getMesh(),
_spatial_dimension = spatial_dimension);
// model.getMesh().initElementTypeMapArray(element_filter, 1,
// spatial_dimension,
// false, _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: Memory(id, model.getMemoryID()), Parsable(ParserType::_material, id),
is_init(false), fem(fe_engine), finite_deformation(false), name(""),
model(model), spatial_dimension(dim),
element_filter("element_filter", id, this->memory_id),
stress("stress", *this, dim, fe_engine, this->element_filter),
eigengradu("eigen_grad_u", *this, dim, fe_engine, this->element_filter),
gradu("gradu", *this, dim, fe_engine, this->element_filter),
green_strain("green_strain", *this, dim, fe_engine, this->element_filter),
piola_kirchhoff_2("piola_kirchhoff_2", *this, dim, fe_engine,
this->element_filter),
potential_energy("potential_energy", *this, dim, fe_engine,
this->element_filter),
is_non_local(false), use_previous_stress(false),
use_previous_gradu(false),
interpolation_inverse_coordinates("interpolation inverse_coordinates",
*this, dim, fe_engine,
this->element_filter),
interpolation_points_matrices("interpolation points matrices", *this, dim,
fe_engine, this->element_filter) {
AKANTU_DEBUG_IN();
element_filter.initialize(mesh, _spatial_dimension = spatial_dimension);
// mesh.initElementTypeMapArray(element_filter, 1, spatial_dimension, false,
// _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::~Material() = default;
/* -------------------------------------------------------------------------- */
void Material::initialize() {
registerParam("rho", rho, Real(0.), _pat_parsable | _pat_modifiable,
"Density");
registerParam("name", name, std::string(), _pat_parsable | _pat_readable);
registerParam("finite_deformation", finite_deformation, false,
_pat_parsable | _pat_readable, "Is finite deformation");
registerParam("inelastic_deformation", inelastic_deformation, false,
_pat_internal, "Is inelastic deformation");
/// allocate gradu stress for local elements
eigengradu.initialize(spatial_dimension * spatial_dimension);
gradu.initialize(spatial_dimension * spatial_dimension);
stress.initialize(spatial_dimension * spatial_dimension);
potential_energy.initialize(1);
this->model.registerEventHandler(*this);
}
/* -------------------------------------------------------------------------- */
void Material::initMaterial() {
AKANTU_DEBUG_IN();
if (finite_deformation) {
this->piola_kirchhoff_2.initialize(spatial_dimension * spatial_dimension);
if (use_previous_stress)
this->piola_kirchhoff_2.initializeHistory();
this->green_strain.initialize(spatial_dimension * spatial_dimension);
}
if (use_previous_stress)
this->stress.initializeHistory();
if (use_previous_gradu)
this->gradu.initializeHistory();
for (auto it = internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it)
it->second->resize();
for (auto it = internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it)
it->second->resize();
for (auto it = internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it)
it->second->resize();
is_init = true;
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::savePreviousState() {
AKANTU_DEBUG_IN();
for (auto 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::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
if (!finite_deformation) {
auto & internal_force = const_cast<Array<Real> &>(model.getInternalForce());
// Mesh & mesh = fem.getMesh();
for (auto && type :
element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element == 0)
continue;
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
/// compute @f$\sigma \frac{\partial \varphi}{\partial X}@f$ by
/// @f$\mathbf{B}^t \mathbf{\sigma}_q@f$
Array<Real> * sigma_dphi_dx =
new Array<Real>(nb_element * nb_quadrature_points,
size_of_shapes_derivatives, "sigma_x_dphi_/_dX");
fem.computeBtD(stress(type, ghost_type), *sigma_dphi_dx, type, ghost_type,
elem_filter);
/**
* compute @f$\int \sigma * \frac{\partial \varphi}{\partial X}dX@f$ by
* @f$ \sum_q \mathbf{B}^t
* \mathbf{\sigma}_q \overline w_q J_q@f$
*/
Array<Real> * int_sigma_dphi_dx =
new Array<Real>(nb_element, nb_nodes_per_element * spatial_dimension,
"int_sigma_x_dphi_/_dX");
fem.integrate(*sigma_dphi_dx, *int_sigma_dphi_dx,
size_of_shapes_derivatives, type, ghost_type, elem_filter);
delete sigma_dphi_dx;
/// assemble
model.getDOFManager().assembleElementalArrayLocalArray(
*int_sigma_dphi_dx, internal_force, type, ghost_type, -1,
elem_filter);
delete int_sigma_dphi_dx;
}
} else {
switch (spatial_dimension) {
case 1:
this->assembleInternalForces<1>(ghost_type);
break;
case 2:
this->assembleInternalForces<2>(ghost_type);
break;
case 3:
this->assembleInternalForces<3>(ghost_type);
break;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stress from the gradu
*
* @param[in] 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();
for (const auto & type :
element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.size() == 0)
continue;
Array<Real> & gradu_vect = gradu(type, ghost_type);
/// compute @f$\nabla u@f$
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect,
spatial_dimension, type, ghost_type,
elem_filter);
gradu_vect -= eigengradu(type, ghost_type);
/// compute @f$\mathbf{\sigma}_q@f$ from @f$\nabla u@f$
computeStress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computeAllCauchyStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(finite_deformation, "The Cauchy stress can only be "
"computed if you are working in "
"finite deformation.");
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
switch (spatial_dimension) {
case 1:
this->computeCauchyStress<1>(type, ghost_type);
break;
case 2:
this->computeCauchyStress<2>(type, ghost_type);
break;
case 3:
this->computeCauchyStress<3>(type, 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();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
/// compute @f$\nabla u@f$
fem.gradientOnIntegrationPoints(displacement, gradu_vect, spatial_dimension,
type, ghost_type, elem_filter);
setToSteadyState(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stiffness matrix by assembling @f$\int_{\omega} B^t \times D
* \times B d\omega @f$
*
* @param[in] 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();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
if (finite_deformation) {
switch (spatial_dimension) {
case 1: {
assembleStiffnessMatrixNL<1>(type, ghost_type);
assembleStiffnessMatrixL2<1>(type, ghost_type);
break;
}
case 2: {
assembleStiffnessMatrixNL<2>(type, ghost_type);
assembleStiffnessMatrixL2<2>(type, ghost_type);
break;
}
case 3: {
assembleStiffnessMatrixNL<3>(type, ghost_type);
assembleStiffnessMatrixL2<3>(type, ghost_type);
break;
}
}
} else {
switch (spatial_dimension) {
case 1: {
assembleStiffnessMatrix<1>(type, ghost_type);
break;
}
case 2: {
assembleStiffnessMatrix<2>(type, ghost_type);
break;
}
case 3: {
assembleStiffnessMatrix<3>(type, ghost_type);
break;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleStiffnessMatrix(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.size() == 0) {
AKANTU_DEBUG_OUT();
return;
}
// const Array<Real> & shapes_derivatives =
// fem.getShapesDerivatives(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect, dim,
type, ghost_type, elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
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);
/// 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");
fem.computeBtDB(*tangent_stiffness_matrix, *bt_d_b, 4, type, ghost_type,
elem_filter);
delete tangent_stiffness_matrix;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * K_e =
new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
fem.integrate(*bt_d_b, *K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
elem_filter);
delete bt_d_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleStiffnessMatrixNL(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
// Array<Real> & gradu_vect = delta_gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
Array<Real> * shapes_derivatives_filtered = new Array<Real>(
nb_element * nb_quadrature_points, dim * nb_nodes_per_element,
"shapes derivatives filtered");
fem.filterElementalData(fem.getMesh(), shapes_derivatives,
*shapes_derivatives_filtered, type, ghost_type,
elem_filter);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_s_b_size = dim * nb_nodes_per_element;
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);
auto shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
spatial_dimension, nb_nodes_per_element);
auto Bt_S_B_it = bt_s_b->begin(bt_s_b_size, bt_s_b_size);
auto Bt_S_B_end = bt_s_b->end(bt_s_b_size, bt_s_b_size);
auto piola_it = piola_kirchhoff_2(type, ghost_type).begin(dim, dim);
for (; Bt_S_B_it != Bt_S_B_end;
++Bt_S_B_it, ++shapes_derivatives_filtered_it, ++piola_it) {
auto & Bt_S_B = *Bt_S_B_it;
const auto & Piola_kirchhoff_matrix = *piola_it;
setCauchyStressMatrix<dim>(Piola_kirchhoff_matrix, S);
VoigtHelper<dim>::transferBMatrixToBNL(*shapes_derivatives_filtered_it, B,
nb_nodes_per_element);
Bt_S.template mul<true, false>(B, S);
Bt_S_B.template mul<false, false>(Bt_S, B);
}
delete shapes_derivatives_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * K_e =
new Array<Real>(nb_element, bt_s_b_size * bt_s_b_size, "K_e");
fem.integrate(*bt_s_b, *K_e, bt_s_b_size * bt_s_b_size, type, ghost_type,
elem_filter);
delete bt_s_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleStiffnessMatrixL2(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect, dim,
type, ghost_type, elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
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");
fem.filterElementalData(fem.getMesh(), shapes_derivatives,
*shapes_derivatives_filtered, type, ghost_type,
elem_filter);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = dim * nb_nodes_per_element;
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);
auto shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
spatial_dimension, nb_nodes_per_element);
auto Bt_D_B_it = bt_d_b->begin(bt_d_b_size, bt_d_b_size);
auto grad_u_it = gradu_vect.begin(dim, dim);
auto D_it = tangent_stiffness_matrix->begin(tangent_size, tangent_size);
auto D_end = tangent_stiffness_matrix->end(tangent_size, tangent_size);
for (; D_it != D_end;
++D_it, ++Bt_D_B_it, ++shapes_derivatives_filtered_it, ++grad_u_it) {
const auto & grad_u = *grad_u_it;
const auto & D = *D_it;
auto & Bt_D_B = *Bt_D_B_it;
// transferBMatrixToBL1<dim > (*shapes_derivatives_filtered_it, B,
// nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToBL2(*shapes_derivatives_filtered_it,
grad_u, B2, nb_nodes_per_element);
B += B2;
Bt_D.template mul<true, false>(B, D);
Bt_D_B.template mul<false, false>(Bt_D, B);
}
delete tangent_stiffness_matrix;
delete shapes_derivatives_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * K_e =
new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
fem.integrate(*bt_d_b, *K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
elem_filter);
delete bt_d_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & internal_force = model.getInternalForce();
Mesh & mesh = fem.getMesh();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.size() == 0)
continue;
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
Array<Real> * shapesd_filtered = new Array<Real>(
nb_element, size_of_shapes_derivatives, "filtered shapesd");
fem.filterElementalData(mesh, shapes_derivatives, *shapesd_filtered, type,
ghost_type, elem_filter);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
// Set stress vectors
UInt stress_size = getTangentStiffnessVoigtSize(dim);
// Set matrices B and BNL*
UInt bt_s_size = dim * nb_nodes_per_element;
auto * bt_s =
new Array<Real>(nb_element * nb_quadrature_points, bt_s_size, "B^t*S");
auto grad_u_it = this->gradu(type, ghost_type).begin(dim, dim);
auto grad_u_end = this->gradu(type, ghost_type).end(dim, dim);
auto stress_it = this->piola_kirchhoff_2(type, ghost_type).begin(dim, dim);
shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator bt_s_it = bt_s->begin(bt_s_size, 1);
Matrix<Real> 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) {
auto & grad_u = *grad_u_it;
auto & r_it = *bt_s_it;
auto & 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.template 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");
fem.integrate(*bt_s, *r_e, bt_s_size, type, ghost_type, elem_filter);
delete bt_s;
model.getDOFManager().assembleElementalArrayLocalArray(
*r_e, internal_force, type, ghost_type, -1., elem_filter);
delete r_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computePotentialEnergyByElements() {
AKANTU_DEBUG_IN();
for (auto type : element_filter.elementTypes(spatial_dimension, _not_ghost)) {
computePotentialEnergy(type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computePotentialEnergy(ElementType, GhostType) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real Material::getPotentialEnergy() {
AKANTU_DEBUG_IN();
Real epot = 0.;
computePotentialEnergyByElements();
/// integrate the potential energy for each type of elements
for (auto type : element_filter.elementTypes(spatial_dimension, _not_ghost)) {
epot += fem.integrate(potential_energy(type, _not_ghost), type, _not_ghost,
element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
Real Material::getPotentialEnergy(ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
Real epot = 0.;
Vector<Real> epot_on_quad_points(fem.getNbIntegrationPoints(type));
computePotentialEnergyByElement(type, index, epot_on_quad_points);
epot = fem.integrate(epot_on_quad_points, type, element_filter(type)(index));
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(const std::string & type) {
AKANTU_DEBUG_IN();
if (type == "potential")
return getPotentialEnergy();
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(const std::string & energy_id, ElementType type,
UInt index) {
AKANTU_DEBUG_IN();
if (energy_id == "potential")
return getPotentialEnergy(type, index);
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
void Material::initElementalFieldInterpolation(
const ElementTypeMapArray<Real> & interpolation_points_coordinates) {
AKANTU_DEBUG_IN();
this->fem.initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates, this->interpolation_points_matrices,
this->interpolation_inverse_coordinates, &(this->element_filter));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStress(ElementTypeMapArray<Real> & result,
const GhostType ghost_type) {
this->fem.interpolateElementalFieldFromIntegrationPoints(
this->stress, this->interpolation_points_matrices,
this->interpolation_inverse_coordinates, result, ghost_type,
&(this->element_filter));
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStressOnFacets(
ElementTypeMapArray<Real> & result,
ElementTypeMapArray<Real> & by_elem_result, const GhostType ghost_type) {
interpolateStress(by_elem_result, ghost_type);
UInt stress_size = this->stress.getNbComponent();
const Mesh & mesh = this->model.getMesh();
const Mesh & mesh_facets = mesh.getMeshFacets();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_fil = element_filter(type, ghost_type);
Array<Real> & by_elem_res = by_elem_result(type, ghost_type);
UInt nb_element = elem_fil.size();
UInt nb_element_full = this->model.getMesh().getNbElement(type, ghost_type);
UInt nb_interpolation_points_per_elem =
by_elem_res.size() / nb_element_full;
const Array<Element> & facet_to_element =
mesh_facets.getSubelementToElement(type, ghost_type);
ElementType type_facet = Mesh::getFacetType(type);
UInt nb_facet_per_elem = facet_to_element.getNbComponent();
UInt nb_quad_per_facet =
nb_interpolation_points_per_elem / nb_facet_per_elem;
Element element_for_comparison{type, 0, ghost_type};
const Array<std::vector<Element>> * element_to_facet = nullptr;
GhostType current_ghost_type = _casper;
Array<Real> * result_vec = nullptr;
Array<Real>::const_matrix_iterator result_it =
by_elem_res.begin_reinterpret(
stress_size, nb_interpolation_points_per_elem, nb_element_full);
for (UInt el = 0; el < nb_element; ++el) {
UInt global_el = elem_fil(el);
element_for_comparison.element = global_el;
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
Element facet_elem = facet_to_element(global_el, f);
UInt global_facet = facet_elem.element;
if (facet_elem.ghost_type != current_ghost_type) {
current_ghost_type = facet_elem.ghost_type;
element_to_facet = &mesh_facets.getElementToSubelement(
type_facet, current_ghost_type);
result_vec = &result(type_facet, current_ghost_type);
}
bool is_second_element =
(*element_to_facet)(global_facet)[0] != element_for_comparison;
for (UInt q = 0; q < nb_quad_per_facet; ++q) {
Vector<Real> result_local(result_vec->storage() +
(global_facet * nb_quad_per_facet + q) *
result_vec->getNbComponent() +
is_second_element * stress_size,
stress_size);
const Matrix<Real> & result_tmp(result_it[global_el]);
result_local = result_tmp(f * nb_quad_per_facet + q);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
const Array<T> & Material::getArray(const ID & /*vect_id*/,
const ElementType & /*type*/,
const GhostType & /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <typename T>
Array<T> & Material::getArray(const ID & /*vect_id*/,
const ElementType & /*type*/,
const GhostType & /*ghost_type*/) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
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_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << " (" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <>
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_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << " (" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <>
const Array<UInt> & 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<UInt>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << " (" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <>
Array<UInt> & 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<UInt>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << "(" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
const InternalField<T> & Material::getInternal(__attribute__((unused))
const ID & int_id) const {
AKANTU_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T> & Material::getInternal(__attribute__((unused))
const ID & int_id) {
AKANTU_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <>
const InternalField<Real> & Material::getInternal(const ID & int_id) const {
auto it = internal_vectors_real.find(getID() + ":" + int_id);
if (it == internal_vectors_real.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <> InternalField<Real> & Material::getInternal(const ID & int_id) {
auto it = internal_vectors_real.find(getID() + ":" + int_id);
if (it == internal_vectors_real.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <>
const InternalField<UInt> & Material::getInternal(const ID & int_id) const {
auto it = internal_vectors_uint.find(getID() + ":" + int_id);
if (it == internal_vectors_uint.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <> InternalField<UInt> & Material::getInternal(const ID & int_id) {
auto it = internal_vectors_uint.find(getID() + ":" + int_id);
if (it == internal_vectors_uint.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
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(), getMemoryID());
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.size(), 1, type,
ghost_type);
Array<UInt> & mat_renumbering =
material_local_new_numbering(type, ghost_type);
UInt nb_element = elem_filter.size();
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.size());
elem_filter.copy(elem_filter_tmp);
}
}
for (auto it = internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
for (auto it = internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
for (auto it = internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::resizeInternals() {
AKANTU_DEBUG_IN();
for (auto it = internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it)
it->second->resize();
for (auto it = internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it)
it->second->resize();
for (auto it = internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it)
it->second->resize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::onElementsAdded(const Array<Element> &,
const NewElementsEvent &) {
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(), getMemoryID());
auto el_begin = element_list.begin();
auto el_end = element_list.end();
for (auto && gt : ghost_types) {
for (auto && type :
new_numbering.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
if (not element_filter.exists(type, gt) ||
element_filter(type, gt).size() == 0)
continue;
auto & elem_filter = element_filter(type, gt);
auto & mat_indexes = this->model.getMaterialByElement(type, gt);
auto & mat_loc_num = this->model.getMaterialLocalNumbering(type, gt);
auto nb_element = this->model.getMesh().getNbElement(type, gt);
// all materials will resize of the same size...
mat_indexes.resize(nb_element);
mat_loc_num.resize(nb_element);
if (!material_local_new_numbering.exists(type, gt))
material_local_new_numbering.alloc(elem_filter.size(), 1, type, gt);
auto & mat_renumbering = material_local_new_numbering(type, gt);
const auto & renumbering = new_numbering(type, gt);
Array<UInt> elem_filter_tmp;
UInt ni = 0;
Element el{type, 0, gt};
for (UInt i = 0; i < elem_filter.size(); ++i) {
el.element = elem_filter(i);
if (std::find(el_begin, el_end, el) == el_end) {
UInt new_el = renumbering(el.element);
AKANTU_DEBUG_ASSERT(new_el != UInt(-1),
"A not removed element as been badly renumbered");
elem_filter_tmp.push_back(new_el);
mat_renumbering(i) = ni;
mat_indexes(new_el) = my_num;
mat_loc_num(new_el) = ni;
++ni;
} else {
mat_renumbering(i) = UInt(-1);
}
}
elem_filter.resize(elem_filter_tmp.size());
elem_filter.copy(elem_filter_tmp);
}
}
for (auto it = internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
for (auto it = internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
for (auto it = internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
}
/* -------------------------------------------------------------------------- */
void Material::beforeSolveStep() { this->savePreviousState(); }
/* -------------------------------------------------------------------------- */
void Material::afterSolveStep() {
for (auto & type : element_filter.elementTypes(_all_dimensions, _not_ghost,
_ek_not_defined)) {
this->updateEnergies(type, _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) {
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;
}
/* -------------------------------------------------------------------------- */
/// extrapolate internal values
void Material::extrapolateInternal(const ID & id, const Element & element,
__attribute__((unused))
const Matrix<Real> & point,
Matrix<Real> & extrapolated) {
if (this->isInternal<Real>(id, element.kind())) {
UInt nb_element =
this->element_filter(element.type, element.ghost_type).size();
const ID name = this->getID() + ":" + id;
UInt nb_quads =
this->internal_vectors_real[name]->getFEEngine().getNbIntegrationPoints(
element.type, element.ghost_type);
const Array<Real> & internal =
this->getArray<Real>(id, element.type, element.ghost_type);
UInt nb_component = internal.getNbComponent();
Array<Real>::const_matrix_iterator internal_it =
internal.begin_reinterpret(nb_component, nb_quads, nb_element);
Element local_element = this->convertToLocalElement(element);
/// instead of really extrapolating, here the value of the first GP
/// is copied into the result vector. This works only for linear
/// elements
/// @todo extrapolate!!!!
AKANTU_DEBUG_WARNING("This is a fix, values are not truly extrapolated");
const Matrix<Real> & values = internal_it[local_element.element];
UInt index = 0;
Vector<Real> tmp(nb_component);
for (UInt j = 0; j < values.cols(); ++j) {
tmp = values(j);
if (tmp.norm() > 0) {
index = j;
break;
}
}
for (UInt i = 0; i < extrapolated.size(); ++i) {
extrapolated(i) = values(index);
}
} else {
Matrix<Real> default_values(extrapolated.rows(), extrapolated.cols(), 0.);
extrapolated = default_values;
}
}
/* -------------------------------------------------------------------------- */
void Material::applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const GhostType ghost_type) {
for (auto && type : element_filter.elementTypes(_all_dimensions, _not_ghost,
_ek_not_defined)) {
if (!element_filter(type, ghost_type).size())
continue;
auto eigen_it = this->eigengradu(type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto eigen_end = this->eigengradu(type, ghost_type)
.end(spatial_dimension, spatial_dimension);
for (; eigen_it != eigen_end; ++eigen_it) {
auto & current_eigengradu = *eigen_it;
current_eigengradu = prescribed_eigen_grad_u;
}
}
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/material.hh b/src/model/solid_mechanics/material.hh
index d66f49984..fae76952a 100644
--- a/src/model/solid_mechanics/material.hh
+++ b/src/model/solid_mechanics/material.hh
@@ -1,680 +1,679 @@
/**
* @file material.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Mother class for all materials
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "aka_voigthelper.hh"
#include "data_accessor.hh"
#include "integration_point.hh"
#include "parsable.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#include "internal_field.hh"
#include "random_internal_field.hh"
/* -------------------------------------------------------------------------- */
#include "mesh_events.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_HH__
#define __AKANTU_MATERIAL_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
class SolidMechanicsModel;
} // namespace akantu
namespace 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<Element>,
public Parsable,
public MeshEventHandler,
protected SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
#if __cplusplus > 199711L
Material(const Material & mat) = delete;
Material & operator=(const Material & mat) = delete;
#endif
/// Initialize material with defaults
Material(SolidMechanicsModel & model, const ID & id = "");
/// Initialize material with custom mesh & fe_engine
Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
/// Destructor
~Material() override;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Function that materials can/should reimplement */
/* ------------------------------------------------------------------------ */
protected:
/// constitutive law
virtual void computeStress(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost) {
AKANTU_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_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_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:
/// extrapolate internal values
virtual void extrapolateInternal(const ID & id, const Element & element,
const Matrix<Real> & points,
Matrix<Real> & extrapolated);
/// compute the p-wave speed in the material
virtual Real getPushWaveSpeed(__attribute__((unused))
const Element & element) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the s-wave speed in the material
virtual Real getShearWaveSpeed(__attribute__((unused))
const Element & element) const {
AKANTU_TO_IMPLEMENT();
}
/// get a material celerity to compute the stable time step (default: is the
/// push wave speed)
virtual Real getCelerity(const Element & element) const {
return getPushWaveSpeed(element);
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename T>
void registerInternal(__attribute__((unused)) InternalField<T> & vect) {
AKANTU_TO_IMPLEMENT();
}
template <typename T>
void unregisterInternal(__attribute__((unused)) InternalField<T> & vect) {
AKANTU_TO_IMPLEMENT();
}
/// initialize the material computed parameter
virtual void initMaterial();
/// compute the residual for this material
// virtual void updateResidual(GhostType ghost_type = _not_ghost);
/// assemble the residual for this material
virtual void assembleInternalForces(GhostType ghost_type);
/// save the stress in the previous_stress if needed
virtual void savePreviousState();
/// compute the stresses for this material
virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
// virtual void
// computeAllStressesFromTangentModuli(GhostType ghost_type = _not_ghost);
virtual void computeAllCauchyStresses(GhostType ghost_type = _not_ghost);
/// set material to steady state
void setToSteadyState(GhostType ghost_type = _not_ghost);
/// compute the stiffness matrix
virtual void assembleStiffnessMatrix(GhostType ghost_type);
/// add an element to the local mesh filter
inline UInt addElement(const ElementType & type, UInt element,
const GhostType & ghost_type);
inline UInt addElement(const Element & element);
/// add many elements at once
void addElements(const Array<Element> & elements_to_add);
/// remove many element at once
void removeElements(const Array<Element> & elements_to_remove);
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
/**
* interpolate stress on given positions for each element by means
* of a geometrical interpolation on quadrature points
*/
void interpolateStress(ElementTypeMapArray<Real> & result,
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,
ElementTypeMapArray<Real> & by_elem_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:
/* ------------------------------------------------------------------------ */
inline UInt getTangentStiffnessVoigtSize(UInt spatial_dimension) const;
/// compute the potential energy by element
void computePotentialEnergyByElements();
/// resize the intenals arrays
virtual void resizeInternals();
/* ------------------------------------------------------------------------ */
/* Finite deformation functions */
/* This functions area implementing what is described in the paper of Bathe */
/* et al, in IJNME, Finite Element Formulations For Large Deformation */
/* Dynamic Analysis, Vol 9, 353-386, 1975 */
/* ------------------------------------------------------------------------ */
protected:
/// assemble the residual
template <UInt dim> void assembleInternalForces(GhostType ghost_type);
/// Computation of Cauchy stress tensor in the case of finite deformation from
/// the 2nd Piola-Kirchhoff for a given element type
template <UInt dim>
void computeCauchyStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// Computation the Cauchy stress the 2nd Piola-Kirchhoff and the deformation
/// gradient
template <UInt dim>
inline void 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);
/// 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> & sigma);
/// write the stress tensor in the Voigt notation.
template <UInt dim>
inline void setCauchyStressArray(const Matrix<Real> & S_t,
Matrix<Real> & sigma_voight);
/* ------------------------------------------------------------------------ */
/* Conversion functions */
/* ------------------------------------------------------------------------ */
public:
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 IntegrationPoint
convertToLocalPoint(const IntegrationPoint & global_point) const;
/// converts local quadrature point to global quadrature point
inline IntegrationPoint
convertToGlobalPoint(const IntegrationPoint & local_point) const;
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
template <typename T>
inline void packElementDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID()) const;
template <typename T>
inline void unpackElementDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID());
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override{};
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) override{};
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override{};
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual void beforeSolveStep();
virtual void afterSolveStep();
void onDamageIteration() override;
void onDamageUpdate() override;
void onDump() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Name, name, const std::string &);
AKANTU_GET_MACRO(Model, model, const SolidMechanicsModel &)
AKANTU_GET_MACRO(ID, Memory::getID(), const ID &);
AKANTU_GET_MACRO(Rho, rho, Real);
AKANTU_SET_MACRO(Rho, rho, Real);
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// return the potential energy for the subset of elements contained by the
/// material
Real getPotentialEnergy();
/// return the potential energy for the provided element
Real getPotentialEnergy(ElementType & type, UInt index);
/// return the energy (identified by id) for the subset of elements contained
/// by the material
virtual Real getEnergy(const std::string & energy_id);
/// return the energy (identified by id) for the provided element
virtual Real getEnergy(const std::string & energy_id, ElementType type,
UInt index);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ElementFilter, element_filter, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(GradU, gradu, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Stress, stress, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(PotentialEnergy, potential_energy,
Real);
AKANTU_GET_MACRO(GradU, gradu, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Stress, stress, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(ElementFilter, element_filter,
const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(FEEngine, fem, FEEngine &);
bool isNonLocal() const { return is_non_local; }
template <typename T>
const Array<T> & getArray(const ID & id, const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
template <typename T>
Array<T> & getArray(const ID & id, const ElementType & type,
const GhostType & ghost_type = _not_ghost);
template <typename T>
const InternalField<T> & getInternal(const ID & id) const;
template <typename T> InternalField<T> & getInternal(const ID & id);
template <typename T>
inline bool isInternal(const ID & id, const ElementKind & element_kind) const;
template <typename T>
ElementTypeMap<UInt>
getInternalDataPerElem(const ID & id, const ElementKind & element_kind) const;
bool isFiniteDeformation() const { return finite_deformation; }
bool isInelasticDeformation() const { return inelastic_deformation; }
template <typename T> inline void setParam(const ID & param, T value);
inline const Parameter & getParam(const ID & param) const;
template <typename T>
void flattenInternal(const std::string & field_id,
ElementTypeMapArray<T> & internal_flat,
const GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) const;
/// apply a constant eigengrad_u everywhere in the material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const GhostType = _not_ghost);
/// specify if the matrix need to be recomputed for this material
virtual bool hasStiffnessMatrixChanged() { return true; }
protected:
bool isInit() const { return is_init; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// 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;
std::map<ID, InternalField<bool> *> internal_vectors_bool;
protected:
/// Link to the fem object in the model
FEEngine & fem;
/// 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;
/// eigengrad_u arrays ordered by element types
InternalField<Real> eigengradu;
/// grad_u arrays ordered by element types
InternalField<Real> gradu;
/// Green Lagrange strain (Finite deformation)
InternalField<Real> green_strain;
/// Second Piola-Kirchhoff stress tensor arrays ordered by element types
/// (Finite deformation)
InternalField<Real> piola_kirchhoff_2;
/// potential energy by element
InternalField<Real> potential_energy;
/// tell if using in non local mode or not
bool is_non_local;
/// 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;
/// vector that contains the names of all the internals that need to
/// be transferred when material interfaces move
std::vector<ID> internals_to_transfer;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Material & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "material_inline_impl.cc"
#include "internal_field_tmpl.hh"
#include "random_internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* Auto loop */
/* -------------------------------------------------------------------------- */
/// This can be used to automatically write the loop on quadrature points in
/// functions such as computeStress. This macro in addition to write the loop
/// provides two tensors (matrices) sigma and grad_u
#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type) \
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).size()); \
\
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).size()); \
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 }
/// This can be used to automatically write the loop on quadrature points in
/// functions such as computeTangentModuli. This macro in addition to write the
/// loop provides two tensors (matrices) sigma_tensor, grad_u, and a matrix
/// where the elemental tangent moduli should be stored in Voigt Notation
#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_mat) \
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).size()); \
\
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 }
/* -------------------------------------------------------------------------- */
namespace akantu {
using MaterialFactory =
Factory<Material, ID, UInt, const ID &, SolidMechanicsModel &, const ID &>;
} // namespace akantu
#define INSTANTIATE_MATERIAL_ONLY(mat_name) \
template class mat_name<1>; \
template class mat_name<2>; \
template class mat_name<3>
#define MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name) \
[](UInt dim, const ID &, SolidMechanicsModel & model, \
const ID & id) -> std::unique_ptr<Material> { \
switch (dim) { \
case 1: \
return std::make_unique<mat_name<1>>(model, id); \
case 2: \
return std::make_unique<mat_name<2>>(model, id); \
case 3: \
return std::make_unique<mat_name<3>>(model, id); \
default: \
AKANTU_EXCEPTION("The dimension " \
<< dim << "is not a valid dimension for the material " \
<< #id); \
} \
}
#define INSTANTIATE_MATERIAL(id, mat_name) \
INSTANTIATE_MATERIAL_ONLY(mat_name); \
static bool material_is_alocated_##id[[gnu::unused]] = \
MaterialFactory::getInstance().registerAllocator( \
#id, MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name))
#endif /* __AKANTU_MATERIAL_HH__ */
diff --git a/src/model/solid_mechanics/material_inline_impl.cc b/src/model/solid_mechanics/material_inline_impl.cc
index 41f6de00b..19d753e5a 100644
--- a/src/model/solid_mechanics/material_inline_impl.cc
+++ b/src/model/solid_mechanics/material_inline_impl.cc
@@ -1,462 +1,461 @@
/**
* @file material_inline_impl.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
- * @date last modification: Wed Nov 25 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the inline functions of the class material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_INLINE_IMPL_CC__
#define __AKANTU_MATERIAL_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt Material::addElement(const ElementType & type, UInt element,
const GhostType & ghost_type) {
Array<UInt> & el_filter = this->element_filter(type, ghost_type);
el_filter.push_back(element);
return el_filter.size() - 1;
}
/* -------------------------------------------------------------------------- */
inline UInt Material::addElement(const Element & element) {
return this->addElement(element.type, element.element, element.ghost_type);
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getTangentStiffnessVoigtSize(UInt dim) const {
return (dim * (dim - 1) / 2 + dim);
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getCauchyStressMatrixSize(UInt dim) const {
return (dim * dim);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToF(const Matrix<Real> & grad_u, Matrix<Real> & F) {
AKANTU_DEBUG_ASSERT(F.size() >= grad_u.size() && grad_u.size() == dim * dim,
"The dimension of the tensor F should be greater or "
"equal to the dimension of the tensor grad_u.");
F.eye();
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
F(i, j) += grad_u(i, j);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::computeCauchyStressOnQuad(const Matrix<Real> & F,
const Matrix<Real> & piola,
Matrix<Real> & sigma,
const Real & C33) const {
Real J = F.det() * sqrt(C33);
Matrix<Real> F_S(dim, dim);
F_S.mul<false, false>(F, piola);
Real constant = J ? 1. / J : 0;
sigma.mul<false, true>(F_S, F, constant);
}
/* -------------------------------------------------------------------------- */
inline void Material::rightCauchy(const Matrix<Real> & F, Matrix<Real> & C) {
C.mul<true, false>(F, F);
}
/* -------------------------------------------------------------------------- */
inline void Material::leftCauchy(const Matrix<Real> & F, Matrix<Real> & B) {
B.mul<false, true>(F, F);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToEpsilon(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon) {
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
epsilon(i, j) = 0.5 * (grad_u(i, j) + grad_u(j, i));
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToGreenStrain(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon) {
epsilon.mul<true, false>(grad_u, grad_u, .5);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
epsilon(i, j) += 0.5 * (grad_u(i, j) + grad_u(j, i));
}
/* -------------------------------------------------------------------------- */
inline Real Material::stressToVonMises(const Matrix<Real> & stress) {
// compute deviatoric stress
UInt dim = stress.cols();
Matrix<Real> deviatoric_stress =
Matrix<Real>::eye(dim, -1. * stress.trace() / 3.);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
deviatoric_stress(i, j) += stress(i, j);
// return Von Mises stress
return std::sqrt(3. * deviatoric_stress.doubleDot(deviatoric_stress) / 2.);
}
/* ---------------------------------------------------------------------------*/
template <UInt dim>
inline void Material::setCauchyStressArray(const Matrix<Real> & S_t,
Matrix<Real> & sigma_voight) {
AKANTU_DEBUG_IN();
sigma_voight.clear();
// see Finite element formulations for large deformation dynamic analysis,
// Bathe et al. IJNME vol 9, 1975, page 364 ^t\tau
/*
* 1d: [ s11 ]'
* 2d: [ s11 s22 s12 ]'
* 3d: [ s11 s22 s33 s23 s13 s12 ]
*/
for (UInt i = 0; i < dim; ++i) // diagonal terms
sigma_voight(i, 0) = S_t(i, i);
for (UInt i = 1; i < dim; ++i) // term s12 in 2D and terms s23 s13 in 3D
sigma_voight(dim + i - 1, 0) = S_t(dim - i - 1, dim - 1);
for (UInt i = 2; i < dim; ++i) // term s13 in 3D
sigma_voight(dim + i, 0) = S_t(0, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::setCauchyStressMatrix(const Matrix<Real> & S_t,
Matrix<Real> & sigma) {
AKANTU_DEBUG_IN();
sigma.clear();
/// see Finite ekement formulations for large deformation dynamic analysis,
/// Bathe et al. IJNME vol 9, 1975, page 364 ^t\tau
for (UInt i = 0; i < dim; ++i) {
for (UInt m = 0; m < dim; ++m) {
for (UInt n = 0; n < dim; ++n) {
sigma(i * dim + m, i * dim + n) = S_t(m, n);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline Element
Material::convertToLocalElement(const Element & global_element) const {
UInt ge = global_element.element;
#ifndef AKANTU_NDEBUG
UInt model_mat_index = this->model.getMaterialByElement(
global_element.type, global_element.ghost_type)(ge);
UInt mat_index = this->model.getMaterialIndex(this->name);
AKANTU_DEBUG_ASSERT(model_mat_index == mat_index,
"Conversion of a global element in a local element for "
"the wrong material "
<< this->name << std::endl);
#endif
UInt le = this->model.getMaterialLocalNumbering(
global_element.type, global_element.ghost_type)(ge);
Element tmp_quad{global_element.type, le, global_element.ghost_type};
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline Element
Material::convertToGlobalElement(const Element & local_element) const {
UInt le = local_element.element;
UInt ge =
this->element_filter(local_element.type, local_element.ghost_type)(le);
Element tmp_quad{local_element.type, ge, local_element.ghost_type};
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline IntegrationPoint
Material::convertToLocalPoint(const IntegrationPoint & global_point) const {
const FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = fem.getNbIntegrationPoints(global_point.type);
Element el =
this->convertToLocalElement(static_cast<const Element &>(global_point));
IntegrationPoint tmp_quad(el, global_point.num_point, nb_quad);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline IntegrationPoint
Material::convertToGlobalPoint(const IntegrationPoint & local_point) const {
const FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = fem.getNbIntegrationPoints(local_point.type);
Element el =
this->convertToGlobalElement(static_cast<const Element &>(local_point));
IntegrationPoint tmp_quad(el, local_point.num_point, nb_quad);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_smm_stress) {
return (this->isFiniteDeformation() ? 3 : 1) * spatial_dimension *
spatial_dimension * sizeof(Real) *
this->getModel().getNbIntegrationPoints(elements);
}
return 0;
}
/* -------------------------------------------------------------------------- */
inline void Material::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_smm_stress) {
if (this->isFiniteDeformation()) {
packElementDataHelper(piola_kirchhoff_2, buffer, elements);
packElementDataHelper(gradu, buffer, elements);
}
packElementDataHelper(stress, buffer, elements);
}
}
/* -------------------------------------------------------------------------- */
inline void Material::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == _gst_smm_stress) {
if (this->isFiniteDeformation()) {
unpackElementDataHelper(piola_kirchhoff_2, buffer, elements);
unpackElementDataHelper(gradu, buffer, elements);
}
unpackElementDataHelper(stress, buffer, elements);
}
}
/* -------------------------------------------------------------------------- */
inline const Parameter & Material::getParam(const ID & param) const {
try {
return get(param);
} catch (...) {
AKANTU_EXCEPTION("No parameter " << param << " in the material "
<< getID());
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::setParam(const ID & param, T value) {
try {
set<T>(param, value);
} catch (...) {
AKANTU_EXCEPTION("No parameter " << param << " in the material "
<< getID());
}
updateInternalParameters();
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::packElementDataHelper(
const ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) const {
DataAccessor::packElementalDataHelper<T>(data_to_pack, buffer, elements, true,
model.getFEEngine(fem_id));
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::unpackElementDataHelper(
ElementTypeMapArray<T> & data_to_unpack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) {
DataAccessor::unpackElementalDataHelper<T>(data_to_unpack, buffer, elements,
true, model.getFEEngine(fem_id));
}
/* -------------------------------------------------------------------------- */
template <>
inline void Material::registerInternal<Real>(InternalField<Real> & vect) {
internal_vectors_real[vect.getID()] = &vect;
}
template <>
inline void Material::registerInternal<UInt>(InternalField<UInt> & vect) {
internal_vectors_uint[vect.getID()] = &vect;
}
template <>
inline void Material::registerInternal<bool>(InternalField<bool> & vect) {
internal_vectors_bool[vect.getID()] = &vect;
}
/* -------------------------------------------------------------------------- */
template <>
inline void Material::unregisterInternal<Real>(InternalField<Real> & vect) {
internal_vectors_real.erase(vect.getID());
}
template <>
inline void Material::unregisterInternal<UInt>(InternalField<UInt> & vect) {
internal_vectors_uint.erase(vect.getID());
}
template <>
inline void Material::unregisterInternal<bool>(InternalField<bool> & vect) {
internal_vectors_bool.erase(vect.getID());
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline bool Material::isInternal(__attribute__((unused)) const ID & id,
__attribute__((unused))
const ElementKind & element_kind) const {
AKANTU_TO_IMPLEMENT();
}
template <>
inline bool Material::isInternal<Real>(const ID & id,
const ElementKind & element_kind) const {
auto internal_array = internal_vectors_real.find(this->getID() + ":" + id);
if (internal_array == internal_vectors_real.end() ||
internal_array->second->getElementKind() != element_kind)
return false;
return true;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMap<UInt>
Material::getInternalDataPerElem(const ID & field_id,
const ElementKind & element_kind) const {
if (!this->template isInternal<T>(field_id, element_kind))
AKANTU_EXCEPTION("Cannot find internal field " << id << " in material "
<< this->name);
const InternalField<T> & internal_field =
this->template getInternal<T>(field_id);
const FEEngine & fe_engine = internal_field.getFEEngine();
UInt nb_data_per_quad = internal_field.getNbComponent();
ElementTypeMap<UInt> res;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
using type_iterator = typename InternalField<T>::type_iterator;
type_iterator tit = internal_field.firstType(*gt);
type_iterator tend = internal_field.lastType(*gt);
for (; tit != tend; ++tit) {
UInt nb_quadrature_points = fe_engine.getNbIntegrationPoints(*tit, *gt);
res(*tit, *gt) = nb_data_per_quad * nb_quadrature_points;
}
}
return res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Material::flattenInternal(const std::string & field_id,
ElementTypeMapArray<T> & internal_flat,
const GhostType ghost_type,
ElementKind element_kind) const {
if (!this->template isInternal<T>(field_id, element_kind))
AKANTU_EXCEPTION("Cannot find internal field " << id << " in material "
<< this->name);
const InternalField<T> & internal_field =
this->template getInternal<T>(field_id);
const FEEngine & fe_engine = internal_field.getFEEngine();
const Mesh & mesh = fe_engine.getMesh();
using type_iterator = typename InternalField<T>::filter_type_iterator;
type_iterator tit = internal_field.filterFirstType(ghost_type);
type_iterator tend = internal_field.filterLastType(ghost_type);
for (; tit != tend; ++tit) {
ElementType type = *tit;
const Array<Real> & src_vect = internal_field(type, ghost_type);
const Array<UInt> & filter = internal_field.getFilter(type, ghost_type);
// total number of elements in the corresponding mesh
UInt nb_element_dst = mesh.getNbElement(type, ghost_type);
// number of element in the internal field
UInt nb_element_src = filter.size();
// number of quadrature points per elem
UInt nb_quad_per_elem = fe_engine.getNbIntegrationPoints(type);
// number of data per quadrature point
UInt nb_data_per_quad = internal_field.getNbComponent();
if (!internal_flat.exists(type, ghost_type)) {
internal_flat.alloc(nb_element_dst * nb_quad_per_elem, nb_data_per_quad,
type, ghost_type);
}
if (nb_element_src == 0)
continue;
// number of data per element
UInt nb_data = nb_quad_per_elem * nb_data_per_quad;
Array<Real> & dst_vect = internal_flat(type, ghost_type);
dst_vect.resize(nb_element_dst * nb_quad_per_elem);
Array<UInt>::const_scalar_iterator it = filter.begin();
Array<UInt>::const_scalar_iterator end = filter.end();
auto it_src = src_vect.begin_reinterpret(nb_data, nb_element_src);
auto it_dst = dst_vect.begin_reinterpret(nb_data, nb_element_dst);
for (; it != end; ++it, ++it_src) {
it_dst[*it] = *it_src;
}
}
}
} // akantu
#endif /* __AKANTU_MATERIAL_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/material_list.hh.in b/src/model/solid_mechanics/material_list.hh.in
index bd556cd36..cd6ca5b68 100644
--- a/src/model/solid_mechanics/material_list.hh.in
+++ b/src/model/solid_mechanics/material_list.hh.in
@@ -1,51 +1,43 @@
/**
* @file material_list.hh.in
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Feb 21 2013
- * @date last modification: Sat Jul 18 2015
+ * @date creation: Wed Sep 01 2010
+ * @date last modification: Wed Feb 03 2016
*
* @brief List of materials and all includes
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
*
- * You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_LIST_HH__
#define __AKANTU_MATERIAL_LIST_HH__
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
/* Material includes */
/* -------------------------------------------------------------------------- */
@AKANTU_MATERIAL_INCLUDES@
/* -------------------------------------------------------------------------- */
/* Material list */
/* -------------------------------------------------------------------------- */
#define AKANTU_MATERIAL_LIST \
@AKANTU_MATERIAL_LISTS@
// leave an empty line after the list
#endif /* __AKANTU_MATERIAL_LIST_HH__ */
diff --git a/src/model/solid_mechanics/material_selector.hh b/src/model/solid_mechanics/material_selector.hh
index eb9d161b8..552274dc9 100644
--- a/src/model/solid_mechanics/material_selector.hh
+++ b/src/model/solid_mechanics/material_selector.hh
@@ -1,160 +1,161 @@
/**
* @file material_selector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Thu Dec 17 2015
+ * @date last modification: Mon Dec 18 2017
*
* @brief class describing how to choose a material for a given element
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "element.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_SELECTOR_HH__
#define __AKANTU_MATERIAL_SELECTOR_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModel;
/**
* main class to assign same or different materials for different
* elements
*/
class MaterialSelector : public std::enable_shared_from_this<MaterialSelector> {
public:
MaterialSelector() = default;
virtual ~MaterialSelector() = default;
virtual inline UInt operator()(const Element & element) {
if (fallback_selector)
return (*fallback_selector)(element);
return fallback_value;
}
inline void setFallback(UInt f) { fallback_value = f; }
inline void
setFallback(const std::shared_ptr<MaterialSelector> & fallback_selector) {
this->fallback_selector = fallback_selector;
}
inline void setFallback(MaterialSelector & fallback_selector) {
this->fallback_selector = fallback_selector.shared_from_this();
}
inline std::shared_ptr<MaterialSelector> & getFallbackSelector() {
return this->fallback_selector;
}
inline UInt getFallbackValue() { return this->fallback_value; }
protected:
UInt fallback_value{0};
std::shared_ptr<MaterialSelector> fallback_selector;
};
/* -------------------------------------------------------------------------- */
/**
* class that assigns the first material to regular elements by default
*/
class DefaultMaterialSelector : public MaterialSelector {
public:
explicit DefaultMaterialSelector(
const ElementTypeMapArray<UInt> & material_index)
: material_index(material_index) {}
UInt operator()(const Element & element) override {
if (not material_index.exists(element.type, element.ghost_type))
return MaterialSelector::operator()(element);
const auto & mat_indexes = material_index(element.type, element.ghost_type);
if (element.element < mat_indexes.size()) {
auto && tmp_mat = mat_indexes(element.element);
if (tmp_mat != UInt(-1))
return tmp_mat;
}
return MaterialSelector::operator()(element);
}
private:
const ElementTypeMapArray<UInt> & material_index;
};
/* -------------------------------------------------------------------------- */
/**
* Use elemental data to assign materials
*/
template <typename T>
class ElementDataMaterialSelector : public MaterialSelector {
public:
ElementDataMaterialSelector(const ElementTypeMapArray<T> & element_data,
const SolidMechanicsModel & model,
UInt first_index = 1)
: element_data(element_data), model(model), first_index(first_index) {}
inline T elementData(const Element & element) {
DebugLevel dbl = debug::getDebugLevel();
debug::setDebugLevel(dblError);
T data = element_data(element.type, element.ghost_type)(element.element);
debug::setDebugLevel(dbl);
return data;
}
inline UInt operator()(const Element & element) override {
return MaterialSelector::operator()(element);
}
protected:
/// list of element with the specified data (i.e. tag value)
const ElementTypeMapArray<T> & element_data;
/// the model that the materials belong
const SolidMechanicsModel & model;
/// first material index: equal to 1 if none specified
UInt first_index;
};
/* -------------------------------------------------------------------------- */
/**
* class to use mesh data information to assign different materials
* where name is the tag value: tag_0, tag_1
*/
template <typename T>
class MeshDataMaterialSelector : public ElementDataMaterialSelector<T> {
public:
MeshDataMaterialSelector(const std::string & name,
const SolidMechanicsModel & model,
UInt first_index = 1);
};
} // namespace akantu
#endif /* __AKANTU_MATERIAL_SELECTOR_HH__ */
diff --git a/src/model/solid_mechanics/material_selector_tmpl.hh b/src/model/solid_mechanics/material_selector_tmpl.hh
index 93fda1636..5c0a9b94b 100644
--- a/src/model/solid_mechanics/material_selector_tmpl.hh
+++ b/src/model/solid_mechanics/material_selector_tmpl.hh
@@ -1,73 +1,74 @@
/**
* @file material_selector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Fri May 01 2015
+ * @date last modification: Tue Nov 07 2017
*
* @brief Implementation of the template MaterialSelector
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material_selector.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_SELECTOR_TMPL_HH__
#define __AKANTU_MATERIAL_SELECTOR_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline UInt ElementDataMaterialSelector<std::string>::
operator()(const Element & element) {
try {
std::string material_name = this->elementData(element);
return model.getMaterialIndex(material_name);
} catch (...) {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
template <>
inline UInt ElementDataMaterialSelector<UInt>::
operator()(const Element & element) {
try {
return this->elementData(element) - first_index;
} catch (...) {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
MeshDataMaterialSelector<T>::MeshDataMaterialSelector(
const std::string & name, const SolidMechanicsModel & model,
UInt first_index)
: ElementDataMaterialSelector<T>(model.getMesh().getData<T>(name), model,
first_index) {}
} // namespace akantu
#endif /* __AKANTU_MATERIAL_SELECTOR_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/internal_field.hh b/src/model/solid_mechanics/materials/internal_field.hh
index af8ae8eaa..54312dbeb 100644
--- a/src/model/solid_mechanics/materials/internal_field.hh
+++ b/src/model/solid_mechanics/materials/internal_field.hh
@@ -1,260 +1,259 @@
/**
* @file internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Thu Feb 08 2018
*
* @brief Material internal properties
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTERNAL_FIELD_HH__
#define __AKANTU_INTERNAL_FIELD_HH__
namespace akantu {
class Material;
class FEEngine;
/**
* class for the internal fields of materials
* to store values for each quadrature
*/
template <typename T> class InternalField : public ElementTypeMapArray<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
InternalField(const ID & id, Material & material);
~InternalField() override;
/// This constructor is only here to let cohesive elements compile
InternalField(const ID & id, Material & material, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter);
/// More general constructor
InternalField(const ID & id, Material & material, UInt dim, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter);
InternalField(const ID & id, const InternalField<T> & other);
private:
InternalField operator=(__attribute__((unused))
const InternalField & other){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to reset the FEEngine for the internal field
virtual void setFEEngine(FEEngine & fe_engine);
/// function to reset the element kind for the internal
virtual void setElementKind(ElementKind element_kind);
/// initialize the field to a given number of component
virtual void initialize(UInt nb_component);
/// activate the history of this field
virtual void initializeHistory();
/// resize the arrays and set the new element to 0
virtual void resize();
/// set the field to a given value v
virtual void setDefaultValue(const T & v);
/// reset all the fields to the default value
virtual void reset();
/// save the current values in the history
virtual void saveCurrentValues();
/// remove the quadrature points corresponding to suppressed elements
virtual void
removeIntegrationPoints(const ElementTypeMapArray<UInt> & new_numbering);
/// print the content
void printself(std::ostream & stream, int /*indent*/ = 0) const override;
/// get the default value
inline operator T() const;
virtual FEEngine & getFEEngine() { return *fem; }
virtual const FEEngine & getFEEngine() const { return *fem; }
/// AKANTU_GET_MACRO(FEEngine, *fem, FEEngine &);
protected:
/// initialize the arrays in the ElementTypeMapArray<T>
void internalInitialize(UInt nb_component);
/// set the values for new internals
virtual void setArrayValues(T * begin, T * end);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
using type_iterator = typename ElementTypeMapArray<T>::type_iterator;
using filter_type_iterator =
typename ElementTypeMapArray<UInt>::type_iterator;
/// get the type iterator on all types contained in the internal field
type_iterator firstType(const GhostType & ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::firstType(this->spatial_dimension,
ghost_type, this->element_kind);
}
/// get the type iterator on the last type contained in the internal field
type_iterator lastType(const GhostType & ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::lastType(this->spatial_dimension, ghost_type,
this->element_kind);
}
/// get the type iterator on all types contained in the internal field
filter_type_iterator
filterFirstType(const GhostType & ghost_type = _not_ghost) const {
return this->element_filter.firstType(this->spatial_dimension, ghost_type,
this->element_kind);
}
/// get the type iterator on the last type contained in the internal field
filter_type_iterator
filterLastType(const GhostType & ghost_type = _not_ghost) const {
return this->element_filter.lastType(this->spatial_dimension, ghost_type,
this->element_kind);
}
/// get the array for a given type of the element_filter
const Array<UInt> getFilter(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
return this->element_filter(type, ghost_type);
}
/// get the Array corresponding to the type en ghost_type specified
virtual Array<T> & operator()(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return ElementTypeMapArray<T>::operator()(type, ghost_type);
}
virtual const Array<T> &
operator()(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::operator()(type, ghost_type);
}
virtual Array<T> & previous(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return this->previous_values->operator()(type, ghost_type);
}
virtual const Array<T> &
previous(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return this->previous_values->operator()(type, ghost_type);
}
virtual InternalField<T> & previous() {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return *(this->previous_values);
}
virtual const InternalField<T> & previous() const {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return *(this->previous_values);
}
/// check if the history is used or not
bool hasHistory() const { return (previous_values != nullptr); }
/// get the kind treated by the internal
const ElementKind & getElementKind() const { return element_kind; }
/// return the number of components
UInt getNbComponent() const { return nb_component; }
/// return the spatial dimension corresponding to the internal element type
/// loop filter
UInt getSpatialDimension() const { return this->spatial_dimension; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the material for which this is an internal parameter
Material & material;
/// the fem containing the mesh and the element informations
FEEngine * fem;
/// Element filter if needed
const ElementTypeMapArray<UInt> & element_filter;
/// default value
T default_value;
/// spatial dimension of the element to consider
UInt spatial_dimension;
/// ElementKind of the element to consider
ElementKind element_kind;
/// Number of component of the internal field
UInt nb_component;
/// Is the field initialized
bool is_init;
/// previous values
InternalField<T> * previous_values;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const InternalField<T> & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#endif /* __AKANTU_INTERNAL_FIELD_HH__ */
diff --git a/src/model/solid_mechanics/materials/internal_field_tmpl.hh b/src/model/solid_mechanics/materials/internal_field_tmpl.hh
index 9f694541b..c6476bcb9 100644
--- a/src/model/solid_mechanics/materials/internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/materials/internal_field_tmpl.hh
@@ -1,317 +1,317 @@
/**
* @file internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Material internal properties
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTERNAL_FIELD_TMPL_HH__
#define __AKANTU_INTERNAL_FIELD_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(const ID & id, Material & material)
: ElementTypeMapArray<T>(id, material.getID(), material.getMemoryID()),
material(material), fem(&(material.getModel().getFEEngine())),
element_filter(material.getElementFilter()), default_value(T()),
spatial_dimension(material.getModel().getSpatialDimension()),
element_kind(_ek_regular), nb_component(0), is_init(false),
previous_values(nullptr) {}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(
const ID & id, Material & material, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter)
: ElementTypeMapArray<T>(id, material.getID(), material.getMemoryID()),
material(material), fem(&fem), element_filter(element_filter),
default_value(T()), spatial_dimension(material.getSpatialDimension()),
element_kind(_ek_regular), nb_component(0), is_init(false),
previous_values(nullptr) {}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(
const ID & id, Material & material, UInt dim, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter)
: ElementTypeMapArray<T>(id, material.getID(), material.getMemoryID()),
material(material), fem(&fem), element_filter(element_filter),
default_value(T()), spatial_dimension(dim), element_kind(_ek_regular),
nb_component(0), is_init(false), previous_values(nullptr) {}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(const ID & id, const InternalField<T> & other)
: ElementTypeMapArray<T>(id, other.material.getID(),
other.material.getMemoryID()),
material(other.material), fem(other.fem),
element_filter(other.element_filter), default_value(other.default_value),
spatial_dimension(other.spatial_dimension),
element_kind(other.element_kind), nb_component(other.nb_component),
is_init(false), previous_values(nullptr) {
AKANTU_DEBUG_ASSERT(other.is_init,
"Cannot create a copy of a non initialized field");
this->internalInitialize(this->nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T> InternalField<T>::~InternalField() {
if (this->is_init) {
this->material.unregisterInternal(*this);
}
delete previous_values;
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::setFEEngine(FEEngine & fe_engine) {
this->fem = &fe_engine;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::setElementKind(ElementKind element_kind) {
this->element_kind = element_kind;
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::initialize(UInt nb_component) {
internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::initializeHistory() {
if (!previous_values)
previous_values = new InternalField<T>("previous_" + this->getID(), *this);
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::resize() {
if (!this->is_init)
return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
filter_type_iterator it = this->filterFirstType(*gt);
filter_type_iterator end = this->filterLastType(*gt);
for (; it != end; ++it) {
UInt nb_element = this->element_filter(*it, *gt).size();
UInt nb_quadrature_points = this->fem->getNbIntegrationPoints(*it, *gt);
UInt new_size = nb_element * nb_quadrature_points;
UInt old_size = 0;
Array<T> * vect = nullptr;
if (this->exists(*it, *gt)) {
vect = &(this->operator()(*it, *gt));
old_size = vect->size();
vect->resize(new_size);
} else {
vect = &(this->alloc(nb_element * nb_quadrature_points, nb_component,
*it, *gt));
}
this->setArrayValues(vect->storage() + old_size * vect->getNbComponent(),
vect->storage() + new_size * vect->getNbComponent());
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::setDefaultValue(const T & value) {
this->default_value = value;
this->reset();
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::reset() {
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
type_iterator it = this->firstType(*gt);
type_iterator end = this->lastType(*gt);
for (; it != end; ++it) {
Array<T> & vect = this->operator()(*it, *gt);
vect.clear();
this->setArrayValues(
vect.storage(), vect.storage() + vect.size() * vect.getNbComponent());
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::internalInitialize(UInt nb_component) {
if (!this->is_init) {
this->nb_component = nb_component;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
filter_type_iterator it = this->filterFirstType(*gt);
filter_type_iterator end = this->filterLastType(*gt);
for (; it != end; ++it) {
UInt nb_element = this->element_filter(*it, *gt).size();
UInt nb_quadrature_points = this->fem->getNbIntegrationPoints(*it, *gt);
if (this->exists(*it, *gt))
this->operator()(*it, *gt).resize(nb_element * nb_quadrature_points);
else
this->alloc(nb_element * nb_quadrature_points, nb_component, *it,
*gt);
}
}
this->material.registerInternal(*this);
this->is_init = true;
}
this->reset();
if (this->previous_values)
this->previous_values->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::setArrayValues(T * begin, T * end) {
for (; begin < end; ++begin)
*begin = this->default_value;
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::saveCurrentValues() {
AKANTU_DEBUG_ASSERT(this->previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
if (!this->is_init)
return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
type_iterator it = this->firstType(*gt);
type_iterator end = this->lastType(*gt);
for (; it != end; ++it) {
this->previous_values->operator()(*it, *gt).copy(
this->operator()(*it, *gt));
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::removeIntegrationPoints(
const ElementTypeMapArray<UInt> & new_numbering) {
for (auto ghost_type : ghost_types) {
for (auto type : new_numbering.elementTypes(_all_dimensions, ghost_type,
_ek_not_defined)) {
if (not this->exists(type, ghost_type))
continue;
Array<T> & vect = this->operator()(type, ghost_type);
if (vect.size() == 0)
continue;
const Array<UInt> & renumbering = new_numbering(type, ghost_type);
UInt nb_quad_per_elem = fem->getNbIntegrationPoints(type, ghost_type);
UInt nb_component = vect.getNbComponent();
Array<T> tmp(renumbering.size() * nb_quad_per_elem, nb_component);
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created from nowhere!!");
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created or disappeared in "
<< vect.getID() << "(" << vect.size() << "!=" << tmp.size()
<< ") "
"!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
memcpy(tmp.storage() + new_i * nb_component * nb_quad_per_elem,
vect.storage() + i * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem * sizeof(T));
++new_size;
}
}
tmp.resize(new_size * nb_quad_per_elem);
vect.copy(tmp);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::printself(std::ostream & stream,
int indent[[gnu::unused]]) const {
stream << "InternalField [ " << this->getID();
#if !defined(AKANTU_NDEBUG)
if (AKANTU_DEBUG_TEST(dblDump)) {
stream << std::endl;
ElementTypeMapArray<T>::printself(stream, indent + 3);
} else {
#endif
stream << " {" << this->getData(_not_ghost).size() << " types - "
<< this->getData(_ghost).size() << " ghost types"
<< "}";
#if !defined(AKANTU_NDEBUG)
}
#endif
stream << " ]";
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<InternalField<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Real r = in_param;
param.setDefaultValue(r);
}
/* -------------------------------------------------------------------------- */
template <typename T> inline InternalField<T>::operator T() const {
return default_value;
}
} // akantu
#endif /* __AKANTU_INTERNAL_FIELD_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_core_includes.hh b/src/model/solid_mechanics/materials/material_core_includes.hh
index 5804db7da..a95a5b1a3 100644
--- a/src/model/solid_mechanics/materials/material_core_includes.hh
+++ b/src/model/solid_mechanics/materials/material_core_includes.hh
@@ -1,68 +1,68 @@
/**
* @file material_core_includes.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Sat Jul 18 2015
+ * @date last modification: Wed Feb 03 2016
*
* @brief List of materials for core package
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_CORE_INCLUDES_HH__
#define __AKANTU_MATERIAL_CORE_INCLUDES_HH__
/* -------------------------------------------------------------------------- */
/* Material list */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_CMAKE_LIST_MATERIALS
// elastic materials
#include "material_elastic.hh"
#include "material_elastic_linear_anisotropic.hh"
#include "material_elastic_orthotropic.hh"
#include "material_neohookean.hh"
// visco-elastic materials
#include "material_standard_linear_solid_deviatoric.hh"
// damage laws
#include "material_marigo.hh"
#include "material_mazars.hh"
// small-deformation plasticity
#include "material_linear_isotropic_hardening.hh"
#endif
#define AKANTU_CORE_MATERIAL_LIST \
((2, (elastic, MaterialElastic)))((2, (neohookean, MaterialNeohookean)))( \
(2, (elastic_orthotropic, MaterialElasticOrthotropic)))( \
(2, (elastic_anisotropic, MaterialElasticLinearAnisotropic)))( \
(2, (sls_deviatoric, MaterialStandardLinearSolidDeviatoric)))( \
(2, (marigo, MaterialMarigo)))((2, (mazars, MaterialMazars)))( \
(2, (plastic_linear_isotropic_hardening, \
MaterialLinearIsotropicHardening)))
#endif /* __AKANTU_MATERIAL_CORE_INCLUDES_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage.hh b/src/model/solid_mechanics/materials/material_damage/material_damage.hh
index fb72e1549..6cefe9796 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage.hh
@@ -1,113 +1,112 @@
/**
* @file material_damage.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sat Jul 11 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Material isotropic elastic
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_DAMAGE_HH__
#define __AKANTU_MATERIAL_DAMAGE_HH__
namespace akantu {
template <UInt spatial_dimension,
template <UInt> class Parent = MaterialElastic>
class MaterialDamage : public Parent<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialDamage(SolidMechanicsModel & model, const ID & id = "");
~MaterialDamage() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
bool hasStiffnessMatrixChanged() override { return true; }
protected:
/// update the dissipated energy, must be called after the stress have been
/// computed
void updateEnergies(ElementType el_type, GhostType ghost_type) override;
/// compute the tangent stiffness matrix for a given quadrature point
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent, Real & dam);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy for the time step
Real getDissipatedEnergy() const;
Real getEnergy(const std::string & type) override;
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override {
return Parent<spatial_dimension>::getEnergy(energy_id, type, index);
};
AKANTU_GET_MACRO_NOT_CONST(Damage, damage, ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Damage, damage, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real)
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage internal variable
InternalField<Real> damage;
/// dissipated energy
InternalField<Real> dissipated_energy;
/// contain the current value of @f$ \int_0^{\epsilon}\sigma(\omega)d\omega
/// @f$ the dissipated energy
InternalField<Real> int_sigma;
};
} // namespace akantu
#include "material_damage_tmpl.hh"
#endif /* __AKANTU_MATERIAL_DAMAGE_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
index 707acab2a..f83923f3e 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
@@ -1,74 +1,73 @@
/**
* @file material_damage_non_local.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 23 2012
- * @date last modification: Wed Oct 21 2015
+ * @date last modification: Mon Sep 11 2017
*
* @brief interface for non local damage material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH__
#define __AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH__
namespace akantu {
template <UInt dim, class MaterialDamageLocal>
class MaterialDamageNonLocal
: public MaterialNonLocal<dim, MaterialDamageLocal> {
public:
using MaterialParent = MaterialNonLocal<dim, MaterialDamageLocal>;
MaterialDamageNonLocal(SolidMechanicsModel & model, const ID & id)
: MaterialParent(model, id){};
protected:
/* ------------------------------------------------------------------------ */
virtual void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost) = 0;
/* ------------------------------------------------------------------------ */
void computeNonLocalStresses(GhostType ghost_type) override {
AKANTU_DEBUG_IN();
for (auto type : this->element_filter.elementTypes(dim, ghost_type)) {
auto & elem_filter = this->element_filter(type, ghost_type);
if (elem_filter.size() == 0)
continue;
computeNonLocalStress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
};
} // namespace akantu
#endif /* __AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh b/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
index 2876eb704..88e744546 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
@@ -1,181 +1,181 @@
/**
* @file material_damage_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Specialization of the material class for the damage material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
MaterialDamage<spatial_dimension, Parent>::MaterialDamage(
SolidMechanicsModel & model, const ID & id)
: Parent<spatial_dimension>(model, id), damage("damage", *this),
dissipated_energy("damage dissipated energy", *this),
int_sigma("integral of sigma", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = false;
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->damage.initialize(1);
this->dissipated_energy.initialize(1);
this->int_sigma.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::initMaterial() {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the dissipated energy in each element by a trapezoidal approximation
* of
* @f$ Ed = \int_0^{\epsilon}\sigma(\omega)d\omega -
* \frac{1}{2}\sigma:\epsilon@f$
*/
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::updateEnergies(
ElementType el_type, GhostType ghost_type) {
Parent<spatial_dimension>::updateEnergies(el_type, ghost_type);
this->computePotentialEnergy(el_type, ghost_type);
Array<Real>::matrix_iterator epsilon_p =
this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator sigma_p =
this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_scalar_iterator epot =
this->potential_energy(el_type, ghost_type).begin();
Array<Real>::scalar_iterator ints =
this->int_sigma(el_type, ghost_type).begin();
Array<Real>::scalar_iterator ed =
this->dissipated_energy(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> delta_gradu_it(*gradu_it);
delta_gradu_it -= *epsilon_p;
Matrix<Real> sigma_h(sigma);
sigma_h += *sigma_p;
Real dint = .5 * sigma_h.doubleDot(delta_gradu_it);
*ints += dint;
*ed = *ints - *epot;
++epsilon_p;
++sigma_p;
++epot;
++ints;
++ed;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::computeTangentModuli(
const ElementType & el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::computeTangentModuli(el_type, tangent_matrix,
ghost_type);
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, *dam);
++dam;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, Real & dam) {
tangent *= (1 - dam);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
Real MaterialDamage<spatial_dimension, Parent>::getDissipatedEnergy() const {
AKANTU_DEBUG_IN();
Real de = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
de +=
this->fem.integrate(dissipated_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
Real MaterialDamage<spatial_dimension, Parent>::getEnergy(
const std::string & type) {
if (type == "dissipated")
return getDissipatedEnergy();
else
return Parent<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo.cc b/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
index 83738f986..d29e96758 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
@@ -1,107 +1,106 @@
/**
* @file material_marigo.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 08 2015
+ * @date last modification: Sun Jul 09 2017
*
* @brief Specialization of the material class for the marigo material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_marigo.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMarigo<spatial_dimension>::MaterialMarigo(SolidMechanicsModel & model,
const ID & id)
: MaterialDamage<spatial_dimension>(model, id), Yd("Yd", *this),
damage_in_y(false), yc_limit(false) {
AKANTU_DEBUG_IN();
this->registerParam("Sd", Sd, Real(5000.), _pat_parsable | _pat_modifiable);
this->registerParam("epsilon_c", epsilon_c, Real(0.), _pat_parsable,
"Critical strain");
this->registerParam("Yc limit", yc_limit, false, _pat_internal,
"As the material a critical Y");
this->registerParam("damage_in_y", damage_in_y, false, _pat_parsable,
"Use threshold (1-D)Y");
this->registerParam("Yd", Yd, _pat_parsable, "Damaging energy threshold");
this->Yd.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialDamage<spatial_dimension>::initMaterial();
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::updateInternalParameters() {
MaterialDamage<spatial_dimension>::updateInternalParameters();
Yc = .5 * epsilon_c * this->E * epsilon_c;
if (std::abs(epsilon_c) > std::numeric_limits<Real>::epsilon())
yc_limit = true;
else
yc_limit = false;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real>::scalar_iterator dam = this->damage(el_type, ghost_type).begin();
Array<Real>::scalar_iterator Yd_q = this->Yd(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Real Y = 0.;
computeStressOnQuad(grad_u, sigma, *dam, Y, *Yd_q);
++dam;
++Yd_q;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(marigo, MaterialMarigo);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
index 39cb01c1e..3f5b63277 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
@@ -1,124 +1,123 @@
/**
* @file material_marigo.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief Marigo damage law
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_MARIGO_HH__
#define __AKANTU_MATERIAL_MARIGO_HH__
namespace akantu {
/**
* Material marigo
*
* parameters in the material files :
* - Yd : (default: 50)
* - Sd : (default: 5000)
* - Ydrandomness : (default:0)
*/
template <UInt spatial_dimension>
class MaterialMarigo : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialMarigo(SolidMechanicsModel & model, const ID & id = "");
~MaterialMarigo() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
void updateInternalParameters() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real & dam, Real & Y, Real & Ydq);
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma, Real & dam,
Real & Y, Real & Ydq);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// resistance to damage
RandomInternalField<Real> Yd;
/// damage threshold
Real Sd;
/// critical epsilon when the material is considered as broken
Real epsilon_c;
Real Yc;
bool damage_in_y;
bool yc_limit;
};
} // akantu
#include "material_marigo_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_MARIGO_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.cc b/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.cc
index a0df92944..1288d566f 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.cc
@@ -1,132 +1,131 @@
/**
* @file material_marigo_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Fri Dec 02 2016
*
* @brief Implementation of the inline functions of the material marigo
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_marigo.hh"
#ifndef __AKANTU_MATERIAL_MARIGO_INLINE_IMPL_CC__
#define __AKANTU_MATERIAL_MARIGO_INLINE_IMPL_CC__
namespace akantu {
template <UInt spatial_dimension>
inline void MaterialMarigo<spatial_dimension>::computeStressOnQuad(
Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam, Real & Y,
Real & Ydq) {
MaterialElastic<spatial_dimension>::computeStressOnQuad(grad_u, sigma);
Y = 0;
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
Y += sigma(i, j) * (grad_u(i, j) + grad_u(j, i)) / 2.;
}
}
Y *= 0.5;
if (damage_in_y)
Y *= (1 - dam);
if (yc_limit)
Y = std::min(Y, Yc);
if (!this->is_non_local) {
computeDamageAndStressOnQuad(sigma, dam, Y, Ydq);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMarigo<spatial_dimension>::computeDamageAndStressOnQuad(
Matrix<Real> & sigma, Real & dam, Real & Y, Real & Ydq) {
Real Fd = Y - Ydq - Sd * dam;
if (Fd > 0)
dam = (Y - Ydq) / Sd;
dam = std::min(dam, Real(1.));
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline UInt MaterialMarigo<spatial_dimension>::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (tag == _gst_smm_init_mat) {
size += sizeof(Real) * this->getModel().getNbIntegrationPoints(elements);
}
size += MaterialDamage<spatial_dimension>::getNbData(elements, tag);
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMarigo<spatial_dimension>::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (tag == _gst_smm_init_mat) {
this->packElementDataHelper(Yd, buffer, elements);
}
MaterialDamage<spatial_dimension>::packData(buffer, elements, tag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void
MaterialMarigo<spatial_dimension>::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (tag == _gst_smm_init_mat) {
this->unpackElementDataHelper(Yd, buffer, elements);
}
MaterialDamage<spatial_dimension>::unpackData(buffer, elements, tag);
AKANTU_DEBUG_OUT();
}
} // akantu
#endif /* __AKANTU_MATERIAL_MARIGO_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.cc b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.cc
index 6eb060efe..731d6e099 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.cc
@@ -1,106 +1,106 @@
/**
* @file material_marigo_non_local.cc
*
+ * @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Mon Sep 11 2017
*
* @brief Marigo non-local inline function implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_marigo_non_local.hh"
#include "non_local_neighborhood_base.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMarigoNonLocal<spatial_dimension>::MaterialMarigoNonLocal(
SolidMechanicsModel & model, const ID & id)
: MaterialMarigoNonLocalParent(model, id), Y("Y", *this),
Ynl("Y non local", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = true;
this->Y.initialize(1);
this->Ynl.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigoNonLocal<spatial_dimension>::registerNonLocalVariables() {
this->model.getNonLocalManager().registerNonLocalVariable(this->Y.getName(),
Ynl.getName(), 1);
this->model.getNonLocalManager()
.getNeighborhood(this->name)
.registerNonLocalVariable(Ynl.getName());
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigoNonLocal<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = this->damage(el_type, ghost_type).storage();
Real * Yt = this->Y(el_type, ghost_type).storage();
Real * Ydq = this->Yd(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
MaterialMarigo<spatial_dimension>::computeStressOnQuad(grad_u, sigma, *dam,
*Yt, *Ydq);
++dam;
++Yt;
++Ydq;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigoNonLocal<spatial_dimension>::computeNonLocalStress(
ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = this->damage(type, ghost_type).storage();
Real * Ydq = this->Yd(type, ghost_type).storage();
Real * Ynlt = this->Ynl(type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(type, ghost_type);
this->computeDamageAndStressOnQuad(sigma, *dam, *Ynlt, *Ydq);
++dam;
++Ynlt;
++Ydq;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(marigo_non_local, MaterialMarigoNonLocal);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
index b9085cdf5..7b563afa8 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
@@ -1,94 +1,93 @@
/**
* @file material_marigo_non_local.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Marigo non-local description
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_non_local.hh"
#include "material_marigo.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH__
#define __AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* Material Marigo
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialMarigoNonLocal
: public MaterialDamageNonLocal<spatial_dimension,
MaterialMarigo<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef MaterialDamageNonLocal<spatial_dimension,
MaterialMarigo<spatial_dimension>>
MaterialMarigoNonLocalParent;
MaterialMarigoNonLocal(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
void registerNonLocalVariables() override;
/// constitutive law
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost) override;
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Y, Y, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> Y;
InternalField<Real> Ynl;
};
} // namespace akantu
#endif /* __AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars.cc b/src/model/solid_mechanics/materials/material_damage/material_mazars.cc
index fdba78438..7ada50bc7 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars.cc
@@ -1,82 +1,81 @@
/**
* @file material_mazars.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Sun Jul 09 2017
*
* @brief Specialization of the material class for the damage material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_mazars.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMazars<spatial_dimension>::MaterialMazars(SolidMechanicsModel & model,
const ID & id)
: MaterialDamage<spatial_dimension>(model, id), K0("K0", *this),
damage_in_compute_stress(true) {
AKANTU_DEBUG_IN();
this->registerParam("K0", K0, _pat_parsable, "K0");
this->registerParam("At", At, Real(0.8), _pat_parsable, "At");
this->registerParam("Ac", Ac, Real(1.4), _pat_parsable, "Ac");
this->registerParam("Bc", Bc, Real(1900.), _pat_parsable, "Bc");
this->registerParam("Bt", Bt, Real(12000.), _pat_parsable, "Bt");
this->registerParam("beta", beta, Real(1.06), _pat_parsable, "beta");
this->K0.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazars<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Real Ehat = 0;
computeStressOnQuad(grad_u, sigma, *dam, Ehat);
++dam;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(mazars, MaterialMazars);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
index 40d5d4358..01a4f7ab6 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
@@ -1,125 +1,125 @@
/**
* @file material_mazars.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
+ * @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief Material Following the Mazars law for damage evolution
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_MAZARS_HH__
#define __AKANTU_MATERIAL_MAZARS_HH__
namespace akantu {
/**
* Material Mazars
*
* parameters in the material files :
* - rho : density (default: 0)
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - K0 : Damage threshold
* - At : Parameter damage traction 1
* - Bt : Parameter damage traction 2
* - Ac : Parameter damage compression 1
* - Bc : Parameter damage compression 2
* - beta : Parameter for shear
*/
template <UInt spatial_dimension>
class MaterialMazars : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialMazars(SolidMechanicsModel & model, const ID & id = "");
~MaterialMazars() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & damage,
Real & Ehat);
inline void computeDamageAndStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & damage,
Real & Ehat);
inline void computeDamageOnQuad(const Real & epsilon_equ,
const Matrix<Real> & sigma,
const Vector<Real> & epsilon_princ,
Real & dam);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage threshold
RandomInternalField<Real> K0;
/// parameter damage traction 1
Real At;
/// parameter damage traction 2
Real Bt;
/// parameter damage compression 1
Real Ac;
/// parameter damage compression 2
Real Bc;
/// parameter for shear
Real beta;
/// specify the variable to average false = ehat, true = damage (only valid
/// for non local version)
bool damage_in_compute_stress;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_mazars_inline_impl.cc"
} // namespace akantu
#endif /* __AKANTU_MATERIAL_MAZARS_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.cc b/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.cc
index 74150eb04..40eadf218 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.cc
@@ -1,155 +1,155 @@
/**
* @file material_mazars_inline_impl.cc
*
+ * @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 06 2011
- * @date last modification: Tue Aug 04 2015
+ * @date last modification: Wed Feb 03 2016
*
* @brief Implementation of the inline functions of the material damage
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMazars<spatial_dimension>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam,
Real & Ehat) {
Matrix<Real> epsilon(3, 3);
epsilon.clear();
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j)
epsilon(i, j) = .5 * (grad_u(i, j) + grad_u(j, i));
Vector<Real> Fdiag(3);
Math::matrixEig(3, epsilon.storage(), Fdiag.storage());
Ehat = 0.;
for (UInt i = 0; i < 3; ++i) {
Real epsilon_p = std::max(Real(0.), Fdiag(i));
Ehat += epsilon_p * epsilon_p;
}
Ehat = sqrt(Ehat);
MaterialElastic<spatial_dimension>::computeStressOnQuad(grad_u, sigma);
if (damage_in_compute_stress) {
computeDamageOnQuad(Ehat, sigma, Fdiag, dam);
}
if (!this->is_non_local) {
computeDamageAndStressOnQuad(grad_u, sigma, dam, Ehat);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMazars<spatial_dimension>::computeDamageAndStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam,
Real & Ehat) {
if (!damage_in_compute_stress) {
Vector<Real> Fdiag(3);
Fdiag.clear();
Matrix<Real> epsilon(3, 3);
epsilon.clear();
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j)
epsilon(i, j) = .5 * (grad_u(i, j) + grad_u(j, i));
Math::matrixEig(3, epsilon.storage(), Fdiag.storage());
computeDamageOnQuad(Ehat, sigma, Fdiag, dam);
}
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMazars<spatial_dimension>::computeDamageOnQuad(
const Real & epsilon_equ,
__attribute__((unused)) const Matrix<Real> & sigma,
const Vector<Real> & epsilon_princ, Real & dam) {
Real Fs = epsilon_equ - K0;
if (Fs > 0.) {
Real dam_t;
Real dam_c;
dam_t =
1 - K0 * (1 - At) / epsilon_equ - At * (exp(-Bt * (epsilon_equ - K0)));
dam_c =
1 - K0 * (1 - Ac) / epsilon_equ - Ac * (exp(-Bc * (epsilon_equ - K0)));
Real Cdiag;
Cdiag = this->E * (1 - this->nu) / ((1 + this->nu) * (1 - 2 * this->nu));
Vector<Real> sigma_princ(3);
sigma_princ(0) = Cdiag * epsilon_princ(0) +
this->lambda * (epsilon_princ(1) + epsilon_princ(2));
sigma_princ(1) = Cdiag * epsilon_princ(1) +
this->lambda * (epsilon_princ(0) + epsilon_princ(2));
sigma_princ(2) = Cdiag * epsilon_princ(2) +
this->lambda * (epsilon_princ(1) + epsilon_princ(0));
Vector<Real> sigma_p(3);
for (UInt i = 0; i < 3; i++)
sigma_p(i) = std::max(Real(0.), sigma_princ(i));
sigma_p *= 1. - dam;
Real trace_p = this->nu / this->E * (sigma_p(0) + sigma_p(1) + sigma_p(2));
Real alpha_t = 0;
for (UInt i = 0; i < 3; ++i) {
Real epsilon_t = (1 + this->nu) / this->E * sigma_p(i) - trace_p;
Real epsilon_p = std::max(Real(0.), epsilon_princ(i));
alpha_t += epsilon_t * epsilon_p;
}
alpha_t /= epsilon_equ * epsilon_equ;
alpha_t = std::min(alpha_t, Real(1.));
Real alpha_c = 1. - alpha_t;
alpha_t = std::pow(alpha_t, beta);
alpha_c = std::pow(alpha_c, beta);
Real damtemp;
damtemp = alpha_t * dam_t + alpha_c * dam_c;
dam = std::max(damtemp, dam);
dam = std::min(dam, Real(1.));
}
}
/* -------------------------------------------------------------------------- */
// template<UInt spatial_dimension>
// inline void
// MaterialMazars<spatial_dimension>::computeTangentModuliOnQuad(Matrix<Real> &
// tangent) {
// MaterialElastic<spatial_dimension>::computeTangentModuliOnQuad(tangent);
// tangent *= (1-dam);
// }
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
index a0df818db..950334fd3 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
@@ -1,124 +1,123 @@
/**
* @file material_mazars_non_local.cc
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Mon Sep 11 2017
*
* @brief Specialization of the material class for the non-local mazars
* material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_mazars_non_local.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMazarsNonLocal<spatial_dimension>::MaterialMazarsNonLocal(
SolidMechanicsModel & model, const ID & id)
: MaterialNonLocalParent(model, id), Ehat("epsilon_equ", *this),
non_local_variable("mazars_non_local", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = true;
this->Ehat.initialize(1);
this->non_local_variable.initialize(1);
this->registerParam("average_on_damage", this->damage_in_compute_stress,
false, _pat_parsable | _pat_modifiable,
"Is D the non local variable");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::registerNonLocalVariables() {
ID local;
if (this->damage_in_compute_stress)
local = this->damage.getName();
else
local = this->Ehat.getName();
this->model.getNonLocalManager().registerNonLocalVariable(
local, non_local_variable.getName(), 1);
this->model.getNonLocalManager()
.getNeighborhood(this->name)
.registerNonLocalVariable(non_local_variable.getName());
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * damage = this->damage(el_type, ghost_type).storage();
Real * epsilon_equ = this->Ehat(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
MaterialMazars<spatial_dimension>::computeStressOnQuad(grad_u, sigma, *damage,
*epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::computeNonLocalStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & non_loc_var = non_local_variable(el_type, ghost_type);
Real * damage;
Real * epsilon_equ;
if (this->damage_in_compute_stress) {
damage = non_loc_var.storage();
epsilon_equ = this->Ehat(el_type, ghost_type).storage();
} else {
damage = this->damage(el_type, ghost_type).storage();
epsilon_equ = non_loc_var.storage();
}
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeDamageAndStressOnQuad(grad_u, sigma, *damage, *epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(mazars_non_local, MaterialMazarsNonLocal);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
index e7f28b042..1b5f0f810 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
@@ -1,92 +1,91 @@
/**
* @file material_mazars_non_local.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 08 2015
+ * @date last modification: Mon Sep 11 2017
*
* @brief Mazars non-local description
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_non_local.hh"
#include "material_mazars.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH__
#define __AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH__
namespace akantu {
/**
* Material Mazars Non local
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialMazarsNonLocal
: public MaterialDamageNonLocal<spatial_dimension,
MaterialMazars<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MaterialNonLocalParent =
MaterialDamageNonLocal<spatial_dimension,
MaterialMazars<spatial_dimension>>;
MaterialMazarsNonLocal(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void computeNonLocalStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void registerNonLocalVariables() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the ehat per quadrature points to perform the averaging
InternalField<Real> Ehat;
InternalField<Real> non_local_variable;
};
} // namespace akantu
#endif /* __AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_elastic.cc b/src/model/solid_mechanics/materials/material_elastic.cc
index 894d86e3c..f605cba65 100644
--- a/src/model/solid_mechanics/materials/material_elastic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic.cc
@@ -1,264 +1,263 @@
/**
* @file material_elastic.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Mon Jan 29 2018
*
* @brief Specialization of the material class for the elastic material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElastic<dim>::MaterialElastic(SolidMechanicsModel & model,
const ID & id)
: Parent(model, id), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElastic<dim>::MaterialElastic(SolidMechanicsModel & model,
__attribute__((unused)) UInt a_dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id)
: Parent(model, dim, mesh, fe_engine, id), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::initialize() {
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Parent::initMaterial();
if (dim == 1)
this->nu = 0.;
this->updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::updateInternalParameters() {
MaterialThermal<dim>::updateInternalParameters();
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - 2 * this->nu));
this->mu = this->E / (2 * (1 + this->nu));
this->kpa = this->lambda + 2. / 3. * this->mu;
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <> void MaterialElastic<2>::updateInternalParameters() {
MaterialThermal<2>::updateInternalParameters();
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - 2 * this->nu));
this->mu = this->E / (2 * (1 + this->nu));
if (this->plane_stress)
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - this->nu));
this->kpa = this->lambda + 2. / 3. * this->mu;
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElastic<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator sigma_th_it =
this->sigma_th(el_type, ghost_type).begin();
if (!this->finite_deformation) {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
const Real & sigma_th = *sigma_th_it;
this->computeStressOnQuad(grad_u, sigma, sigma_th);
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
/// finite gradus
Matrix<Real> E(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
/// compute E
this->template gradUToGreenStrain<spatial_dimension>(grad_u, E);
const Real & sigma_th = *sigma_th_it;
/// compute second Piola-Kirchhoff stress tensor
this->computeStressOnQuad(E, sigma, sigma_th);
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElastic<spatial_dimension>::computeTangentModuli(
const ElementType & el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialElastic<spatial_dimension>::getPushWaveSpeed(
const Element &) const {
return sqrt((lambda + 2 * mu) / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialElastic<spatial_dimension>::getShearWaveSpeed(
const Element &) const {
return sqrt(mu / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElastic<spatial_dimension>::computePotentialEnergy(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialThermal<spatial_dimension>::computePotentialEnergy(el_type,
ghost_type);
if (ghost_type != _not_ghost)
return;
auto epot = this->potential_energy(el_type, ghost_type).begin();
if (!this->finite_deformation) {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computePotentialEnergyOnQuad(grad_u, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
Matrix<Real> E(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->template gradUToGreenStrain<spatial_dimension>(grad_u, E);
this->computePotentialEnergyOnQuad(E, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElastic<spatial_dimension>::computePotentialEnergyByElement(
ElementType type, UInt index, Vector<Real> & epot_on_quad_points) {
auto gradu_it = this->gradu(type).begin(spatial_dimension, spatial_dimension);
auto gradu_end =
this->gradu(type).begin(spatial_dimension, spatial_dimension);
auto stress_it =
this->stress(type).begin(spatial_dimension, spatial_dimension);
if (this->finite_deformation)
stress_it = this->piola_kirchhoff_2(type).begin(spatial_dimension,
spatial_dimension);
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
gradu_it += index * nb_quadrature_points;
gradu_end += (index + 1) * nb_quadrature_points;
stress_it += index * nb_quadrature_points;
Real * epot_quad = epot_on_quad_points.storage();
Matrix<Real> grad_u(spatial_dimension, spatial_dimension);
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
if (this->finite_deformation)
this->template gradUToGreenStrain<spatial_dimension>(*gradu_it, grad_u);
else
grad_u.copy(*gradu_it);
this->computePotentialEnergyOnQuad(grad_u, *stress_it, *epot_quad);
}
}
/* -------------------------------------------------------------------------- */
template <>
Real MaterialElastic<1>::getPushWaveSpeed(const Element & /*element*/) const {
return std::sqrt(this->E / this->rho);
}
template <>
Real MaterialElastic<1>::getShearWaveSpeed(const Element & /*element*/) const {
AKANTU_EXCEPTION("There is no shear wave speed in 1D");
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(elastic, MaterialElastic);
} // akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic.hh b/src/model/solid_mechanics/materials/material_elastic.hh
index 805a05107..e442831a7 100644
--- a/src/model/solid_mechanics/materials/material_elastic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic.hh
@@ -1,157 +1,156 @@
/**
* @file material_elastic.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Nov 15 2015
+ * @date last modification: Fri Nov 17 2017
*
* @brief Material isotropic elastic
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_thermal.hh"
#include "plane_stress_toolbox.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_ELASTIC_HH__
#define __AKANTU_MATERIAL_ELASTIC_HH__
namespace akantu {
/**
* Material elastic isotropic
*
* parameters in the material files :
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - Plane_Stress : if 0: plane strain, else: plane stress (default: 0)
*/
template <UInt spatial_dimension>
class MaterialElastic
: public PlaneStressToolbox<spatial_dimension,
MaterialThermal<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
using Parent =
PlaneStressToolbox<spatial_dimension, MaterialThermal<spatial_dimension>>;
public:
MaterialElastic(SolidMechanicsModel & model, const ID & id = "");
MaterialElastic(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
~MaterialElastic() override = default;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) override;
/// compute the p-wave speed in the material
Real getPushWaveSpeed(const Element & element) const override;
/// compute the s-wave speed in the material
Real getShearWaveSpeed(const Element & element) const override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
const Real sigma_th = 0) const;
/// compute the tangent stiffness matrix for an element
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent) const;
/// recompute the lame coefficient if E or nu changes
void updateInternalParameters() override;
static inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot);
bool hasStiffnessMatrixChanged() override {
return (!was_stiffness_assembled);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get first Lame constant
AKANTU_GET_MACRO(Lambda, lambda, Real);
/// get second Lame constant
AKANTU_GET_MACRO(Mu, mu, Real);
/// get bulk modulus
AKANTU_GET_MACRO(Kappa, kpa, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// Bulk modulus
Real kpa;
/// defines if the stiffness was computed
bool was_stiffness_assembled;
};
} // akantu
#include "material_elastic_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_ELASTIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_inline_impl.cc b/src/model/solid_mechanics/materials/material_elastic_inline_impl.cc
index 6c7160500..606e7bb73 100644
--- a/src/model/solid_mechanics/materials/material_elastic_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_inline_impl.cc
@@ -1,121 +1,120 @@
/**
* @file material_elastic_inline_impl.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Fri Dec 16 2016
*
* @brief Implementation of the inline functions of the material elastic
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_CC__
#define __AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialElastic<spatial_dimension>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma,
const Real sigma_th) const {
Real trace = grad_u.trace(); // trace = (\nabla u)_{kk}
// \sigma_{ij} = \lambda * (\nabla u)_{kk} * \delta_{ij} + \mu * (\nabla
// u_{ij} + \nabla u_{ji})
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
sigma(i, j) = (i == j) * lambda * trace +
mu * (grad_u(i, j) + grad_u(j, i)) + (i == j) * sigma_th;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void MaterialElastic<1>::computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
Real sigma_th) const {
sigma(0, 0) = this->E * grad_u(0, 0) + sigma_th;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialElastic<spatial_dimension>::computeTangentModuliOnQuad(
Matrix<Real> & tangent) const {
UInt n = tangent.cols();
// Real Ep = E/((1+nu)*(1-2*nu));
Real Miiii = lambda + 2 * mu;
Real Miijj = lambda;
Real Mijij = mu;
if (spatial_dimension == 1)
tangent(0, 0) = this->E;
else
tangent(0, 0) = Miiii;
// test of dimension should by optimized out by the compiler due to the
// template
if (spatial_dimension >= 2) {
tangent(1, 1) = Miiii;
tangent(0, 1) = Miijj;
tangent(1, 0) = Miijj;
tangent(n - 1, n - 1) = Mijij;
}
if (spatial_dimension == 3) {
tangent(2, 2) = Miiii;
tangent(0, 2) = Miijj;
tangent(1, 2) = Miijj;
tangent(2, 0) = Miijj;
tangent(2, 1) = Miijj;
tangent(3, 3) = Mijij;
tangent(4, 4) = Mijij;
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElastic<dim>::computePotentialEnergyOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & sigma, Real & epot) {
epot = .5 * sigma.doubleDot(grad_u);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
MaterialElastic<1>::computeTangentModuliOnQuad(Matrix<Real> & tangent) const {
tangent(0, 0) = E;
}
} // akantu
#endif /* __AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
index 84c1608fa..0b8a34b78 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
@@ -1,263 +1,265 @@
/**
* @file material_elastic_linear_anisotropic.cc
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
+ * @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 25 2013
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Anisotropic elastic material
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "material_elastic_linear_anisotropic.hh"
#include "solid_mechanics_model.hh"
#include <algorithm>
#include <sstream>
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElasticLinearAnisotropic<dim>::MaterialElasticLinearAnisotropic(
SolidMechanicsModel & model, const ID & id, bool symmetric)
: Material(model, id), rot_mat(dim, dim), Cprime(dim * dim, dim * dim),
C(voigt_h::size, voigt_h::size), eigC(voigt_h::size),
symmetric(symmetric), alpha(0), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->dir_vecs.push_back(std::make_unique<Vector<Real>>(dim));
(*this->dir_vecs.back())[0] = 1.;
this->registerParam("n1", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of main material axis");
if (dim > 1) {
this->dir_vecs.push_back(std::make_unique<Vector<Real>>(dim));
(*this->dir_vecs.back())[1] = 1.;
this->registerParam("n2", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of secondary material axis");
}
if (dim > 2) {
this->dir_vecs.push_back(std::make_unique<Vector<Real>>(dim));
(*this->dir_vecs.back())[2] = 1.;
this->registerParam("n3", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of tertiary material axis");
}
for (UInt i = 0; i < voigt_h::size; ++i) {
UInt start = 0;
if (this->symmetric) {
start = i;
}
for (UInt j = start; j < voigt_h::size; ++j) {
std::stringstream param("C");
param << "C" << i + 1 << j + 1;
this->registerParam(param.str(), this->Cprime(i, j), Real(0.),
_pat_parsmod, "Coefficient " + param.str());
}
}
this->registerParam("alpha", this->alpha, _pat_parsmod,
"Proportion of viscous stress");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElasticLinearAnisotropic<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::updateInternalParameters() {
Material::updateInternalParameters();
if (this->symmetric) {
for (UInt i = 0; i < voigt_h::size; ++i) {
for (UInt j = i + 1; j < voigt_h::size; ++j) {
this->Cprime(j, i) = this->Cprime(i, j);
}
}
}
this->rotateCprime();
this->C.eig(this->eigC);
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <UInt Dim> void MaterialElasticLinearAnisotropic<Dim>::rotateCprime() {
// start by filling the empty parts fo Cprime
UInt diff = Dim * Dim - voigt_h::size;
for (UInt i = voigt_h::size; i < Dim * Dim; ++i) {
for (UInt j = 0; j < Dim * Dim; ++j) {
this->Cprime(i, j) = this->Cprime(i - diff, j);
}
}
for (UInt i = 0; i < Dim * Dim; ++i) {
for (UInt j = voigt_h::size; j < Dim * Dim; ++j) {
this->Cprime(i, j) = this->Cprime(i, j - diff);
}
}
// construction of rotator tensor
// normalise rotation matrix
for (UInt j = 0; j < Dim; ++j) {
Vector<Real> rot_vec = this->rot_mat(j);
rot_vec = *this->dir_vecs[j];
rot_vec.normalize();
}
// make sure the vectors form a right-handed base
Vector<Real> test_axis(3);
Vector<Real> v1(3), v2(3), v3(3);
if (Dim == 2) {
for (UInt i = 0; i < Dim; ++i) {
v1[i] = this->rot_mat(0, i);
v2[i] = this->rot_mat(1, i);
v3[i] = 0.;
}
v3[2] = 1.;
v1[2] = 0.;
v2[2] = 0.;
} else if (Dim == 3) {
v1 = this->rot_mat(0);
v2 = this->rot_mat(1);
v3 = this->rot_mat(2);
}
test_axis.crossProduct(v1, v2);
test_axis -= v3;
if (test_axis.norm() > 8 * std::numeric_limits<Real>::epsilon()) {
AKANTU_ERROR("The axis vectors do not form a right-handed coordinate "
<< "system. I. e., ||n1 x n2 - n3|| should be zero, but "
<< "it is " << test_axis.norm() << ".");
}
// create the rotator and the reverse rotator
Matrix<Real> rotator(Dim * Dim, Dim * Dim);
Matrix<Real> revrotor(Dim * Dim, Dim * Dim);
for (UInt i = 0; i < Dim; ++i) {
for (UInt j = 0; j < Dim; ++j) {
for (UInt k = 0; k < Dim; ++k) {
for (UInt l = 0; l < Dim; ++l) {
UInt I = voigt_h::mat[i][j];
UInt J = voigt_h::mat[k][l];
rotator(I, J) = this->rot_mat(k, i) * this->rot_mat(l, j);
revrotor(I, J) = this->rot_mat(i, k) * this->rot_mat(j, l);
}
}
}
}
// create the full rotated matrix
Matrix<Real> Cfull(Dim * Dim, Dim * Dim);
Cfull = rotator * Cprime * revrotor;
for (UInt i = 0; i < voigt_h::size; ++i) {
for (UInt j = 0; j < voigt_h::size; ++j) {
this->C(i, j) = Cfull(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computeStress(
ElementType el_type, GhostType ghost_type) {
// Wikipedia convention:
// 2*eps_ij (i!=j) = voigt_eps_I
// http://en.wikipedia.org/wiki/Voigt_notation
AKANTU_DEBUG_IN();
Matrix<Real> strain(dim, dim);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeStressOnQuad(strain, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computeTangentModuli(
const ElementType & el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computePotentialEnergy(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Material::computePotentialEnergy(el_type, ghost_type);
AKANTU_DEBUG_ASSERT(!this->finite_deformation,
"finite deformation not possible in material anisotropic "
"(TO BE IMPLEMENTED)");
if (ghost_type != _not_ghost)
return;
Array<Real>::scalar_iterator epot =
this->potential_energy(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computePotentialEnergyOnQuad(grad_u, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialElasticLinearAnisotropic<dim>::getCelerity(
__attribute__((unused)) const Element & element) const {
return std::sqrt(this->eigC(0) / rho);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(elastic_anisotropic, MaterialElasticLinearAnisotropic);
} // akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
index 2cfa119bb..363378550 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
@@ -1,139 +1,140 @@
/**
* @file material_elastic_linear_anisotropic.hh
*
* @author Till Junge <till.junge@epfl.ch>
+ * @author Enrico Milanese <enrico.milanese@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Fri Feb 16 2018
*
* @brief Orthotropic elastic material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH__
#define __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH__
namespace akantu {
/**
* General linear anisotropic elastic material
* The only constraint on the elastic tensor is that it can be represented
* as a symmetric 6x6 matrix (3D) or 3x3 (2D).
*
* parameters in the material files :
* - rho : density (default: 0)
* - C_ij : entry on the stiffness
*/
template <UInt Dim> class MaterialElasticLinearAnisotropic : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialElasticLinearAnisotropic(SolidMechanicsModel & model,
const ID & id = "", bool symmetric = true);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void updateInternalParameters() override;
bool hasStiffnessMatrixChanged() override {
return (!was_stiffness_assembled);
}
protected:
// compute C from Cprime
void rotateCprime();
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma) const;
/// tangent matrix for a given quadrature point
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent) const;
inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// compute max wave celerity
Real getCelerity(const Element & element) const override;
AKANTU_GET_MACRO(VoigtStiffness, C, Matrix<Real>);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
using voigt_h = VoigtHelper<Dim>;
/// direction matrix and vectors
std::vector<std::unique_ptr<Vector<Real>>> dir_vecs;
Matrix<Real> rot_mat;
/// Elastic stiffness tensor in material frame and full vectorised notation
Matrix<Real> Cprime;
/// Elastic stiffness tensor in voigt notation
Matrix<Real> C;
/// eigenvalues of stiffness tensor
Vector<Real> eigC;
bool symmetric;
/// viscous proportion
Real alpha;
/// defines if the stiffness was computed
bool was_stiffness_assembled;
};
} // akantu
#include "material_elastic_linear_anisotropic_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.cc b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.cc
index 1d608fe60..716978f67 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.cc
@@ -1,93 +1,92 @@
/**
* @file material_elastic_linear_anisotropic_inline_impl.cc
*
* @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Feb 12 2018
- * @date last modification: Mon Feb 12 2018
+ * @date creation: Fri Feb 16 2018
+ * @date last modification: Fri Feb 16 2018
*
- * @brief Implementation of the inline functions of the material elastic linear
+ * @brief Implementation of the inline functions of the material elastic linear
* anisotropic
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic_linear_anisotropic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_CC__
#define __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElasticLinearAnisotropic<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma) const {
// Wikipedia convention:
// 2*eps_ij (i!=j) = voigt_eps_I
// http://en.wikipedia.org/wiki/Voigt_notation
Vector<Real> voigt_strain(voigt_h::size);
Vector<Real> voigt_stress(voigt_h::size);
for (UInt I = 0; I < voigt_h::size; ++I) {
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_strain(I) = voigt_factor * (grad_u(i, j) + grad_u(j, i)) / 2.;
}
voigt_stress = this->C * voigt_strain;
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
sigma(i, j) = sigma(j, i) = voigt_stress(I);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElasticLinearAnisotropic<dim>::computeTangentModuliOnQuad(
Matrix<Real> & tangent) const {
tangent.copy(this->C);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElasticLinearAnisotropic<dim>::computePotentialEnergyOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & sigma, Real & epot) {
AKANTU_DEBUG_ASSERT(this->symmetric,
"The elastic constants matrix is not symmetric,"
"energy is not path independent.");
epot = .5 * sigma.doubleDot(grad_u);
}
} // akantu
#endif /* __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc b/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
index 320f2bb44..d701bf394 100644
--- a/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
@@ -1,168 +1,168 @@
/**
* @file material_elastic_orthotropic.cc
*
* @author Till Junge <till.junge@epfl.ch>
+ * @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Orthotropic elastic material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "material_elastic_orthotropic.hh"
#include "solid_mechanics_model.hh"
#include <algorithm>
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt Dim>
MaterialElasticOrthotropic<Dim>::MaterialElasticOrthotropic(
SolidMechanicsModel & model, const ID & id)
: MaterialElasticLinearAnisotropic<Dim>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("E1", E1, Real(0.), _pat_parsmod, "Young's modulus (n1)");
this->registerParam("E2", E2, Real(0.), _pat_parsmod, "Young's modulus (n2)");
this->registerParam("nu12", nu12, Real(0.), _pat_parsmod,
"Poisson's ratio (12)");
this->registerParam("G12", G12, Real(0.), _pat_parsmod, "Shear modulus (12)");
if (Dim > 2) {
this->registerParam("E3", E3, Real(0.), _pat_parsmod,
"Young's modulus (n3)");
this->registerParam("nu13", nu13, Real(0.), _pat_parsmod,
"Poisson's ratio (13)");
this->registerParam("nu23", nu23, Real(0.), _pat_parsmod,
"Poisson's ratio (23)");
this->registerParam("G13", G13, Real(0.), _pat_parsmod,
"Shear modulus (13)");
this->registerParam("G23", G23, Real(0.), _pat_parsmod,
"Shear modulus (23)");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt Dim> void MaterialElasticOrthotropic<Dim>::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt Dim>
void MaterialElasticOrthotropic<Dim>::updateInternalParameters() {
/* 1) construction of temporary material frame stiffness tensor------------ */
// http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real nu31 = nu13 * E3 / E1;
Real nu32 = nu23 * E3 / E2;
// Full (i.e. dim^2 by dim^2) stiffness tensor in material frame
if (Dim == 1) {
AKANTU_ERROR("Dimensions 1 not implemented: makes no sense to have "
"orthotropy for 1D");
}
Real Gamma;
if (Dim == 3)
Gamma = 1 / (1 - nu12 * nu21 - nu23 * nu32 - nu31 * nu13 -
2 * nu21 * nu32 * nu13);
if (Dim == 2)
Gamma = 1 / (1 - nu12 * nu21);
// Lamé's first parameters
this->Cprime(0, 0) = E1 * (1 - nu23 * nu32) * Gamma;
this->Cprime(1, 1) = E2 * (1 - nu13 * nu31) * Gamma;
if (Dim == 3)
this->Cprime(2, 2) = E3 * (1 - nu12 * nu21) * Gamma;
// normalised poisson's ratio's
this->Cprime(1, 0) = this->Cprime(0, 1) = E1 * (nu21 + nu31 * nu23) * Gamma;
if (Dim == 3) {
this->Cprime(2, 0) = this->Cprime(0, 2) = E1 * (nu31 + nu21 * nu32) * Gamma;
this->Cprime(2, 1) = this->Cprime(1, 2) = E2 * (nu32 + nu12 * nu31) * Gamma;
}
// Lamé's second parameters (shear moduli)
if (Dim == 3) {
this->Cprime(3, 3) = G23;
this->Cprime(4, 4) = G13;
this->Cprime(5, 5) = G12;
} else
this->Cprime(2, 2) = G12;
/* 1) rotation of C into the global frame */
this->rotateCprime();
this->C.eig(this->eigC);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElasticOrthotropic<spatial_dimension>::
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) {
AKANTU_DEBUG_ASSERT(!this->finite_deformation,
"finite deformation not possible in material orthotropic "
"(TO BE IMPLEMENTED)");
Array<Real>::matrix_iterator gradu_it =
this->gradu(type).begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator gradu_end =
this->gradu(type).begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator stress_it =
this->stress(type).begin(spatial_dimension, spatial_dimension);
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
gradu_it += index * nb_quadrature_points;
gradu_end += (index + 1) * nb_quadrature_points;
stress_it += index * nb_quadrature_points;
Real * epot_quad = epot_on_quad_points.storage();
Matrix<Real> grad_u(spatial_dimension, spatial_dimension);
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
grad_u.copy(*gradu_it);
this->computePotentialEnergyOnQuad(grad_u, *stress_it, *epot_quad);
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(elastic_orthotropic, MaterialElasticOrthotropic);
} // akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh b/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
index 60110342c..0cea87042 100644
--- a/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
@@ -1,136 +1,136 @@
/**
* @file material_elastic_orthotropic.hh
*
* @author Till Junge <till.junge@epfl.ch>
+ * @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Fri Feb 16 2018
*
* @brief Orthotropic elastic material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic_linear_anisotropic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH__
#define __AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH__
namespace akantu {
/**
* Orthotropic elastic material
*
* parameters in the material files :
* - n1 : direction of x-axis in material base, normalisation not necessary
* (default: {1, 0, 0})
* - n2 : direction of y-axis in material base, normalisation not necessary
* (default: {0, 1, 0})
* - n3 : direction of z-axis in material base, normalisation not necessary
* (default: {0, 0, 1})
* - rho : density (default: 0)
* - E1 : Young's modulus along n1 (default: 0)
* - E2 : Young's modulus along n2 (default: 0)
* - E3 : Young's modulus along n3 (default: 0)
* - nu12 : Poisson's ratio along 12 (default: 0)
* - nu13 : Poisson's ratio along 13 (default: 0)
* - nu23 : Poisson's ratio along 23 (default: 0)
* - G12 : Shear modulus along 12 (default: 0)
* - G13 : Shear modulus along 13 (default: 0)
* - G23 : Shear modulus along 23 (default: 0)
*/
template <UInt Dim>
class MaterialElasticOrthotropic
: public MaterialElasticLinearAnisotropic<Dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialElasticOrthotropic(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
void updateInternalParameters() override;
void
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(E1, E1, Real);
AKANTU_GET_MACRO(E2, E2, Real);
AKANTU_GET_MACRO(E3, E3, Real);
AKANTU_GET_MACRO(Nu12, nu12, Real);
AKANTU_GET_MACRO(Nu13, nu13, Real);
AKANTU_GET_MACRO(Nu23, nu23, Real);
AKANTU_GET_MACRO(G12, G12, Real);
AKANTU_GET_MACRO(G13, G13, Real);
AKANTU_GET_MACRO(G23, G23, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the n1 young modulus
Real E1;
/// the n2 young modulus
Real E2;
/// the n3 young modulus
Real E3;
/// 12 Poisson coefficient
Real nu12;
/// 13 Poisson coefficient
Real nu13;
/// 23 Poisson coefficient
Real nu23;
/// 12 shear modulus
Real G12;
/// 13 shear modulus
Real G13;
/// 23 shear modulus
Real G23;
};
} // akantu
#endif /* __AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh b/src/model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh
index 29362ed2c..fa1a1f523 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh
@@ -1,41 +1,41 @@
/**
* @file material_embedded_includes.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Fri May 29 2015
+ * @date last modification: Fri Feb 09 2018
*
* @brief List of includes for embedded elements
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_CMAKE_LIST_MATERIALS
#include "material_reinforcement.hh"
#endif
#define AKANTU_MATERIAL_REINFORCEMENT_LAW_TMPL_LIST \
((elastic, (MaterialElastic<1>)))( \
(plastic, (MaterialLinearIsotropicHardening<1>)))
#define AKANTU_EMBEDDED_MATERIAL_LIST \
((2, (reinforcement, MaterialReinforcement)))
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
index 172508a2e..36a04ab7f 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
@@ -1,209 +1,209 @@
/**
* @file material_reinforcement.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
- * @date last modification: Tue Nov 24 2015
+ * @date last modification: Fri Feb 09 2018
*
* @brief Reinforcement material
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_REINFORCEMENT_HH__
#define __AKANTU_MATERIAL_REINFORCEMENT_HH__
#include "aka_common.hh"
#include "embedded_interface_model.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Material used to represent embedded reinforcements
*
* This class is used for computing the reinforcement stiffness matrix
* along with the reinforcement residual. Room is made for constitutive law,
* but actual use of contitutive laws is made in MaterialReinforcementTemplate.
*
* Be careful with the dimensions in this class :
* - this->spatial_dimension is always 1
* - the template parameter dim is the dimension of the problem
*/
template <class Mat, UInt dim> class MaterialReinforcement : public Mat {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/// Constructor
MaterialReinforcement(EmbeddedInterfaceModel & model, const ID & id = "");
/// Destructor
~MaterialReinforcement() override;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Init the material
void initMaterial() override;
/// Init the filters for background elements
void initFilters();
/// Init the background shape derivatives
void initBackgroundShapeDerivatives();
/// Init the cosine matrices
void initDirectingCosines();
/// Assemble stiffness matrix
void assembleStiffnessMatrix(GhostType ghost_type) override;
/// Compute all the stresses !
void computeAllStresses(GhostType ghost_type) override;
/// Compute energy
Real getEnergy(const std::string & id) override;
/// Assemble the residual of one type of element (typically _segment_2)
void assembleInternalForces(GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Protected methods */
/* ------------------------------------------------------------------------ */
protected:
/// Allocate the background shape derivatives
void allocBackgroundShapeDerivatives();
/// Compute the directing cosines matrix for one element type
void computeDirectingCosines(const ElementType & type, GhostType ghost_type);
/// Compute the directing cosines matrix on quadrature points.
inline void computeDirectingCosinesOnQuad(const Matrix<Real> & nodes,
Matrix<Real> & cosines);
/// Add the prestress to the computed stress
void addPrestress(const ElementType & type, GhostType ghost_type);
/// Compute displacement gradient in reinforcement
void computeGradU(const ElementType & interface_type, GhostType ghost_type);
/// 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
void assembleStiffnessMatrixInterface(const ElementType & interface_type,
const ElementType & background_type,
GhostType ghost_type);
/// Compute the background shape derivatives for a type
void computeBackgroundShapeDerivatives(const ElementType & type,
GhostType ghost_type);
/// Compute the background shape derivatives for a type pair
void computeBackgroundShapeDerivatives(const ElementType & interface_type,
const ElementType & bg_type,
GhostType ghost_type,
const Array<UInt> & filter);
/// Filter elements crossed by interface of a type
void filterInterfaceBackgroundElements(Array<UInt> & foreground,
Array<UInt> & background,
const ElementType & type,
const ElementType & interface_type,
GhostType ghost_type);
/// Assemble the residual of one type of element (typically _segment_2)
void assembleInternalForces(const ElementType & type, GhostType ghost_type);
/// Assemble the residual for a pair of elements
void assembleInternalForcesInterface(const ElementType & interface_type,
const ElementType & background_type,
GhostType ghost_type);
// TODO figure out why voigt size is 4 in 2D
inline void stressTensorToVoigtVector(const Matrix<Real> & tensor,
Vector<Real> & vector);
inline void strainTensorToVoigtVector(const Matrix<Real> & tensor,
Vector<Real> & vector);
/// Get background filter
Array<UInt> & getBackgroundFilter(const ElementType & fg_type,
const ElementType & bg_type,
GhostType ghost_type) {
return (*background_filter(fg_type, ghost_type))(bg_type, ghost_type);
}
/// Get foreground filter
Array<UInt> & getForegroundFilter(const ElementType & fg_type,
const ElementType & bg_type,
GhostType ghost_type) {
return (*foreground_filter(fg_type, ghost_type))(bg_type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Embedded model
EmbeddedInterfaceModel & emodel;
/// Gradu of concrete on reinforcement
InternalField<Real> gradu_embedded;
/// C matrix on quad
InternalField<Real> directing_cosines;
/// Prestress on quad
InternalField<Real> pre_stress;
/// Cross-sectional area
Real area;
template <typename T>
using CrossMap = ElementTypeMap<std::unique_ptr<ElementTypeMapArray<T>>>;
/// Background mesh shape derivatives
CrossMap<Real> shape_derivatives;
/// Foreground mesh filter (contains segment ids)
CrossMap<UInt> foreground_filter;
/// Background element filter (contains bg ids)
CrossMap<UInt> background_filter;
};
} // akantu
#include "material_reinforcement_tmpl.hh"
#endif // __AKANTU_MATERIAL_REINFORCEMENT_HH__
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
index e8f8c5ef9..dadf9e27e 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
@@ -1,800 +1,801 @@
/**
* @file material_reinforcement_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
- * @date creation: Thu Feb 1 2018
+ * @date creation: Wed Mar 25 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Reinforcement material
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_reinforcement.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
MaterialReinforcement<Mat, dim>::MaterialReinforcement(
EmbeddedInterfaceModel & model, const ID & id)
: Mat(model, 1, model.getInterfaceMesh(),
model.getFEEngine("EmbeddedInterfaceFEEngine"), id),
emodel(model),
gradu_embedded("gradu_embedded", *this, 1,
model.getFEEngine("EmbeddedInterfaceFEEngine"),
this->element_filter),
directing_cosines("directing_cosines", *this, 1,
model.getFEEngine("EmbeddedInterfaceFEEngine"),
this->element_filter),
pre_stress("pre_stress", *this, 1,
model.getFEEngine("EmbeddedInterfaceFEEngine"),
this->element_filter),
area(1.0), shape_derivatives() {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initialize() {
AKANTU_DEBUG_IN();
this->registerParam("area", area, _pat_parsable | _pat_modifiable,
"Reinforcement cross-sectional area");
this->registerParam("pre_stress", pre_stress, _pat_parsable | _pat_modifiable,
"Uniform pre-stress");
// this->unregisterInternal(this->stress);
// Fool the AvgHomogenizingFunctor
// stress.initialize(dim * dim);
// Reallocate the element filter
this->element_filter.initialize(this->emodel.getInterfaceMesh(),
_spatial_dimension = 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
MaterialReinforcement<Mat, dim>::~MaterialReinforcement() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initMaterial() {
Mat::initMaterial();
gradu_embedded.initialize(dim * dim);
pre_stress.initialize(1);
/// We initialise the stuff that is not going to change during the simulation
this->initFilters();
this->allocBackgroundShapeDerivatives();
this->initBackgroundShapeDerivatives();
this->initDirectingCosines();
}
/* -------------------------------------------------------------------------- */
/// Initialize the filter for background elements
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initFilters() {
for (auto gt : ghost_types) {
for (auto && type : emodel.getInterfaceMesh().elementTypes(1, gt)) {
std::string shaped_id = "filter";
if (gt == _ghost)
shaped_id += ":ghost";
auto & background =
background_filter(std::make_unique<ElementTypeMapArray<UInt>>(
"bg_" + shaped_id, this->name),
type, gt);
auto & foreground = foreground_filter(
std::make_unique<ElementTypeMapArray<UInt>>(shaped_id, this->name),
type, gt);
foreground->initialize(emodel.getMesh(), _nb_component = 1,
_ghost_type = gt);
background->initialize(emodel.getMesh(), _nb_component = 1,
_ghost_type = gt);
// Computing filters
for (auto && bg_type : background->elementTypes(dim, gt)) {
filterInterfaceBackgroundElements(
(*foreground)(bg_type), (*background)(bg_type), bg_type, type, gt);
}
}
}
}
/* -------------------------------------------------------------------------- */
/// Construct a filter for a (interface_type, background_type) pair
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::filterInterfaceBackgroundElements(
Array<UInt> & foreground, Array<UInt> & background,
const ElementType & type, const ElementType & interface_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
foreground.resize(0);
background.resize(0);
Array<Element> & elements =
emodel.getInterfaceAssociatedElements(interface_type, ghost_type);
Array<UInt> & elem_filter = this->element_filter(interface_type, ghost_type);
for (auto & elem_id : elem_filter) {
Element & elem = elements(elem_id);
if (elem.type == type) {
background.push_back(elem.element);
foreground.push_back(elem_id);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
namespace detail {
class BackgroundShapeDInitializer : public ElementTypeMapArrayInitializer {
public:
BackgroundShapeDInitializer(UInt spatial_dimension, FEEngine & engine,
const ElementType & foreground_type,
const ElementTypeMapArray<UInt> & filter,
const GhostType & ghost_type)
: ElementTypeMapArrayInitializer(
[](const ElementType & bgtype, const GhostType &) {
return ShapeFunctions::getShapeDerivativesSize(bgtype);
},
spatial_dimension, ghost_type, _ek_regular) {
auto nb_quad = engine.getNbIntegrationPoints(foreground_type);
// Counting how many background elements are affected by elements of
// interface_type
for (auto type : filter.elementTypes(this->spatial_dimension)) {
// Inserting size
array_size_per_bg_type(filter(type).size() * nb_quad, type,
this->ghost_type);
}
}
auto elementTypes() const -> decltype(auto) {
return array_size_per_bg_type.elementTypes();
}
UInt size(const ElementType & bgtype) const {
return array_size_per_bg_type(bgtype, this->ghost_type);
}
protected:
ElementTypeMap<UInt> array_size_per_bg_type;
};
}
/**
* Background shape derivatives need to be stored per background element
* types but also per embedded element type, which is why they are stored
* in an ElementTypeMap<ElementTypeMapArray<Real> *>. The outer ElementTypeMap
* refers to the embedded types, and the inner refers to the background types.
*/
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::allocBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
for (auto gt : ghost_types) {
for (auto && type : emodel.getInterfaceMesh().elementTypes(1, gt)) {
std::string shaped_id = "embedded_shape_derivatives";
if (gt == _ghost)
shaped_id += ":ghost";
auto & shaped_etma = shape_derivatives(
std::make_unique<ElementTypeMapArray<Real>>(shaped_id, this->name),
type, gt);
shaped_etma->initialize(
detail::BackgroundShapeDInitializer(
emodel.getSpatialDimension(),
emodel.getFEEngine("EmbeddedInterfaceFEEngine"), type,
*background_filter(type, gt), gt),
0, true);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
for (auto interface_type :
this->element_filter.elementTypes(this->spatial_dimension)) {
for (auto type : background_filter(interface_type)->elementTypes(dim)) {
computeBackgroundShapeDerivatives(interface_type, type, _not_ghost,
this->element_filter(interface_type));
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeBackgroundShapeDerivatives(
const ElementType & interface_type, const ElementType & bg_type,
GhostType ghost_type, const Array<UInt> & filter) {
auto & interface_engine = emodel.getFEEngine("EmbeddedInterfaceFEEngine");
auto & engine = emodel.getFEEngine();
auto & interface_mesh = emodel.getInterfaceMesh();
const auto nb_nodes_elem_bg = Mesh::getNbNodesPerElement(bg_type);
// const auto nb_strss = VoigtHelper<dim>::size;
const auto nb_quads_per_elem =
interface_engine.getNbIntegrationPoints(interface_type);
Array<Real> quad_pos(0, dim, "interface_quad_pos");
interface_engine.interpolateOnIntegrationPoints(interface_mesh.getNodes(),
quad_pos, dim, interface_type,
ghost_type, filter);
auto & background_shapesd =
(*shape_derivatives(interface_type, ghost_type))(bg_type, ghost_type);
auto & background_elements =
(*background_filter(interface_type, ghost_type))(bg_type, ghost_type);
auto & foreground_elements =
(*foreground_filter(interface_type, ghost_type))(bg_type, ghost_type);
auto shapesd_begin =
background_shapesd.begin(dim, nb_nodes_elem_bg, nb_quads_per_elem);
auto quad_begin = quad_pos.begin(dim, nb_quads_per_elem);
for (auto && tuple : zip(background_elements, foreground_elements)) {
UInt bg = std::get<0>(tuple), fg = std::get<1>(tuple);
for (UInt i = 0; i < nb_quads_per_elem; ++i) {
Matrix<Real> shapesd = Tensor3<Real>(shapesd_begin[fg])(i);
Vector<Real> quads = Matrix<Real>(quad_begin[fg])(i);
engine.computeShapeDerivatives(quads, bg, bg_type, shapesd, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initDirectingCosines() {
AKANTU_DEBUG_IN();
Mesh & mesh = emodel.getInterfaceMesh();
Mesh::type_iterator type_it = mesh.firstType(1, _not_ghost);
Mesh::type_iterator type_end = mesh.lastType(1, _not_ghost);
const UInt voigt_size = VoigtHelper<dim>::size;
directing_cosines.initialize(voigt_size);
for (; type_it != type_end; ++type_it) {
computeDirectingCosines(*type_it, _not_ghost);
// computeDirectingCosines(*type_it, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleStiffnessMatrix(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
Mesh::type_iterator type_it = interface_mesh.firstType(1, _not_ghost);
Mesh::type_iterator type_end = interface_mesh.lastType(1, _not_ghost);
for (; type_it != type_end; ++type_it) {
assembleStiffnessMatrix(*type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleInternalForces(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
Mesh::type_iterator type_it = interface_mesh.firstType(1, _not_ghost);
Mesh::type_iterator type_end = interface_mesh.lastType(1, _not_ghost);
for (; type_it != type_end; ++type_it) {
this->assembleInternalForces(*type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeAllStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = emodel.getInterfaceMesh().firstType();
Mesh::type_iterator last_type = emodel.getInterfaceMesh().lastType();
for (; it != last_type; ++it) {
computeGradU(*it, ghost_type);
this->computeStress(*it, ghost_type);
addPrestress(*it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::addPrestress(const ElementType & type,
GhostType ghost_type) {
auto & stress = this->stress(type, ghost_type);
auto & sigma_p = this->pre_stress(type, ghost_type);
for (auto && tuple : zip(stress, sigma_p)) {
std::get<0>(tuple) += std::get<1>(tuple);
}
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleInternalForces(
const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = emodel.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) {
assembleInternalForcesInterface(type, *type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Computes and assemble the residual. Residual in reinforcement is computed as:
*
* \f[
* \vec{r} = A_s \int_S{\mathbf{B}^T\mathbf{C}^T \vec{\sigma_s}\,\mathrm{d}s}
* \f]
*/
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleInternalForcesInterface(
const ElementType & interface_type, const ElementType & background_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt voigt_size = VoigtHelper<dim>::size;
FEEngine & interface_engine = emodel.getFEEngine("EmbeddedInterfaceFEEngine");
Array<UInt> & elem_filter = this->element_filter(interface_type, ghost_type);
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points =
interface_engine.getNbIntegrationPoints(interface_type, ghost_type);
UInt nb_element = elem_filter.size();
UInt back_dof = dim * nodes_per_background_e;
Array<Real> & shapesd = (*shape_derivatives(interface_type, ghost_type))(
background_type, ghost_type);
Array<Real> integrant(nb_quadrature_points * nb_element, back_dof,
"integrant");
auto integrant_it = integrant.begin(back_dof);
auto integrant_end = integrant.end(back_dof);
Array<Real>::matrix_iterator B_it =
shapesd.begin(dim, nodes_per_background_e);
auto C_it = directing_cosines(interface_type, ghost_type).begin(voigt_size);
auto sigma_it = this->stress(interface_type, ghost_type).begin();
Matrix<Real> Bvoigt(voigt_size, back_dof);
for (; integrant_it != integrant_end;
++integrant_it, ++B_it, ++C_it, ++sigma_it) {
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(*B_it, Bvoigt,
nodes_per_background_e);
Vector<Real> & C = *C_it;
Vector<Real> & BtCt_sigma = *integrant_it;
BtCt_sigma.mul<true>(Bvoigt, C);
BtCt_sigma *= *sigma_it * area;
}
Array<Real> residual_interface(nb_element, back_dof, "residual_interface");
interface_engine.integrate(integrant, residual_interface, back_dof,
interface_type, ghost_type, elem_filter);
integrant.resize(0);
Array<UInt> background_filter(nb_element, 1, "background_filter");
auto & filter =
getBackgroundFilter(interface_type, background_type, ghost_type);
emodel.getDOFManager().assembleElementalArrayLocalArray(
residual_interface, emodel.getInternalForce(), background_type,
ghost_type, -1., filter);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeDirectingCosines(
const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const UInt steel_dof = dim * nb_nodes_per_element;
const UInt voigt_size = VoigtHelper<dim>::size;
const UInt nb_quad_points = emodel.getFEEngine("EmbeddedInterfaceFEEngine")
.getNbIntegrationPoints(type, ghost_type);
Array<Real> node_coordinates(this->element_filter(type, ghost_type).size(),
steel_dof);
this->emodel.getFEEngine().template extractNodalToElementField<Real>(
interface_mesh, interface_mesh.getNodes(), node_coordinates, type,
ghost_type, this->element_filter(type, ghost_type));
Array<Real>::matrix_iterator directing_cosines_it =
directing_cosines(type, ghost_type).begin(1, voigt_size);
Array<Real>::matrix_iterator node_coordinates_it =
node_coordinates.begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator node_coordinates_end =
node_coordinates.end(dim, nb_nodes_per_element);
for (; node_coordinates_it != node_coordinates_end; ++node_coordinates_it) {
for (UInt i = 0; i < nb_quad_points; i++, ++directing_cosines_it) {
Matrix<Real> & nodes = *node_coordinates_it;
Matrix<Real> & cosines = *directing_cosines_it;
computeDirectingCosinesOnQuad(nodes, cosines);
}
}
// Mauro: the directing_cosines internal is defined on the quadrature points
// of each element
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleStiffnessMatrix(
const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = emodel.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) {
assembleStiffnessMatrixInterface(type, *type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Computes the reinforcement stiffness matrix (Gomes & Awruch, 2001)
* \f[
* \mathbf{K}_e = \sum_{i=1}^R{A_i\int_{S_i}{\mathbf{B}^T
* \mathbf{C}_i^T \mathbf{D}_{s, i} \mathbf{C}_i \mathbf{B}\,\mathrm{d}s}}
* \f]
*/
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleStiffnessMatrixInterface(
const ElementType & interface_type, const ElementType & background_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt voigt_size = VoigtHelper<dim>::size;
FEEngine & interface_engine = emodel.getFEEngine("EmbeddedInterfaceFEEngine");
Array<UInt> & elem_filter = this->element_filter(interface_type, ghost_type);
Array<Real> & grad_u = gradu_embedded(interface_type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points =
interface_engine.getNbIntegrationPoints(interface_type, ghost_type);
UInt back_dof = dim * nodes_per_background_e;
UInt integrant_size = back_dof;
grad_u.resize(nb_quadrature_points * nb_element);
Array<Real> tangent_moduli(nb_element * nb_quadrature_points, 1,
"interface_tangent_moduli");
this->computeTangentModuli(interface_type, tangent_moduli, ghost_type);
Array<Real> & shapesd = (*shape_derivatives(interface_type, ghost_type))(
background_type, ghost_type);
Array<Real> integrant(nb_element * nb_quadrature_points,
integrant_size * integrant_size, "B^t*C^t*D*C*B");
/// Temporary matrices for integrant product
Matrix<Real> Bvoigt(voigt_size, back_dof);
Matrix<Real> DCB(1, back_dof);
Matrix<Real> CtDCB(voigt_size, back_dof);
Array<Real>::scalar_iterator D_it = tangent_moduli.begin();
Array<Real>::scalar_iterator D_end = tangent_moduli.end();
Array<Real>::matrix_iterator C_it =
directing_cosines(interface_type, ghost_type).begin(1, voigt_size);
Array<Real>::matrix_iterator B_it =
shapesd.begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator integrant_it =
integrant.begin(integrant_size, integrant_size);
for (; D_it != D_end; ++D_it, ++C_it, ++B_it, ++integrant_it) {
Real & D = *D_it;
Matrix<Real> & C = *C_it;
Matrix<Real> & B = *B_it;
Matrix<Real> & BtCtDCB = *integrant_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(B, Bvoigt,
nodes_per_background_e);
DCB.mul<false, false>(C, Bvoigt);
DCB *= D * area;
CtDCB.mul<true, false>(C, DCB);
BtCtDCB.mul<true, false>(Bvoigt, CtDCB);
}
tangent_moduli.resize(0);
Array<Real> K_interface(nb_element, integrant_size * integrant_size,
"K_interface");
interface_engine.integrate(integrant, K_interface,
integrant_size * integrant_size, interface_type,
ghost_type, elem_filter);
integrant.resize(0);
// Mauro: Here K_interface contains the local stiffness matrices,
// directing_cosines contains the information about the orientation
// of the reinforcements, any rotation of the local stiffness matrix
// can be done here
auto & filter =
getBackgroundFilter(interface_type, background_type, ghost_type);
emodel.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", K_interface, background_type, ghost_type, _symmetric,
filter);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
Real MaterialReinforcement<Mat, dim>::getEnergy(const std::string & id) {
AKANTU_DEBUG_IN();
if (id == "potential") {
Real epot = 0.;
this->computePotentialEnergyByElements();
Mesh::type_iterator it = this->element_filter.firstType(
this->spatial_dimension),
end = this->element_filter.lastType(
this->spatial_dimension);
for (; it != end; ++it) {
FEEngine & interface_engine =
emodel.getFEEngine("EmbeddedInterfaceFEEngine");
epot += interface_engine.integrate(
this->potential_energy(*it, _not_ghost), *it, _not_ghost,
this->element_filter(*it, _not_ghost));
epot *= area;
}
return epot;
}
AKANTU_DEBUG_OUT();
return 0;
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeGradU(
const ElementType & interface_type, GhostType ghost_type) {
// Looping over background types
for (auto && bg_type :
background_filter(interface_type, ghost_type)->elementTypes(dim)) {
const UInt nodes_per_background_e = Mesh::getNbNodesPerElement(bg_type);
const UInt voigt_size = VoigtHelper<dim>::size;
auto & bg_shapesd =
(*shape_derivatives(interface_type, ghost_type))(bg_type, ghost_type);
auto & filter = getBackgroundFilter(interface_type, bg_type, ghost_type);
Array<Real> disp_per_element(0, dim * nodes_per_background_e, "disp_elem");
FEEngine::extractNodalToElementField(
emodel.getMesh(), emodel.getDisplacement(), disp_per_element, bg_type,
ghost_type, filter);
Matrix<Real> concrete_du(dim, dim);
Matrix<Real> epsilon(dim, dim);
Vector<Real> evoigt(voigt_size);
for (auto && tuple :
zip(make_view(disp_per_element, dim, nodes_per_background_e),
make_view(bg_shapesd, dim, nodes_per_background_e),
this->gradu(interface_type, ghost_type),
make_view(this->directing_cosines(interface_type, ghost_type),
voigt_size))) {
auto & u = std::get<0>(tuple);
auto & B = std::get<1>(tuple);
auto & du = std::get<2>(tuple);
auto & C = std::get<3>(tuple);
concrete_du.mul<false, true>(u, B);
auto epsilon = 0.5 * (concrete_du + concrete_du.transpose());
strainTensorToVoigtVector(epsilon, evoigt);
du = C.dot(evoigt);
}
}
}
/* -------------------------------------------------------------------------- */
/**
* The structure of the directing cosines matrix is :
* \f{eqnarray*}{
* C_{1,\cdot} & = & (l^2, m^2, n^2, mn, ln, lm) \\
* C_{i,j} & = & 0
* \f}
*
* with :
* \f[
* (l, m, n) = \frac{1}{\|\frac{\mathrm{d}\vec{r}(s)}{\mathrm{d}s}\|} \cdot
* \frac{\mathrm{d}\vec{r}(s)}{\mathrm{d}s}
* \f]
*/
template <class Mat, UInt dim>
inline void MaterialReinforcement<Mat, dim>::computeDirectingCosinesOnQuad(
const Matrix<Real> & nodes, Matrix<Real> & cosines) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(nodes.cols() == 2,
"Higher order reinforcement elements not implemented");
const Vector<Real> a = nodes(0), b = nodes(1);
Vector<Real> delta = b - a;
Real sq_length = 0.;
for (UInt i = 0; i < dim; i++) {
sq_length += delta(i) * delta(i);
}
if (dim == 2) {
cosines(0, 0) = delta(0) * delta(0); // l^2
cosines(0, 1) = delta(1) * delta(1); // m^2
cosines(0, 2) = delta(0) * delta(1); // lm
} else if (dim == 3) {
cosines(0, 0) = delta(0) * delta(0); // l^2
cosines(0, 1) = delta(1) * delta(1); // m^2
cosines(0, 2) = delta(2) * delta(2); // n^2
cosines(0, 3) = delta(1) * delta(2); // mn
cosines(0, 4) = delta(0) * delta(2); // ln
cosines(0, 5) = delta(0) * delta(1); // lm
}
cosines /= sq_length;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
inline void MaterialReinforcement<Mat, dim>::stressTensorToVoigtVector(
const Matrix<Real> & tensor, Vector<Real> & vector) {
AKANTU_DEBUG_IN();
for (UInt i = 0; i < dim; i++) {
vector(i) = tensor(i, i);
}
if (dim == 2) {
vector(2) = tensor(0, 1);
} else if (dim == 3) {
vector(3) = tensor(1, 2);
vector(4) = tensor(0, 2);
vector(5) = tensor(0, 1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
inline void MaterialReinforcement<Mat, dim>::strainTensorToVoigtVector(
const Matrix<Real> & tensor, Vector<Real> & vector) {
AKANTU_DEBUG_IN();
for (UInt i = 0; i < dim; i++) {
vector(i) = tensor(i, i);
}
if (dim == 2) {
vector(2) = 2 * tensor(0, 1);
} else if (dim == 3) {
vector(3) = 2 * tensor(1, 2);
vector(4) = 2 * tensor(0, 2);
vector(5) = 2 * tensor(0, 1);
}
AKANTU_DEBUG_OUT();
}
} // akantu
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
index 1f2e92ac8..bf8906b65 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
@@ -1,287 +1,287 @@
/**
* @file material_neohookean.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Mon Apr 08 2013
- * @date last modification: Tue Aug 04 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Specialization of the material class for finite deformation
* neo-hookean material
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_neohookean.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialNeohookean<spatial_dimension>::MaterialNeohookean(
SolidMechanicsModel & model, const ID & id)
: PlaneStressToolbox<spatial_dimension>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("E", E, Real(0.), _pat_parsable | _pat_modifiable,
"Young's modulus");
this->registerParam("nu", nu, Real(0.5), _pat_parsable | _pat_modifiable,
"Poisson's ratio");
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
this->finite_deformation = true;
this->initialize_third_axis_deformation = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
PlaneStressToolbox<spatial_dimension>::initMaterial();
if (spatial_dimension == 1)
nu = 0.;
this->updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <> void MaterialNeohookean<2>::initMaterial() {
AKANTU_DEBUG_IN();
PlaneStressToolbox<2>::initMaterial();
this->updateInternalParameters();
if (this->plane_stress)
this->third_axis_deformation.setDefaultValue(1.);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::updateInternalParameters() {
lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
mu = E / (2 * (1 + nu));
kpa = lambda + 2. / 3. * mu;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeCauchyStressPlaneStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
PlaneStressToolbox<dim>::computeCauchyStressPlaneStress(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeCauchyStressPlaneStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real>::matrix_iterator gradu_it =
this->gradu(el_type, ghost_type).begin(2, 2);
Array<Real>::matrix_iterator gradu_end =
this->gradu(el_type, ghost_type).end(2, 2);
Array<Real>::matrix_iterator piola_it =
this->piola_kirchhoff_2(el_type, ghost_type).begin(2, 2);
Array<Real>::matrix_iterator stress_it =
this->stress(el_type, ghost_type).begin(2, 2);
Array<Real>::const_scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
Matrix<Real> F_tensor(2, 2);
for (; gradu_it != gradu_end; ++gradu_it, ++piola_it, ++stress_it, ++c33_it) {
Matrix<Real> & grad_u = *gradu_it;
Matrix<Real> & piola = *piola_it;
Matrix<Real> & sigma = *stress_it;
gradUToF<2>(grad_u, F_tensor);
computeCauchyStressOnQuad<2>(F_tensor, piola, sigma, *c33_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
PlaneStressToolbox<2>::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma, *c33_it);
++c33_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeThirdAxisDeformation(
ElementType /*el_type*/, GhostType /*ghost_type*/) {}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeThirdAxisDeformation(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(this->plane_stress, "The third component of the strain "
"can only be computed for 2D "
"problems in Plane Stress!!");
Array<Real>::scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeThirdAxisDeformationOnQuad(grad_u, *c33_it);
++c33_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::computePotentialEnergy(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Material::computePotentialEnergy(el_type, ghost_type);
if (ghost_type != _not_ghost)
return;
Array<Real>::scalar_iterator epot =
this->potential_energy(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computePotentialEnergyOnQuad(grad_u, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::computeTangentModuli(
__attribute__((unused)) const ElementType & el_type,
Array<Real> & tangent_matrix,
__attribute__((unused)) GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeTangentModuli(__attribute__((unused))
const ElementType & el_type,
Array<Real> & tangent_matrix,
__attribute__((unused))
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
PlaneStressToolbox<2>::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u, *c33_it);
++c33_it;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialNeohookean<spatial_dimension>::getPushWaveSpeed(
__attribute__((unused)) const Element & element) const {
return sqrt((this->lambda + 2 * this->mu) / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialNeohookean<spatial_dimension>::getShearWaveSpeed(
__attribute__((unused)) const Element & element) const {
return sqrt(this->mu / this->rho);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(neohookean, MaterialNeohookean);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
index 96d6b1b7c..77a934ded 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
@@ -1,169 +1,168 @@
/**
* @file material_neohookean.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 08 2015
+ * @date last modification: Wed Nov 29 2017
*
* @brief Material isotropic elastic
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "plane_stress_toolbox.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_NEOHOOKEAN_HH__
#define __AKANTU_MATERIAL_NEOHOOKEAN_HH__
namespace akantu {
/**
* Material elastic isotropic
*
* parameters in the material files :
* - rho : density (default: 0)
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - Plane_Stress : if 0: plane strain, else: plane stress (default: 0)
*/
template <UInt spatial_dimension>
class MaterialNeohookean : public PlaneStressToolbox<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialNeohookean(SolidMechanicsModel & model, const ID & id = "");
~MaterialNeohookean() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// Computation of the cauchy stress for plane strain materials
void
computeCauchyStressPlaneStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// Non linear computation of the third direction strain in 2D plane stress
/// case
void computeThirdAxisDeformation(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the p-wave speed in the material
Real getPushWaveSpeed(const Element & element) const override;
/// compute the s-wave speed in the material
Real getShearWaveSpeed(const Element & element) const override;
protected:
/// constitutive law for a given quadrature point
inline void computePiolaKirchhoffOnQuad(const Matrix<Real> & E,
Matrix<Real> & S);
/// constitutive law for a given quadrature point (first piola)
inline void computeFirstPiolaKirchhoffOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & S,
Matrix<Real> & P);
/// constitutive law for a given quadrature point
inline void computeDeltaStressOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & grad_delta_u,
Matrix<Real> & delta_S);
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & S,
const Real & C33 = 1.0);
/// constitutive law for a given quadrature point
inline void computeThirdAxisDeformationOnQuad(Matrix<Real> & grad_u,
Real & c33_value);
/// constitutive law for a given quadrature point
// inline void updateStressOnQuad(const Matrix<Real> & sigma,
// Matrix<Real> & cauchy_sigma);
/// compute the potential energy for a quadrature point
inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
Real & epot);
/// compute the tangent stiffness matrix for an element
void computeTangentModuliOnQuad(Matrix<Real> & tangent, Matrix<Real> & grad_u,
const Real & C33 = 1.0);
/// recompute the lame coefficient if E or nu changes
void updateInternalParameters() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// Bulk modulus
Real kpa;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_neohookean_inline_impl.cc"
} // akantu
#endif /* __AKANTU_MATERIAL_NEOHOOKEAN_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.cc b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.cc
index b99d4e14f..c46c352bb 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.cc
@@ -1,191 +1,191 @@
/**
* @file material_neohookean_inline_impl.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Mon Apr 08 2013
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the inline functions of the material elastic
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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 "material_neohookean.hh"
#include <cmath>
#include <utility>
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeDeltaStressOnQuad(
__attribute__((unused)) const Matrix<Real> & grad_u,
__attribute__((unused)) const Matrix<Real> & grad_delta_u,
__attribute__((unused)) Matrix<Real> & delta_S) {}
//! computes the second piola kirchhoff stress, called S
template <UInt dim>
inline void MaterialNeohookean<dim>::computeStressOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & S,
const Real & C33) {
// Neo hookean book
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
Matrix<Real> Cminus(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Real J = F.det() * sqrt(C33); // the term sqrt(C33) corresponds to the off
// plane strain (2D plane stress)
// std::cout<<"det(F) -> "<<J<<std::endl;
Cminus.inverse(C);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
S(i, j) = (i == j) * mu + (lambda * log(J) - mu) * Cminus(i, j);
}
/* -------------------------------------------------------------------------- */
class C33_NR : public Math::NewtonRaphsonFunctor {
public:
C33_NR(std::string name, const Real & lambda, const Real & mu,
const Matrix<Real> & C)
: NewtonRaphsonFunctor(std::move(name)), lambda(lambda), mu(mu), C(C) {}
inline Real f(Real x) const override {
return (this->lambda / 2. *
(std::log(x) + std::log(this->C(0, 0) * this->C(1, 1) -
Math::pow<2>(this->C(0, 1)))) +
this->mu * (x - 1.));
}
inline Real f_prime(Real x) const override {
AKANTU_DEBUG_ASSERT(std::abs(x) > Math::getTolerance(),
"x is zero (x should be the off plane right Cauchy"
<< " measure in this function so you made a mistake"
<< " somewhere else that lead to a zero here!!!");
return (this->lambda / (2. * x) + this->mu);
}
private:
const Real & lambda;
const Real & mu;
const Matrix<Real> & C;
};
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeThirdAxisDeformationOnQuad(
Matrix<Real> & grad_u, Real & c33_value) {
// Neo hookean book
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Math::NewtonRaphson nr(1e-5, 100);
c33_value = nr.solve(
C33_NR("Neohookean_plan_stress", this->lambda, this->mu, C), c33_value);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void
MaterialNeohookean<dim>::computePiolaKirchhoffOnQuad(const Matrix<Real> & E,
Matrix<Real> & S) {
Real trace = E.trace(); /// trace = (\nabla u)_{kk}
/// \sigma_{ij} = \lambda * (\nabla u)_{kk} * \delta_{ij} + \mu * (\nabla
/// u_{ij} + \nabla u_{ji})
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
S(i, j) = (i == j) * lambda * trace + 2.0 * mu * E(i, j);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeFirstPiolaKirchhoffOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & S, Matrix<Real> & P) {
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
// first Piola-Kirchhoff is computed as the product of the deformation
// gracient
// tensor and the second Piola-Kirchhoff stress tensor
P = F * S;
}
/**************************************************************************************/
/* Computation of the potential energy for a this neo hookean material */
template <UInt dim>
inline void MaterialNeohookean<dim>::computePotentialEnergyOnQuad(
const Matrix<Real> & grad_u, Real & epot) {
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Real J = F.det();
// std::cout<<"det(F) -> "<<J<<std::endl;
epot =
0.5 * lambda * pow(log(J), 2.) + mu * (-log(J) + 0.5 * (C.trace() - dim));
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, Matrix<Real> & grad_u, const Real & C33) {
// Neo hookean book
UInt cols = tangent.cols();
UInt rows = tangent.rows();
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim);
Matrix<Real> Cminus(dim, dim);
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Real J = F.det() * sqrt(C33);
// std::cout<<"det(F) -> "<<J<<std::endl;
Cminus.inverse(C);
for (UInt m = 0; m < rows; m++) {
UInt i = VoigtHelper<dim>::vec[m][0];
UInt j = VoigtHelper<dim>::vec[m][1];
for (UInt n = 0; n < cols; n++) {
UInt k = VoigtHelper<dim>::vec[n][0];
UInt l = VoigtHelper<dim>::vec[n][1];
// book belytchko
tangent(m, n) = lambda * Cminus(i, j) * Cminus(k, l) +
(mu - lambda * log(J)) * (Cminus(i, k) * Cminus(j, l) +
Cminus(i, l) * Cminus(k, j));
}
}
}
/* -------------------------------------------------------------------------- */
diff --git a/src/model/solid_mechanics/materials/material_non_local.hh b/src/model/solid_mechanics/materials/material_non_local.hh
index acff2d771..763a06ae4 100644
--- a/src/model/solid_mechanics/materials/material_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_non_local.hh
@@ -1,120 +1,119 @@
/**
* @file material_non_local.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Mon Sep 11 2017
*
* @brief Material class that handle the non locality of a law for example
* damage.
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_NON_LOCAL_HH__
#define __AKANTU_MATERIAL_NON_LOCAL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
class MaterialNonLocalInterface {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material the non local parts of the material
void initMaterialNonLocal() {
this->registerNeighborhood();
this->registerNonLocalVariables();
};
/// insert the quadrature points in the neighborhoods of the non-local manager
virtual void insertIntegrationPointsInNeighborhoods(
const GhostType & ghost_type,
const ElementTypeMapReal & quadrature_points_coordinates) = 0;
/// update the values in the non-local internal fields
virtual void updateNonLocalInternals(ElementTypeMapReal & non_local_flattened,
const ID & field_id,
const GhostType & ghost_type,
const ElementKind & kind) = 0;
/// constitutive law
virtual void computeNonLocalStresses(GhostType ghost_type = _not_ghost) = 0;
protected:
/// get the name of the neighborhood for this material
virtual ID getNeighborhoodName() = 0;
/// register the neighborhoods for the material
virtual void registerNeighborhood() = 0;
/// register the non local internal variable
virtual void registerNonLocalVariables() = 0;
virtual inline void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) {}
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
class MaterialNonLocal : public MaterialNonLocalInterface, public LocalParent {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit MaterialNonLocal(SolidMechanicsModel & model, const ID & id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// insert the quadrature points in the neighborhoods of the non-local manager
void insertIntegrationPointsInNeighborhoods(
const GhostType & ghost_type,
const ElementTypeMapReal & quadrature_points_coordinates) override;
/// update the values in the non-local internal fields
void updateNonLocalInternals(ElementTypeMapReal & non_local_flattened,
const ID & field_id,
const GhostType & ghost_type,
const ElementKind & kind) override;
/// register the neighborhoods for the material
void registerNeighborhood() override;
protected:
/// get the name of the neighborhood for this material
ID getNeighborhoodName() override { return this->name; }
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "material_non_local_tmpl.hh"
#endif /* __AKANTU_MATERIAL_NON_LOCAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_non_local_includes.hh b/src/model/solid_mechanics/materials/material_non_local_includes.hh
index d3b20179f..4a0c657be 100644
--- a/src/model/solid_mechanics/materials/material_non_local_includes.hh
+++ b/src/model/solid_mechanics/materials/material_non_local_includes.hh
@@ -1,40 +1,39 @@
/**
* @file material_non_local_includes.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 31 2012
- * @date last modification: Wed Nov 18 2015
+ * @date last modification: Thu Jul 06 2017
*
* @brief Non local materials includes
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_CMAKE_LIST_MATERIALS
#include "material_marigo_non_local.hh"
#include "material_mazars_non_local.hh"
#endif
#define AKANTU_DAMAGE_NON_LOCAL_MATERIAL_LIST \
((2, (marigo_non_local, MaterialMarigoNonLocal)))( \
(2, (mazars_non_local, MaterialMazarsNonLocal)))
diff --git a/src/model/solid_mechanics/materials/material_non_local_tmpl.hh b/src/model/solid_mechanics/materials/material_non_local_tmpl.hh
index ccfd93508..de6046f3c 100644
--- a/src/model/solid_mechanics/materials/material_non_local_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_non_local_tmpl.hh
@@ -1,128 +1,128 @@
/**
- * @file material_non_local.cc
+ * @file material_non_local_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Sat Sep 26 2015
- * @date last modification: Tue Dec 08 2015
+ * @date creation: Thu Jul 06 2017
+ * @date last modification: Tue Nov 07 2017
*
* @brief Implementation of material non-local
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "material_non_local.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
MaterialNonLocal<dim, LocalParent>::MaterialNonLocal(
SolidMechanicsModel & model, const ID & id)
: LocalParent(model, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
void MaterialNonLocal<dim, LocalParent>::insertIntegrationPointsInNeighborhoods(
const GhostType & ghost_type,
const ElementTypeMapReal & quadrature_points_coordinates) {
IntegrationPoint q;
q.ghost_type = ghost_type;
auto & neighborhood = this->model.getNonLocalManager().getNeighborhood(
this->getNeighborhoodName());
for (auto & type :
this->element_filter.elementTypes(dim, ghost_type, _ek_regular)) {
q.type = type;
const auto & elem_filter = this->element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element) {
UInt nb_quad =
this->getFEEngine().getNbIntegrationPoints(type, ghost_type);
const auto & quads = quadrature_points_coordinates(type, ghost_type);
auto nb_total_element =
this->model.getMesh().getNbElement(type, ghost_type);
auto quads_it = quads.begin_reinterpret(dim, nb_quad, nb_total_element);
for (auto & elem : elem_filter) {
Matrix<Real> quads = quads_it[elem];
q.element = elem;
for (UInt nq = 0; nq < nb_quad; ++nq) {
q.num_point = nq;
q.global_num = q.element * nb_quad + nq;
neighborhood.insertIntegrationPoint(q, quads(nq));
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
void MaterialNonLocal<dim, LocalParent>::updateNonLocalInternals(
ElementTypeMapReal & non_local_flattened, const ID & field_id,
const GhostType & ghost_type, const ElementKind & kind) {
/// loop over all types in the material
for (auto & el_type :
this->element_filter.elementTypes(dim, ghost_type, kind)) {
Array<Real> & internal =
this->template getInternal<Real>(field_id)(el_type, ghost_type);
auto & internal_flat = non_local_flattened(el_type, ghost_type);
auto nb_component = internal_flat.getNbComponent();
auto internal_it = internal.begin(nb_component);
auto internal_flat_it = internal_flat.begin(nb_component);
/// loop all elements for the given type
const auto & filter = this->element_filter(el_type, ghost_type);
UInt nb_quads =
this->getFEEngine().getNbIntegrationPoints(el_type, ghost_type);
for (auto & elem : filter) {
for (UInt q = 0; q < nb_quads; ++q, ++internal_it) {
UInt global_quad = elem * nb_quads + q;
*internal_it = internal_flat_it[global_quad];
}
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
void MaterialNonLocal<dim, LocalParent>::registerNeighborhood() {
ID name = this->getNeighborhoodName();
this->model.getNonLocalManager().registerNeighborhood(name, name);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
index d5db9fa1a..0e287d59c 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
@@ -1,201 +1,202 @@
/**
* @file material_linear_isotropic_hardening.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Sat Dec 02 2017
*
* @brief Specialization of the material class for isotropic finite deformation
* linear hardening plasticity
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_linear_isotropic_hardening.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialLinearIsotropicHardening<dim>::MaterialLinearIsotropicHardening(
SolidMechanicsModel & model, const ID & id)
: MaterialPlastic<dim>(model, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialLinearIsotropicHardening<spatial_dimension>::
MaterialLinearIsotropicHardening(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id)
: MaterialPlastic<spatial_dimension>(model, dim, mesh, fe_engine, id) {}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialLinearIsotropicHardening<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialThermal<spatial_dimension>::computeStress(el_type, ghost_type);
// infinitesimal and finite deformation
auto sigma_th_it = this->sigma_th(el_type, ghost_type).begin();
auto previous_sigma_th_it =
this->sigma_th.previous(el_type, ghost_type).begin();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto inelastic_strain_it = this->inelastic_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto iso_hardening_it = this->iso_hardening(el_type, ghost_type).begin();
auto previous_iso_hardening_it =
this->iso_hardening.previous(el_type, ghost_type).begin();
//
// Finite Deformations
//
if (this->finite_deformation) {
auto previous_piola_kirchhoff_2_it =
this->piola_kirchhoff_2.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto green_strain_it = this->green_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_piola_kirchhoff_2_it;
auto & green_strain = *green_strain_it;
this->template gradUToGreenStrain<spatial_dimension>(grad_u, green_strain);
Matrix<Real> previous_green_strain(spatial_dimension, spatial_dimension);
this->template gradUToGreenStrain<spatial_dimension>(previous_grad_u,
previous_green_strain);
Matrix<Real> F_tensor(spatial_dimension, spatial_dimension);
this->template gradUToF<spatial_dimension>(grad_u, F_tensor);
computeStressOnQuad(green_strain, previous_green_strain, sigma,
previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it,
*previous_sigma_th_it, F_tensor);
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
//++previous_stress_it;
++previous_gradu_it;
++green_strain_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
++previous_piola_kirchhoff_2_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
// Infinitesimal deformations
else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_stress_it;
computeStressOnQuad(
grad_u, previous_grad_u, sigma, previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it, *previous_sigma_th_it);
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
++previous_stress_it;
++previous_gradu_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialLinearIsotropicHardening<spatial_dimension>::computeTangentModuli(
const ElementType & el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto iso_hardening = this->iso_hardening(el_type, ghost_type).begin();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u, *previous_gradu_it, sigma_tensor,
*previous_stress_it, *iso_hardening);
++previous_gradu_it;
++previous_stress_it;
++iso_hardening;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(plastic_linear_isotropic_hardening,
MaterialLinearIsotropicHardening);
} // akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
index 78aa000cd..dea48f6b9 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
@@ -1,113 +1,113 @@
/**
* @file material_linear_isotropic_hardening.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Jun 01 2015
+ * @date last modification: Sat Dec 02 2017
*
* @brief Specialization of the material class for isotropic finite deformation
* linear hardening plasticity
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH__
#define __AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH__
namespace akantu {
/**
* Material plastic with a linear evolution of the yielding stress
*/
template <UInt spatial_dimension>
class MaterialLinearIsotropicHardening
: public MaterialPlastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialLinearIsotropicHardening(SolidMechanicsModel & model,
const ID & id = "");
MaterialLinearIsotropicHardening(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
protected:
/// Infinitesimal deformations
inline void computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelas_strain, const Matrix<Real> & previous_inelas_strain,
Real & iso_hardening, const Real & previous_iso_hardening,
const Real & sigma_th, const Real & previous_sigma_th);
/// Finite deformations
inline void computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelas_strain, const Matrix<Real> & previous_inelas_strain,
Real & iso_hardening, const Real & previous_iso_hardening,
const Real & sigma_th, const Real & previous_sigma_th,
const Matrix<Real> & F_tensor);
inline void computeTangentModuliOnQuad(
Matrix<Real> & tangent, const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u, const Matrix<Real> & sigma_tensor,
const Matrix<Real> & previous_sigma_tensor,
const Real & iso_hardening) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // akantu
#include "material_linear_isotropic_hardening_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.cc b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.cc
index 8fb7dbff4..06bb421f4 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.cc
@@ -1,297 +1,298 @@
/**
* @file material_linear_isotropic_hardening_inline_impl.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
- * @date last modification: Fri May 29 2015
+ * @date last modification: Thu Nov 30 2017
*
* @brief Implementation of the inline functions of the material plasticity
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "material_linear_isotropic_hardening.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/// Infinitesimal deformations
template <UInt dim>
inline void MaterialLinearIsotropicHardening<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain, Real & iso_hardening,
const Real & previous_iso_hardening, const Real & sigma_th,
const Real & previous_sigma_th) {
Real delta_sigma_th = sigma_th - previous_sigma_th;
Matrix<Real> grad_delta_u(grad_u);
grad_delta_u -= previous_grad_u;
// Compute trial stress, sigma_tr
Matrix<Real> sigma_tr(dim, dim);
MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr,
delta_sigma_th);
sigma_tr += previous_sigma;
// We need a full stress tensor, otherwise the VM stress is messed up
Matrix<Real> sigma_tr_dev(3, 3, 0);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
sigma_tr_dev(i, j) = sigma_tr(i, j);
sigma_tr_dev -= Matrix<Real>::eye(3, sigma_tr.trace() / 3.0);
// Compute effective deviatoric trial stress
Real s = sigma_tr_dev.doubleDot(sigma_tr_dev);
Real sigma_tr_dev_eff = std::sqrt(3. / 2. * s);
bool initial_yielding =
((sigma_tr_dev_eff - iso_hardening - this->sigma_y) > 0);
Real dp = (initial_yielding)
? (sigma_tr_dev_eff - this->sigma_y - previous_iso_hardening) /
(3 * this->mu + this->h)
: 0;
iso_hardening = previous_iso_hardening + this->h * dp;
// Compute inelastic strain (ignore last components in 1-2D)
Matrix<Real> delta_inelastic_strain(dim, dim, 0.);
if (std::abs(sigma_tr_dev_eff) >
sigma_tr_dev.norm<L_inf>() * Math::getTolerance()) {
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
delta_inelastic_strain(i, j) = sigma_tr_dev(i, j);
delta_inelastic_strain *= 3. / 2. * dp / sigma_tr_dev_eff;
}
MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
grad_delta_u, sigma, previous_sigma, inelastic_strain,
previous_inelastic_strain, delta_inelastic_strain);
}
/* -------------------------------------------------------------------------- */
/// Finite deformations
template <UInt dim>
inline void MaterialLinearIsotropicHardening<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain, Real & iso_hardening,
const Real & previous_iso_hardening, const Real & sigma_th,
const Real & previous_sigma_th, const Matrix<Real> & F_tensor) {
// Finite plasticity
Real dp = 0.0;
Real d_dp = 0.0;
UInt n = 0;
Real delta_sigma_th = sigma_th - previous_sigma_th;
Matrix<Real> grad_delta_u(grad_u);
grad_delta_u -= previous_grad_u;
// Compute trial stress, sigma_tr
Matrix<Real> sigma_tr(dim, dim);
MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr,
delta_sigma_th);
sigma_tr += previous_sigma;
// Compute deviatoric trial stress, sigma_tr_dev
Matrix<Real> sigma_tr_dev(sigma_tr);
sigma_tr_dev -= Matrix<Real>::eye(dim, sigma_tr.trace() / 3.0);
// Compute effective deviatoric trial stress
Real s = sigma_tr_dev.doubleDot(sigma_tr_dev);
Real sigma_tr_dev_eff = std::sqrt(3. / 2. * s);
// compute the cauchy stress to apply the Von-Mises criterion
Matrix<Real> cauchy_stress(dim, dim);
Material::computeCauchyStressOnQuad<dim>(F_tensor, sigma_tr, cauchy_stress);
Matrix<Real> cauchy_stress_dev(cauchy_stress);
cauchy_stress_dev -= Matrix<Real>::eye(dim, cauchy_stress.trace() / 3.0);
Real c = cauchy_stress_dev.doubleDot(cauchy_stress_dev);
Real cauchy_stress_dev_eff = std::sqrt(3. / 2. * c);
const Real iso_hardening_t = previous_iso_hardening;
iso_hardening = iso_hardening_t;
// Loop for correcting stress based on yield function
// F is written in terms of S
// bool initial_yielding = ( (sigma_tr_dev_eff - iso_hardening -
// this->sigma_y) > 0) ;
// while ( initial_yielding && std::abs(sigma_tr_dev_eff - iso_hardening -
// this->sigma_y) > Math::getTolerance() ) {
// d_dp = (sigma_tr_dev_eff - 3. * this->mu *dp - iso_hardening -
// this->sigma_y)
// / (3. * this->mu + this->h);
// //r = r + h * dp;
// dp = dp + d_dp;
// iso_hardening = iso_hardening_t + this->h * dp;
// ++n;
// /// TODO : explicit this criterion with an error message
// if ((std::abs(d_dp) < 1e-9) || (n>50)){
// AKANTU_DEBUG_INFO("convergence of increment of plastic strain. d_dp:"
// << d_dp << "\tNumber of iteration:"<<n);
// break;
// }
// }
// F is written in terms of cauchy stress
bool initial_yielding =
((cauchy_stress_dev_eff - iso_hardening - this->sigma_y) > 0);
while (initial_yielding &&
std::abs(cauchy_stress_dev_eff - iso_hardening - this->sigma_y) >
Math::getTolerance()) {
d_dp = (cauchy_stress_dev_eff - 3. * this->mu * dp - iso_hardening -
this->sigma_y) /
(3. * this->mu + this->h);
// r = r + h * dp;
dp = dp + d_dp;
iso_hardening = iso_hardening_t + this->h * dp;
++n;
/// TODO : explicit this criterion with an error message
if ((d_dp < 1e-5) || (n > 50)) {
AKANTU_DEBUG_INFO("convergence of increment of plastic strain. d_dp:"
<< d_dp << "\tNumber of iteration:" << n);
break;
}
}
// Update internal variable
Matrix<Real> delta_inelastic_strain(dim, dim, 0.);
if (std::abs(sigma_tr_dev_eff) >
sigma_tr_dev.norm<L_inf>() * Math::getTolerance()) {
// /// compute the direction of the plastic strain as \frac{\partial
// F}{\partial S} = \frac{3}{2J\sigma_{effective}}} Ft \sigma_{dev} F
Matrix<Real> cauchy_dev_F(dim, dim);
cauchy_dev_F.mul<false, false>(F_tensor, cauchy_stress_dev);
Real J = F_tensor.det();
Real constant = J ? 1. / J : 0;
constant *= 3. * dp / (2. * cauchy_stress_dev_eff);
delta_inelastic_strain.mul<true, false>(F_tensor, cauchy_dev_F, constant);
// Direction given by the piola kirchhoff deviatoric tensor \frac{\partial
// F}{\partial S} = \frac{3}{2\sigma_{effective}}}S_{dev}
// delta_inelastic_strain.copy(sigma_tr_dev);
// delta_inelastic_strain *= 3./2. * dp / sigma_tr_dev_eff;
}
MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
grad_delta_u, sigma, previous_sigma, inelastic_strain,
previous_inelastic_strain, delta_inelastic_strain);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialLinearIsotropicHardening<dim>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, __attribute__((unused)) const Matrix<Real> & grad_u,
__attribute__((unused)) const Matrix<Real> & previous_grad_u,
__attribute__((unused)) const Matrix<Real> & sigma_tensor,
__attribute__((unused)) const Matrix<Real> & previous_sigma_tensor,
__attribute__((unused)) const Real & iso_hardening) const {
// Real r=iso_hardening;
// Matrix<Real> grad_delta_u(grad_u);
// grad_delta_u -= previous_grad_u;
// //Compute trial stress, sigma_tr
// Matrix<Real> sigma_tr(dim, dim);
// MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr);
// sigma_tr += previous_sigma_tensor;
// // Compute deviatoric trial stress, sigma_tr_dev
// Matrix<Real> sigma_tr_dev(sigma_tr);
// sigma_tr_dev -= Matrix<Real>::eye(dim, sigma_tr.trace() / 3.0);
// // Compute effective deviatoric trial stress
// Real s = sigma_tr_dev.doubleDot(sigma_tr_dev);
// Real sigma_tr_dev_eff=std::sqrt(3./2. * s);
// // Compute deviatoric stress, sigma_dev
// Matrix<Real> sigma_dev(sigma_tensor);
// sigma_dev -= Matrix<Real>::eye(dim, sigma_tensor.trace() / 3.0);
// // Compute effective deviatoric stress
// s = sigma_dev.doubleDot(sigma_dev);
// Real sigma_dev_eff = std::sqrt(3./2. * s);
// Real xr = 0.0;
// if(sigma_tr_dev_eff > sigma_dev_eff * Math::getTolerance())
// xr = sigma_dev_eff / sigma_tr_dev_eff;
// Real __attribute__((unused)) q = 1.5 * (1. / (1. + 3. * this->mu /
// this->h) - xr);
/*
UInt cols = tangent.cols();
UInt rows = tangent.rows();
for (UInt m = 0; m < rows; ++m) {
UInt i = VoigtHelper<dim>::vec[m][0];
UInt j = VoigtHelper<dim>::vec[m][1];
for (UInt n = 0; n < cols; ++n) {
UInt k = VoigtHelper<dim>::vec[n][0];
UInt l = VoigtHelper<dim>::vec[n][1];
*/
// This section of the code is commented
// There were some problems with the convergence of plastic-coupled
// simulations with thermal expansion
// XXX: DO NOT REMOVE
/*if (((sigma_tr_dev_eff-iso_hardening-sigmay) > 0) && (xr > 0)) {
tangent(m,n) =
2. * this->mu * q * (sigma_tr_dev (i,j) / sigma_tr_dev_eff) * (sigma_tr_dev
(k,l) / sigma_tr_dev_eff) +
(i==k) * (j==l) * 2. * this->mu * xr +
(i==j) * (k==l) * (this->kpa - 2./3. * this->mu * xr);
if ((m == n) && (m>=dim))
tangent(m, n) = tangent(m, n) - this->mu * xr;
} else {*/
/*
tangent(m,n) = (i==k) * (j==l) * 2. * this->mu +
(i==j) * (k==l) * this->lambda;
tangent(m,n) -= (m==n) * (m>=dim) * this->mu;
*/
//}
// correct tangent stiffness for shear component
//}
//}
MaterialElastic<dim>::computeTangentModuliOnQuad(tangent);
}
} // akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc b/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
index bfe07f012..1032eab13 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
@@ -1,209 +1,209 @@
/**
* @file material_plastic.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Implemantation of the akantu::MaterialPlastic class
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialPlastic<spatial_dimension>::MaterialPlastic(SolidMechanicsModel & model,
const ID & id)
: MaterialElastic<spatial_dimension>(model, id),
iso_hardening("iso_hardening", *this),
inelastic_strain("inelastic_strain", *this),
plastic_energy("plastic_energy", *this),
d_plastic_energy("d_plastic_energy", *this) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
template <UInt spatial_dimension>
MaterialPlastic<spatial_dimension>::MaterialPlastic(SolidMechanicsModel & model,
UInt dim, const Mesh & mesh,
FEEngine & fe_engine,
const ID & id)
: MaterialElastic<spatial_dimension>(model, dim, mesh, fe_engine, id),
iso_hardening("iso_hardening", *this, dim, fe_engine,
this->element_filter),
inelastic_strain("inelastic_strain", *this, dim, fe_engine,
this->element_filter),
plastic_energy("plastic_energy", *this, dim, fe_engine,
this->element_filter),
d_plastic_energy("d_plastic_energy", *this, dim, fe_engine,
this->element_filter) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::initialize() {
this->registerParam("h", h, Real(0.), _pat_parsable | _pat_modifiable,
"Hardening modulus");
this->registerParam("sigma_y", sigma_y, Real(0.),
_pat_parsable | _pat_modifiable, "Yield stress");
this->iso_hardening.initialize(1);
this->iso_hardening.initializeHistory();
this->plastic_energy.initialize(1);
this->d_plastic_energy.initialize(1);
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->use_previous_stress_thermal = true;
this->inelastic_strain.initialize(spatial_dimension * spatial_dimension);
this->inelastic_strain.initializeHistory();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialPlastic<spatial_dimension>::getEnergy(const std::string & type) {
if (type == "plastic")
return getPlasticEnergy();
else
return MaterialElastic<spatial_dimension>::getEnergy(type);
return 0.;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialPlastic<spatial_dimension>::getPlasticEnergy() {
AKANTU_DEBUG_IN();
Real penergy = 0.;
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
penergy +=
this->fem.integrate(plastic_energy(type, _not_ghost), type, _not_ghost,
this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return penergy;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::computePotentialEnergy(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (ghost_type != _not_ghost)
return;
Array<Real>::scalar_iterator epot =
this->potential_energy(el_type, ghost_type).begin();
Array<Real>::const_iterator<Matrix<Real>> inelastic_strain_it =
this->inelastic_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> elastic_strain(spatial_dimension, spatial_dimension);
elastic_strain.copy(grad_u);
elastic_strain -= *inelastic_strain_it;
MaterialElastic<spatial_dimension>::computePotentialEnergyOnQuad(
elastic_strain, sigma, *epot);
++epot;
++inelastic_strain_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::updateEnergies(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialElastic<spatial_dimension>::updateEnergies(el_type, ghost_type);
Array<Real>::iterator<> pe_it =
this->plastic_energy(el_type, ghost_type).begin();
Array<Real>::iterator<> wp_it =
this->d_plastic_energy(el_type, ghost_type).begin();
Array<Real>::iterator<Matrix<Real>> inelastic_strain_it =
this->inelastic_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
Array<Real>::iterator<Matrix<Real>> previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator previous_sigma =
this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> delta_strain_it(*inelastic_strain_it);
delta_strain_it -= *previous_inelastic_strain_it;
Matrix<Real> sigma_h(sigma);
sigma_h += *previous_sigma;
*wp_it = .5 * sigma_h.doubleDot(delta_strain_it);
*pe_it += *wp_it;
++pe_it;
++wp_it;
++inelastic_strain_it;
++previous_inelastic_strain_it;
++previous_sigma;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL_ONLY(MaterialPlastic);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh b/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
index 1b1b2749b..36ac049c8 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
@@ -1,130 +1,130 @@
/**
* @file material_plastic.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 08 2015
+ * @date last modification: Thu Dec 07 2017
*
* @brief Common interface for plastic materials
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_PLASTIC_HH__
#define __AKANTU_MATERIAL_PLASTIC_HH__
namespace akantu {
/**
* Parent class for the plastic constitutive laws
* parameters in the material files :
* - h : Hardening parameter (default: 0)
* - sigmay : Yield stress
*/
template <UInt dim> class MaterialPlastic : public MaterialElastic<dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialPlastic(SolidMechanicsModel & model, const ID & id = "");
MaterialPlastic(SolidMechanicsModel & model, UInt a_dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the energy specifying the type for the time step
Real getEnergy(const std::string & type) override;
/// Compute the plastic energy
void updateEnergies(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// Compute the true potential energy
void computePotentialEnergy(ElementType el_type,
GhostType ghost_type) override;
protected:
/// compute the stress and inelastic strain for the quadrature point
inline void computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelas_strain, const Matrix<Real> & previous_inelas_strain,
const Matrix<Real> & delta_inelastic_strain) const;
inline void computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & delta_grad_u, Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma, Matrix<Real> & inelas_strain,
const Matrix<Real> & previous_inelas_strain,
const Matrix<Real> & delta_inelastic_strain) const;
/// get the plastic energy for the time step
Real getPlasticEnergy();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Yield stresss
Real sigma_y;
/// hardening modulus
Real h;
/// isotropic hardening, r
InternalField<Real> iso_hardening;
/// inelastic strain arrays ordered by element types (inelastic deformation)
InternalField<Real> inelastic_strain;
/// Plastic energy
InternalField<Real> plastic_energy;
/// @todo : add a coefficient beta that will multiply the plastic energy
/// increment
/// to compute the energy converted to heat
/// Plastic energy increment
InternalField<Real> d_plastic_energy;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // akantu
#include "material_plastic_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_PLASTIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.cc b/src/model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.cc
index 1c8172c80..f70afb3a2 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.cc
@@ -1,75 +1,76 @@
/**
* @file material_plastic_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: Mon Apr 07 2014
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Wed Jan 24 2018
*
* @brief Implementation of the inline functions of akantu::MaterialPlastic
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef MATERIAL_PLASTIC_INLINE_IMPL_H
#define MATERIAL_PLASTIC_INLINE_IMPL_H
#include "material_plastic.hh"
namespace akantu {
template <UInt dim>
inline void MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & delta_grad_u, Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma, Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain,
const Matrix<Real> & delta_inelastic_strain) const {
Matrix<Real> grad_u_elastic(dim, dim);
grad_u_elastic.copy(delta_grad_u);
grad_u_elastic -= delta_inelastic_strain;
Matrix<Real> sigma_elastic(dim, dim);
MaterialElastic<dim>::computeStressOnQuad(grad_u_elastic, sigma_elastic);
sigma.copy(previous_sigma);
sigma += sigma_elastic;
inelastic_strain.copy(previous_inelastic_strain);
inelastic_strain += delta_inelastic_strain;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain,
const Matrix<Real> & delta_inelastic_strain) const {
Matrix<Real> delta_grad_u(grad_u);
delta_grad_u -= previous_grad_u;
computeStressAndInelasticStrainOnQuad(
delta_grad_u, sigma, previous_sigma, inelastic_strain,
previous_inelastic_strain, delta_inelastic_strain);
}
} // Akantu
#endif /* MATERIAL_PLASTIC_INLINE_IMPL_H */
diff --git a/src/model/solid_mechanics/materials/material_python/material_python.cc b/src/model/solid_mechanics/materials/material_python/material_python.cc
index 3c3087c87..c48b3ae85 100644
--- a/src/model/solid_mechanics/materials/material_python/material_python.cc
+++ b/src/model/solid_mechanics/materials/material_python/material_python.cc
@@ -1,214 +1,215 @@
/**
* @file material_python.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Nov 13 2015
- * @date last modification: Fri Nov 13 2015
+ * @date last modification: Wed Feb 07 2018
*
* @brief Material python implementation
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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_python.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MaterialPython::MaterialPython(SolidMechanicsModel & model, PyObject * obj,
const ID & id)
: Material(model, id), PythonFunctor(obj) {
AKANTU_DEBUG_IN();
this->registerInternals();
std::vector<std::string> param_names =
this->callFunctor<std::vector<std::string>>("registerParam");
for (UInt i = 0; i < param_names.size(); ++i) {
std::stringstream sstr;
sstr << "PythonParameter" << i;
this->registerParam(param_names[i], local_params[param_names[i]], 0.,
_pat_parsable | _pat_readable, sstr.str());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialPython::registerInternals() {
std::vector<std::string> internal_names =
this->callFunctor<std::vector<std::string>>("registerInternals");
std::vector<UInt> internal_sizes;
try {
internal_sizes =
this->callFunctor<std::vector<UInt>>("registerInternalSizes");
} catch (...) {
internal_sizes.assign(internal_names.size(), 1);
}
for (UInt i = 0; i < internal_names.size(); ++i) {
std::stringstream sstr;
sstr << "PythonInternal" << i;
this->internals[internal_names[i]] =
std::make_unique<InternalField<Real>>(internal_names[i], *this);
AKANTU_DEBUG_INFO("alloc internal " << internal_names[i] << " "
<< &this->internals[internal_names[i]]);
this->internals[internal_names[i]]->initialize(internal_sizes[i]);
}
// making an internal with the quadrature points coordinates
this->internals["quad_coordinates"] =
std::make_unique<InternalField<Real>>("quad_coordinates", *this);
auto && coords = *this->internals["quad_coordinates"];
coords.initialize(this->getSpatialDimension());
}
/* -------------------------------------------------------------------------- */
void MaterialPython::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
auto && coords = *this->internals["quad_coordinates"];
this->model.getFEEngine().computeIntegrationPointsCoordinates(
coords, &this->element_filter);
auto params = local_params;
params["rho"] = this->rho;
try {
this->callFunctor<void>("initMaterial", this->internals, params);
} catch (...) {
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialPython::computeStress(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto params = local_params;
params["rho"] = this->rho;
std::map<std::string, Array<Real> *> internal_arrays;
for (auto & i : this->internals) {
auto & array = (*i.second)(el_type, ghost_type);
auto & name = i.first;
internal_arrays[name] = &array;
}
this->callFunctor<void>("computeStress", this->gradu(el_type, ghost_type),
this->stress(el_type, ghost_type), internal_arrays,
params);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialPython::computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type) {
auto params = local_params;
params["rho"] = this->rho;
std::map<std::string, Array<Real> *> internal_arrays;
for (auto & i : this->internals) {
auto & array = (*i.second)(el_type, ghost_type);
auto & name = i.first;
internal_arrays[name] = &array;
}
this->callFunctor<void>("computeTangentModuli",
this->gradu(el_type, ghost_type), tangent_matrix,
internal_arrays, params);
}
/* -------------------------------------------------------------------------- */
Real MaterialPython::getPushWaveSpeed(const Element &) const {
auto params = local_params;
params["rho"] = this->rho;
return this->callFunctor<Real>("getPushWaveSpeed", params);
}
/* -------------------------------------------------------------------------- */
Real MaterialPython::getEnergyForType(const std::string & type,
ElementType el_type) {
AKANTU_DEBUG_IN();
std::map<std::string, Array<Real> *> internal_arrays;
for (auto & i : this->internals) {
auto & array = (*i.second)(el_type, _not_ghost);
auto & name = i.first;
internal_arrays[name] = &array;
}
auto params = local_params;
params["rho"] = this->rho;
auto & energy_density = *internal_arrays[type];
this->callFunctor<void>("getEnergyDensity", type, energy_density,
this->gradu(el_type, _not_ghost),
this->stress(el_type, _not_ghost), internal_arrays,
params);
Real energy = fem.integrate(energy_density, el_type, _not_ghost,
element_filter(el_type, _not_ghost));
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real MaterialPython::getEnergy(const std::string & type) {
AKANTU_DEBUG_IN();
if (this->internals.find(type) == this->internals.end()) {
AKANTU_EXCEPTION("unknown energy type: "
<< type << " you must declare an internal named " << type);
}
Real energy = 0.;
/// 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) {
energy += this->getEnergyForType(type, *it);
}
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/solid_mechanics/materials/material_python/material_python.hh b/src/model/solid_mechanics/materials/material_python/material_python.hh
index e675b338b..a16c88b1e 100644
--- a/src/model/solid_mechanics/materials/material_python/material_python.hh
+++ b/src/model/solid_mechanics/materials/material_python/material_python.hh
@@ -1,97 +1,98 @@
/**
* @file material_python.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Nov 13 2015
- * @date last modification: Fri Nov 13 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Tue Feb 06 2018
*
* @brief Python material
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/**
* @file material_python.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
*/
/* -------------------------------------------------------------------------- */
#include "python_functor.hh"
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_PYTHON_HH__
#define __AKANTU_MATERIAL_PYTHON_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class MaterialPython : public Material, PythonFunctor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialPython(SolidMechanicsModel & model, PyObject * obj,
const ID & id = "");
~MaterialPython() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void registerInternals();
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the push wave speed of the material
Real getPushWaveSpeed(const Element & element) const override;
/// compute an energy of the material
Real getEnergy(const std::string & type) override;
/// compute an energy of the material
Real getEnergyForType(const std::string & type, ElementType el_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
std::map<std::string, Real> local_params;
std::map<std::string, std::unique_ptr<InternalField<Real>>> internals;
};
} // akantu
#endif /* __AKANTU_MATERIAL_PYTHON_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_thermal.cc b/src/model/solid_mechanics/materials/material_thermal.cc
index 70222c54f..22a29b48d 100644
--- a/src/model/solid_mechanics/materials/material_thermal.cc
+++ b/src/model/solid_mechanics/materials/material_thermal.cc
@@ -1,111 +1,110 @@
/**
* @file material_thermal.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Aug 04 2015
+ * @date last modification: Mon Jan 29 2018
*
* @brief Specialization of the material class for the thermal material
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_thermal.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialThermal<spatial_dimension>::MaterialThermal(SolidMechanicsModel & model,
const ID & id)
: Material(model, id), delta_T("delta_T", *this),
sigma_th("sigma_th", *this), use_previous_stress_thermal(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialThermal<spatial_dimension>::MaterialThermal(SolidMechanicsModel & model,
UInt dim, const Mesh & mesh,
FEEngine & fe_engine,
const ID & id)
: Material(model, dim, mesh, fe_engine, id),
delta_T("delta_T", *this, dim, fe_engine, this->element_filter),
sigma_th("sigma_th", *this, dim, fe_engine, this->element_filter),
use_previous_stress_thermal(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
template <UInt spatial_dimension>
void MaterialThermal<spatial_dimension>::initialize() {
this->registerParam("E", E, Real(0.), _pat_parsable | _pat_modifiable,
"Young's modulus");
this->registerParam("nu", nu, Real(0.5), _pat_parsable | _pat_modifiable,
"Poisson's ratio");
this->registerParam("alpha", alpha, Real(0.), _pat_parsable | _pat_modifiable,
"Thermal expansion coefficient");
this->registerParam("delta_T", delta_T, _pat_parsable | _pat_modifiable,
"Uniform temperature field");
delta_T.initialize(1);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialThermal<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
sigma_th.initialize(1);
if (use_previous_stress_thermal) {
sigma_th.initializeHistory();
}
Material::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialThermal<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
for (auto && tuple : zip(this->delta_T(el_type, ghost_type),
this->sigma_th(el_type, ghost_type))) {
computeStressOnQuad(std::get<1>(tuple), std::get<0>(tuple));
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL_ONLY(MaterialThermal);
} // akantu
diff --git a/src/model/solid_mechanics/materials/material_thermal.hh b/src/model/solid_mechanics/materials/material_thermal.hh
index ee1a0fe94..d7e1d3555 100644
--- a/src/model/solid_mechanics/materials/material_thermal.hh
+++ b/src/model/solid_mechanics/materials/material_thermal.hh
@@ -1,108 +1,107 @@
/**
* @file material_thermal.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Mon Jan 29 2018
*
* @brief Material isotropic thermo-elastic
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_THERMAL_HH__
#define __AKANTU_MATERIAL_THERMAL_HH__
namespace akantu {
template <UInt spatial_dimension> class MaterialThermal : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialThermal(SolidMechanicsModel & model, const ID & id = "");
MaterialThermal(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
~MaterialThermal() override = default;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type) override;
/// local computation of thermal stress
inline void computeStressOnQuad(Real & sigma, const Real & deltaT);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Young modulus
Real E;
/// Poisson ratio
Real nu;
/// Thermal expansion coefficient
/// TODO : implement alpha as a matrix
Real alpha;
/// Temperature field
InternalField<Real> delta_T;
/// Current thermal stress
InternalField<Real> sigma_th;
/// Tell if we need to use the previous thermal stress
bool use_previous_stress_thermal;
};
/* ------------------------------------------------------------------------ */
/* Inline impl */
/* ------------------------------------------------------------------------ */
template <UInt dim>
inline void MaterialThermal<dim>::computeStressOnQuad(Real & sigma,
const Real & deltaT) {
sigma = -this->E / (1. - 2. * this->nu) * this->alpha * deltaT;
}
template <>
inline void MaterialThermal<1>::computeStressOnQuad(Real & sigma,
const Real & deltaT) {
sigma = -this->E * this->alpha * deltaT;
}
} // akantu
#endif /* __AKANTU_MATERIAL_THERMAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
index f21887a1b..e103076ac 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
@@ -1,325 +1,324 @@
/**
* @file material_standard_linear_solid_deviatoric.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Vladislav Yastrebov <vladislav.yastrebov@epfl.ch>
*
* @date creation: Wed May 04 2011
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Material Visco-elastic
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_standard_linear_solid_deviatoric.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialStandardLinearSolidDeviatoric<spatial_dimension>::
MaterialStandardLinearSolidDeviatoric(SolidMechanicsModel & model,
const ID & id)
: MaterialElastic<spatial_dimension>(model, id),
stress_dev("stress_dev", *this),
history_integral("history_integral", *this),
dissipated_energy("dissipated_energy", *this) {
AKANTU_DEBUG_IN();
this->registerParam("Eta", eta, Real(1.), _pat_parsable | _pat_modifiable,
"Viscosity");
this->registerParam("Ev", Ev, Real(1.), _pat_parsable | _pat_modifiable,
"Stiffness of the viscous element");
this->registerParam("Einf", E_inf, Real(1.), _pat_readable,
"Stiffness of the elastic element");
UInt stress_size = spatial_dimension * spatial_dimension;
this->stress_dev.initialize(stress_size);
this->history_integral.initialize(stress_size);
this->dissipated_energy.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
updateInternalParameters();
MaterialElastic<spatial_dimension>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<
spatial_dimension>::updateInternalParameters() {
MaterialElastic<spatial_dimension>::updateInternalParameters();
E_inf = this->E - this->Ev;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<spatial_dimension>::setToSteadyState(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d =
stress_dev_vect.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator history_int =
history_int_vect.begin(spatial_dimension, spatial_dimension);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
/// Compute the first invariant of strain
Real Theta = grad_u.trace();
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j) {
dev_s(i, j) = 2 * this->mu * (.5 * (grad_u(i, j) + grad_u(j, i)) -
1. / 3. * Theta * (i == j));
h(i, j) = 0.;
}
/// Save the deviator of stress
++stress_d;
++history_int;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real tau = 0.;
// if(std::abs(Ev) > std::numeric_limits<Real>::epsilon())
tau = eta / Ev;
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d =
stress_dev_vect.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator history_int =
history_int_vect.begin(spatial_dimension, spatial_dimension);
Matrix<Real> s(spatial_dimension, spatial_dimension);
Real dt = this->model.getTimeStep();
Real exp_dt_tau = exp(-dt / tau);
Real exp_dt_tau_2 = exp(-.5 * dt / tau);
Matrix<Real> epsilon_d(spatial_dimension, spatial_dimension);
Matrix<Real> epsilon_v(spatial_dimension, spatial_dimension);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
s.clear();
sigma.clear();
/// Compute the first invariant of strain
Real gamma_inf = E_inf / this->E;
Real gamma_v = Ev / this->E;
this->template gradUToEpsilon<spatial_dimension>(grad_u, epsilon_d);
Real Theta = epsilon_d.trace();
epsilon_v.eye(Theta / Real(3.));
epsilon_d -= epsilon_v;
Matrix<Real> U_rond_prim(spatial_dimension, spatial_dimension);
U_rond_prim.eye(gamma_inf * this->kpa * Theta);
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j) {
s(i, j) = 2 * this->mu * epsilon_d(i, j);
h(i, j) = exp_dt_tau * h(i, j) + exp_dt_tau_2 * (s(i, j) - dev_s(i, j));
dev_s(i, j) = s(i, j);
sigma(i, j) = U_rond_prim(i, j) + gamma_inf * s(i, j) + gamma_v * h(i, j);
}
/// Save the deviator of stress
++stress_d;
++history_int;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
this->updateDissipatedEnergy(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<
spatial_dimension>::updateDissipatedEnergy(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
// if(ghost_type == _ghost) return 0.;
Real tau = 0.;
tau = eta / Ev;
Real * dis_energy = dissipated_energy(el_type, ghost_type).storage();
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d =
stress_dev_vect.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator history_int =
history_int_vect.begin(spatial_dimension, spatial_dimension);
Matrix<Real> q(spatial_dimension, spatial_dimension);
Matrix<Real> q_rate(spatial_dimension, spatial_dimension);
Matrix<Real> epsilon_d(spatial_dimension, spatial_dimension);
Matrix<Real> epsilon_v(spatial_dimension, spatial_dimension);
Real dt = this->model.getTimeStep();
Real gamma_v = Ev / this->E;
Real alpha = 1. / (2. * this->mu * gamma_v);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
/// Compute the first invariant of strain
this->template gradUToEpsilon<spatial_dimension>(grad_u, epsilon_d);
Real Theta = epsilon_d.trace();
epsilon_v.eye(Theta / Real(3.));
epsilon_d -= epsilon_v;
q.copy(dev_s);
q -= h;
q *= gamma_v;
q_rate.copy(dev_s);
q_rate *= gamma_v;
q_rate -= q;
q_rate /= tau;
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j)
*dis_energy += (epsilon_d(i, j) - alpha * q(i, j)) * q_rate(i, j) * dt;
/// Save the deviator of stress
++stress_d;
++history_int;
++dis_energy;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialStandardLinearSolidDeviatoric<
spatial_dimension>::getDissipatedEnergy() const {
AKANTU_DEBUG_IN();
Real de = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
de +=
this->fem.integrate(dissipated_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialStandardLinearSolidDeviatoric<
spatial_dimension>::getDissipatedEnergy(ElementType type,
UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
auto it =
this->dissipated_energy(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->fem.integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialStandardLinearSolidDeviatoric<spatial_dimension>::getEnergy(
const std::string & type) {
if (type == "dissipated")
return getDissipatedEnergy();
else if (type == "dissipated_sls_deviatoric")
return getDissipatedEnergy();
else
return MaterialElastic<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialStandardLinearSolidDeviatoric<spatial_dimension>::getEnergy(
const std::string & energy_id, ElementType type, UInt index) {
if (energy_id == "dissipated")
return getDissipatedEnergy(type, index);
else if (energy_id == "dissipated_sls_deviatoric")
return getDissipatedEnergy(type, index);
else
return MaterialElastic<spatial_dimension>::getEnergy(energy_id, type,
index);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(sls_deviatoric, MaterialStandardLinearSolidDeviatoric);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
index a5a70a7ff..6b39c6d49 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
@@ -1,136 +1,135 @@
/**
* @file material_standard_linear_solid_deviatoric.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Vladislav Yastrebov <vladislav.yastrebov@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 08 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Material Visco-elastic, based on Standard Solid rheological model,
* see
* [] J.C. Simo, T.J.R. Hughes, "Computational Inelasticity", Springer (1998),
* see Sections 10.2 and 10.3
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH__
#define __AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH__
namespace akantu {
/**
* Material standard linear solid deviatoric
*
*
* @verbatim
E_\inf
------|\/\/\|------
| |
---| |---
| |
----|\/\/\|--[|----
E_v \eta
@endverbatim
*
* keyword : sls_deviatoric
*
* parameters in the material files :
* - E : Initial Young's modulus @f$ E = E_i + E_v @f$
* - eta : viscosity
* - Ev : stiffness of the viscous element
*/
template <UInt spatial_dimension>
class MaterialStandardLinearSolidDeviatoric
: public MaterialElastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialStandardLinearSolidDeviatoric(SolidMechanicsModel & model,
const ID & id = "");
~MaterialStandardLinearSolidDeviatoric() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// update the internal parameters (for modifiable parameters)
void updateInternalParameters() override;
/// set material to steady state
void setToSteadyState(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// update the dissipated energy, is called after the stress have been
/// computed
void updateDissipatedEnergy(ElementType el_type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy for the time step
Real getDissipatedEnergy() const;
Real getDissipatedEnergy(ElementType type, UInt index) const;
/// get the energy using an energy type string for the time step
Real getEnergy(const std::string & type) override;
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// viscosity, viscous elastic modulus
Real eta, Ev, E_inf;
/// history of deviatoric stress
InternalField<Real> stress_dev;
/// Internal variable: history integral
InternalField<Real> history_integral;
/// Dissipated energy
InternalField<Real> dissipated_energy;
};
} // namespace akantu
#endif /* __AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
index 1387b8f97..00c017adc 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
@@ -1,102 +1,103 @@
/**
* @file plane_stress_toolbox.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 16 2014
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Tools to implement the plane stress behavior in a material
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PLANE_STRESS_TOOLBOX_HH__
#define __AKANTU_PLANE_STRESS_TOOLBOX_HH__
namespace akantu {
class SolidMechanicsModel;
class FEEngine;
} // akantu
namespace akantu {
/**
* Empty class in dimensions different from 2
* This class is only specialized for 2D in the tmpl file
*/
template <UInt dim, class ParentMaterial = Material>
class PlaneStressToolbox : public ParentMaterial {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PlaneStressToolbox(SolidMechanicsModel & model, const ID & id = "")
: ParentMaterial(model, id) {}
PlaneStressToolbox(SolidMechanicsModel & model, UInt spatial_dimension,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "")
: ParentMaterial(model, spatial_dimension, mesh, fe_engine, id) {}
~PlaneStressToolbox() override = default;
protected:
void initialize();
public:
void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) override {
ParentMaterial::computeAllCauchyStresses(ghost_type);
}
virtual void computeCauchyStressPlaneStress(ElementType /*el_type*/,
GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
AKANTU_ERROR("The function \"computeCauchyStressPlaneStress\" can "
"only be used in 2D Plane stress problems, which means "
"that you made a mistake somewhere!! ");
AKANTU_DEBUG_OUT();
}
virtual void computeThirdAxisDeformation(ElementType, GhostType) {}
protected:
bool initialize_third_axis_deformation{false};
};
#define AKANTU_PLANE_STRESS_TOOL_SPEC(dim) \
template <> \
inline PlaneStressToolbox<dim, Material>::PlaneStressToolbox( \
SolidMechanicsModel & model, const ID & id) \
: Material(model, id) {}
AKANTU_PLANE_STRESS_TOOL_SPEC(1)
AKANTU_PLANE_STRESS_TOOL_SPEC(3)
} // namespace akantu
#include "plane_stress_toolbox_tmpl.hh"
#endif /* __AKANTU_PLANE_STRESS_TOOLBOX_HH__ */
diff --git a/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh b/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
index 9ef31be49..5cfdcdf1e 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
@@ -1,169 +1,169 @@
/**
* @file plane_stress_toolbox_tmpl.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Tue Sep 16 2014
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief 2D specialization of the akantu::PlaneStressToolbox class
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH__
#define __AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class ParentMaterial>
class PlaneStressToolbox<2, ParentMaterial> : public ParentMaterial {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PlaneStressToolbox(SolidMechanicsModel & model, const ID & id = "");
PlaneStressToolbox(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
~PlaneStressToolbox() override = default;
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ThirdAxisDeformation,
third_axis_deformation, Real);
protected:
void initialize() {
this->registerParam("Plane_Stress", plane_stress, false, _pat_parsmod,
"Is plane stress");
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
void initMaterial() override {
ParentMaterial::initMaterial();
if (this->plane_stress && this->initialize_third_axis_deformation) {
this->third_axis_deformation.initialize(1);
this->third_axis_deformation.resize();
}
}
/* ------------------------------------------------------------------------ */
void computeStress(ElementType el_type, GhostType ghost_type) override {
ParentMaterial::computeStress(el_type, ghost_type);
if (this->plane_stress)
computeThirdAxisDeformation(el_type, ghost_type);
}
/* ------------------------------------------------------------------------ */
virtual void computeThirdAxisDeformation(ElementType, GhostType) {}
/// Computation of Cauchy stress tensor in the case of finite deformation
void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) override {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
AKANTU_DEBUG_ASSERT(this->finite_deformation,
"The Cauchy stress can only be computed if you are "
"working in finite deformation.");
// resizeInternalArray(stress);
Mesh::type_iterator it = this->fem.getMesh().firstType(2, ghost_type);
Mesh::type_iterator last_type =
this->fem.getMesh().lastType(2, ghost_type);
for (; it != last_type; ++it)
this->computeCauchyStressPlaneStress(*it, ghost_type);
} else
ParentMaterial::computeAllCauchyStresses(ghost_type);
AKANTU_DEBUG_OUT();
}
virtual void
computeCauchyStressPlaneStress(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost){};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// third axis strain measure value
InternalField<Real> third_axis_deformation;
/// Plane stress or plane strain
bool plane_stress;
/// For non linear materials, the \epsilon_{zz} might be required
bool initialize_third_axis_deformation;
};
template <class ParentMaterial>
inline PlaneStressToolbox<2, ParentMaterial>::PlaneStressToolbox(
SolidMechanicsModel & model, const ID & id)
: ParentMaterial(model, id),
third_axis_deformation("third_axis_deformation", *this),
plane_stress(false), initialize_third_axis_deformation(false) {
/// @todo Plane_Stress should not be possible to be modified after
/// initMaterial (but before)
this->initialize();
}
template <class ParentMaterial>
inline PlaneStressToolbox<2, ParentMaterial>::PlaneStressToolbox(
SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: ParentMaterial(model, dim, mesh, fe_engine, id),
third_axis_deformation("third_axis_deformation", *this, dim, fe_engine,
this->element_filter),
plane_stress(false), initialize_third_axis_deformation(false) {
this->initialize();
}
template <>
inline PlaneStressToolbox<2, Material>::PlaneStressToolbox(
SolidMechanicsModel & model, const ID & id)
: Material(model, id),
third_axis_deformation("third_axis_deformation", *this),
plane_stress(false), initialize_third_axis_deformation(false) {
/// @todo Plane_Stress should not be possible to be modified after
/// initMaterial (but before)
this->registerParam("Plane_Stress", plane_stress, false, _pat_parsmod,
"Is plane stress");
}
} // namespace akantu
#endif /* __AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/random_internal_field.hh b/src/model/solid_mechanics/materials/random_internal_field.hh
index ebb9c03c6..a6511b6c9 100644
--- a/src/model/solid_mechanics/materials/random_internal_field.hh
+++ b/src/model/solid_mechanics/materials/random_internal_field.hh
@@ -1,105 +1,104 @@
/**
* @file random_internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Random internal material parameter
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "internal_field.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_RANDOM_INTERNAL_FIELD_HH__
#define __AKANTU_RANDOM_INTERNAL_FIELD_HH__
namespace akantu {
/**
* class for the internal fields of materials with a random
* distribution
*/
template <typename T, template <typename> class BaseField = InternalField,
template <typename> class Generator = RandomGenerator>
class RandomInternalField : public BaseField<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
RandomInternalField(const ID & id, Material & material);
~RandomInternalField() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
RandomInternalField operator=(const RandomInternalField &) = delete;
public:
AKANTU_GET_MACRO(RandomParameter, random_parameter, const RandomParameter<T>);
/// initialize the field to a given number of component
void initialize(UInt nb_component) override;
/// set the field to a given value
void setDefaultValue(const T & value) override;
/// set the specified random distribution to a given parameter
void setRandomDistribution(const RandomParameter<T> & param);
/// print the content
void printself(std::ostream & stream, int indent = 0) const override;
protected:
void setArrayValues(T * begin, T * end) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline operator Real() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// random parameter containing the distribution and base value
RandomParameter<T> random_parameter;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const RandomInternalField<T> & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#endif /* __AKANTU_RANDOM_INTERNAL_FIELD_HH__ */
diff --git a/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh b/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
index ed64c4371..4f2769960 100644
--- a/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
@@ -1,125 +1,125 @@
/**
* @file random_internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Thu Feb 08 2018
*
* @brief Random internal material parameter implementation
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH__
#define __AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
RandomInternalField<T, BaseField, Generator>::RandomInternalField(
const ID & id, Material & material)
: BaseField<T>(id, material), random_parameter(T()) {}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
RandomInternalField<T, BaseField, Generator>::~RandomInternalField() = default;
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::initialize(
UInt nb_component) {
this->internalInitialize(nb_component);
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setDefaultValue(
const T & value) {
random_parameter.setBaseValue(value);
this->reset();
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setRandomDistribution(
const RandomParameter<T> & param) {
random_parameter = param;
this->reset();
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::printself(
std::ostream & stream, int indent[[gnu::unused]]) const {
stream << "RandomInternalField [ ";
random_parameter.printself(stream);
stream << " ]";
#if !defined(AKANTU_NDEBUG)
if (AKANTU_DEBUG_TEST(dblDump)) {
stream << std::endl;
InternalField<T>::printself(stream, indent);
}
#endif
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setArrayValues(T * begin,
T * end) {
random_parameter.template setValues<Generator>(begin, end);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
inline RandomInternalField<T, BaseField, Generator>::operator Real() const {
return random_parameter.getBaseValue();
}
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<RandomInternalField<Real>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
index 7ffbfdbf3..95d494d05 100644
--- a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
@@ -1,82 +1,82 @@
/**
* @file damaged_weight_function.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Damaged weight function for non local materials
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DAMAGED_WEIGHT_FUNCTION_HH__
#define __AKANTU_DAMAGED_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Damage weight function */
/* -------------------------------------------------------------------------- */
class DamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
DamagedWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "damaged"), damage(nullptr) {
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
/// set the pointers of internals to the right flattend version
void init() override;
inline Real operator()(Real r,
const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2);
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// internal pointer to the current damage vector
ElementTypeMapReal * damage;
};
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "damaged_weight_function_inline_impl.cc"
#endif
} // namespace akantu
#endif /* __AKANTU_DAMAGED_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function_inline_impl.cc b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function_inline_impl.cc
index 8752fe003..c6595d2a9 100644
--- a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function_inline_impl.cc
@@ -1,75 +1,75 @@
/**
* @file damaged_weight_function_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Feb 03 2016
*
* @brief Implementation of inline function of damaged weight function
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 Real DamagedWeightFunction::operator()(Real r,
const __attribute__((unused))
IntegrationPoint & q1,
const IntegrationPoint & q2) {
/// compute the weight
UInt quad = q2.global_num;
Array<Real> & dam_array = (*this->damage)(q2.type, q2.ghost_type);
Real D = dam_array(quad);
Real Radius_t = 0;
Real Radius_init = this->R2;
// if(D <= 0.5)
// {
// Radius_t = 2*D*Radius_init;
// }
// else
// {
// Radius_t = 2*Radius_init*(1-D);
// }
//
Radius_t = Radius_init * (1 - D);
Radius_init *= Radius_init;
Radius_t *= Radius_t;
if (Radius_t < Math::getTolerance()) {
Radius_t = 0.001 * Radius_init;
}
Real expb =
(2 * std::log(0.51)) / (std::log(1.0 - 0.49 * Radius_t / Radius_init));
Int expb_floor = std::floor(expb);
Real b = expb_floor + expb_floor % 2;
Real alpha = std::max(0., 1. - r * r / Radius_init);
Real w = std::pow(alpha, b);
return w;
}
/* -------------------------------------------------------------------------- */
inline void DamagedWeightFunction::init() {
this->damage = &(this->manager.registerWeightFunctionInternal("damage"));
}
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
index 3a5ca0524..b79e308bf 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
@@ -1,96 +1,96 @@
/**
* @file remove_damaged_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Removed damaged weight function for non local materials
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH__
#define __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Remove damaged weight function */
/* -------------------------------------------------------------------------- */
class RemoveDamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
RemoveDamagedWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "remove_damaged"), damage(nullptr) {
this->registerParam("damage_limit", this->damage_limit, 1., _pat_parsable,
"Damage Threshold");
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
inline void init() override;
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2);
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// limit at which a point is considered as complitely broken
Real damage_limit;
/// internal pointer to the current damage vector
ElementTypeMapReal * damage;
};
} // namespace akantu
#include "remove_damaged_weight_function_inline_impl.cc"
#endif /* __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.cc b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.cc
index 326454778..ea10a3db2 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.cc
@@ -1,103 +1,104 @@
/**
* @file remove_damaged_weight_function_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Wed Oct 21 2015
+ * @date last modification: Thu Jul 06 2017
*
* @brief Implementation of inline function of remove damaged weight function
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "remove_damaged_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_CC__
#define __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline Real RemoveDamagedWeightFunction::
operator()(Real r, const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2) {
/// compute the weight
UInt quad = q2.global_num;
if (q1 == q2)
return 1.;
Array<Real> & dam_array = (*this->damage)(q2.type, q2.ghost_type);
Real D = dam_array(quad);
Real w = 0.;
if (D < damage_limit * (1 - Math::getTolerance())) {
Real alpha = std::max(0., 1. - r * r / this->R2);
w = alpha * alpha;
}
return w;
}
/* -------------------------------------------------------------------------- */
inline void RemoveDamagedWeightFunction::init() {
this->damage = &(this->manager.registerWeightFunctionInternal("damage"));
}
/* -------------------------------------------------------------------------- */
inline UInt
RemoveDamagedWeightFunction::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_mnl_weight)
return this->manager.getModel().getNbIntegrationPoints(elements) *
sizeof(Real);
return 0;
}
/* -------------------------------------------------------------------------- */
inline void
RemoveDamagedWeightFunction::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_mnl_weight) {
DataAccessor<Element>::packElementalDataHelper<Real>(
*damage, buffer, elements, true,
this->manager.getModel().getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
inline void
RemoveDamagedWeightFunction::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == _gst_mnl_weight) {
DataAccessor<Element>::unpackElementalDataHelper<Real>(
*damage, buffer, elements, true,
this->manager.getModel().getFEEngine());
}
}
} // namespace akantu
#endif /* __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
index e4664c861..fc956fa1a 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
@@ -1,86 +1,85 @@
/**
* @file remove_damaged_with_damage_rate_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Removed damaged weight function for non local materials
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH__
#define __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Remove damaged with damage rate weight function */
/* -------------------------------------------------------------------------- */
class RemoveDamagedWithDamageRateWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
RemoveDamagedWithDamageRateWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "remove_damage_with_damage_rate"),
damage_with_damage_rate(nullptr) {
this->registerParam<Real>("damage_limit",
this->damage_limit_with_damage_rate, 1,
_pat_parsable, "Damage Threshold");
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
inline Real operator()(Real r,
const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2);
inline void init() override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// limit at which a point is considered as complitely broken
Real damage_limit_with_damage_rate;
/// internal pointer to the current damage vector
ElementTypeMapReal * damage_with_damage_rate;
};
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "remove_damaged_with_damage_rate_weight_function_inline_impl.cc"
#endif
} // akantu
#endif /* __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.cc b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.cc
index 2c9b3d939..f36ed8b8b 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.cc
@@ -1,62 +1,62 @@
/**
* @file remove_damaged_with_damage_rate_weight_function_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Feb 03 2016
*
* @brief Implementation of inline function of remove damaged with
* damage rate weight function
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
inline void RemoveDamagedWithDamageRateWeightFunction::init() {
this->damage_with_damage_rate =
&(this->manager.registerWeightFunctionInternal("damage-rate"));
}
/* -------------------------------------------------------------------------- */
inline Real RemoveDamagedWithDamageRateWeightFunction::
operator()(Real r, const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2) {
/// compute the weight
UInt quad = q2.global_num;
if (q1.global_num == quad)
return 1.;
Array<Real> & dam_array =
(*this->damage_with_damage_rate)(q2.type, q2.ghost_type);
Real D = dam_array(quad);
Real w = 0.;
Real alphaexp = 1.;
Real betaexp = 2.;
if (D < damage_limit_with_damage_rate) {
Real alpha = std::max(0., 1. - pow((r * r / this->R2), alphaexp));
w = pow(alpha, betaexp);
}
return w;
}
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
index 992297710..e3913c320 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
@@ -1,123 +1,123 @@
/**
* @file stress_based_weight_function.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Wed Oct 07 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief implementation of the stres based weight function classes
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "stress_based_weight_function.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
StressBasedWeightFunction::StressBasedWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "stress_based")
// stress_diag("stress_diag", material), selected_stress_diag(NULL),
// stress_base("stress_base", material), selected_stress_base(NULL),
// characteristic_size("lc", material), selected_characteristic_size(NULL)
{
// this->registerParam("ft", this->ft, 0., _pat_parsable, "Tensile strength");
// stress_diag.initialize(spatial_dimension);
// stress_base.initialize(spatial_dimension * spatial_dimension);
// characteristic_size.initialize(1);
}
/* -------------------------------------------------------------------------- */
/// During intialization the characteristic sizes for all quadrature
/// points are computed
void StressBasedWeightFunction::init() {
// const Mesh & mesh = this->material.getModel().getFEEngine().getMesh();
// for (UInt g = _not_ghost; g <= _ghost; ++g) {
// GhostType gt = GhostType(g);
// Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt);
// Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, gt);
// for(; it != last_type; ++it) {
// UInt nb_quadrature_points =
// this->material.getModel().getFEEngine().getNbQuadraturePoints(*it, gt);
// const Array<UInt> & element_filter =
// this->material.getElementFilter(*it, gt);
// UInt nb_element = element_filter.size();
// Array<Real> ones(nb_element*nb_quadrature_points, 1, 1.);
// Array<Real> & lc = characteristic_size(*it, gt);
// this->material.getModel().getFEEngine().integrateOnQuadraturePoints(ones,
// lc,
// 1,
// *it,
// gt,
// element_filter);
// for (UInt q = 0; q < nb_quadrature_points * nb_element; q++) {
// lc(q) = pow(lc(q), 1./ Real(spatial_dimension));
// }
// }
// }
}
/* -------------------------------------------------------------------------- */
/// computation of principals stresses and principal directions
void StressBasedWeightFunction::updatePrincipalStress(__attribute__((unused))
GhostType ghost_type) {
// AKANTU_DEBUG_IN();
// const Mesh & mesh = this->material.getModel().getFEEngine().getMesh();
// Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
// Mesh::type_iterator last_type = mesh.lastType(spatial_dimension,
// ghost_type);
// for(; it != last_type; ++it) {
// Array<Real>::const_matrix_iterator sigma =
// this->material.getStress(*it, ghost_type).begin(spatial_dimension,
// spatial_dimension);
// auto eigenvalues =
// stress_diag(*it, ghost_type).begin(spatial_dimension);
// auto eigenvalues_end =
// stress_diag(*it, ghost_type).end(spatial_dimension);
// Array<Real>::matrix_iterator eigenvector =
// stress_base(*it, ghost_type).begin(spatial_dimension,
// spatial_dimension);
// #ifndef __trick__
// auto cl = characteristic_size(*it, ghost_type).begin();
// #endif
// UInt q = 0;
// for(;eigenvalues != eigenvalues_end; ++sigma, ++eigenvalues,
// ++eigenvector, ++cl, ++q) {
// sigma->eig(*eigenvalues, *eigenvector);
// *eigenvalues /= ft;
// #ifndef __trick__
// // specify a lower bound for principal stress based on the size of
// the element
// for (UInt i = 0; i < spatial_dimension; ++i) {
// (*eigenvalues)(i) = std::max(*cl / this->R, (*eigenvalues)(i));
// }
// #endif
// }
// }
// AKANTU_DEBUG_OUT();
}
} // akantu
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
index a2e1debd7..60897da5c 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
@@ -1,101 +1,101 @@
/**
* @file stress_based_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Removed damaged weight function for non local materials
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__
#define __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Stress Based Weight */
/* -------------------------------------------------------------------------- */
/// based on based on Giry et al.: Stress-based nonlocal damage model,
/// IJSS, 48, 2011
class StressBasedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
StressBasedWeightFunction(NonLocalManager & manager);
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
void init() override;
inline void updateInternals() override;
void updatePrincipalStress(GhostType ghost_type);
inline void updateQuadraturePointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates);
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2);
/// computation of ellipsoid
inline Real computeRhoSquare(Real r, Vector<Real> & eigs,
Matrix<Real> & eigenvects, Vector<Real> & x_s);
protected:
inline void setInternal();
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// tensile strength
Real ft;
/// prinicipal stresses
ElementTypeMapReal * stress_diag;
/// for preselection of types (optimization)
ElementTypeMapReal * selected_stress_diag;
/// principal directions
ElementTypeMapReal * stress_base;
/// lenght intrinisic to the material
ElementTypeMapReal * characteristic_size;
};
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "stress_based_weight_function_inline_impl.cc"
#endif
} // akantu
#endif /* __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.cc b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.cc
index 2990dd1d4..3ac8d4cb9 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.cc
@@ -1,191 +1,190 @@
/**
* @file stress_based_weight_function_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Feb 03 2016
*
* @brief Implementation of inline function of remove damaged with
* damage rate weight function
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
inline void StressBasedWeightFunction::updateInternals() {
// updatePrincipalStress(_not_ghost);
// updatePrincipalStress(_ghost);
}
/* -------------------------------------------------------------------------- */
// inline void StressBasedWeightFunction::selectType(ElementType type1,
// GhostType ghost_type1,
// ElementType type2,
// GhostType ghost_type2) {
// selected_stress_diag = &stress_diag(type2, ghost_type2);
// selected_stress_base = &stress_base(type2, ghost_type2);
// selected_characteristic_size = &characteristic_size(type1, ghost_type1);
// }
/* -------------------------------------------------------------------------- */
inline Real StressBasedWeightFunction::computeRhoSquare(
__attribute__((unused)) Real r, __attribute__((unused)) Vector<Real> & eigs,
__attribute__((unused)) Matrix<Real> & eigenvects,
__attribute__((unused)) Vector<Real> & x_s) {
// if (spatial_dimension == 1)
// return eigs[0];
// else if (spatial_dimension == 2) {
// Vector<Real> u1(eigenvects.storage(), 2);
// Real cos_t = x_s.dot(u1) / (x_s.norm() * u1.norm());
// Real cos_t_2;
// Real sin_t_2;
// Real sigma1_2 = eigs[0]*eigs[0];
// Real sigma2_2 = eigs[1]*eigs[1];
// #ifdef __trick__
// Real zero = std::numeric_limits<Real>::epsilon();
// if(std::abs(cos_t) < zero) {
// cos_t_2 = 0;
// sin_t_2 = 1;
// } else {
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// }
// Real rhop1 = std::max(0., cos_t_2 / sigma1_2);
// Real rhop2 = std::max(0., sin_t_2 / sigma2_2);
// #else
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// Real rhop1 = cos_t_2 / sigma1_2;
// Real rhop2 = sin_t_2 / sigma2_2;
// #endif
// return 1./ (rhop1 + rhop2);
// } else if (spatial_dimension == 3) {
// Vector<Real> u1(eigenvects.storage() + 0*3, 3);
// //Vector<Real> u2(eigenvects.storage() + 1*3, 3);
// Vector<Real> u3(eigenvects.storage() + 2*3, 3);
// Real zero = std::numeric_limits<Real>::epsilon();
// Vector<Real> tmp(3);
// tmp.crossProduct(x_s, u3);
// Vector<Real> u3_C_x_s_C_u3(3);
// u3_C_x_s_C_u3.crossProduct(u3, tmp);
// Real norm_u3_C_x_s_C_u3 = u3_C_x_s_C_u3.norm();
// Real cos_t = 0.;
// if(std::abs(norm_u3_C_x_s_C_u3) > zero) {
// Real inv_norm_u3_C_x_s_C_u3 = 1. / norm_u3_C_x_s_C_u3;
// cos_t = u1.dot(u3_C_x_s_C_u3) * inv_norm_u3_C_x_s_C_u3;
// }
// Real cos_p = u3.dot(x_s) / r;
// Real cos_t_2;
// Real sin_t_2;
// Real cos_p_2;
// Real sin_p_2;
// Real sigma1_2 = eigs[0]*eigs[0];
// Real sigma2_2 = eigs[1]*eigs[1];
// Real sigma3_2 = eigs[2]*eigs[2];
// #ifdef __trick__
// if(std::abs(cos_t) < zero) {
// cos_t_2 = 0;
// sin_t_2 = 1;
// } else {
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// }
// if(std::abs(cos_p) < zero) {
// cos_p_2 = 0;
// sin_p_2 = 1;
// } else {
// cos_p_2 = cos_p * cos_p;
// sin_p_2 = (1 - cos_p_2);
// }
// Real rhop1 = std::max(0., sin_p_2 * cos_t_2 / sigma1_2);
// Real rhop2 = std::max(0., sin_p_2 * sin_t_2 / sigma2_2);
// Real rhop3 = std::max(0., cos_p_2 / sigma3_2);
// #else
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// cos_p_2 = cos_p * cos_p;
// sin_p_2 = (1 - cos_p_2);
// Real rhop1 = sin_p_2 * cos_t_2 / sigma1_2;
// Real rhop2 = sin_p_2 * sin_t_2 / sigma2_2;
// Real rhop3 = cos_p_2 / sigma3_2;
// #endif
// return 1./ (rhop1 + rhop2 + rhop3);
// }
return 0.;
}
/* -------------------------------------------------------------------------- */
inline Real StressBasedWeightFunction::
operator()(__attribute__((unused)) Real r,
__attribute__((unused)) const IntegrationPoint & q1,
__attribute__((unused)) const IntegrationPoint & q2) {
// Real zero = std::numeric_limits<Real>::epsilon();
// if(r < zero) return 1.; // means x and s are the same points
// const Vector<Real> & x = q1.getPosition();
// const Vector<Real> & s = q2.getPosition();
// Vector<Real> eigs =
// selected_stress_diag->begin(spatial_dimension)[q2.global_num];
// Matrix<Real> eigenvects =
// selected_stress_base->begin(spatial_dimension,
// spatial_dimension)[q2.global_num];
// Real min_rho_lc = selected_characteristic_size->begin()[q1.global_num];
// Vector<Real> x_s(spatial_dimension);
// x_s = x;
// x_s -= s;
// Real rho_2 = computeRhoSquare(r, eigs, eigenvects, x_s);
// Real rho_lc_2 = std::max(this->R2 * rho_2, min_rho_lc*min_rho_lc);
// // Real w = std::max(0., 1. - r*r / rho_lc_2);
// // w = w*w;
// Real w = exp(- 2*2*r*r / rho_lc_2);
// return w;
return 0.;
}
diff --git a/src/model/solid_mechanics/solid_mechanics_model.cc b/src/model/solid_mechanics/solid_mechanics_model.cc
index ba8c9bcd2..61b9662de 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model.cc
@@ -1,1212 +1,1211 @@
/**
* @file solid_mechanics_model.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Implementation of the SolidMechanicsModel class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "integrator_gauss.hh"
#include "shape_lagrange.hh"
#include "solid_mechanics_model_tmpl.hh"
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "sparse_matrix.hh"
#include "synchronizer_registry.hh"
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_iohelper_paraview.hh"
#endif
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* A solid mechanics model need a mesh and a dimension to be created. the model
* by it self can not do a lot, the good init functions should be called in
* order to configure the model depending on what we want to do.
*
* @param mesh mesh representing the model we want to simulate
* @param dim spatial dimension of the problem, if dim = 0 (default value) the
* dimension of the problem is assumed to be the on of the mesh
* @param id an id to identify the model
*/
SolidMechanicsModel::SolidMechanicsModel(Mesh & mesh, UInt dim, const ID & id,
const MemoryID & memory_id,
const ModelType model_type)
: Model(mesh, model_type, dim, id, memory_id),
BoundaryCondition<SolidMechanicsModel>(), f_m2a(1.0),
displacement(nullptr), previous_displacement(nullptr),
displacement_increment(nullptr), mass(nullptr), velocity(nullptr),
acceleration(nullptr), external_force(nullptr), internal_force(nullptr),
blocked_dofs(nullptr), current_position(nullptr),
material_index("material index", id, memory_id),
material_local_numbering("material local numbering", id, memory_id),
increment_flag(false), are_materials_instantiated(false) {
AKANTU_DEBUG_IN();
this->registerFEEngineObject<MyFEEngineType>("SolidMechanicsFEEngine", mesh,
Model::spatial_dimension);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
this->mesh.addDumpMesh(mesh, Model::spatial_dimension, _not_ghost,
_ek_regular);
#endif
material_selector = std::make_shared<DefaultMaterialSelector>(material_index),
this->initDOFManager();
this->registerDataAccessor(*this);
if (this->mesh.isDistributed()) {
auto & synchronizer = this->mesh.getElementSynchronizer();
this->registerSynchronizer(synchronizer, _gst_material_id);
this->registerSynchronizer(synchronizer, _gst_smm_mass);
this->registerSynchronizer(synchronizer, _gst_smm_stress);
this->registerSynchronizer(synchronizer, _gst_smm_boundary);
this->registerSynchronizer(synchronizer, _gst_for_dump);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModel::~SolidMechanicsModel() {
AKANTU_DEBUG_IN();
for (auto & internal : this->registered_internals) {
delete internal.second;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::setTimeStep(Real time_step, const ID & solver_id) {
Model::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper().setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
/* Initialization */
/* -------------------------------------------------------------------------- */
/**
* This function groups many of the initialization in on function. For most of
* basics case the function should be enough. The functions initialize the
* model, the internal vectors, set them to 0, and depending on the parameters
* it also initialize the explicit or implicit solver.
*
* @param 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::initFullImpl(const ModelOptions & options) {
material_index.initialize(mesh, _element_kind = _ek_not_defined,
_default_value = UInt(-1), _with_nb_element = true);
material_local_numbering.initialize(mesh, _element_kind = _ek_not_defined,
_with_nb_element = true);
Model::initFullImpl(options);
// initialize pbc
if (this->pbc_pair.size() != 0)
this->initPBC();
// initialize the materials
if (this->parser.getLastParsedFile() != "") {
this->instantiateMaterials();
}
this->initMaterials();
this->initBC(*this, *displacement, *displacement_increment, *external_force);
}
/* -------------------------------------------------------------------------- */
TimeStepSolverType SolidMechanicsModel::getDefaultSolverType() const {
return _tsst_dynamic_lumped;
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions SolidMechanicsModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case _tsst_dynamic_lumped: {
options.non_linear_solver_type = _nls_lumped;
options.integration_scheme_type["displacement"] = _ist_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
break;
}
case _tsst_static: {
options.non_linear_solver_type = _nls_newton_raphson;
options.integration_scheme_type["displacement"] = _ist_pseudo_time;
options.solution_type["displacement"] = IntegrationScheme::_not_defined;
break;
}
case _tsst_dynamic: {
if (this->method == _explicit_consistent_mass) {
options.non_linear_solver_type = _nls_newton_raphson;
options.integration_scheme_type["displacement"] = _ist_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
} else {
options.non_linear_solver_type = _nls_newton_raphson;
options.integration_scheme_type["displacement"] = _ist_trapezoidal_rule_2;
options.solution_type["displacement"] = IntegrationScheme::_displacement;
}
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
std::tuple<ID, TimeStepSolverType>
SolidMechanicsModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _explicit_lumped_mass: {
return std::make_tuple("explicit_lumped", _tsst_dynamic_lumped);
}
case _explicit_consistent_mass: {
return std::make_tuple("explicit", _tsst_dynamic);
}
case _static: {
return std::make_tuple("static", _tsst_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", _tsst_dynamic);
}
default:
return std::make_tuple("unknown", _tsst_not_defined);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType) {
auto & dof_manager = this->getDOFManager();
/* ------------------------------------------------------------------------ */
// for alloc type of solvers
this->allocNodalField(this->displacement, spatial_dimension, "displacement");
this->allocNodalField(this->previous_displacement, spatial_dimension,
"previous_displacement");
this->allocNodalField(this->displacement_increment, spatial_dimension,
"displacement_increment");
this->allocNodalField(this->internal_force, spatial_dimension,
"internal_force");
this->allocNodalField(this->external_force, spatial_dimension,
"external_force");
this->allocNodalField(this->blocked_dofs, spatial_dimension, "blocked_dofs");
this->allocNodalField(this->current_position, spatial_dimension,
"current_position");
// initialize the current positions
this->current_position->copy(this->mesh.getNodes());
/* ------------------------------------------------------------------------ */
if (!dof_manager.hasDOFs("displacement")) {
dof_manager.registerDOFs("displacement", *this->displacement, _dst_nodal);
dof_manager.registerBlockedDOFs("displacement", *this->blocked_dofs);
dof_manager.registerDOFsIncrement("displacement",
*this->displacement_increment);
dof_manager.registerDOFsPrevious("displacement",
*this->previous_displacement);
}
/* ------------------------------------------------------------------------ */
// for dynamic
if (time_step_solver_type == _tsst_dynamic ||
time_step_solver_type == _tsst_dynamic_lumped) {
this->allocNodalField(this->velocity, spatial_dimension, "velocity");
this->allocNodalField(this->acceleration, spatial_dimension,
"acceleration");
if (!dof_manager.hasDOFsDerivatives("displacement", 1)) {
dof_manager.registerDOFsDerivative("displacement", 1, *this->velocity);
dof_manager.registerDOFsDerivative("displacement", 2,
*this->acceleration);
}
}
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*/
void SolidMechanicsModel::initModel() {
/// \todo add the current position as a parameter to initShapeFunctions for
/// large deformation
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleResidual() {
AKANTU_DEBUG_IN();
/* ------------------------------------------------------------------------ */
// computes the internal forces
this->assembleInternalForces();
/* ------------------------------------------------------------------------ */
this->getDOFManager().assembleToResidual("displacement",
*this->external_force, 1);
this->getDOFManager().assembleToResidual("displacement",
*this->internal_force, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_IN();
if ("external" == residual_part) {
this->getDOFManager().assembleToResidual("displacement",
*this->external_force, 1);
AKANTU_DEBUG_OUT();
return;
}
if ("internal" == residual_part) {
this->getDOFManager().assembleToResidual("displacement",
*this->internal_force, 1);
AKANTU_DEBUG_OUT();
return;
}
AKANTU_CUSTOM_EXCEPTION(
debug::SolverCallbackResidualPartUnknown(residual_part));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MatrixType SolidMechanicsModel::getMatrixType(const ID & matrix_id) {
// \TODO check the materials to know what is the correct answer
if (matrix_id == "C")
return _mt_not_defined;
return _symmetric;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleStiffnessMatrix();
} else if (matrix_id == "M") {
this->assembleMass();
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleLumpedMatrix(const ID & matrix_id) {
if (matrix_id == "M") {
this->assembleMassLumped();
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::beforeSolveStep() {
for (auto & material : materials)
material->beforeSolveStep();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::afterSolveStep() {
for (auto & material : materials)
material->afterSolveStep();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::predictor() { ++displacement_release; }
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::corrector() { ++displacement_release; }
/* -------------------------------------------------------------------------- */
/**
* This function computes the internal forces as F_{int} = \int_{\Omega} N
* \sigma d\Omega@f$
*/
void SolidMechanicsModel::assembleInternalForces() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the internal forces");
this->internal_force->clear();
// compute the stresses of local elements
AKANTU_DEBUG_INFO("Compute local stresses");
for (auto & material : materials) {
material->computeAllStresses(_not_ghost);
}
/* ------------------------------------------------------------------------ */
/* Computation of the non local part */
if (this->non_local_manager)
this->non_local_manager->computeAllNonLocalStresses();
// communicate the stresses
AKANTU_DEBUG_INFO("Send data for residual assembly");
this->asynchronousSynchronize(_gst_smm_stress);
// assemble the forces due to local stresses
AKANTU_DEBUG_INFO("Assemble residual for local elements");
for (auto & material : materials) {
material->assembleInternalForces(_not_ghost);
}
// finalize communications
AKANTU_DEBUG_INFO("Wait distant stresses");
this->waitEndSynchronize(_gst_smm_stress);
// assemble the stresses due to ghost elements
AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
for (auto & material : materials) {
material->assembleInternalForces(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix.");
// Check if materials need to recompute the matrix
bool need_to_reassemble = false;
for (auto & material : materials) {
need_to_reassemble |= material->hasStiffnessMatrixChanged();
}
if (need_to_reassemble) {
this->getDOFManager().getMatrix("K").clear();
// call compute stiffness matrix on each local elements
for (auto & material : materials) {
material->assembleStiffnessMatrix(_not_ghost);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateCurrentPosition() {
if (this->current_position_release == this->displacement_release)
return;
this->current_position->copy(this->mesh.getNodes());
auto cpos_it = this->current_position->begin(Model::spatial_dimension);
auto cpos_end = this->current_position->end(Model::spatial_dimension);
auto disp_it = this->displacement->begin(Model::spatial_dimension);
for (; cpos_it != cpos_end; ++cpos_it, ++disp_it) {
*cpos_it += *disp_it;
}
this->current_position_release = this->displacement_release;
}
/* -------------------------------------------------------------------------- */
const Array<Real> & SolidMechanicsModel::getCurrentPosition() {
this->updateCurrentPosition();
return *this->current_position;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateDataForNonLocalCriterion(
ElementTypeMapReal & criterion) {
const ID field_name = criterion.getName();
for (auto & material : materials) {
if (!material->isInternal<Real>(field_name, _ek_regular))
continue;
for (auto ghost_type : ghost_types) {
material->flattenInternal(field_name, criterion, ghost_type, _ek_regular);
}
}
}
/* -------------------------------------------------------------------------- */
/* Information */
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real min_dt = getStableTimeStep(_not_ghost);
/// reduction min over all processors
mesh.getCommunicator().allReduce(min_dt, SynchronizerOperation::_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep(const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Real min_dt = std::numeric_limits<Real>::max();
this->updateCurrentPosition();
Element elem;
elem.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, _ek_regular)) {
elem.type = type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type);
auto mat_indexes = material_index(type, ghost_type).begin();
auto mat_loc_num = material_local_numbering(type, ghost_type).begin();
Array<Real> X(0, nb_nodes_per_element * Model::spatial_dimension);
FEEngine::extractNodalToElementField(mesh, *current_position, X, type,
_not_ghost);
auto X_el = X.begin(Model::spatial_dimension, nb_nodes_per_element);
for (UInt el = 0; el < nb_element;
++el, ++X_el, ++mat_indexes, ++mat_loc_num) {
elem.element = *mat_loc_num;
Real el_h = getFEEngine().getElementInradius(*X_el, type);
Real el_c = this->materials[*mat_indexes]->getCelerity(elem);
Real el_dt = el_h / el_c;
min_dt = std::min(min_dt, el_dt);
}
}
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy() {
AKANTU_DEBUG_IN();
Real ekin = 0.;
UInt nb_nodes = mesh.getNbNodes();
if (this->getDOFManager().hasLumpedMatrix("M")) {
auto m_it = this->mass->begin(Model::spatial_dimension);
auto m_end = this->mass->end(Model::spatial_dimension);
auto v_it = this->velocity->begin(Model::spatial_dimension);
for (UInt n = 0; m_it != m_end; ++n, ++m_it, ++v_it) {
const Vector<Real> & v = *v_it;
const Vector<Real> & m = *m_it;
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;
if (count_node) {
for (UInt i = 0; i < Model::spatial_dimension; ++i) {
if (m(i) > std::numeric_limits<Real>::epsilon())
mv2 += v(i) * v(i) * m(i);
}
}
ekin += mv2;
}
} else if (this->getDOFManager().hasMatrix("M")) {
Array<Real> Mv(nb_nodes, Model::spatial_dimension);
this->getDOFManager().getMatrix("M").matVecMul(*this->velocity, Mv);
auto mv_it = Mv.begin(Model::spatial_dimension);
auto mv_end = Mv.end(Model::spatial_dimension);
auto v_it = this->velocity->begin(Model::spatial_dimension);
for (; mv_it != mv_end; ++mv_it, ++v_it) {
ekin += v_it->dot(*mv_it);
}
} else {
AKANTU_ERROR("No function called to assemble the mass matrix.");
}
mesh.getCommunicator().allReduce(ekin, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return ekin * .5;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy(const ElementType & type,
UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
Array<Real> vel_on_quad(nb_quadrature_points, Model::spatial_dimension);
Array<UInt> filter_element(1, 1, index);
getFEEngine().interpolateOnIntegrationPoints(*velocity, vel_on_quad,
Model::spatial_dimension, type,
_not_ghost, filter_element);
auto vit = vel_on_quad.begin(Model::spatial_dimension);
auto vend = vel_on_quad.end(Model::spatial_dimension);
Vector<Real> rho_v2(nb_quadrature_points);
Real rho = materials[material_index(type)(index)]->getRho();
for (UInt q = 0; vit != vend; ++vit, ++q) {
rho_v2(q) = rho * vit->dot(*vit);
}
AKANTU_DEBUG_OUT();
return .5 * getFEEngine().integrate(rho_v2, type, index);
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getExternalWork() {
AKANTU_DEBUG_IN();
auto ext_force_it = external_force->begin(Model::spatial_dimension);
auto int_force_it = internal_force->begin(Model::spatial_dimension);
auto boun_it = blocked_dofs->begin(Model::spatial_dimension);
decltype(ext_force_it) incr_or_velo_it;
if (this->method == _static) {
incr_or_velo_it =
this->displacement_increment->begin(Model::spatial_dimension);
} else {
incr_or_velo_it = this->velocity->begin(Model::spatial_dimension);
}
Real work = 0.;
UInt nb_nodes = this->mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes;
++n, ++ext_force_it, ++int_force_it, ++boun_it, ++incr_or_velo_it) {
const auto & int_force = *int_force_it;
const auto & ext_force = *ext_force_it;
const auto & boun = *boun_it;
const auto & incr_or_velo = *incr_or_velo_it;
bool is_local_node = this->mesh.isLocalOrMasterNode(n);
// bool is_not_pbc_slave_node = !this->isPBCSlaveNode(n);
bool count_node = is_local_node; // && is_not_pbc_slave_node;
if (count_node) {
for (UInt i = 0; i < Model::spatial_dimension; ++i) {
if (boun(i))
work -= int_force(i) * incr_or_velo(i);
else
work += ext_force(i) * incr_or_velo(i);
}
}
}
mesh.getCommunicator().allReduce(work, SynchronizerOperation::_sum);
if (this->method != _static)
work *= this->getTimeStep();
AKANTU_DEBUG_OUT();
return work;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy();
} else if (energy_id == "external work") {
return getExternalWork();
}
Real energy = 0.;
for (auto & material : materials)
energy += material->getEnergy(energy_id);
/// reduction sum over all processors
mesh.getCommunicator().allReduce(energy, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id,
const ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy(type, index);
}
UInt mat_index = this->material_index(type, _not_ghost)(index);
UInt mat_loc_num = this->material_local_numbering(type, _not_ghost)(index);
Real energy =
this->materials[mat_index]->getEnergy(energy_id, type, mat_loc_num);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
this->material_index.initialize(mesh, _element_kind = _ek_not_defined,
_with_nb_element = true,
_default_value = UInt(-1));
this->material_local_numbering.initialize(
mesh, _element_kind = _ek_not_defined, _with_nb_element = true,
_default_value = UInt(-1));
ElementTypeMapArray<UInt> filter("new_element_filter", this->getID(),
this->getMemoryID());
for (auto & elem : element_list) {
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);
for (auto & material : materials)
material->onElementsAdded(element_list, event);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
for (auto & material : materials) {
material->onElementsRemoved(element_list, new_numbering, event);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
if (displacement) {
displacement->resize(nb_nodes, 0.);
++displacement_release;
}
if (mass)
mass->resize(nb_nodes, 0.);
if (velocity)
velocity->resize(nb_nodes, 0.);
if (acceleration)
acceleration->resize(nb_nodes, 0.);
if (external_force)
external_force->resize(nb_nodes, 0.);
if (internal_force)
internal_force->resize(nb_nodes, 0.);
if (blocked_dofs)
blocked_dofs->resize(nb_nodes, 0.);
if (current_position)
current_position->resize(nb_nodes, 0.);
if (previous_displacement)
previous_displacement->resize(nb_nodes, 0.);
if (displacement_increment)
displacement_increment->resize(nb_nodes, 0.);
for (auto & material : materials) {
material->onNodesAdded(nodes_list, event);
}
need_to_reassemble_lumped_mass = true;
need_to_reassemble_mass = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesRemoved(const Array<UInt> & /*element_list*/,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & /*event*/) {
if (displacement) {
mesh.removeNodesFromArray(*displacement, new_numbering);
++displacement_release;
}
if (mass)
mesh.removeNodesFromArray(*mass, new_numbering);
if (velocity)
mesh.removeNodesFromArray(*velocity, new_numbering);
if (acceleration)
mesh.removeNodesFromArray(*acceleration, new_numbering);
if (internal_force)
mesh.removeNodesFromArray(*internal_force, new_numbering);
if (external_force)
mesh.removeNodesFromArray(*external_force, new_numbering);
if (blocked_dofs)
mesh.removeNodesFromArray(*blocked_dofs, new_numbering);
// if (increment_acceleration)
// mesh.removeNodesFromArray(*increment_acceleration, new_numbering);
if (displacement_increment)
mesh.removeNodesFromArray(*displacement_increment, new_numbering);
if (previous_displacement)
mesh.removeNodesFromArray(*previous_displacement, new_numbering);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::printself(std::ostream & stream, int indent) const {
std::string space;
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 : " << Model::spatial_dimension
<< std::endl;
stream << space << " + fem [" << std::endl;
getFEEngine().printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + nodals information [" << std::endl;
displacement->printself(stream, indent + 2);
if (velocity)
velocity->printself(stream, indent + 2);
if (acceleration)
acceleration->printself(stream, indent + 2);
if (mass)
mass->printself(stream, indent + 2);
external_force->printself(stream, indent + 2);
internal_force->printself(stream, indent + 2);
blocked_dofs->printself(stream, indent + 2);
stream << space << 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;
for (auto & material : materials) {
material->printself(stream, indent + 1);
}
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initializeNonLocal() {
this->non_local_manager->synchronize(*this, _gst_material_id);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::insertIntegrationPointsInNeighborhoods(
const GhostType & ghost_type) {
for (auto & mat : materials) {
MaterialNonLocalInterface * mat_non_local;
if ((mat_non_local =
dynamic_cast<MaterialNonLocalInterface *>(mat.get())) == nullptr)
continue;
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_tmp_nl", this->id, this->memory_id);
quadrature_points_coordinates.initialize(this->getFEEngine(),
_nb_component = spatial_dimension,
_ghost_type = ghost_type);
for (auto & type : quadrature_points_coordinates.elementTypes(
Model::spatial_dimension, ghost_type)) {
this->getFEEngine().computeIntegrationPointsCoordinates(
quadrature_points_coordinates(type, ghost_type), type, ghost_type);
}
mat_non_local->initMaterialNonLocal();
mat_non_local->insertIntegrationPointsInNeighborhoods(
ghost_type, quadrature_points_coordinates);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::computeNonLocalStresses(
const GhostType & ghost_type) {
for (auto & mat : materials) {
if (dynamic_cast<MaterialNonLocalInterface *>(mat.get()) == nullptr)
continue;
auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
mat_non_local.computeNonLocalStresses(ghost_type);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateLocalInternal(
ElementTypeMapReal & internal_flat, const GhostType & ghost_type,
const ElementKind & kind) {
const ID field_name = internal_flat.getName();
for (auto & material : materials) {
if (material->isInternal<Real>(field_name, kind))
material->flattenInternal(field_name, internal_flat, ghost_type, kind);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateNonLocalInternal(
ElementTypeMapReal & internal_flat, const GhostType & ghost_type,
const ElementKind & kind) {
const ID field_name = internal_flat.getName();
for (auto & mat : materials) {
if (dynamic_cast<MaterialNonLocalInterface *>(mat.get()) == nullptr)
continue;
auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
mat_non_local.updateNonLocalInternals(internal_flat, field_name, ghost_type,
kind);
}
}
/* -------------------------------------------------------------------------- */
FEEngine & SolidMechanicsModel::getFEEngineBoundary(const ID & name) {
return dynamic_cast<FEEngine &>(
getFEEngineClassBoundary<MyFEEngineType>(name));
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::splitElementByMaterial(
const Array<Element> & elements,
std::vector<Array<Element>> & elements_per_mat) const {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
const Array<UInt> * mat_indexes = nullptr;
const Array<UInt> * mat_loc_num = nullptr;
for (const auto & el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
mat_indexes = &(this->material_index(el.type, el.ghost_type));
mat_loc_num = &(this->material_local_numbering(el.type, el.ghost_type));
}
Element mat_el = el;
mat_el.element = (*mat_loc_num)(el.element);
elements_per_mat[(*mat_indexes)(el.element)].push_back(mat_el);
}
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModel::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes_per_element = 0;
for (const Element & el : elements) {
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
switch (tag) {
case _gst_material_id: {
size += elements.size() * sizeof(UInt);
break;
}
case _gst_smm_mass: {
size += nb_nodes_per_element * sizeof(Real) *
Model::spatial_dimension; // mass vector
break;
}
case _gst_smm_for_gradu: {
size += nb_nodes_per_element * Model::spatial_dimension *
sizeof(Real); // displacement
break;
}
case _gst_smm_boundary: {
// force, displacement, boundary
size += nb_nodes_per_element * Model::spatial_dimension *
(2 * sizeof(Real) + sizeof(bool));
break;
}
case _gst_for_dump: {
// displacement, velocity, acceleration, residual, force
size += nb_nodes_per_element * Model::spatial_dimension * sizeof(Real) * 5;
break;
}
default: {}
}
if (tag != _gst_material_id) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
size += mat.getNbData(elements, tag);
});
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
switch (tag) {
case _gst_material_id: {
this->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_for_dump: {
packNodalDataHelper(*displacement, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*acceleration, buffer, elements, mesh);
packNodalDataHelper(*internal_force, buffer, elements, mesh);
packNodalDataHelper(*external_force, buffer, elements, mesh);
break;
}
case _gst_smm_boundary: {
packNodalDataHelper(*external_force, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {}
}
if (tag != _gst_material_id) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.packData(buffer, elements, tag);
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
switch (tag) {
case _gst_material_id: {
for (auto && element : elements) {
UInt recv_mat_index;
buffer >> recv_mat_index;
UInt & mat_index = material_index(element);
if (mat_index != UInt(-1))
continue;
// add ghosts element to the correct material
mat_index = recv_mat_index;
UInt index = materials[mat_index]->addElement(element);
material_local_numbering(element) = index;
}
break;
}
case _gst_smm_mass: {
unpackNodalDataHelper(*mass, buffer, elements, mesh);
break;
}
case _gst_smm_for_gradu: {
unpackNodalDataHelper(*displacement, buffer, elements, mesh);
break;
}
case _gst_for_dump: {
unpackNodalDataHelper(*displacement, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*acceleration, buffer, elements, mesh);
unpackNodalDataHelper(*internal_force, buffer, elements, mesh);
unpackNodalDataHelper(*external_force, buffer, elements, mesh);
break;
}
case _gst_smm_boundary: {
unpackNodalDataHelper(*external_force, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {}
}
if (tag != _gst_material_id) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.unpackData(buffer, elements, tag);
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModel::getNbData(const Array<UInt> & dofs,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
// UInt nb_nodes = mesh.getNbNodes();
switch (tag) {
case _gst_smm_uv: {
size += sizeof(Real) * Model::spatial_dimension * 2;
break;
}
case _gst_smm_res: {
size += sizeof(Real) * Model::spatial_dimension;
break;
}
case _gst_smm_mass: {
size += sizeof(Real) * Model::spatial_dimension;
break;
}
case _gst_for_dump: {
size += sizeof(Real) * Model::spatial_dimension * 5;
break;
}
default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
}
AKANTU_DEBUG_OUT();
return size * dofs.size();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
const Array<UInt> & dofs,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
switch (tag) {
case _gst_smm_uv: {
packDOFDataHelper(*displacement, buffer, dofs);
packDOFDataHelper(*velocity, buffer, dofs);
break;
}
case _gst_smm_res: {
packDOFDataHelper(*internal_force, buffer, dofs);
break;
}
case _gst_smm_mass: {
packDOFDataHelper(*mass, buffer, dofs);
break;
}
case _gst_for_dump: {
packDOFDataHelper(*displacement, buffer, dofs);
packDOFDataHelper(*velocity, buffer, dofs);
packDOFDataHelper(*acceleration, buffer, dofs);
packDOFDataHelper(*internal_force, buffer, dofs);
packDOFDataHelper(*external_force, buffer, dofs);
break;
}
default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
const Array<UInt> & dofs,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
switch (tag) {
case _gst_smm_uv: {
unpackDOFDataHelper(*displacement, buffer, dofs);
unpackDOFDataHelper(*velocity, buffer, dofs);
break;
}
case _gst_smm_res: {
unpackDOFDataHelper(*internal_force, buffer, dofs);
break;
}
case _gst_smm_mass: {
unpackDOFDataHelper(*mass, buffer, dofs);
break;
}
case _gst_for_dump: {
unpackDOFDataHelper(*displacement, buffer, dofs);
unpackDOFDataHelper(*velocity, buffer, dofs);
unpackDOFDataHelper(*acceleration, buffer, dofs);
unpackDOFDataHelper(*internal_force, buffer, dofs);
unpackDOFDataHelper(*external_force, buffer, dofs);
break;
}
default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model.hh b/src/model/solid_mechanics/solid_mechanics_model.hh
index 57e489704..37c45ef56 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model.hh
@@ -1,559 +1,559 @@
/**
* @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 Jan 19 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Model of Solid Mechanics
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "boundary_condition.hh"
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "model.hh"
#include "non_local_manager.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_HH__
namespace akantu {
class Material;
class MaterialSelector;
class DumperIOHelper;
class NonLocalManager;
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
class SolidMechanicsModel
: public Model,
public DataAccessor<Element>,
public DataAccessor<UInt>,
public BoundaryCondition<SolidMechanicsModel>,
public NonLocalManagerCallback,
public EventHandlerManager<SolidMechanicsModelEventHandler> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
class NewMaterialElementsEvent : public NewElementsEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(MaterialList, material, Array<UInt> &);
AKANTU_GET_MACRO(MaterialList, material, const Array<UInt> &);
protected:
Array<UInt> material;
};
using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
protected:
using EventManager = EventHandlerManager<SolidMechanicsModelEventHandler>;
public:
SolidMechanicsModel(
Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model", const MemoryID & memory_id = 0,
const ModelType model_type = ModelType::_solid_mechanics_model);
~SolidMechanicsModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize completely the model
void initFullImpl(
const ModelOptions & options = SolidMechanicsModelOptions()) override;
/// initialize all internal arrays for materials
virtual void initMaterials();
/// initialize the model
void initModel() override;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
/* ------------------------------------------------------------------------ */
/* Solver interface */
/* ------------------------------------------------------------------------ */
public:
/// assembles the stiffness matrix,
virtual void assembleStiffnessMatrix();
/// assembles the internal forces in the array internal_forces
virtual void assembleInternalForces();
protected:
/// callback for the solver, this adds f_{ext} - f_{int} to the residual
void assembleResidual() override;
/// callback for the solver, this adds f_{ext} or f_{int} to the residual
void assembleResidual(const ID & residual_part) override;
bool canSplitResidual() override { return true; }
/// get the type of matrix needed
MatrixType getMatrixType(const ID & matrix_id) override;
/// callback for the solver, this assembles different matrices
void assembleMatrix(const ID & matrix_id) override;
/// callback for the solver, this assembles the stiffness matrix
void assembleLumpedMatrix(const ID & matrix_id) override;
/// callback for the solver, this is called at beginning of solve
void predictor() override;
/// callback for the solver, this is called at end of solve
void corrector() override;
/// callback for the solver, this is called at beginning of solve
void beforeSolveStep() override;
/// callback for the solver, this is called at end of solve
void afterSolveStep() override;
/// Callback for the model to instantiate the matricees when needed
void initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) override;
protected:
/* ------------------------------------------------------------------------ */
TimeStepSolverType getDefaultSolverType() const override;
/* ------------------------------------------------------------------------ */
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
public:
bool isDefaultSolverExplicit() {
return method == _explicit_lumped_mass ||
method == _explicit_consistent_mass;
}
protected:
/// update the current position vector
void updateCurrentPosition();
/* ------------------------------------------------------------------------ */
/* Materials (solid_mechanics_model_material.cc) */
/* ------------------------------------------------------------------------ */
public:
/// register an empty material of a given type
Material & registerNewMaterial(const ID & mat_name, const ID & mat_type,
const ID & opt_param);
/// reassigns materials depending on the material selector
virtual void reassignMaterial();
/// apply a constant eigen_grad_u on all quadrature points of a given material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const ID & material_name,
const GhostType ghost_type = _not_ghost);
protected:
/// register a material in the dynamic database
Material & registerNewMaterial(const ParserSection & mat_section);
/// read the material files to instantiate all the materials
void instantiateMaterials();
/// set the element_id_by_material and add the elements to the good materials
virtual void
assignMaterialToElements(const ElementTypeMapArray<UInt> * filter = nullptr);
/* ------------------------------------------------------------------------ */
/* Mass (solid_mechanics_model_mass.cc) */
/* ------------------------------------------------------------------------ */
public:
/// assemble the lumped mass matrix
void assembleMassLumped();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
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);
/// 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();
/* ------------------------------------------------------------------------ */
/* NonLocalManager inherited members */
/* ------------------------------------------------------------------------ */
protected:
void initializeNonLocal() override;
void updateDataForNonLocalCriterion(ElementTypeMapReal & criterion) override;
void computeNonLocalStresses(const GhostType & ghost_type) override;
void
insertIntegrationPointsInNeighborhoods(const GhostType & ghost_type) override;
/// update the values of the non local internal
void updateLocalInternal(ElementTypeMapReal & internal_flat,
const GhostType & ghost_type,
const ElementKind & kind) override;
/// copy the results of the averaging in the materials
void updateNonLocalInternal(ElementTypeMapReal & internal_flat,
const GhostType & ghost_type,
const ElementKind & kind) override;
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override;
UInt getNbData(const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) override;
protected:
void
splitElementByMaterial(const Array<Element> & elements,
std::vector<Array<Element>> & elements_per_mat) const;
template <typename Operation>
void splitByMaterial(const Array<Element> & elements, Operation && op) const;
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
void onNodesRemoved(const Array<UInt> & element_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) override;
void onElementsAdded(const Array<Element> & nodes_list,
const NewElementsEvent & event) override;
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override{};
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
public:
virtual void onDump();
//! decide wether a field is a material internal or not
bool isInternal(const std::string & field_name,
const ElementKind & element_kind);
#ifndef SWIG
//! give the amount of data per element
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
dumper::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
dumper::Field * createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
dumper::Field * createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
const UInt & spatial_dimension,
const ElementKind & kind) override;
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);
void dump() override;
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, Model::spatial_dimension, UInt);
/// set the value of the time step
void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// get the value of the conversion from forces/ mass to acceleration
AKANTU_GET_MACRO(F_M2A, f_m2a, Real);
/// set the value of the conversion from forces/ mass to acceleration
AKANTU_SET_MACRO(F_M2A, f_m2a, Real);
/// get the SolidMechanicsModel::displacement 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
const Array<Real> & getCurrentPosition();
/// get the SolidMechanicsModel::increment vector \warn only consistent if
/// SolidMechanicsModel::setIncrementFlagOn has been called before
AKANTU_GET_MACRO(Increment, *displacement_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 (external forces)
AKANTU_GET_MACRO(Force, *external_force, Array<Real> &);
/// get the SolidMechanicsModel::internal_force vector (internal forces)
AKANTU_GET_MACRO(InternalForce, *internal_force, Array<Real> &);
/// get the SolidMechanicsModel::blocked_dofs vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool> &);
/// 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(); }
/// give the material internal index from its id
Int getInternalIndexFromID(const ID & id) const;
/// compute the stable time step
Real getStableTimeStep();
/// 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);
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);
AKANTU_GET_MACRO_NOT_CONST(MaterialSelector, *material_selector,
MaterialSelector &);
AKANTU_SET_MACRO(MaterialSelector, material_selector,
std::shared_ptr<MaterialSelector>);
/// Access the non_local_manager interface
AKANTU_GET_MACRO(NonLocalManager, *non_local_manager, NonLocalManager &);
/// get the FEEngine object to integrate or interpolate on the boundary
FEEngine & getFEEngineBoundary(const ID & name = "") override;
protected:
friend class Material;
protected:
/// compute the stable time step
Real getStableTimeStep(const GhostType & ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
Array<Real> * displacement;
UInt displacement_release{0};
/// displacements array at the previous time step (used in finite deformation)
Array<Real> * previous_displacement{nullptr};
/// increment of displacement
Array<Real> * displacement_increment{nullptr};
/// lumped mass array
Array<Real> * mass{nullptr};
/// Check if materials need to recompute the mass array
bool need_to_reassemble_lumped_mass{true};
/// Check if materials need to recompute the mass matrix
bool need_to_reassemble_mass{true};
/// velocities array
Array<Real> * velocity{nullptr};
/// accelerations array
Array<Real> * acceleration{nullptr};
/// accelerations array
// Array<Real> * increment_acceleration;
/// external forces array
Array<Real> * external_force{nullptr};
/// internal forces array
Array<Real> * internal_force{nullptr};
/// array specifing if a degree of freedom is blocked or not
Array<bool> * blocked_dofs{nullptr};
/// array of current position used during update residual
Array<Real> * current_position{nullptr};
UInt current_position_release{0};
/// Arrays containing the material index for each element
ElementTypeMapArray<UInt> material_index;
/// Arrays containing the position in the element filter of the material
/// (material's local numbering)
ElementTypeMapArray<UInt> material_local_numbering;
/// list of used materials
std::vector<std::unique_ptr<Material>> materials;
/// mapping between material name and material internal id
std::map<std::string, UInt> materials_names_to_id;
/// class defining of to choose a material
std::shared_ptr<MaterialSelector> material_selector;
/// flag defining if the increment must be computed or not
bool increment_flag;
/// tells if the material are instantiated
bool are_materials_instantiated;
using flatten_internal_map = std::map<std::pair<std::string, ElementKind>,
ElementTypeMapArray<Real> *>;
/// map a registered internals to be flattened for dump purposes
flatten_internal_map registered_internals;
/// non local manager
std::unique_ptr<NonLocalManager> non_local_manager;
};
/* -------------------------------------------------------------------------- */
namespace BC {
namespace Neumann {
using FromStress = FromHigherDim;
using FromTraction = FromSameDim;
} // namespace Neumann
} // namespace BC
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "parser.hh"
#include "solid_mechanics_model_inline_impl.cc"
#include "solid_mechanics_model_tmpl.hh"
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
index 63396a1b8..9f1a72dd2 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
@@ -1,611 +1,612 @@
/**
* @file fragment_manager.cc
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jan 23 2014
- * @date last modification: Mon Dec 14 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Group manager to handle fragments
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fragment_manager.hh"
#include "aka_iterators.hh"
#include "communicator.hh"
#include "material_cohesive.hh"
#include "mesh_iterators.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <functional>
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
FragmentManager::FragmentManager(SolidMechanicsModelCohesive & model,
bool dump_data, const ID & id,
const MemoryID & memory_id)
: GroupManager(model.getMesh(), id, memory_id), model(model),
mass_center(0, model.getSpatialDimension(), "mass_center"),
mass(0, model.getSpatialDimension(), "mass"),
velocity(0, model.getSpatialDimension(), "velocity"),
inertia_moments(0, model.getSpatialDimension(), "inertia_moments"),
principal_directions(
0, model.getSpatialDimension() * model.getSpatialDimension(),
"principal_directions"),
quad_coordinates("quad_coordinates", id),
mass_density("mass_density", id),
nb_elements_per_fragment(0, 1, "nb_elements_per_fragment"),
dump_data(dump_data) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
/// compute quadrature points' coordinates
quad_coordinates.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(quad_coordinates, spatial_dimension,
// spatial_dimension, _not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getMesh().getNodes(),
quad_coordinates);
/// store mass density per quadrature point
mass_density.initialize(mesh, _spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(mass_density, 1, spatial_dimension,
// _not_ghost);
storeMassDensityPerIntegrationPoint();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
class CohesiveElementFilter : public GroupManager::ClusteringFilter {
public:
CohesiveElementFilter(const SolidMechanicsModelCohesive & model,
const Real max_damage = 1.)
: model(model), is_unbroken(max_damage) {}
bool operator()(const Element & el) const override {
if (Mesh::getKind(el.type) == _ek_regular)
return true;
const Array<UInt> & mat_indexes =
model.getMaterialByElement(el.type, el.ghost_type);
const Array<UInt> & mat_loc_num =
model.getMaterialLocalNumbering(el.type, el.ghost_type);
const auto & mat = static_cast<const MaterialCohesive &>(
model.getMaterial(mat_indexes(el.element)));
UInt el_index = mat_loc_num(el.element);
UInt nb_quad_per_element =
model.getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(el.type, el.ghost_type);
const Array<Real> & damage_array = mat.getDamage(el.type, el.ghost_type);
AKANTU_DEBUG_ASSERT(nb_quad_per_element * el_index < damage_array.size(),
"This quadrature point is out of range");
const Real * element_damage =
damage_array.storage() + nb_quad_per_element * el_index;
UInt unbroken_quads = std::count_if(
element_damage, element_damage + nb_quad_per_element, is_unbroken);
if (unbroken_quads > 0)
return true;
return false;
}
private:
struct IsUnbrokenFunctor {
IsUnbrokenFunctor(const Real & max_damage) : max_damage(max_damage) {}
bool operator()(const Real & x) { return x < max_damage; }
const Real max_damage;
};
const SolidMechanicsModelCohesive & model;
const IsUnbrokenFunctor is_unbroken;
};
/* -------------------------------------------------------------------------- */
void FragmentManager::buildFragments(Real damage_limit) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
ElementSynchronizer * cohesive_synchronizer =
const_cast<ElementSynchronizer *>(model.getCohesiveSynchronizer());
if (cohesive_synchronizer) {
cohesive_synchronizer->computeBufferSize(model, _gst_smmc_damage);
cohesive_synchronizer->asynchronousSynchronize(model, _gst_smmc_damage);
cohesive_synchronizer->waitEndSynchronize(model, _gst_smmc_damage);
}
#endif
auto & mesh_facets = const_cast<Mesh &>(mesh.getMeshFacets());
UInt spatial_dimension = model.getSpatialDimension();
std::string fragment_prefix("fragment");
/// generate fragments
global_nb_fragment =
createClusters(spatial_dimension, mesh_facets, fragment_prefix,
CohesiveElementFilter(model, damage_limit));
nb_fragment = getNbElementGroups(spatial_dimension);
fragment_index.resize(nb_fragment);
UInt * fragment_index_it = fragment_index.storage();
/// loop over fragments
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
/// get fragment index
std::string fragment_index_string =
it->first.substr(fragment_prefix.size() + 1);
std::stringstream sstr(fragment_index_string.c_str());
sstr >> *fragment_index_it;
AKANTU_DEBUG_ASSERT(!sstr.fail(), "fragment_index is not an integer");
}
/// compute fragments' mass
computeMass();
if (dump_data) {
createDumpDataArray(fragment_index, "fragments", true);
createDumpDataArray(mass, "fragments mass");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeMass() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// create a unit field per quadrature point, since to compute mass
/// it's neccessary to integrate only density
ElementTypeMapArray<Real> unit_field("unit_field", id);
unit_field.initialize(model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost, _default_value = 1.);
// mesh.initElementTypeMapArray(unit_field, spatial_dimension,
// spatial_dimension,
// _not_ghost);
// ElementTypeMapArray<Real>::type_iterator it =
// unit_field.firstType(spatial_dimension, _not_ghost, _ek_regular);
// ElementTypeMapArray<Real>::type_iterator end =
// unit_field.lastType(spatial_dimension, _not_ghost, _ek_regular);
// for (; it != end; ++it) {
// ElementType type = *it;
// Array<Real> & field_array = unit_field(type);
// UInt nb_element = mesh.getNbElement(type);
// UInt nb_quad_per_element =
// model.getFEEngine().getNbIntegrationPoints(type);
// field_array.resize(nb_element * nb_quad_per_element);
// field_array.set(1.);
// }
integrateFieldOnFragments(unit_field, mass);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeCenterOfMass() {
AKANTU_DEBUG_IN();
/// integrate position multiplied by density
integrateFieldOnFragments(quad_coordinates, mass_center);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * mass_center_storage = mass_center.storage();
UInt total_components = mass_center.size() * mass_center.getNbComponent();
for (UInt i = 0; i < total_components; ++i)
mass_center_storage[i] /= mass_storage[i];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeVelocity() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// compute velocity per quadrature point
ElementTypeMapArray<Real> velocity_field("velocity_field", id);
velocity_field.initialize(
model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension, _ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(velocity_field, spatial_dimension,
// spatial_dimension, _not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getVelocity(),
velocity_field);
/// integrate on fragments
integrateFieldOnFragments(velocity_field, velocity);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * velocity_storage = velocity.storage();
UInt total_components = velocity.size() * velocity.getNbComponent();
for (UInt i = 0; i < total_components; ++i)
velocity_storage[i] /= mass_storage[i];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Given the distance @f$ \mathbf{r} @f$ between a quadrature point
* and its center of mass, the moment of inertia is computed as \f[
* I_\mathrm{CM} = \mathrm{tr}(\mathbf{r}\mathbf{r}^\mathrm{T})
* \mathbf{I} - \mathbf{r}\mathbf{r}^\mathrm{T} \f] for more
* information check Wikipedia
* (http://en.wikipedia.org/wiki/Moment_of_inertia#Identities_for_a_skew-symmetric_matrix)
*
*/
void FragmentManager::computeInertiaMoments() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
computeCenterOfMass();
/// compute local coordinates products with respect to the center of match
ElementTypeMapArray<Real> moments_coords("moments_coords", id);
moments_coords.initialize(model.getFEEngine(),
_nb_component =
spatial_dimension * spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost, _default_value = 1.);
// mesh.initElementTypeMapArray(moments_coords,
// spatial_dimension * spatial_dimension,
// spatial_dimension, _not_ghost);
// /// resize the by element type
// ElementTypeMapArray<Real>::type_iterator it =
// moments_coords.firstType(spatial_dimension, _not_ghost, _ek_regular);
// ElementTypeMapArray<Real>::type_iterator end =
// moments_coords.lastType(spatial_dimension, _not_ghost, _ek_regular);
// for (; it != end; ++it) {
// ElementType type = *it;
// Array<Real> & field_array = moments_coords(type);
// UInt nb_element = mesh.getNbElement(type);
// UInt nb_quad_per_element =
// model.getFEEngine().getNbIntegrationPoints(type);
// field_array.resize(nb_element * nb_quad_per_element);
// }
/// compute coordinates
auto mass_center_it = mass_center.begin(spatial_dimension);
/// loop over fragments
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++mass_center_it) {
const ElementTypeMapArray<UInt> & el_list = it->second->getElements();
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_quad_per_element =
model.getFEEngine().getNbIntegrationPoints(type);
Array<Real> & moments_coords_array = moments_coords(type);
const Array<Real> & quad_coordinates_array = quad_coordinates(type);
const Array<UInt> & el_list_array = el_list(type);
Array<Real>::matrix_iterator moments_begin =
moments_coords_array.begin(spatial_dimension, spatial_dimension);
auto quad_coordinates_begin =
quad_coordinates_array.begin(spatial_dimension);
Vector<Real> relative_coords(spatial_dimension);
for (UInt el = 0; el < el_list_array.size(); ++el) {
UInt global_el = el_list_array(el);
/// loop over quadrature points
for (UInt q = 0; q < nb_quad_per_element; ++q) {
UInt global_q = global_el * nb_quad_per_element + q;
Matrix<Real> moments_matrix = moments_begin[global_q];
const Vector<Real> & quad_coord_vector =
quad_coordinates_begin[global_q];
/// to understand this read the documentation written just
/// before this function
relative_coords = quad_coord_vector;
relative_coords -= *mass_center_it;
moments_matrix.outerProduct(relative_coords, relative_coords);
Real trace = moments_matrix.trace();
moments_matrix *= -1.;
moments_matrix += Matrix<Real>::eye(spatial_dimension, trace);
}
}
}
}
/// integrate moments
Array<Real> integrated_moments(global_nb_fragment,
spatial_dimension * spatial_dimension);
integrateFieldOnFragments(moments_coords, integrated_moments);
/// compute and store principal moments
inertia_moments.resize(global_nb_fragment);
principal_directions.resize(global_nb_fragment);
Array<Real>::matrix_iterator integrated_moments_it =
integrated_moments.begin(spatial_dimension, spatial_dimension);
auto inertia_moments_it = inertia_moments.begin(spatial_dimension);
Array<Real>::matrix_iterator principal_directions_it =
principal_directions.begin(spatial_dimension, spatial_dimension);
for (UInt frag = 0; frag < global_nb_fragment; ++frag,
++integrated_moments_it, ++inertia_moments_it,
++principal_directions_it) {
integrated_moments_it->eig(*inertia_moments_it, *principal_directions_it);
}
if (dump_data)
createDumpDataArray(inertia_moments, "moments of inertia");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeAllData() {
AKANTU_DEBUG_IN();
buildFragments();
computeVelocity();
computeInertiaMoments();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::storeMassDensityPerIntegrationPoint() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator end = mesh.lastType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
Array<Real> & mass_density_array = mass_density(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
mass_density_array.resize(nb_element * nb_quad_per_element);
const Array<UInt> & mat_indexes = model.getMaterialByElement(type);
Real * mass_density_it = mass_density_array.storage();
/// store mass_density for each element and quadrature point
for (UInt el = 0; el < nb_element; ++el) {
Material & mat = model.getMaterial(mat_indexes(el));
for (UInt q = 0; q < nb_quad_per_element; ++q, ++mass_density_it)
*mass_density_it = mat.getRho();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::integrateFieldOnFragments(
ElementTypeMapArray<Real> & field, Array<Real> & output) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
UInt nb_component = output.getNbComponent();
/// integration part
output.resize(global_nb_fragment);
output.clear();
UInt * fragment_index_it = fragment_index.storage();
auto output_begin = output.begin(nb_component);
/// loop over fragments
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
const ElementTypeMapArray<UInt> & el_list = it->second->getElements();
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_quad_per_element =
model.getFEEngine().getNbIntegrationPoints(type);
const Array<Real> & density_array = mass_density(type);
Array<Real> & field_array = field(type);
const Array<UInt> & elements = el_list(type);
UInt nb_element = elements.size();
/// generate array to be integrated by filtering fragment's elements
Array<Real> integration_array(elements.size() * nb_quad_per_element,
nb_component);
Array<Real>::matrix_iterator int_array_it =
integration_array.begin_reinterpret(nb_quad_per_element, nb_component,
nb_element);
Array<Real>::matrix_iterator int_array_end =
integration_array.end_reinterpret(nb_quad_per_element, nb_component,
nb_element);
Array<Real>::matrix_iterator field_array_begin =
field_array.begin_reinterpret(nb_quad_per_element, nb_component,
field_array.size() /
nb_quad_per_element);
auto density_array_begin = density_array.begin_reinterpret(
nb_quad_per_element, density_array.size() / nb_quad_per_element);
for (UInt el = 0; int_array_it != int_array_end; ++int_array_it, ++el) {
UInt global_el = elements(el);
*int_array_it = field_array_begin[global_el];
/// multiply field by density
const Vector<Real> & density_vector = density_array_begin[global_el];
for (UInt i = 0; i < nb_quad_per_element; ++i) {
for (UInt j = 0; j < nb_component; ++j) {
(*int_array_it)(i, j) *= density_vector(i);
}
}
}
/// integrate the field over the fragment
Array<Real> integrated_array(elements.size(), nb_component);
model.getFEEngine().integrate(integration_array, integrated_array,
nb_component, type, _not_ghost, elements);
/// sum over all elements and store the result
Vector<Real> output_tmp(output_begin[*fragment_index_it]);
output_tmp += std::accumulate(integrated_array.begin(nb_component),
integrated_array.end(nb_component),
Vector<Real>(nb_component));
}
}
/// sum output over all processors
const Communicator & comm = mesh.getCommunicator();
comm.allReduce(output, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeNbElementsPerFragment() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
nb_elements_per_fragment.resize(global_nb_fragment);
nb_elements_per_fragment.clear();
UInt * fragment_index_it = fragment_index.storage();
/// loop over fragments
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
const ElementTypeMapArray<UInt> & el_list = it->second->getElements();
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_element = el_list(type).size();
nb_elements_per_fragment(*fragment_index_it) += nb_element;
}
}
/// sum values over all processors
const auto & comm = mesh.getCommunicator();
comm.allReduce(nb_elements_per_fragment, SynchronizerOperation::_sum);
if (dump_data)
createDumpDataArray(nb_elements_per_fragment, "elements per fragment");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void FragmentManager::createDumpDataArray(Array<T> & data, std::string name,
bool fragment_index_output) {
AKANTU_DEBUG_IN();
if (data.size() == 0)
return;
auto & mesh_not_const = const_cast<Mesh &>(mesh);
auto && spatial_dimension = mesh.getSpatialDimension();
auto && nb_component = data.getNbComponent();
auto && data_begin = data.begin(nb_component);
auto fragment_index_it = fragment_index.begin();
/// loop over fragments
for (const auto & fragment : ElementGroupsIterable(*this)) {
const auto & fragment_idx = *fragment_index_it;
/// loop over cluster types
for (auto & type : fragment.elementTypes(spatial_dimension)) {
/// init mesh data
auto & mesh_data = mesh_not_const.getDataPointer<T>(
name, type, _not_ghost, nb_component);
auto mesh_data_begin = mesh_data.begin(nb_component);
/// fill mesh data
for (const auto & elem : fragment.getElements(type)) {
Vector<T> md_tmp = mesh_data_begin[elem];
if (fragment_index_output) {
md_tmp(0) = fragment_idx;
} else {
md_tmp = data_begin[fragment_idx];
}
}
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
index 74f676cd4..eaf2025f7 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
@@ -1,169 +1,169 @@
/**
* @file fragment_manager.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jan 23 2014
- * @date last modification: Mon Dec 14 2015
+ * @date last modification: Thu Jul 06 2017
*
* @brief Group manager to handle fragments
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "group_manager.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_FRAGMENT_MANAGER_HH__
#define __AKANTU_FRAGMENT_MANAGER_HH__
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
class FragmentManager : public GroupManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FragmentManager(SolidMechanicsModelCohesive & model, bool dump_data = true,
const ID & id = "fragment_manager",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/// store mass density per integration point
void storeMassDensityPerIntegrationPoint();
/// integrate an elemental field multiplied by density on global
/// fragments
void integrateFieldOnFragments(ElementTypeMapArray<Real> & field,
Array<Real> & output);
/// compute fragments' mass
void computeMass();
/// create dump data for a single array
template <typename T>
void createDumpDataArray(Array<T> & data, std::string name,
bool fragment_index_output = false);
public:
/// build fragment list (cohesive elements are considered broken if
/// damage >= damage_limit)
void buildFragments(Real damage_limit = 1.);
/// compute fragments' center of mass
void computeCenterOfMass();
/// compute fragments' velocity
void computeVelocity();
/// computes principal moments of inertia with respect to the center
/// of mass of each fragment
void computeInertiaMoments();
/// compute all fragments' data
void computeAllData();
/// compute number of elements per fragment
void computeNbElementsPerFragment();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get number of fragments
AKANTU_GET_MACRO(NbFragment, global_nb_fragment, UInt);
/// get fragments' mass
AKANTU_GET_MACRO(Mass, mass, const Array<Real> &);
/// get fragments' center of mass
AKANTU_GET_MACRO(CenterOfMass, mass_center, const Array<Real> &);
/// get fragments' velocity
AKANTU_GET_MACRO(Velocity, velocity, const Array<Real> &);
/// get fragments' principal moments of inertia
AKANTU_GET_MACRO(MomentsOfInertia, inertia_moments, const Array<Real> &);
/// get fragments' principal directions
AKANTU_GET_MACRO(PrincipalDirections, principal_directions,
const Array<Real> &);
/// get number of elements per fragment
AKANTU_GET_MACRO(NbElementsPerFragment, nb_elements_per_fragment,
const Array<UInt> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// local_fragment index
Array<UInt> fragment_index;
/// global number of fragments (parallel simulations)
UInt global_nb_fragment;
/// number of fragments
UInt nb_fragment;
/// cohesive solid mechanics model associated
SolidMechanicsModelCohesive & model;
/// fragments' center of mass
Array<Real> mass_center;
/// fragments' mass
Array<Real> mass;
/// fragments' velocity
Array<Real> velocity;
/// fragments' principal moments of inertia with respect to the
/// center of mass
Array<Real> inertia_moments;
/// fragments' principal directions
Array<Real> principal_directions;
/// quadrature points' coordinates
ElementTypeMapArray<Real> quad_coordinates;
/// mass density per quadrature point
ElementTypeMapArray<Real> mass_density;
/// fragment filter
Array<UInt> nb_elements_per_fragment;
/// dump data
bool dump_data;
};
} // akantu
#endif /* __AKANTU_FRAGMENT_MANAGER_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
index cfed39f0e..3f052a5fb 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
@@ -1,159 +1,159 @@
/**
* @file material_selector_cohesive.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Dec 11 2015
- * @date last modification: Mon Dec 14 2015
+ * @date last modification: Mon Dec 18 2017
*
* @brief Material selector for cohesive elements
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_selector_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DefaultMaterialCohesiveSelector::DefaultMaterialCohesiveSelector(
const SolidMechanicsModelCohesive & model)
: facet_material(model.getFacetMaterial()), mesh(model.getMesh()) {
// backward compatibility v3: to get the former behavior back when the user
// creates its own selector
this->fallback_selector =
std::make_shared<DefaultMaterialSelector>(model.getMaterialByElement());
}
/* -------------------------------------------------------------------------- */
UInt DefaultMaterialCohesiveSelector::operator()(const Element & element) {
if (Mesh::getKind(element.type) == _ek_cohesive) {
try {
const Array<Element> & cohesive_el_to_facet =
mesh.getMeshFacets().getSubelementToElement(element.type,
element.ghost_type);
bool third_dimension = (mesh.getSpatialDimension() == 3);
const Element & facet =
cohesive_el_to_facet(element.element, third_dimension);
if (facet_material.exists(facet.type, facet.ghost_type)) {
return facet_material(facet.type, facet.ghost_type)(facet.element);
} else {
return fallback_value;
}
} catch (...) {
return fallback_value;
}
} else if (Mesh::getSpatialDimension(element.type) ==
mesh.getSpatialDimension() - 1) {
return facet_material(element.type, element.ghost_type)(element.element);
} else {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
MeshDataMaterialCohesiveSelector::MeshDataMaterialCohesiveSelector(
const SolidMechanicsModelCohesive & model)
: model(model), mesh_facets(model.getMeshFacets()),
material_index(mesh_facets.getData<std::string>("physical_names")) {
third_dimension = (model.getSpatialDimension() == 3);
// backward compatibility v3: to get the former behavior back when the user
// creates its own selector
this->fallback_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
}
/* -------------------------------------------------------------------------- */
UInt MeshDataMaterialCohesiveSelector::operator()(const Element & element) {
if (Mesh::getKind(element.type) == _ek_cohesive) {
const auto & facet = mesh_facets.getSubelementToElement(
element.type, element.ghost_type)(element.element, third_dimension);
try {
std::string material_name = this->material_index(facet);
return this->model.getMaterialIndex(material_name);
} catch (...) {
return fallback_value;
}
} else
return MaterialSelector::operator()(element);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
MaterialCohesiveRulesSelector::MaterialCohesiveRulesSelector(
const SolidMechanicsModelCohesive & model,
const MaterialCohesiveRules & rules,
ID mesh_data_id) // what we have here is the name of model and also
// the name of different materials
: model(model), mesh_data_id(std::move(mesh_data_id)),
mesh(model.getMesh()), mesh_facets(model.getMeshFacets()),
spatial_dimension(model.getSpatialDimension()), rules(rules) {
// cohesive fallback
this->fallback_selector =
std::make_shared<DefaultMaterialCohesiveSelector>(model);
// non cohesive fallback
this->fallback_selector->setFallback(
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model));
}
/* -------------------------------------------------------------------------- */
UInt MaterialCohesiveRulesSelector::operator()(const Element & element) {
if (mesh_facets.getSpatialDimension(element.type) ==
(spatial_dimension - 1)) {
const std::vector<Element> & element_to_subelement =
mesh_facets.getElementToSubelement(element.type,
element.ghost_type)(element.element);
// Array<bool> & facets_check = model.getFacetsCheck();
const Element & el1 = element_to_subelement[0];
const Element & el2 = element_to_subelement[1];
ID id1 = mesh.getData<std::string>(mesh_data_id, el1.type,
el1.ghost_type)(el1.element);
ID id2 = id1;
if (el2 != ElementNull) {
id2 = mesh.getData<std::string>(mesh_data_id, el2.type,
el2.ghost_type)(el2.element);
}
auto rit = rules.find(std::make_pair(id1, id2));
if (rit == rules.end()) {
rit = rules.find(std::make_pair(id2, id1));
}
if (rit != rules.end()) {
return model.getMaterialIndex(rit->second);
}
}
return MaterialSelector::operator()(element);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
index a5dd25995..a6ef7c4ed 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
@@ -1,98 +1,99 @@
/**
* @file material_selector_cohesive.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Dec 11 2015
- * @date last modification: Mon Dec 14 2015
+ * @date last modification: Mon Dec 18 2017
*
* @brief Material selectors for cohesive elements
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material_selector.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
#ifndef __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__
#define __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__
/* -------------------------------------------------------------------------- */
/**
* class that assigns the first cohesive material by default to the
* cohesive elements
*/
class DefaultMaterialCohesiveSelector : public MaterialSelector {
public:
DefaultMaterialCohesiveSelector(const SolidMechanicsModelCohesive & model);
UInt operator()(const Element & element) override;
private:
const ElementTypeMapArray<UInt> & facet_material;
const Mesh & mesh;
};
/* -------------------------------------------------------------------------- */
/// To be used with intrinsic elements inserted along mesh physical surfaces
class MeshDataMaterialCohesiveSelector : public MaterialSelector {
public:
MeshDataMaterialCohesiveSelector(const SolidMechanicsModelCohesive & model);
UInt operator()(const Element & element) override;
protected:
const SolidMechanicsModelCohesive & model;
const Mesh & mesh_facets;
const ElementTypeMapArray<std::string> & material_index;
bool third_dimension;
};
/// bulk1, bulk2 -> cohesive
using MaterialCohesiveRules = std::map<std::pair<ID, ID>, ID>;
/* -------------------------------------------------------------------------- */
class MaterialCohesiveRulesSelector : public MaterialSelector {
public:
MaterialCohesiveRulesSelector(const SolidMechanicsModelCohesive & model,
const MaterialCohesiveRules & rules,
ID mesh_data_id = "physical_names");
UInt operator()(const Element & element);
private:
const SolidMechanicsModelCohesive & model;
ID mesh_data_id;
const Mesh & mesh;
const Mesh & mesh_facets;
UInt spatial_dimension;
MaterialCohesiveRules rules;
};
#endif /* __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__ */
} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
index 22e2c96dd..c67ea80fd 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
@@ -1,68 +1,67 @@
/**
* @file cohesive_internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Oct 08 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Internal field for cohesive elements
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "internal_field.hh"
#ifndef __AKANTU_COHESIVE_INTERNAL_FIELD_HH__
#define __AKANTU_COHESIVE_INTERNAL_FIELD_HH__
namespace akantu {
/// internal field class for cohesive materials
template <typename T> class CohesiveInternalField : public InternalField<T> {
public:
CohesiveInternalField(const ID & id, Material & material);
~CohesiveInternalField() override;
/// initialize the field to a given number of component
void initialize(UInt nb_component) override;
private:
CohesiveInternalField operator=(__attribute__((unused))
const CohesiveInternalField & other){};
};
/* -------------------------------------------------------------------------- */
/* Facet Internal Field */
/* -------------------------------------------------------------------------- */
template <typename T> class FacetInternalField : public InternalField<T> {
public:
FacetInternalField(const ID & id, Material & material);
~FacetInternalField() override;
/// initialize the field to a given number of component
void initialize(UInt nb_component) override;
};
} // akantu
#endif /* __AKANTU_COHESIVE_INTERNAL_FIELD_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
index 0b2c80de8..52c688752 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
@@ -1,95 +1,95 @@
/**
* @file cohesive_internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Wed Nov 08 2017
*
* @brief implementation of the cohesive internal field
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH__
#define __AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH__
namespace akantu {
template <typename T>
CohesiveInternalField<T>::CohesiveInternalField(const ID & id,
Material & material)
: InternalField<T>(
id, material, material.getModel().getFEEngine("CohesiveFEEngine"),
dynamic_cast<MaterialCohesive &>(material).getElementFilter()) {
this->element_kind = _ek_cohesive;
}
template <typename T>
CohesiveInternalField<T>::~CohesiveInternalField() = default;
template <typename T>
void CohesiveInternalField<T>::initialize(UInt nb_component) {
this->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T>
FacetInternalField<T>::FacetInternalField(const ID & id, Material & material)
: InternalField<T>(
id, material, material.getModel().getFEEngine("FacetsFEEngine"),
dynamic_cast<MaterialCohesive &>(material).getFacetFilter()) {
this->spatial_dimension -= 1;
this->element_kind = _ek_regular;
}
template <typename T> FacetInternalField<T>::~FacetInternalField() = default;
template <typename T>
void FacetInternalField<T>::initialize(UInt nb_component) {
this->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<RandomInternalField<Real, FacetInternalField>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<RandomInternalField<Real, CohesiveInternalField>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
} // akantu
#endif /* __AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
index 1be65c688..dffd4f680 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
@@ -1,217 +1,216 @@
/**
* @file material_cohesive_bilinear.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Bilinear cohesive constitutive law
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_bilinear.hh"
//#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveBilinear<spatial_dimension>::MaterialCohesiveBilinear(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesiveLinear<spatial_dimension>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("delta_0", delta_0, Real(0.),
_pat_parsable | _pat_readable,
"Elastic limit displacement");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
this->sigma_c_eff.setRandomDistribution(this->sigma_c.getRandomParameter());
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
this->delta_max.setDefaultValue(delta_0);
this->insertion_stress.setDefaultValue(0);
this->delta_max.reset();
this->insertion_stress.reset();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::onElementsAdded(
const Array<Element> & element_list, const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::onElementsAdded(element_list,
event);
bool scale_traction = false;
// don't scale sigma_c if volume_s hasn't been specified by the user
if (!Math::are_float_equal(this->volume_s, 0.))
scale_traction = true;
Array<Element>::const_scalar_iterator el_it = element_list.begin();
Array<Element>::const_scalar_iterator el_end = element_list.end();
for (; el_it != el_end; ++el_it) {
// filter not ghost cohesive elements
if (el_it->ghost_type != _not_ghost ||
Mesh::getKind(el_it->type) != _ek_cohesive)
continue;
UInt index = el_it->element;
ElementType type = el_it->type;
UInt nb_element = this->model->getMesh().getNbElement(type);
UInt nb_quad_per_element = this->fem_cohesive.getNbIntegrationPoints(type);
auto sigma_c_begin = this->sigma_c_eff(type).begin_reinterpret(
nb_quad_per_element, nb_element);
Vector<Real> sigma_c_vec = sigma_c_begin[index];
auto delta_c_begin = this->delta_c_eff(type).begin_reinterpret(
nb_quad_per_element, nb_element);
Vector<Real> delta_c_vec = delta_c_begin[index];
if (scale_traction)
scaleTraction(*el_it, sigma_c_vec);
/**
* Recompute sigma_c as
* @f$ {\sigma_c}_\textup{new} =
* \frac{{\sigma_c}_\textup{old} \delta_c} {\delta_c - \delta_0} @f$
*/
for (UInt q = 0; q < nb_quad_per_element; ++q) {
delta_c_vec(q) = 2 * this->G_c / sigma_c_vec(q);
if (delta_c_vec(q) - delta_0 < Math::getTolerance())
AKANTU_ERROR("delta_0 = " << delta_0 << " must be lower than delta_c = "
<< delta_c_vec(q)
<< ", modify your material file");
sigma_c_vec(q) *= delta_c_vec(q) / (delta_c_vec(q) - delta_0);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::scaleTraction(
const Element & el, Vector<Real> & sigma_c_vec) {
AKANTU_DEBUG_IN();
Real base_sigma_c = this->sigma_c_eff;
const Mesh & mesh_facets = this->model->getMeshFacets();
const FEEngine & fe_engine = this->model->getFEEngine();
auto coh_element_to_facet_begin =
mesh_facets.getSubelementToElement(el.type).begin(2);
const Vector<Element> & coh_element_to_facet =
coh_element_to_facet_begin[el.element];
// compute bounding volume
Real volume = 0;
// loop over facets
for (UInt f = 0; f < 2; ++f) {
const Element & facet = coh_element_to_facet(f);
const Array<std::vector<Element>> & facet_to_element =
mesh_facets.getElementToSubelement(facet.type, facet.ghost_type);
const std::vector<Element> & element_list = facet_to_element(facet.element);
auto elem = element_list.begin();
auto elem_end = element_list.end();
// loop over elements connected to each facet
for (; elem != elem_end; ++elem) {
// skip cohesive elements and dummy elements
if (*elem == ElementNull || Mesh::getKind(elem->type) == _ek_cohesive)
continue;
// unit vector for integration in order to obtain the volume
UInt nb_quadrature_points = fe_engine.getNbIntegrationPoints(elem->type);
Vector<Real> unit_vector(nb_quadrature_points, 1);
volume += fe_engine.integrate(unit_vector, elem->type, elem->element,
elem->ghost_type);
}
}
// scale sigma_c
sigma_c_vec -= base_sigma_c;
sigma_c_vec *= std::pow(this->volume_s / volume, 1. / this->m_s);
sigma_c_vec += base_sigma_c;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::computeTraction(normal, el_type,
ghost_type);
// adjust damage
Array<Real>::scalar_iterator delta_c_it =
this->delta_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_max_it =
this->delta_max(el_type, ghost_type).begin();
Array<Real>::scalar_iterator damage_it =
this->damage(el_type, ghost_type).begin();
Array<Real>::scalar_iterator damage_end =
this->damage(el_type, ghost_type).end();
for (; damage_it != damage_end; ++damage_it, ++delta_max_it, ++delta_c_it) {
*damage_it =
std::max((*delta_max_it - delta_0) / (*delta_c_it - delta_0), Real(0.));
*damage_it = std::min(*damage_it, Real(1.));
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_bilinear, MaterialCohesiveBilinear);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
index 4c5b6a09d..5653bf663 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
@@ -1,106 +1,105 @@
/**
* @file material_cohesive_bilinear.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Sun Dec 03 2017
*
* @brief Bilinear cohesive constitutive law
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#ifndef __AKANTU_MATERIAL_COHESIVE_BILINEAR_HH__
#define __AKANTU_MATERIAL_COHESIVE_BILINEAR_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material bilinear
*
* parameters in the material files :
* - delta_0 : elastic limit displacement (default: 0)
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default:
* 0)
* - G_cI : fracture energy for mode I (default: 0)
* - G_cII : fracture energy for mode II (default: 0)
* - penalty : stiffness in compression to prevent penetration
*/
template <UInt spatial_dimension>
class MaterialCohesiveBilinear
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveBilinear(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// set material parameters for new elements
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/**
* Scale traction sigma_c according to the volume of the
* two elements surrounding an element
*/
void scaleTraction(const Element & el, Vector<Real> & sigma_c_vec);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// elastic limit displacement
Real delta_0;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "material_cohesive_elastic_inline_impl.cc"
} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_BILINEAR_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
index 35ecec09e..139d64a96 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
@@ -1,349 +1,349 @@
/**
* @file material_cohesive_exponential.cc
*
+ * @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Mon Jul 09 2012
- * @date last modification: Tue Aug 04 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Exponential irreversible cohesive law of mixed mode loading
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_exponential.hh"
#include "dof_synchronizer.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveExponential<spatial_dimension>::MaterialCohesiveExponential(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesive(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("beta", beta, Real(0.), _pat_parsable, "Beta parameter");
this->registerParam("exponential_penalty", exp_penalty, true, _pat_parsable,
"Is contact penalty following the exponential law?");
this->registerParam(
"contact_tangent", contact_tangent, Real(1.0), _pat_parsable,
"Ratio of contact tangent over the initial exponential tangent");
// this->initInternalArray(delta_max, 1, _ek_cohesive);
use_previous_delta_max = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesive::initMaterial();
if ((exp_penalty) && (contact_tangent != 1)) {
contact_tangent = 1;
AKANTU_DEBUG_WARNING("The parsed paramter <contact_tangent> is forced to "
"1.0 when the contact penalty follows the exponential "
"law");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto traction_it = tractions(el_type, ghost_type).begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto traction_end = tractions(el_type, ghost_type).end(spatial_dimension);
auto delta_max_it = delta_max(el_type, ghost_type).begin();
auto delta_max_prev_it = delta_max.previous(el_type, ghost_type).begin();
/// compute scalars
Real beta2 = beta * beta;
/// loop on each quadrature point
for (; traction_it != traction_end; ++traction_it, ++opening_it, ++normal_it,
++delta_max_it, ++delta_max_prev_it) {
/// compute normal and tangential opening vectors
Real normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening(spatial_dimension);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \beta^2 \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta = tangential_opening_norm;
delta *= delta * beta2;
delta += normal_opening_norm * normal_opening_norm;
delta = sqrt(delta);
if ((normal_opening_norm < 0) &&
(std::abs(normal_opening_norm) > Math::getTolerance())) {
Vector<Real> op_n(*normal_it);
op_n *= normal_opening_norm;
Vector<Real> delta_s(*opening_it);
delta_s -= op_n;
delta = tangential_opening_norm * beta;
computeCoupledTraction(*traction_it, *normal_it, delta, delta_s,
*delta_max_it, *delta_max_prev_it);
computeCompressiveTraction(*traction_it, *normal_it, normal_opening_norm,
*opening_it);
} else
computeCoupledTraction(*traction_it, *normal_it, delta, *opening_it,
*delta_max_it, *delta_max_prev_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCoupledTraction(
Vector<Real> & tract, const Vector<Real> & normal, Real delta,
const Vector<Real> & opening, Real & delta_max_new, Real delta_max) {
AKANTU_DEBUG_IN();
/// full damage case
if (std::abs(delta) < Math::getTolerance()) {
/// set traction to zero
tract.clear();
} else { /// element not fully damaged
/**
* Compute traction loading @f$ \mathbf{T} =
* e \sigma_c \frac{\delta}{\delta_c} e^{-\delta/ \delta_c}@f$
*/
/**
* Compute traction unloading @f$ \mathbf{T} =
* \frac{t_{max}}{\delta_{max}} \delta @f$
*/
Real beta2 = beta * beta;
Real normal_open_norm = opening.dot(normal);
Vector<Real> op_n_n(spatial_dimension);
op_n_n = normal;
op_n_n *= (1 - beta2);
op_n_n *= normal_open_norm;
tract = beta2 * opening;
tract += op_n_n;
delta_max_new = std::max(delta_max, delta);
tract *= exp(1) * sigma_c * exp(-delta_max_new / delta_c) / delta_c;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCompressiveTraction(
Vector<Real> & tract, const Vector<Real> & normal, Real delta_n,
__attribute__((unused)) const Vector<Real> & opening) {
Vector<Real> temp_tract(normal);
if (exp_penalty) {
temp_tract *=
delta_n * exp(1) * sigma_c * exp(-delta_n / delta_c) / delta_c;
} else {
Real initial_tg = contact_tangent * exp(1) * sigma_c * delta_n / delta_c;
temp_tract *= initial_tg;
}
tract += temp_tract;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeTangentTraction(
const ElementType & el_type, Array<Real> & tangent_matrix,
const Array<Real> & normal, GhostType ghost_type) {
AKANTU_DEBUG_IN();
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);
auto normal_it = normal.begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
auto delta_max_it = delta_max.previous(el_type, ghost_type).begin();
Real beta2 = beta * beta;
/**
* compute tangent matrix @f$ \frac{\partial \mathbf{t}}
* {\partial \delta} = \hat{\mathbf{t}} \otimes
* \frac{\partial (t/\delta)}{\partial \delta}
* \frac{\hat{\mathbf{t}}}{\delta}+ \frac{t}{\delta} [ \beta^2 \mathbf{I} +
* (1-\beta^2) (\mathbf{n} \otimes \mathbf{n})] @f$
**/
/**
* In which @f$
* \frac{\partial(t/ \delta)}{\partial \delta} =
* \left\{\begin{array} {l l}
* -e \frac{\sigma_c}{\delta_c^2 }e^{-\delta / \delta_c} & \quad if
* \delta \geq \delta_{max} \\
* 0 & \quad if \delta < \delta_{max}, \delta_n > 0
* \end{array}\right. @f$
**/
for (; tangent_it != tangent_end;
++tangent_it, ++normal_it, ++opening_it, ++delta_max_it) {
Real normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening(spatial_dimension);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
Real delta = tangential_opening_norm;
delta *= delta * beta2;
delta += normal_opening_norm * normal_opening_norm;
delta = sqrt(delta);
if ((normal_opening_norm < 0) &&
(std::abs(normal_opening_norm) > Math::getTolerance())) {
Vector<Real> op_n(*normal_it);
op_n *= normal_opening_norm;
Vector<Real> delta_s(*opening_it);
delta_s -= op_n;
delta = tangential_opening_norm * beta;
computeCoupledTangent(*tangent_it, *normal_it, delta, delta_s,
*delta_max_it);
computeCompressivePenalty(*tangent_it, *normal_it, normal_opening_norm);
} else
computeCoupledTangent(*tangent_it, *normal_it, delta, *opening_it,
*delta_max_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCoupledTangent(
Matrix<Real> & tangent, const Vector<Real> & normal, Real delta,
const Vector<Real> & opening, Real) {
AKANTU_DEBUG_IN();
Real beta2 = beta * beta;
Matrix<Real> J(spatial_dimension, spatial_dimension);
J.eye(beta2);
if (std::abs(delta) < Math::getTolerance()) {
delta = Math::getTolerance();
}
Real opening_normal;
opening_normal = opening.dot(normal);
Vector<Real> delta_e(normal);
delta_e *= opening_normal;
delta_e *= (1 - beta2);
delta_e += (beta2 * opening);
Real exponent = exp(1 - delta / delta_c) * sigma_c / delta_c;
Matrix<Real> first_term(spatial_dimension, spatial_dimension);
first_term.outerProduct(normal, normal);
first_term *= (1 - beta2);
first_term += J;
Matrix<Real> second_term(spatial_dimension, spatial_dimension);
second_term.outerProduct(delta_e, delta_e);
second_term /= delta;
second_term /= delta_c;
Matrix<Real> diff(first_term);
diff -= second_term;
tangent = diff;
tangent *= exponent;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCompressivePenalty(
Matrix<Real> & tangent, const Vector<Real> & normal, Real delta_n) {
if (!exp_penalty)
delta_n = 0;
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(normal, normal);
Real normal_tg = contact_tangent * exp(1) * sigma_c *
exp(-delta_n / delta_c) * (1 - delta_n / delta_c) / delta_c;
n_outer_n *= normal_tg;
tangent += n_outer_n;
}
INSTANTIATE_MATERIAL(cohesive_exponential, MaterialCohesiveExponential);
} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
index 3b2b569c0..17e667827 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
@@ -1,123 +1,122 @@
/**
* @file material_cohesive_exponential.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 06 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Exponential irreversible cohesive law of mixed mode loading
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH__
#define __AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material Exponential damage
*
* parameters in the material files :
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default:
* 0)
* - delta_c : critical opening (default: 0)
*/
template <UInt spatial_dimension>
class MaterialCohesiveExponential : public MaterialCohesive {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveExponential(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// Initialization
void initMaterial() override;
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type = _not_ghost) override;
private:
void computeCoupledTraction(Vector<Real> & tract, const Vector<Real> & normal,
Real delta, const Vector<Real> & opening,
Real & delta_max_new, Real delta_max);
void computeCompressiveTraction(Vector<Real> & tract,
const Vector<Real> & normal, Real delta_n,
const Vector<Real> & opening);
void computeCoupledTangent(Matrix<Real> & tangent,
const Vector<Real> & normal, Real delta,
const Vector<Real> & opening, Real delta_max_new);
void computeCompressivePenalty(Matrix<Real> & tangent,
const Vector<Real> & normal, Real delta_n);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// beta parameter
Real beta;
/// contact penalty = initial slope ?
bool exp_penalty;
/// Ratio of contact tangent over the initial exponential tangent
Real contact_tangent;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
// #include "material_cohesive_exponential_inline_impl.cc"
} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
index 806cb7ef9..e63e3154a 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
@@ -1,419 +1,419 @@
/**
* @file material_cohesive_linear.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <numeric>
/* -------------------------------------------------------------------------- */
#include "dof_synchronizer.hh"
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinear<spatial_dimension>::MaterialCohesiveLinear(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesive(model, id), sigma_c_eff("sigma_c_eff", *this),
delta_c_eff("delta_c_eff", *this),
insertion_stress("insertion_stress", *this) {
AKANTU_DEBUG_IN();
this->registerParam("beta", beta, Real(0.), _pat_parsable | _pat_readable,
"Beta parameter");
this->registerParam("G_c", G_c, Real(0.), _pat_parsable | _pat_readable,
"Mode I fracture energy");
this->registerParam("penalty", penalty, Real(0.),
_pat_parsable | _pat_readable, "Penalty coefficient");
this->registerParam("volume_s", volume_s, Real(0.),
_pat_parsable | _pat_readable,
"Reference volume for sigma_c scaling");
this->registerParam("m_s", m_s, Real(1.), _pat_parsable | _pat_readable,
"Weibull exponent for sigma_c scaling");
this->registerParam("kappa", kappa, Real(1.), _pat_parsable | _pat_readable,
"Kappa parameter");
this->registerParam(
"contact_after_breaking", contact_after_breaking, false,
_pat_parsable | _pat_readable,
"Activation of contact when the elements are fully damaged");
this->registerParam("max_quad_stress_insertion", max_quad_stress_insertion,
false, _pat_parsable | _pat_readable,
"Insertion of cohesive element when stress is high "
"enough just on one quadrature point");
this->registerParam("recompute", recompute, false,
_pat_parsable | _pat_modifiable, "recompute solution");
this->use_previous_delta_max = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesive::initMaterial();
sigma_c_eff.initialize(1);
delta_c_eff.initialize(1);
insertion_stress.initialize(spatial_dimension);
if (not Math::are_float_equal(delta_c, 0.))
delta_c_eff.setDefaultValue(delta_c);
else
delta_c_eff.setDefaultValue(2 * G_c / sigma_c);
if (model->getIsExtrinsic())
scaleInsertionTraction();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::updateInternalParameters() {
/// compute scalars
beta2_kappa2 = beta * beta / kappa / kappa;
beta2_kappa = beta * beta / kappa;
if (Math::are_float_equal(beta, 0))
beta2_inv = 0;
else
beta2_inv = 1. / beta / beta;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::scaleInsertionTraction() {
AKANTU_DEBUG_IN();
// do nothing if volume_s hasn't been specified by the user
if (Math::are_float_equal(volume_s, 0.))
return;
const Mesh & mesh_facets = model->getMeshFacets();
const auto & fe_engine = model->getFEEngine();
const auto & fe_engine_facet = model->getFEEngine("FacetsFEEngine");
Real base_sigma_c = sigma_c;
for (auto && type_facet : mesh_facets.elementTypes(spatial_dimension - 1)) {
const Array<std::vector<Element>> & facet_to_element =
mesh_facets.getElementToSubelement(type_facet);
UInt nb_facet = facet_to_element.size();
UInt nb_quad_per_facet = fe_engine_facet.getNbIntegrationPoints(type_facet);
// iterator to modify sigma_c for all the quadrature points of a facet
auto sigma_c_iterator =
sigma_c(type_facet).begin_reinterpret(nb_quad_per_facet, nb_facet);
for (UInt f = 0; f < nb_facet; ++f, ++sigma_c_iterator) {
const std::vector<Element> & element_list = facet_to_element(f);
// compute bounding volume
Real volume = 0;
auto elem = element_list.begin();
auto elem_end = element_list.end();
for (; elem != elem_end; ++elem) {
if (*elem == ElementNull)
continue;
// unit vector for integration in order to obtain the volume
UInt nb_quadrature_points =
fe_engine.getNbIntegrationPoints(elem->type);
Vector<Real> unit_vector(nb_quadrature_points, 1);
volume += fe_engine.integrate(unit_vector, elem->type, elem->element,
elem->ghost_type);
}
// scale sigma_c
*sigma_c_iterator -= base_sigma_c;
*sigma_c_iterator *= std::pow(volume_s / volume, 1. / m_s);
*sigma_c_iterator += base_sigma_c;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::checkInsertion(
bool check_only) {
AKANTU_DEBUG_IN();
const Mesh & mesh_facets = model->getMeshFacets();
CohesiveElementInserter & inserter = model->getElementInserter();
for (auto && type_facet : mesh_facets.elementTypes(spatial_dimension - 1)) {
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
const auto & facets_check = inserter.getCheckFacets(type_facet);
auto & f_insertion = inserter.getInsertionFacets(type_facet);
auto & f_filter = facet_filter(type_facet);
auto & sig_c_eff = sigma_c_eff(type_cohesive);
auto & del_c = delta_c_eff(type_cohesive);
auto & ins_stress = insertion_stress(type_cohesive);
auto & trac_old = tractions.previous(type_cohesive);
const auto & f_stress = model->getStressOnFacets(type_facet);
const auto & sigma_lim = sigma_c(type_facet);
UInt nb_quad_facet =
model->getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
UInt nb_quad_cohesive = model->getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(type_cohesive);
AKANTU_DEBUG_ASSERT(nb_quad_cohesive == nb_quad_facet,
"The cohesive element and the corresponding facet do "
"not have the same numbers of integration points");
UInt nb_facet = f_filter.size();
// if (nb_facet == 0) continue;
auto sigma_lim_it = sigma_lim.begin();
Matrix<Real> stress_tmp(spatial_dimension, spatial_dimension);
Matrix<Real> normal_traction(spatial_dimension, nb_quad_facet);
Vector<Real> stress_check(nb_quad_facet);
UInt sp2 = spatial_dimension * spatial_dimension;
const auto & tangents = model->getTangents(type_facet);
const auto & normals = model->getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(type_facet);
auto normal_begin = normals.begin(spatial_dimension);
auto tangent_begin = tangents.begin(tangents.getNbComponent());
auto facet_stress_begin =
f_stress.begin(spatial_dimension, spatial_dimension * 2);
std::vector<Real> new_sigmas;
std::vector<Vector<Real>> new_normal_traction;
std::vector<Real> new_delta_c;
// loop over each facet belonging to this material
for (UInt f = 0; f < nb_facet; ++f, ++sigma_lim_it) {
UInt facet = f_filter(f);
// skip facets where check shouldn't be realized
if (!facets_check(facet))
continue;
// compute the effective norm on each quadrature point of the facet
for (UInt q = 0; q < nb_quad_facet; ++q) {
UInt current_quad = facet * nb_quad_facet + q;
const Vector<Real> & normal = normal_begin[current_quad];
const Vector<Real> & tangent = tangent_begin[current_quad];
const Matrix<Real> & facet_stress_it = facet_stress_begin[current_quad];
// compute average stress on the current quadrature point
Matrix<Real> stress_1(facet_stress_it.storage(), spatial_dimension,
spatial_dimension);
Matrix<Real> stress_2(facet_stress_it.storage() + sp2,
spatial_dimension, spatial_dimension);
stress_tmp.copy(stress_1);
stress_tmp += stress_2;
stress_tmp /= 2.;
Vector<Real> normal_traction_vec(normal_traction(q));
// compute normal and effective stress
stress_check(q) = computeEffectiveNorm(stress_tmp, normal, tangent,
normal_traction_vec);
}
// verify if the effective stress overcomes the threshold
Real final_stress = stress_check.mean();
if (max_quad_stress_insertion)
final_stress = *std::max_element(
stress_check.storage(), stress_check.storage() + nb_quad_facet);
if (final_stress > *sigma_lim_it) {
f_insertion(facet) = true;
if (check_only)
continue;
// store the new cohesive material parameters for each quadrature
// point
for (UInt q = 0; q < nb_quad_facet; ++q) {
Real new_sigma = stress_check(q);
Vector<Real> normal_traction_vec(normal_traction(q));
if (spatial_dimension != 3)
normal_traction_vec *= -1.;
new_sigmas.push_back(new_sigma);
new_normal_traction.push_back(normal_traction_vec);
Real new_delta;
// set delta_c in function of G_c or a given delta_c value
if (Math::are_float_equal(delta_c, 0.))
new_delta = 2 * G_c / new_sigma;
else
new_delta = (*sigma_lim_it) / new_sigma * delta_c;
new_delta_c.push_back(new_delta);
}
}
}
// update material data for the new elements
UInt old_nb_quad_points = sig_c_eff.size();
UInt new_nb_quad_points = new_sigmas.size();
sig_c_eff.resize(old_nb_quad_points + new_nb_quad_points);
ins_stress.resize(old_nb_quad_points + new_nb_quad_points);
trac_old.resize(old_nb_quad_points + new_nb_quad_points);
del_c.resize(old_nb_quad_points + new_nb_quad_points);
for (UInt q = 0; q < new_nb_quad_points; ++q) {
sig_c_eff(old_nb_quad_points + q) = new_sigmas[q];
del_c(old_nb_quad_points + q) = new_delta_c[q];
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
ins_stress(old_nb_quad_points + q, dim) = new_normal_traction[q](dim);
trac_old(old_nb_quad_points + q, dim) = new_normal_traction[q](dim);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto traction_it = tractions(el_type, ghost_type).begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto traction_end = tractions(el_type, ghost_type).end(spatial_dimension);
auto sigma_c_it = sigma_c_eff(el_type, ghost_type).begin();
auto delta_max_it = delta_max(el_type, ghost_type).begin();
auto delta_c_it = delta_c_eff(el_type, ghost_type).begin();
auto damage_it = damage(el_type, ghost_type).begin();
auto insertion_stress_it =
insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++normal_it, ++sigma_c_it, ++delta_max_it,
++delta_c_it, ++damage_it, ++contact_traction_it, ++insertion_stress_it,
++contact_opening_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
this->computeTractionOnQuad(
*traction_it, *opening_it, *normal_it, *delta_max_it, *delta_c_it,
*insertion_stress_it, *sigma_c_it, normal_opening, tangential_opening,
normal_opening_norm, tangential_opening_norm, *damage_it, penetration,
*contact_traction_it, *contact_opening_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
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
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
/// NB: delta_max_it points on delta_max_previous, i.e. the
/// delta_max related to the solution of the previous incremental
/// step
auto delta_max_it = delta_max.previous(el_type, ghost_type).begin();
auto sigma_c_it = sigma_c_eff(el_type, ghost_type).begin();
auto delta_c_it = delta_c_eff(el_type, ghost_type).begin();
auto damage_it = damage(el_type, ghost_type).begin();
auto contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end; ++tangent_it, ++normal_it, ++opening_it,
++delta_max_it, ++sigma_c_it, ++delta_c_it,
++damage_it, ++contact_opening_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
this->computeTangentTractionOnQuad(
*tangent_it, *delta_max_it, *delta_c_it, *sigma_c_it, *opening_it,
*normal_it, normal_opening, tangential_opening, normal_opening_norm,
tangential_opening_norm, *damage_it, penetration, *contact_opening_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear, MaterialCohesiveLinear);
} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
index 56dd8570e..6102277b5 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
@@ -1,188 +1,188 @@
/**
* @file material_cohesive_linear.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__
namespace akantu {
/**
* Cohesive material linear damage for extrinsic case
*
* parameters in the material files :
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default:
* 0)
* - G_cI : fracture energy for mode I (default: 0)
* - G_cII : fracture energy for mode II (default: 0)
* - penalty : stiffness in compression to prevent penetration
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinear : public MaterialCohesive {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveLinear(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
void updateInternalParameters() override;
/// check stress for cohesive elements' insertion
void checkInsertion(bool check_only = false) override;
/// compute effective stress norm for insertion check
Real computeEffectiveNorm(const Matrix<Real> & stress,
const Vector<Real> & normal,
const Vector<Real> & tangent,
Vector<Real> & normal_stress) const;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute tangent stiffness matrix
void computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) override;
/**
* Scale insertion traction sigma_c according to the volume of the
* two elements surrounding a facet
*
* see the article: F. Zhou and J. F. Molinari "Dynamic crack
* propagation with cohesive elements: a methodology to address mesh
* dependency" International Journal for Numerical Methods in
* Engineering (2004)
*/
void scaleInsertionTraction();
/// compute the traction for a given quadrature point
inline void computeTractionOnQuad(
Vector<Real> & traction, Vector<Real> & opening,
const Vector<Real> & normal, Real & delta_max, const Real & delta_c,
const Vector<Real> & insertion_stress, const Real & sigma_c,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_traction,
Vector<Real> & contact_opening);
inline void computeTangentTractionOnQuad(
Matrix<Real> & tangent, Real & delta_max, const Real & delta_c,
const Real & sigma_c, Vector<Real> & opening, const Vector<Real> & normal,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_opening);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get sigma_c_eff
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(InsertionTraction, sigma_c_eff, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// beta parameter
Real beta;
/// beta square inverse to compute effective norm
Real beta2_inv;
/// mode I fracture energy
Real G_c;
/// kappa parameter
Real kappa;
/// constitutive law scalar to compute delta
Real beta2_kappa2;
/// constitutive law scalar to compute traction
Real beta2_kappa;
/// penalty coefficient
Real penalty;
/// reference volume used to scale sigma_c
Real volume_s;
/// weibull exponent used to scale sigma_c
Real m_s;
/// variable defining if we are recomputing the last loading step
/// after load_reduction
bool recompute;
/// critical effective stress
RandomInternalField<Real, CohesiveInternalField> sigma_c_eff;
/// effective critical displacement (each element can have a
/// different value)
CohesiveInternalField<Real> delta_c_eff;
/// stress at insertion
CohesiveInternalField<Real> insertion_stress;
/// variable saying if there should be penalty contact also after
/// breaking the cohesive elements
bool contact_after_breaking;
/// insertion of cohesive element when stress is high enough just on
/// one quadrature point
bool max_quad_stress_insertion;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // akantu
#include "material_cohesive_linear_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
index 432b7e673..0f931e311 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
@@ -1,298 +1,298 @@
/**
* @file material_cohesive_linear_fatigue.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 20 2015
- * @date last modification: Tue Jan 12 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief See material_cohesive_linear_fatigue.hh for information
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_fatigue.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearFatigue<spatial_dimension>::MaterialCohesiveLinearFatigue(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesiveLinear<spatial_dimension>(model, id),
delta_prec("delta_prec", *this), K_plus("K_plus", *this),
K_minus("K_minus", *this), T_1d("T_1d", *this),
switches("switches", *this), delta_dot_prec("delta_dot_prec", *this),
normal_regime("normal_regime", *this) {
this->registerParam("delta_f", delta_f, Real(-1.),
_pat_parsable | _pat_readable, "delta_f");
this->registerParam("progressive_delta_f", progressive_delta_f, false,
_pat_parsable | _pat_readable,
"Whether or not delta_f is equal to delta_max");
this->registerParam("count_switches", count_switches, false,
_pat_parsable | _pat_readable,
"Count the opening/closing switches per element");
this->registerParam(
"fatigue_ratio", fatigue_ratio, Real(1.), _pat_parsable | _pat_readable,
"What portion of the cohesive law is subjected to fatigue");
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFatigue<spatial_dimension>::initMaterial() {
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
// check that delta_f has a proper value or assign a defaul value
if (delta_f < 0)
delta_f = this->delta_c_eff;
else if (delta_f < this->delta_c_eff)
AKANTU_ERROR("Delta_f must be greater or equal to delta_c");
delta_prec.initialize(1);
K_plus.initialize(1);
K_minus.initialize(1);
T_1d.initialize(1);
normal_regime.initialize(1);
if (count_switches) {
switches.initialize(1);
delta_dot_prec.initialize(1);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFatigue<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
const Array<Real> & sigma_c_array = this->sigma_c_eff(el_type, ghost_type);
Array<Real> & delta_max_array = this->delta_max(el_type, ghost_type);
const Array<Real> & delta_c_array = this->delta_c_eff(el_type, ghost_type);
Array<Real> & damage_array = this->damage(el_type, ghost_type);
auto insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Array<Real> & delta_prec_array = delta_prec(el_type, ghost_type);
Array<Real> & K_plus_array = K_plus(el_type, ghost_type);
Array<Real> & K_minus_array = K_minus(el_type, ghost_type);
Array<Real> & T_1d_array = T_1d(el_type, ghost_type);
Array<bool> & normal_regime_array = normal_regime(el_type, ghost_type);
Array<UInt> * switches_array = nullptr;
Array<Real> * delta_dot_prec_array = nullptr;
if (count_switches) {
switches_array = &switches(el_type, ghost_type);
delta_dot_prec_array = &delta_dot_prec(el_type, ghost_type);
}
auto * memory_space = new Real[2 * spatial_dimension];
Vector<Real> normal_opening(memory_space, spatial_dimension);
Vector<Real> tangential_opening(memory_space + spatial_dimension,
spatial_dimension);
Real tolerance = Math::getTolerance();
/// loop on each quadrature point
for (UInt q = 0; traction_it != traction_end; ++traction_it, ++opening_it,
++normal_it, ++contact_traction_it, ++insertion_stress_it,
++contact_opening_it, ++q) {
/// compute normal and tangential opening vectors
Real normal_opening_norm = opening_it->dot(*normal_it);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \frac{\beta^2}{\kappa^2} \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
bool penetration = normal_opening_norm < -tolerance;
if (this->contact_after_breaking == false &&
Math::are_float_equal(damage_array(q), 1.))
penetration = false;
if (penetration) {
/// use penalty coefficient in case of penetration
*contact_traction_it = normal_opening;
*contact_traction_it *= this->penalty;
*contact_opening_it = normal_opening;
/// don't consider penetration contribution for delta
*opening_it = tangential_opening;
normal_opening.clear();
} else {
delta += normal_opening_norm * normal_opening_norm;
contact_traction_it->clear();
contact_opening_it->clear();
}
delta = std::sqrt(delta);
/**
* Compute traction @f$ \mathbf{T} = \left(
* \frac{\beta^2}{\kappa} \Delta_t \mathbf{t} + \Delta_n
* \mathbf{n} \right) \frac{\sigma_c}{\delta} \left( 1-
* \frac{\delta}{\delta_c} \right)@f$
*/
// update maximum displacement and damage
delta_max_array(q) = std::max(delta, delta_max_array(q));
damage_array(q) = std::min(delta_max_array(q) / delta_c_array(q), Real(1.));
Real delta_dot = delta - delta_prec_array(q);
// count switches if asked
if (count_switches) {
if ((delta_dot > 0. && (*delta_dot_prec_array)(q) <= 0.) ||
(delta_dot < 0. && (*delta_dot_prec_array)(q) >= 0.))
++((*switches_array)(q));
(*delta_dot_prec_array)(q) = delta_dot;
}
// set delta_f equal to delta_max if desired
if (progressive_delta_f)
delta_f = delta_max_array(q);
// broken element case
if (Math::are_float_equal(damage_array(q), 1.))
traction_it->clear();
// just inserted element case
else if (Math::are_float_equal(damage_array(q), 0.)) {
if (penetration)
traction_it->clear();
else
*traction_it = *insertion_stress_it;
// initialize the 1d traction to sigma_c
T_1d_array(q) = sigma_c_array(q);
}
// normal case
else {
// if element is closed then there are zero tractions
if (delta <= tolerance)
traction_it->clear();
// otherwise compute new tractions if the new delta is different
// than the previous one
else if (std::abs(delta_dot) > tolerance) {
// loading case
if (delta_dot > 0.) {
if (!normal_regime_array(q)) {
// equation (4) of the article
K_plus_array(q) *= 1. - delta_dot / delta_f;
// equivalent to equation (2) of the article
T_1d_array(q) += K_plus_array(q) * delta_dot;
// in case of reloading, traction must not exceed that of the
// envelop of the cohesive law
Real max_traction =
sigma_c_array(q) * (1 - delta / delta_c_array(q));
bool max_traction_exceeded = T_1d_array(q) > max_traction;
if (max_traction_exceeded)
T_1d_array(q) = max_traction;
// switch to standard linear cohesive law
if (delta_max_array(q) > fatigue_ratio * delta_c_array(q)) {
// reset delta_max to avoid big jumps in the traction
delta_max_array(q) =
sigma_c_array(q) /
(T_1d_array(q) / delta + sigma_c_array(q) / delta_c_array(q));
damage_array(q) =
std::min(delta_max_array(q) / delta_c_array(q), Real(1.));
K_minus_array(q) = sigma_c_array(q) / delta_max_array(q) *
(1. - damage_array(q));
normal_regime_array(q) = true;
} else {
// equation (3) of the article
K_minus_array(q) = T_1d_array(q) / delta;
// if the traction is following the cohesive envelop, then
// K_plus has to be reset
if (max_traction_exceeded)
K_plus_array(q) = K_minus_array(q);
}
} else {
// compute stiffness according to the standard law
K_minus_array(q) =
sigma_c_array(q) / delta_max_array(q) * (1. - damage_array(q));
}
}
// unloading case
else if (!normal_regime_array(q)) {
// equation (4) of the article
K_plus_array(q) +=
(K_plus_array(q) - K_minus_array(q)) * delta_dot / delta_f;
// equivalent to equation (2) of the article
T_1d_array(q) = K_minus_array(q) * delta;
}
// applying the actual stiffness
*traction_it = tangential_opening;
*traction_it *= this->beta2_kappa;
*traction_it += normal_opening;
*traction_it *= K_minus_array(q);
}
}
// update precendent delta
delta_prec_array(q) = delta;
}
delete[] memory_space;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear_fatigue, MaterialCohesiveLinearFatigue);
} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
index 93d3329d2..7c204eadc 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
@@ -1,133 +1,132 @@
/**
* @file material_cohesive_linear_fatigue.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Jun 25 2015
+ * @date last modification: Sun Dec 03 2017
*
* @brief Linear irreversible cohesive law with dissipative
* unloading-reloading cycles
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Linear irreversible cohesive law with dissipative
* unloading-reloading cycles
*
* This law uses two different stiffnesses during unloading and
* reloading. The implementation is based on the article entitled "A
* cohesive model for fatigue crack growth" by Nguyen, Repetto, Ortiz
* and Radovitzky (2001). This law is identical to the
* MaterialCohesiveLinear one except for the unloading-reloading
* phase.
*
* input parameter:
*
* - delta_f : it must be greater than delta_c and it is inversely
* proportional to the dissipation in the unloading-reloading
* cycles (default: delta_c)
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearFatigue
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveLinearFatigue(SolidMechanicsModel & model,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the switches
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Switches, switches, UInt);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// delta_f parameter
Real delta_f;
/// variable saying if delta_f is equal to delta_max for each
/// element when the traction is computed
bool progressive_delta_f;
/// count the opening/closing switches per element
bool count_switches;
/// delta of the previous step
CohesiveInternalField<Real> delta_prec;
/// stiffness for reloading
CohesiveInternalField<Real> K_plus;
/// stiffness for unloading
CohesiveInternalField<Real> K_minus;
/// 1D traction in the cohesive law
CohesiveInternalField<Real> T_1d;
/// Number of opening/closing switches
CohesiveInternalField<UInt> switches;
/// delta increment of the previous time step
CohesiveInternalField<Real> delta_dot_prec;
/// has the element passed to normal regime (not in fatigue anymore)
CohesiveInternalField<bool> normal_regime;
/// ratio indicating until what point fatigue is applied in the cohesive law
Real fatigue_ratio;
};
} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
index 9de56ad9b..0379b2531 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
@@ -1,277 +1,277 @@
/**
* @file material_cohesive_linear_friction.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Tue Jan 12 2016
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_friction.hh"
#include "solid_mechanics_model_cohesive.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearFriction<spatial_dimension>::
MaterialCohesiveLinearFriction(SolidMechanicsModel & model, const ID & id)
: MaterialParent(model, id), residual_sliding("residual_sliding", *this),
friction_force("friction_force", *this) {
AKANTU_DEBUG_IN();
this->registerParam("mu", mu_max, Real(0.), _pat_parsable | _pat_readable,
"Maximum value of the friction coefficient");
this->registerParam("penalty_for_friction", friction_penalty, Real(0.),
_pat_parsable | _pat_readable,
"Penalty parameter for the friction behavior");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialParent::initMaterial();
friction_force.initialize(spatial_dimension);
residual_sliding.initialize(1);
residual_sliding.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::computeTraction(
__attribute__((unused)) const Array<Real> & normal, ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
residual_sliding.resize();
friction_force.resize();
/// define iterators
auto traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
auto traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto previous_opening_it =
this->opening.previous(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_max_it = this->delta_max(el_type, ghost_type).begin();
auto delta_max_prev_it =
this->delta_max.previous(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_it = this->damage(el_type, ghost_type).begin();
auto insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
auto res_sliding_it = this->residual_sliding(el_type, ghost_type).begin();
auto res_sliding_prev_it =
this->residual_sliding.previous(el_type, ghost_type).begin();
auto friction_force_it =
this->friction_force(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
if (not this->model->isDefaultSolverExplicit())
this->delta_max(el_type, ghost_type)
.copy(this->delta_max.previous(el_type, ghost_type));
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++normal_it, ++sigma_c_it, ++delta_max_it,
++delta_c_it, ++damage_it, ++contact_traction_it, ++insertion_stress_it,
++contact_opening_it, ++delta_max_prev_it, ++res_sliding_it,
++res_sliding_prev_it, ++friction_force_it, ++previous_opening_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
this->computeTractionOnQuad(
*traction_it, *opening_it, *normal_it, *delta_max_it, *delta_c_it,
*insertion_stress_it, *sigma_c_it, normal_opening, tangential_opening,
normal_opening_norm, tangential_opening_norm, *damage_it, penetration,
*contact_traction_it, *contact_opening_it);
if (penetration) {
/// the friction coefficient mu increases with the damage. It
/// equals the maximum value when damage = 1.
// Real damage = std::min(*delta_max_prev_it / *delta_c_it,
// Real(1.));
Real mu = mu_max; // * damage;
/// the definition of tau_max refers to the opening
/// (penetration) of the previous incremental step
Real normal_opening_prev_norm =
std::min(previous_opening_it->dot(*normal_it), Real(0.));
// Vector<Real> normal_opening_prev = (*normal_it);
// normal_opening_prev *= normal_opening_prev_norm;
Real tau_max = mu * this->penalty * (std::abs(normal_opening_prev_norm));
Real delta_sliding_norm =
std::abs(tangential_opening_norm - *res_sliding_prev_it);
/// tau is the norm of the friction force, acting tangentially to the
/// surface
Real tau = std::min(friction_penalty * delta_sliding_norm, tau_max);
if ((tangential_opening_norm - *res_sliding_prev_it) < 0.0)
tau = -tau;
/// from tau get the x and y components of friction, to be added in the
/// force vector
Vector<Real> tangent_unit_vector(spatial_dimension);
tangent_unit_vector = tangential_opening / tangential_opening_norm;
*friction_force_it = tau * tangent_unit_vector;
/// update residual_sliding
*res_sliding_it =
tangential_opening_norm - (std::abs(tau) / friction_penalty);
} else {
friction_force_it->clear();
}
*traction_it += *friction_force_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::computeTangentTraction(
const ElementType & el_type, Array<Real> & tangent_matrix,
__attribute__((unused)) const Array<Real> & normal, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto previous_opening_it =
this->opening.previous(el_type, ghost_type).begin(spatial_dimension);
/**
* NB: delta_max_it points on delta_max_previous, i.e. the
* delta_max related to the solution of the previous incremental
* step
*/
auto delta_max_it = this->delta_max.previous(el_type, ghost_type).begin();
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_it = this->damage(el_type, ghost_type).begin();
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto res_sliding_prev_it =
this->residual_sliding.previous(el_type, ghost_type).begin();
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end;
++tangent_it, ++normal_it, ++opening_it, ++previous_opening_it,
++delta_max_it, ++sigma_c_it, ++delta_c_it, ++damage_it,
++contact_opening_it, ++res_sliding_prev_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
this->computeTangentTractionOnQuad(
*tangent_it, *delta_max_it, *delta_c_it, *sigma_c_it, *opening_it,
*normal_it, normal_opening, tangential_opening, normal_opening_norm,
tangential_opening_norm, *damage_it, penetration, *contact_opening_it);
if (penetration) {
// Real damage = std::min(*delta_max_it / *delta_c_it, Real(1.));
Real mu = mu_max; // * damage;
Real normal_opening_prev_norm =
std::min(previous_opening_it->dot(*normal_it), Real(0.));
// Vector<Real> normal_opening_prev = (*normal_it);
// normal_opening_prev *= normal_opening_prev_norm;
Real tau_max = mu * this->penalty * (std::abs(normal_opening_prev_norm));
Real delta_sliding_norm =
std::abs(tangential_opening_norm - *res_sliding_prev_it);
// tau is the norm of the friction force, acting tangentially to the
// surface
Real tau = std::min(friction_penalty * delta_sliding_norm, tau_max);
if (tau < tau_max && tau_max > Math::getTolerance()) {
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye(1.);
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(*normal_it, *normal_it);
Matrix<Real> nn(n_outer_n);
I -= nn;
*tangent_it += I * friction_penalty;
}
}
// check if the tangential stiffness matrix is symmetric
// for (UInt h = 0; h < spatial_dimension; ++h){
// for (UInt l = h; l < spatial_dimension; ++l){
// if (l > h){
// Real k_ls = (*tangent_it)[spatial_dimension*h+l];
// Real k_us = (*tangent_it)[spatial_dimension*l+h];
// // std::cout << "k_ls = " << k_ls << std::endl;
// // std::cout << "k_us = " << k_us << std::endl;
// if (std::abs(k_ls) > 1e-13 && std::abs(k_us) > 1e-13){
// Real error = std::abs((k_ls - k_us) / k_us);
// if (error > 1e-10){
// std::cout << "non symmetric cohesive matrix" << std::endl;
// // std::cout << "error " << error << std::endl;
// }
// }
// }
// }
// }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear_friction, MaterialCohesiveLinearFriction);
} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
index f928863f1..8df782f9c 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
@@ -1,106 +1,105 @@
/**
* @file material_cohesive_linear_friction.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Jan 12 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material linear with friction force
*
* parameters in the material files :
* - mu : friction coefficient
* - penalty_for_friction : Penalty parameter for the friction behavior
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearFriction
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
using MaterialParent = MaterialCohesiveLinear<spatial_dimension>;
public:
MaterialCohesiveLinearFriction(SolidMechanicsModel & model,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute tangent stiffness matrix
void computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// maximum value of the friction coefficient
Real mu_max;
/// penalty parameter for the friction law
Real friction_penalty;
/// history parameter for the friction law
CohesiveInternalField<Real> residual_sliding;
/// friction force
CohesiveInternalField<Real> friction_force;
};
} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.cc
index 08322ed07..448c63ea2 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.cc
@@ -1,264 +1,266 @@
/**
* @file material_cohesive_linear_inline_impl.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 22 2015
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Inline functions of the MaterialCohesiveLinear
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_CC__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_CC__
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline Real MaterialCohesiveLinear<dim>::computeEffectiveNorm(
const Matrix<Real> & stress, const Vector<Real> & normal,
const Vector<Real> & tangent, Vector<Real> & normal_traction) const {
normal_traction.mul<false>(stress, normal);
Real normal_contrib = normal_traction.dot(normal);
/// in 3D tangential components must be summed
Real tangent_contrib = 0;
if (dim == 2) {
Real tangent_contrib_tmp = normal_traction.dot(tangent);
tangent_contrib += tangent_contrib_tmp * tangent_contrib_tmp;
} else if (dim == 3) {
for (UInt s = 0; s < dim - 1; ++s) {
const Vector<Real> tangent_v(tangent.storage() + s * dim, dim);
Real tangent_contrib_tmp = normal_traction.dot(tangent_v);
tangent_contrib += tangent_contrib_tmp * tangent_contrib_tmp;
}
}
tangent_contrib = std::sqrt(tangent_contrib);
normal_contrib = std::max(Real(0.), normal_contrib);
return std::sqrt(normal_contrib * normal_contrib +
tangent_contrib * tangent_contrib * beta2_inv);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialCohesiveLinear<dim>::computeTractionOnQuad(
Vector<Real> & traction, Vector<Real> & opening,
const Vector<Real> & normal, Real & delta_max, const Real & delta_c,
const Vector<Real> & insertion_stress, const Real & sigma_c,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_traction,
Vector<Real> & contact_opening) {
/// compute normal and tangential opening vectors
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
tangential_opening = opening;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \frac{\beta^2}{\kappa^2} \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm / delta_c < -Math::getTolerance();
// penetration = normal_opening_norm < 0.;
if (this->contact_after_breaking == false &&
Math::are_float_equal(damage, 1.))
penetration = false;
if (penetration) {
/// use penalty coefficient in case of penetration
contact_traction = normal_opening;
contact_traction *= this->penalty;
contact_opening = normal_opening;
/// don't consider penetration contribution for delta
opening = tangential_opening;
normal_opening.clear();
} else {
delta += normal_opening_norm * normal_opening_norm;
contact_traction.clear();
contact_opening.clear();
}
delta = std::sqrt(delta);
/// update maximum displacement and damage
delta_max = std::max(delta_max, delta);
damage = std::min(delta_max / delta_c, Real(1.));
/**
* Compute traction @f$ \mathbf{T} = \left(
* \frac{\beta^2}{\kappa} \Delta_t \mathbf{t} + \Delta_n
* \mathbf{n} \right) \frac{\sigma_c}{\delta} \left( 1-
* \frac{\delta}{\delta_c} \right)@f$
*/
if (Math::are_float_equal(damage, 1.))
traction.clear();
else if (Math::are_float_equal(damage, 0.)) {
if (penetration)
traction.clear();
else
traction = insertion_stress;
} else {
traction = tangential_opening;
traction *= this->beta2_kappa;
traction += normal_opening;
AKANTU_DEBUG_ASSERT(delta_max != 0.,
"Division by zero, tolerance might be too low");
traction *= sigma_c / delta_max * (1. - damage);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialCohesiveLinear<dim>::computeTangentTractionOnQuad(
Matrix<Real> & tangent, Real & delta_max, const Real & delta_c,
const Real & sigma_c, Vector<Real> & opening, const Vector<Real> & normal,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_opening) {
/**
* During the update of the residual the interpenetrations are
* stored in the array "contact_opening", therefore, in the case
* of penetration, in the array "opening" there are only the
* tangential components.
*/
opening += contact_opening;
/// compute normal and tangential opening vectors
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
tangential_opening = opening;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
Real delta =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (this->contact_after_breaking == false &&
Math::are_float_equal(damage, 1.))
penetration = false;
Real derivative = 0; // derivative = d(t/delta)/ddelta
Real t = 0;
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(normal, normal);
if (penetration) {
/// stiffness in compression given by the penalty parameter
tangent += n_outer_n;
tangent *= penalty;
opening = tangential_opening;
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
} else {
delta += normal_opening_norm * normal_opening_norm;
}
delta = std::sqrt(delta);
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
if (delta < Math::getTolerance())
delta = delta_c / 1000.;
if (delta >= delta_max) {
if (delta <= delta_c) {
derivative = -sigma_c / (delta * delta);
t = sigma_c * (1 - delta / delta_c);
} else {
derivative = 0.;
t = 0.;
}
} else if (delta < delta_max) {
Real tmax = sigma_c * (1 - delta_max / delta_c);
t = tmax / delta_max * delta;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye(this->beta2_kappa);
Matrix<Real> nn(n_outer_n);
nn *= (1. - this->beta2_kappa);
nn += I;
nn *= t / delta;
Vector<Real> t_tilde(normal_opening);
t_tilde *= (1. - this->beta2_kappa2);
Vector<Real> mm(opening);
mm *= this->beta2_kappa2;
t_tilde += mm;
Vector<Real> t_hat(normal_opening);
t_hat += this->beta2_kappa * tangential_opening;
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(t_hat, t_tilde);
prov *= derivative / delta;
prov += nn;
Matrix<Real> prov_t = prov.transpose();
tangent += prov_t;
}
/* -------------------------------------------------------------------------- */
} // akantu
/* -------------------------------------------------------------------------- */
#endif //__AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_CC__
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
index f31411171..622b5e77b 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
@@ -1,414 +1,413 @@
/**
* @file material_cohesive_linear_uncoupled.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
- * @date creation: Wed Feb 22 2012
- * @date last modification: Thu Jan 14 2016
+ * @date creation: Mon Jul 25 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <numeric>
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_uncoupled.hh"
#include "solid_mechanics_model_cohesive.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearUncoupled<spatial_dimension>::
MaterialCohesiveLinearUncoupled(SolidMechanicsModel & model, const ID & id)
: MaterialCohesiveLinear<spatial_dimension>(model, id),
delta_n_max("delta_n_max", *this), delta_t_max("delta_t_max", *this),
damage_n("damage_n", *this), damage_t("damage_t", *this) {
AKANTU_DEBUG_IN();
this->registerParam(
"roughness", R, Real(1.), _pat_parsable | _pat_readable,
"Roughness to define coupling between mode II and mode I");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
delta_n_max.initialize(1);
delta_t_max.initialize(1);
damage_n.initialize(1);
damage_t.initialize(1);
delta_n_max.initializeHistory();
delta_t_max.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::computeTraction(
const Array<Real> &, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
delta_n_max.resize();
delta_t_max.resize();
damage_n.resize();
damage_t.resize();
/// define iterators
auto traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
auto traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_n_max_it = delta_n_max(el_type, ghost_type).begin();
auto delta_t_max_it = delta_t_max(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_n_it = damage_n(el_type, ghost_type).begin();
auto damage_t_it = damage_t(el_type, ghost_type).begin();
auto insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++contact_traction_it, ++contact_opening_it,
++normal_it, ++sigma_c_it, ++delta_n_max_it, ++delta_t_max_it,
++delta_c_it, ++damage_n_it, ++damage_t_it, ++insertion_stress_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
Real delta_c2_R2 = *delta_c_it * (*delta_c_it) / R / R;
/// compute normal and tangential opening vectors
normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening = *normal_it;
normal_opening *= normal_opening_norm;
// std::cout<< "normal_opening_norm = " << normal_opening_norm
// <<std::endl;
Vector<Real> tangential_opening = *opening_it;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
/// compute effective opening displacement
Real delta_n =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
Real delta_t =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (this->contact_after_breaking == false &&
Math::are_float_equal(*damage_n_it, 1.))
penetration = false;
if (penetration) {
/// use penalty coefficient in case of penetration
*contact_traction_it = normal_opening;
*contact_traction_it *= this->penalty;
*contact_opening_it = normal_opening;
/// don't consider penetration contribution for delta
//*opening_it = tangential_opening;
normal_opening.clear();
} else {
delta_n += normal_opening_norm * normal_opening_norm;
delta_t += normal_opening_norm * normal_opening_norm * delta_c2_R2;
contact_traction_it->clear();
contact_opening_it->clear();
}
delta_n = std::sqrt(delta_n);
delta_t = std::sqrt(delta_t);
/// update maximum displacement and damage
*delta_n_max_it = std::max(*delta_n_max_it, delta_n);
*damage_n_it = std::min(*delta_n_max_it / *delta_c_it, Real(1.));
*delta_t_max_it = std::max(*delta_t_max_it, delta_t);
*damage_t_it = std::min(*delta_t_max_it / *delta_c_it, Real(1.));
Vector<Real> normal_traction(spatial_dimension);
Vector<Real> shear_traction(spatial_dimension);
/// NORMAL TRACTIONS
if (Math::are_float_equal(*damage_n_it, 1.))
normal_traction.clear();
else if (Math::are_float_equal(*damage_n_it, 0.)) {
if (penetration)
normal_traction.clear();
else
normal_traction = *insertion_stress_it;
} else {
// the following formulation holds both in loading and in
// unloading-reloading
normal_traction = normal_opening;
AKANTU_DEBUG_ASSERT(*delta_n_max_it != 0.,
"Division by zero, tolerance might be too low");
normal_traction *= *sigma_c_it / (*delta_n_max_it) * (1. - *damage_n_it);
}
/// SHEAR TRACTIONS
if (Math::are_float_equal(*damage_t_it, 1.))
shear_traction.clear();
else if (Math::are_float_equal(*damage_t_it, 0.)) {
shear_traction.clear();
} else {
shear_traction = tangential_opening;
AKANTU_DEBUG_ASSERT(*delta_t_max_it != 0.,
"Division by zero, tolerance might be too low");
shear_traction *= this->beta2_kappa;
shear_traction *= *sigma_c_it / (*delta_t_max_it) * (1. - *damage_t_it);
}
*traction_it = normal_traction;
*traction_it += shear_traction;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::computeTangentTraction(
const ElementType & el_type, Array<Real> & tangent_matrix,
const Array<Real> &, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
/// NB: delta_max_it points on delta_max_previous, i.e. the
/// delta_max related to the solution of the previous incremental
/// step
auto delta_n_max_it = delta_n_max.previous(el_type, ghost_type).begin();
auto delta_t_max_it = delta_t_max.previous(el_type, ghost_type).begin();
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_n_it = damage_n(el_type, ghost_type).begin();
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end; ++tangent_it, ++normal_it, ++opening_it,
++sigma_c_it, ++delta_c_it,
++delta_n_max_it, ++delta_t_max_it,
++damage_n_it, ++contact_opening_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
Real delta_c2_R2 = *delta_c_it * (*delta_c_it) / R / R;
/**
* During the update of the residual the interpenetrations are
* stored in the array "contact_opening", therefore, in the case
* of penetration, in the array "opening" there are only the
* tangential components.
*/
*opening_it += *contact_opening_it;
/// compute normal and tangential opening vectors
normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening = *normal_it;
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening = *opening_it;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
Real delta_n =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
Real delta_t =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (this->contact_after_breaking == false &&
Math::are_float_equal(*damage_n_it, 1.))
penetration = false;
Real derivative = 0; // derivative = d(t/delta)/ddelta
Real T = 0;
/// TANGENT STIFFNESS FOR NORMAL TRACTIONS
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(*normal_it, *normal_it);
if (penetration) {
/// stiffness in compression given by the penalty parameter
*tangent_it = n_outer_n;
*tangent_it *= this->penalty;
//*opening_it = tangential_opening;
normal_opening.clear();
} else {
delta_n += normal_opening_norm * normal_opening_norm;
delta_n = std::sqrt(delta_n);
delta_t += normal_opening_norm * normal_opening_norm * delta_c2_R2;
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
if (delta_n < Math::getTolerance())
delta_n = *delta_c_it / 1000.;
// loading
if (delta_n >= *delta_n_max_it) {
if (delta_n <= *delta_c_it) {
derivative = -(*sigma_c_it) / (delta_n * delta_n);
T = *sigma_c_it * (1 - delta_n / *delta_c_it);
} else {
derivative = 0.;
T = 0.;
}
// unloading-reloading
} else if (delta_n < *delta_n_max_it) {
Real T_max = *sigma_c_it * (1 - *delta_n_max_it / *delta_c_it);
derivative = 0.;
T = T_max / *delta_n_max_it * delta_n;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> nn(n_outer_n);
nn *= T / delta_n;
Vector<Real> Delta_tilde(normal_opening);
Delta_tilde *= (1. - this->beta2_kappa2);
Vector<Real> mm(*opening_it);
mm *= this->beta2_kappa2;
Delta_tilde += mm;
const Vector<Real> & Delta_hat(normal_opening);
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(Delta_hat, Delta_tilde);
prov *= derivative / delta_n;
prov += nn;
Matrix<Real> prov_t = prov.transpose();
*tangent_it = prov_t;
}
derivative = 0.;
T = 0.;
/// TANGENT STIFFNESS FOR SHEAR TRACTIONS
delta_t = std::sqrt(delta_t);
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
if (delta_t < Math::getTolerance())
delta_t = *delta_c_it / 1000.;
// loading
if (delta_t >= *delta_t_max_it) {
if (delta_t <= *delta_c_it) {
derivative = -(*sigma_c_it) / (delta_t * delta_t);
T = *sigma_c_it * (1 - delta_t / *delta_c_it);
} else {
derivative = 0.;
T = 0.;
}
// unloading-reloading
} else if (delta_t < *delta_t_max_it) {
Real T_max = *sigma_c_it * (1 - *delta_t_max_it / *delta_c_it);
derivative = 0.;
T = T_max / *delta_t_max_it * delta_t;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye();
Matrix<Real> nn(n_outer_n);
I -= nn;
I *= T / delta_t;
Vector<Real> Delta_tilde(normal_opening);
Delta_tilde *= (delta_c2_R2 - this->beta2_kappa2);
Vector<Real> mm(*opening_it);
mm *= this->beta2_kappa2;
Delta_tilde += mm;
Vector<Real> Delta_hat(tangential_opening);
Delta_hat *= this->beta2_kappa;
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(Delta_hat, Delta_tilde);
prov *= derivative / delta_t;
prov += I;
Matrix<Real> prov_t = prov.transpose();
*tangent_it += prov_t;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear_uncoupled,
MaterialCohesiveLinearUncoupled);
} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
index f63de86de..4a7d61404 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
@@ -1,103 +1,102 @@
/**
- * @file material_cohesive_linear.hh
+ * @file material_cohesive_linear_uncoupled.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material linear with two different laws for mode I and
* mode II, for extrinsic case
*
* parameters in the material files :
* - roughness : define the interaction between mode I and mode II (default: 0)
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearUncoupled
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
// typedef MaterialCohesiveLinear<spatial_dimension> MaterialParent;
public:
MaterialCohesiveLinearUncoupled(SolidMechanicsModel & model,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute tangent stiffness matrix
void computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// parameter to tune the interaction between mode II and mode I
Real R;
/// maximum normal displacement
CohesiveInternalField<Real> delta_n_max;
/// maximum tangential displacement
CohesiveInternalField<Real> delta_t_max;
/// damage associated to normal tractions
CohesiveInternalField<Real> damage_n;
/// damage associated to shear tractions
CohesiveInternalField<Real> damage_t;
};
} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
index 4d55b04ce..e22a4f934 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
@@ -1,573 +1,574 @@
/**
* @file material_cohesive.cc
*
+ * @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
- * @date last modification: Tue Jan 12 2016
+ * @date last modification: Mon Feb 19 2018
*
* @brief Specialization of the material class for cohesive elements
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
#include "aka_random_generator.hh"
#include "dof_synchronizer.hh"
#include "fe_engine_template.hh"
#include "integrator_gauss.hh"
#include "shape_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MaterialCohesive::MaterialCohesive(SolidMechanicsModel & model, const ID & id)
: Material(model, id),
facet_filter("facet_filter", id, this->getMemoryID()),
fem_cohesive(
model.getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine")),
reversible_energy("reversible_energy", *this),
total_energy("total_energy", *this), opening("opening", *this),
tractions("tractions", *this),
contact_tractions("contact_tractions", *this),
contact_opening("contact_opening", *this), delta_max("delta max", *this),
use_previous_delta_max(false), use_previous_opening(false),
damage("damage", *this), sigma_c("sigma_c", *this),
normal(0, spatial_dimension, "normal") {
AKANTU_DEBUG_IN();
this->model = dynamic_cast<SolidMechanicsModelCohesive *>(&model);
this->registerParam("sigma_c", sigma_c, _pat_parsable | _pat_readable,
"Critical stress");
this->registerParam("delta_c", delta_c, Real(0.),
_pat_parsable | _pat_readable, "Critical displacement");
this->element_filter.initialize(this->model->getMesh(),
_spatial_dimension = spatial_dimension,
_element_kind = _ek_cohesive);
// this->model->getMesh().initElementTypeMapArray(
// this->element_filter, 1, spatial_dimension, false, _ek_cohesive);
if (this->model->getIsExtrinsic())
this->facet_filter.initialize(this->model->getMeshFacets(),
_spatial_dimension = spatial_dimension - 1,
_element_kind = _ek_regular);
// this->model->getMeshFacets().initElementTypeMapArray(facet_filter, 1,
// spatial_dimension -
// 1);
this->reversible_energy.initialize(1);
this->total_energy.initialize(1);
this->tractions.initialize(spatial_dimension);
this->tractions.initializeHistory();
this->contact_tractions.initialize(spatial_dimension);
this->contact_opening.initialize(spatial_dimension);
this->opening.initialize(spatial_dimension);
this->opening.initializeHistory();
this->delta_max.initialize(1);
this->damage.initialize(1);
if (this->model->getIsExtrinsic())
this->sigma_c.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MaterialCohesive::~MaterialCohesive() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
if (this->use_previous_delta_max)
this->delta_max.initializeHistory();
if (this->use_previous_opening)
this->opening.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_material_cohesive,
"Cohesive Tractions", tractions);
#endif
auto & internal_force = const_cast<Array<Real> &>(model->getInternalForce());
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type,
_ek_cohesive)) {
auto & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element == 0)
continue;
const auto & shapes = fem_cohesive.getShapes(type, ghost_type);
auto & traction = tractions(type, ghost_type);
auto & contact_traction = contact_tractions(type, ghost_type);
UInt size_of_shapes = shapes.getNbComponent();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points =
fem_cohesive.getNbIntegrationPoints(type, ghost_type);
/// compute @f$t_i N_a@f$
Array<Real> * traction_cpy = new Array<Real>(
nb_element * nb_quadrature_points, spatial_dimension * size_of_shapes);
auto traction_it = traction.begin(spatial_dimension, 1);
auto contact_traction_it = contact_traction.begin(spatial_dimension, 1);
auto shapes_filtered_begin = shapes.begin(1, size_of_shapes);
auto traction_cpy_it =
traction_cpy->begin(spatial_dimension, size_of_shapes);
Matrix<Real> traction_tmp(spatial_dimension, 1);
for (UInt el = 0; el < nb_element; ++el) {
UInt current_quad = elem_filter(el) * nb_quadrature_points;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++traction_it,
++contact_traction_it, ++current_quad, ++traction_cpy_it) {
const Matrix<Real> & shapes_filtered =
shapes_filtered_begin[current_quad];
traction_tmp.copy(*traction_it);
traction_tmp += *contact_traction_it;
traction_cpy_it->mul<false, false>(traction_tmp, shapes_filtered);
}
}
/**
* compute @f$\int t \cdot N\, dS@f$ by @f$ \sum_q \mathbf{N}^t
* \mathbf{t}_q \overline w_q J_q@f$
*/
Array<Real> * int_t_N = new Array<Real>(
nb_element, spatial_dimension * size_of_shapes, "int_t_N");
fem_cohesive.integrate(*traction_cpy, *int_t_N,
spatial_dimension * size_of_shapes, type, ghost_type,
elem_filter);
delete traction_cpy;
int_t_N->extendComponentsInterlaced(2, int_t_N->getNbComponent());
Real * int_t_N_val = int_t_N->storage();
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < size_of_shapes * spatial_dimension; ++n)
int_t_N_val[n] *= -1.;
int_t_N_val += nb_nodes_per_element * spatial_dimension;
}
/// assemble
model->getDOFManager().assembleElementalArrayLocalArray(
*int_t_N, internal_force, type, ghost_type, -1, elem_filter);
delete int_t_N;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type,
_ek_cohesive)) {
UInt nb_quadrature_points =
fem_cohesive.getNbIntegrationPoints(type, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<Real> & shapes = fem_cohesive.getShapes(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (!nb_element)
continue;
UInt size_of_shapes = shapes.getNbComponent();
Array<Real> * shapes_filtered = new Array<Real>(
nb_element * nb_quadrature_points, size_of_shapes, "filtered shapes");
Real * shapes_filtered_val = shapes_filtered->storage();
UInt * elem_filter_val = elem_filter.storage();
for (UInt el = 0; el < nb_element; ++el) {
auto shapes_val =
shapes.storage() +
elem_filter_val[el] * size_of_shapes * nb_quadrature_points;
memcpy(shapes_filtered_val, shapes_val,
size_of_shapes * nb_quadrature_points * sizeof(Real));
shapes_filtered_val += size_of_shapes * nb_quadrature_points;
}
/**
* compute A matrix @f$ \mathbf{A} = \left[\begin{array}{c c c c c c c c c c
*c c}
* 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 & 0 & 0 & 0 & 0 \\
* 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 & 0 & 0 & 0 \\
* 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 & 0 & 0 \\
* 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 & 0 \\
* 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 \\
* 0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1
* \end{array} \right]@f$
**/
// UInt size_of_A =
// spatial_dimension*size_of_shapes*spatial_dimension*nb_nodes_per_element;
// Real * A = new Real[size_of_A];
// memset(A, 0, size_of_A*sizeof(Real));
Matrix<Real> A(spatial_dimension * size_of_shapes,
spatial_dimension * nb_nodes_per_element);
for (UInt i = 0; i < spatial_dimension * size_of_shapes; ++i) {
A(i, i) = 1;
A(i, i + spatial_dimension * size_of_shapes) = -1;
}
// compute traction. This call is not necessary for the linear
// cohesive law that, currently, is the only one used for the
// extrinsic approach.
// if (!model->getIsExtrinsic()){
// computeTraction(ghost_type);
//}
/// get the tangent matrix @f$\frac{\partial{(t/\delta)}}{\partial{\delta}}
/// @f$
Array<Real> * tangent_stiffness_matrix = new Array<Real>(
nb_element * nb_quadrature_points,
spatial_dimension * spatial_dimension, "tangent_stiffness_matrix");
// Array<Real> * normal = new Array<Real>(nb_element *
// nb_quadrature_points, spatial_dimension, "normal");
normal.resize(nb_quadrature_points);
computeNormal(model->getCurrentPosition(), normal, type, ghost_type);
/// compute openings @f$\mathbf{\delta}@f$
// computeOpening(model->getDisplacement(), opening(type, ghost_type), type,
// ghost_type);
tangent_stiffness_matrix->clear();
computeTangentTraction(type, *tangent_stiffness_matrix, normal, ghost_type);
// delete normal;
UInt size_at_nt_d_n_a = spatial_dimension * nb_nodes_per_element *
spatial_dimension * nb_nodes_per_element;
Array<Real> * at_nt_d_n_a = new Array<Real>(
nb_element * nb_quadrature_points, size_at_nt_d_n_a, "A^t*N^t*D*N*A");
Array<Real>::iterator<Vector<Real>> shapes_filt_it =
shapes_filtered->begin(size_of_shapes);
Array<Real>::matrix_iterator D_it =
tangent_stiffness_matrix->begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator At_Nt_D_N_A_it =
at_nt_d_n_a->begin(spatial_dimension * nb_nodes_per_element,
spatial_dimension * nb_nodes_per_element);
Array<Real>::matrix_iterator At_Nt_D_N_A_end =
at_nt_d_n_a->end(spatial_dimension * nb_nodes_per_element,
spatial_dimension * nb_nodes_per_element);
Matrix<Real> N(spatial_dimension, spatial_dimension * size_of_shapes);
Matrix<Real> N_A(spatial_dimension,
spatial_dimension * nb_nodes_per_element);
Matrix<Real> D_N_A(spatial_dimension,
spatial_dimension * nb_nodes_per_element);
for (; At_Nt_D_N_A_it != At_Nt_D_N_A_end;
++At_Nt_D_N_A_it, ++D_it, ++shapes_filt_it) {
N.clear();
/**
* store the shapes in voigt notations matrix @f$\mathbf{N} =
* \begin{array}{cccccc} N_0(\xi) & 0 & N_1(\xi) &0 & N_2(\xi) & 0 \\
* 0 & * N_0(\xi)& 0 &N_1(\xi)& 0 & N_2(\xi) \end{array} @f$
**/
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt n = 0; n < size_of_shapes; ++n)
N(i, i + spatial_dimension * n) = (*shapes_filt_it)(n);
/**
* compute stiffness matrix @f$ \mathbf{K} = \delta \mathbf{U}^T
* \int_{\Gamma_c} {\mathbf{P}^t \frac{\partial{\mathbf{t}}}
*{\partial{\delta}}
* \mathbf{P} d\Gamma \Delta \mathbf{U}} @f$
**/
N_A.mul<false, false>(N, A);
D_N_A.mul<false, false>(*D_it, N_A);
(*At_Nt_D_N_A_it).mul<true, false>(D_N_A, N_A);
}
delete tangent_stiffness_matrix;
delete shapes_filtered;
Array<Real> * K_e = new Array<Real>(nb_element, size_at_nt_d_n_a, "K_e");
fem_cohesive.integrate(*at_nt_d_n_a, *K_e, size_at_nt_d_n_a, type,
ghost_type, elem_filter);
delete at_nt_d_n_a;
model->getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _unsymmetric, elem_filter);
delete K_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- *
* Compute traction from displacements
*
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void MaterialCohesive::computeTraction(GhostType ghost_type) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_material_cohesive,
"Cohesive Openings", opening);
#endif
for (auto & type : element_filter.elementTypes(spatial_dimension, ghost_type,
_ek_cohesive)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element == 0)
continue;
UInt nb_quadrature_points =
nb_element * fem_cohesive.getNbIntegrationPoints(type, ghost_type);
normal.resize(nb_quadrature_points);
/// compute normals @f$\mathbf{n}@f$
computeNormal(model->getCurrentPosition(), normal, type, ghost_type);
/// compute openings @f$\mathbf{\delta}@f$
computeOpening(model->getDisplacement(), opening(type, ghost_type), type,
ghost_type);
/// compute traction @f$\mathbf{t}@f$
computeTraction(normal, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::computeNormal(const Array<Real> & position,
Array<Real> & normal, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem_cohesive =
this->model->getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine");
#define COMPUTE_NORMAL(type) \
fem_cohesive.getShapeFunctions() \
.computeNormalsOnIntegrationPoints<type, CohesiveReduceFunctionMean>( \
position, normal, ghost_type, element_filter(type, ghost_type));
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(COMPUTE_NORMAL);
#undef COMPUTE_NORMAL
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::computeOpening(const Array<Real> & displacement,
Array<Real> & opening, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem_cohesive =
this->model->getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine");
#define COMPUTE_OPENING(type) \
fem_cohesive.getShapeFunctions() \
.interpolateOnIntegrationPoints<type, CohesiveReduceFunctionOpening>( \
displacement, opening, spatial_dimension, ghost_type, \
element_filter(type, ghost_type));
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(COMPUTE_OPENING);
#undef COMPUTE_OPENING
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::updateEnergies(ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (Mesh::getKind(type) != _ek_cohesive)
return;
Vector<Real> b(spatial_dimension);
Vector<Real> h(spatial_dimension);
auto erev = reversible_energy(type, ghost_type).begin();
auto etot = total_energy(type, ghost_type).begin();
auto traction_it = tractions(type, ghost_type).begin(spatial_dimension);
auto traction_old_it =
tractions.previous(type, ghost_type).begin(spatial_dimension);
auto opening_it = opening(type, ghost_type).begin(spatial_dimension);
auto opening_old_it =
opening.previous(type, ghost_type).begin(spatial_dimension);
auto traction_end = tractions(type, ghost_type).end(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end; ++traction_it, ++traction_old_it,
++opening_it, ++opening_old_it, ++erev,
++etot) {
/// trapezoidal integration
b = *opening_it;
b -= *opening_old_it;
h = *traction_old_it;
h += *traction_it;
*etot += .5 * b.dot(h);
*erev = .5 * traction_it->dot(*opening_it);
}
/// update old values
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getReversibleEnergy() {
AKANTU_DEBUG_IN();
Real erev = 0.;
/// integrate reversible energy for each type of elements
for (auto & type : element_filter.elementTypes(spatial_dimension, _not_ghost,
_ek_cohesive)) {
erev +=
fem_cohesive.integrate(reversible_energy(type, _not_ghost), type,
_not_ghost, element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return erev;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getDissipatedEnergy() {
AKANTU_DEBUG_IN();
Real edis = 0.;
/// integrate dissipated energy for each type of elements
for (auto & type : element_filter.elementTypes(spatial_dimension, _not_ghost,
_ek_cohesive)) {
Array<Real> dissipated_energy(total_energy(type, _not_ghost));
dissipated_energy -= reversible_energy(type, _not_ghost);
edis += fem_cohesive.integrate(dissipated_energy, type, _not_ghost,
element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return edis;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getContactEnergy() {
AKANTU_DEBUG_IN();
Real econ = 0.;
/// integrate contact energy for each type of elements
for (auto & type : element_filter.elementTypes(spatial_dimension, _not_ghost,
_ek_cohesive)) {
auto & el_filter = element_filter(type, _not_ghost);
UInt nb_quad_per_el = fem_cohesive.getNbIntegrationPoints(type, _not_ghost);
UInt nb_quad_points = el_filter.size() * nb_quad_per_el;
Array<Real> contact_energy(nb_quad_points);
auto contact_traction_it =
contact_tractions(type, _not_ghost).begin(spatial_dimension);
auto contact_opening_it =
contact_opening(type, _not_ghost).begin(spatial_dimension);
/// loop on each quadrature point
for (UInt q = 0; q < nb_quad_points;
++contact_traction_it, ++contact_opening_it, ++q) {
contact_energy(q) = .5 * contact_traction_it->dot(*contact_opening_it);
}
econ += fem_cohesive.integrate(contact_energy, type, _not_ghost, el_filter);
}
AKANTU_DEBUG_OUT();
return econ;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getEnergy(const std::string & type) {
AKANTU_DEBUG_IN();
if (type == "reversible")
return getReversibleEnergy();
else if (type == "dissipated")
return getDissipatedEnergy();
else if (type == "cohesive contact")
return getContactEnergy();
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
index 2f854eb40..40ad8a6f3 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
@@ -1,238 +1,237 @@
/**
* @file material_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Jan 12 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Specialization of the material class for cohesive elements
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#include "cohesive_internal_field.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_HH__
#define __AKANTU_MATERIAL_COHESIVE_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
class MaterialCohesive : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MyFEEngineCohesiveType =
FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive>;
public:
MaterialCohesive(SolidMechanicsModel & model, const ID & id = "");
~MaterialCohesive() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// compute tractions (including normals and openings)
void computeTraction(GhostType ghost_type = _not_ghost);
/// assemble residual
void assembleInternalForces(GhostType ghost_type = _not_ghost) override;
/// check stress for cohesive elements' insertion, by default it
/// also updates the cohesive elements' data
virtual void checkInsertion(bool /*check_only*/ = false) {
AKANTU_TO_IMPLEMENT();
}
/// interpolate stress on given positions for each element (empty
/// implemantation to avoid the generic call to be done on cohesive elements)
virtual void interpolateStress(const ElementType /*type*/,
Array<Real> & /*result*/) {}
/// compute the stresses
void computeAllStresses(GhostType /*ghost_type*/ = _not_ghost) override{};
// add the facet to be handled by the material
UInt addFacet(const Element & element);
protected:
virtual void computeTangentTraction(const ElementType & /*el_type*/,
Array<Real> & /*tangent_matrix*/,
const Array<Real> & /*normal*/,
GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// compute the normal
void computeNormal(const Array<Real> & position, Array<Real> & normal,
ElementType type, GhostType ghost_type);
/// compute the opening
void computeOpening(const Array<Real> & displacement, Array<Real> & opening,
ElementType type, GhostType ghost_type);
template <ElementType type>
void computeNormal(const Array<Real> & position, Array<Real> & normal,
GhostType ghost_type);
/// assemble stiffness
void assembleStiffnessMatrix(GhostType ghost_type) override;
/// constitutive law
virtual void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) = 0;
/// parallelism functions
inline UInt 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);
protected:
void updateEnergies(ElementType el_type, GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the opening
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Opening, opening, Real);
/// get the traction
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Traction, tractions, Real);
/// get damage
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
/// get facet filter
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(FacetFilter, facet_filter, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(FacetFilter, facet_filter, UInt);
AKANTU_GET_MACRO(FacetFilter, facet_filter,
const ElementTypeMapArray<UInt> &);
// AKANTU_GET_MACRO(ElementFilter, element_filter, const
// ElementTypeMapArray<UInt> &);
/// compute reversible energy
Real getReversibleEnergy();
/// compute dissipated energy
Real getDissipatedEnergy();
/// compute contact energy
Real getContactEnergy();
/// get energy
Real getEnergy(const std::string & type) override;
/// return the energy (identified by id) for the provided element
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override {
return Material::getEnergy(energy_id, type, index);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// list of facets assigned to this material
ElementTypeMapArray<UInt> facet_filter;
/// Link to the cohesive fem object in the model
FEEngine & fem_cohesive;
private:
/// reversible energy by quadrature point
CohesiveInternalField<Real> reversible_energy;
/// total energy by quadrature point
CohesiveInternalField<Real> total_energy;
protected:
/// opening in all elements and quadrature points
CohesiveInternalField<Real> opening;
/// traction in all elements and quadrature points
CohesiveInternalField<Real> tractions;
/// traction due to contact
CohesiveInternalField<Real> contact_tractions;
/// normal openings for contact tractions
CohesiveInternalField<Real> contact_opening;
/// maximum displacement
CohesiveInternalField<Real> delta_max;
/// tell if the previous delta_max state is needed (in iterative schemes)
bool use_previous_delta_max;
/// tell if the previous opening state is needed (in iterative schemes)
bool use_previous_opening;
/// damage
CohesiveInternalField<Real> damage;
/// pointer to the solid mechanics model for cohesive elements
SolidMechanicsModelCohesive * model;
/// critical stress
RandomInternalField<Real, FacetInternalField> sigma_c;
/// critical displacement
Real delta_c;
/// array to temporarily store the normals
Array<Real> normal;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_cohesive_inline_impl.cc"
} // namespace akantu
#include "cohesive_internal_field_tmpl.hh"
#endif /* __AKANTU_MATERIAL_COHESIVE_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_includes.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_includes.hh
index 6548a282c..5cd373e11 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_includes.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_includes.hh
@@ -1,49 +1,48 @@
/**
* @file material_cohesive_includes.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
- * @date last modification: Tue Jan 12 2016
+ * @date last modification: Fri Oct 13 2017
*
* @brief List of includes for cohesive elements
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_CMAKE_LIST_MATERIALS
#include "material_cohesive.hh"
#include "material_cohesive_bilinear.hh"
#include "material_cohesive_exponential.hh"
#include "material_cohesive_linear.hh"
#include "material_cohesive_linear_fatigue.hh"
#include "material_cohesive_linear_friction.hh"
#include "material_cohesive_linear_uncoupled.hh"
#endif
#define AKANTU_COHESIVE_MATERIAL_LIST \
((2, (cohesive_linear, MaterialCohesiveLinear)))( \
(2, (cohesive_linear_fatigue, MaterialCohesiveLinearFatigue)))( \
(2, (cohesive_linear_friction, MaterialCohesiveLinearFriction)))( \
(2, (cohesive_linear_uncoupled, MaterialCohesiveLinearUncoupled)))( \
(2, (cohesive_bilinear, MaterialCohesiveBilinear)))( \
(2, (cohesive_exponential, MaterialCohesiveExponential)))
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.cc
index 5e6a2cf69..469d804e8 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.cc
@@ -1,102 +1,101 @@
/**
* @file material_cohesive_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Mon Feb 19 2018
*
* @brief MaterialCohesive inline implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
inline UInt MaterialCohesive::addFacet(const Element & element) {
Array<UInt> & f_filter = facet_filter(element.type, element.ghost_type);
f_filter.push_back(element.element);
return f_filter.size() - 1;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void MaterialCohesive::computeNormal(const Array<Real> & /*position*/,
Array<Real> & /*normal*/,
GhostType /*ghost_type*/) {}
/* -------------------------------------------------------------------------- */
inline UInt
MaterialCohesive::getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
switch (tag) {
case _gst_smm_stress: {
return 2 * spatial_dimension * sizeof(Real) *
this->getModel().getNbIntegrationPoints(elements,
"CohesiveFEEngine");
}
case _gst_smmc_damage: {
return sizeof(Real) *
this->getModel().getNbIntegrationPoints(elements,
"CohesiveFEEngine");
}
default: {}
}
return 0;
}
/* -------------------------------------------------------------------------- */
inline void MaterialCohesive::packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
switch (tag) {
case _gst_smm_stress: {
packElementDataHelper(tractions, buffer, elements, "CohesiveFEEngine");
packElementDataHelper(contact_tractions, buffer, elements,
"CohesiveFEEngine");
break;
}
case _gst_smmc_damage:
packElementDataHelper(damage, buffer, elements, "CohesiveFEEngine");
break;
default: {}
}
}
/* -------------------------------------------------------------------------- */
inline void MaterialCohesive::unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
switch (tag) {
case _gst_smm_stress: {
unpackElementDataHelper(tractions, buffer, elements, "CohesiveFEEngine");
unpackElementDataHelper(contact_tractions, buffer, elements,
"CohesiveFEEngine");
break;
}
case _gst_smmc_damage:
unpackElementDataHelper(damage, buffer, elements, "CohesiveFEEngine");
break;
default: {}
}
}
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
index 9e2a9eb12..b6b1bc5cd 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
@@ -1,713 +1,714 @@
/**
* @file solid_mechanics_model_cohesive.cc
*
+ * @author Fabian Barras <fabian.barras@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
- * @date last modification: Wed Jan 13 2016
+ * @date last modification: Wed Feb 21 2018
*
* @brief Solid mechanics model for cohesive elements
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
#include "aka_iterators.hh"
#include "cohesive_element_inserter.hh"
#include "element_synchronizer.hh"
#include "facet_synchronizer.hh"
#include "fe_engine_template.hh"
#include "integrator_gauss.hh"
#include "material_cohesive.hh"
#include "parser.hh"
#include "shape_cohesive.hh"
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::SolidMechanicsModelCohesive(
Mesh & mesh, UInt dim, const ID & id, const MemoryID & memory_id)
: SolidMechanicsModel(mesh, dim, id, memory_id,
ModelType::_solid_mechanics_model_cohesive),
tangents("tangents", id), facet_stress("facet_stress", id),
facet_material("facet_material", id) {
AKANTU_DEBUG_IN();
registerFEEngineObject<MyFEEngineCohesiveType>("CohesiveFEEngine", mesh,
Model::spatial_dimension);
auto && tmp_material_selector =
std::make_shared<DefaultMaterialCohesiveSelector>(*this);
tmp_material_selector->setFallback(this->material_selector);
this->material_selector = tmp_material_selector;
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("cohesive elements", id);
this->mesh.addDumpMeshToDumper("cohesive elements", mesh,
Model::spatial_dimension, _not_ghost,
_ek_cohesive);
#endif
if (this->mesh.isDistributed()) {
/// create the distributed synchronizer for cohesive elements
this->cohesive_synchronizer = std::make_unique<ElementSynchronizer>(
mesh, "cohesive_distributed_synchronizer");
auto & synchronizer = mesh.getElementSynchronizer();
this->cohesive_synchronizer->split(synchronizer, [](auto && el) {
return Mesh::getKind(el.type) == _ek_cohesive;
});
this->registerSynchronizer(*cohesive_synchronizer, _gst_material_id);
this->registerSynchronizer(*cohesive_synchronizer, _gst_smm_stress);
this->registerSynchronizer(*cohesive_synchronizer, _gst_smm_boundary);
}
this->inserter = std::make_unique<CohesiveElementInserter>(
this->mesh, id + ":cohesive_element_inserter");
registerFEEngineObject<MyFEEngineFacetType>(
"FacetsFEEngine", mesh.getMeshFacets(), Model::spatial_dimension - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::~SolidMechanicsModelCohesive() = default;
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::setTimeStep(Real time_step,
const ID & solver_id) {
SolidMechanicsModel::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper("cohesive elements").setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initFullImpl(const ModelOptions & options) {
AKANTU_DEBUG_IN();
const auto & smmc_options =
dynamic_cast<const SolidMechanicsModelCohesiveOptions &>(options);
this->is_extrinsic = smmc_options.extrinsic;
inserter->setIsExtrinsic(is_extrinsic);
if (mesh.isDistributed()) {
auto & mesh_facets = inserter->getMeshFacets();
auto & synchronizer =
dynamic_cast<FacetSynchronizer &>(mesh_facets.getElementSynchronizer());
this->registerSynchronizer(synchronizer, _gst_smmc_facets);
this->registerSynchronizer(synchronizer, _gst_smmc_facets_conn);
synchronizeGhostFacetsConnectivity();
/// create the facet synchronizer for extrinsic simulations
if (is_extrinsic) {
facet_stress_synchronizer = std::make_unique<ElementSynchronizer>(
synchronizer, id + ":facet_stress_synchronizer");
this->registerSynchronizer(*facet_stress_synchronizer,
_gst_smmc_facets_stress);
}
inserter->initParallel(*cohesive_synchronizer);
}
ParserSection section;
bool is_empty;
std::tie(section, is_empty) = this->getParserSection();
if (not is_empty) {
auto inserter_section =
section.getSubSections(ParserType::_cohesive_inserter);
if (inserter_section.begin() != inserter_section.end()) {
inserter->parseSection(*inserter_section.begin());
}
}
SolidMechanicsModel::initFullImpl(options);
AKANTU_DEBUG_OUT();
} // namespace akantu
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initMaterials() {
AKANTU_DEBUG_IN();
// make sure the material are instantiated
if (!are_materials_instantiated)
instantiateMaterials();
/// find the first cohesive material
UInt cohesive_index = UInt(-1);
for (auto && material : enumerate(materials)) {
if (dynamic_cast<MaterialCohesive *>(std::get<1>(material).get())) {
cohesive_index = std::get<0>(material);
break;
}
}
if (cohesive_index == UInt(-1))
AKANTU_EXCEPTION("No cohesive materials in the material input file");
material_selector->setFallback(cohesive_index);
// set the facet information in the material in case of dynamic insertion
// to know what material to call for stress checks
if (is_extrinsic) {
this->initExtrinsicMaterials();
} else {
this->initIntrinsicMaterials();
}
AKANTU_DEBUG_OUT();
} // namespace akantu
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initExtrinsicMaterials() {
const Mesh & mesh_facets = inserter->getMeshFacets();
facet_material.initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_element = true,
_default_value = material_selector->getFallbackValue());
for_each_element(
mesh_facets,
[&](auto && element) {
auto mat_index = (*material_selector)(element);
auto & mat = dynamic_cast<MaterialCohesive &>(*materials[mat_index]);
facet_material(element) = mat_index;
mat.addFacet(element);
},
_spatial_dimension = spatial_dimension - 1, _ghost_type = _not_ghost);
SolidMechanicsModel::initMaterials();
this->initAutomaticInsertion();
}
/* -------------------------------------------------------------------------- */
#if 0
void SolidMechanicsModelCohesive::initIntrinsicCohesiveMaterials(
const std::string & cohesive_surfaces) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_synchronizer != nullptr)
inserter->initParallel(facet_synchronizer, cohesive_element_synchronizer);
// inserter->initParallel(facet_synchronizer, synch_parallel);
#endif
std::istringstream split(cohesive_surfaces);
std::string physname;
while (std::getline(split, physname, ',')) {
AKANTU_DEBUG_INFO(
"Pre-inserting cohesive elements along facets from physical surface: "
<< physname);
insertElementsFromMeshData(physname);
}
synchronizeInsertionData();
SolidMechanicsModel::initMaterials();
auto && tmp = std::make_shared<MeshDataMaterialCohesiveSelector>(*this);
tmp->setFallback(material_selector->getFallbackValue());
tmp->setFallback(material_selector->getFallbackSelector());
material_selector = tmp;
// UInt nb_new_elements =
inserter->insertElements();
// if (nb_new_elements > 0) {
// this->reinitializeSolver();
// }
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::synchronizeInsertionData() {
if (inserter->getMeshFacets().isDistributed()) {
inserter->getMeshFacets().getElementSynchronizer().synchronizeOnce(
*inserter, _gst_ce_groups);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initIntrinsicMaterials() {
AKANTU_DEBUG_IN();
SolidMechanicsModel::initMaterials();
this->insertIntrinsicElements();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*/
void SolidMechanicsModelCohesive::initModel() {
AKANTU_DEBUG_IN();
SolidMechanicsModel::initModel();
/// add cohesive type connectivity
ElementType type = _not_defined;
for (auto && type_ghost : ghost_types) {
for (const auto & tmp_type :
mesh.elementTypes(spatial_dimension, type_ghost)) {
const auto & connectivity = mesh.getConnectivity(tmp_type, type_ghost);
if (connectivity.size() == 0)
continue;
type = tmp_type;
auto type_facet = Mesh::getFacetType(type);
auto type_cohesive = FEEngine::getCohesiveElementType(type_facet);
mesh.addConnectivityType(type_cohesive, type_ghost);
}
}
AKANTU_DEBUG_ASSERT(type != _not_defined, "No elements in the mesh");
getFEEngine("CohesiveFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("CohesiveFEEngine").initShapeFunctions(_ghost);
if (is_extrinsic) {
getFEEngine("FacetsFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("FacetsFEEngine").initShapeFunctions(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::insertIntrinsicElements() {
AKANTU_DEBUG_IN();
inserter->insertIntrinsicElements();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initAutomaticInsertion() {
AKANTU_DEBUG_IN();
this->inserter->limitCheckFacets();
this->updateFacetStressSynchronizer();
this->resizeFacetStress();
/// compute normals on facets
this->computeNormals();
this->initStressInterpolation();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateAutomaticInsertion() {
AKANTU_DEBUG_IN();
this->inserter->limitCheckFacets();
this->updateFacetStressSynchronizer();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initStressInterpolation() {
Mesh & mesh_facets = inserter->getMeshFacets();
/// compute quadrature points coordinates on facets
Array<Real> & position = mesh.getNodes();
ElementTypeMapArray<Real> quad_facets("quad_facets", id);
quad_facets.initialize(mesh_facets, _nb_component = Model::spatial_dimension,
_spatial_dimension = Model::spatial_dimension - 1);
// mesh_facets.initElementTypeMapArray(quad_facets, Model::spatial_dimension,
// Model::spatial_dimension - 1);
getFEEngine("FacetsFEEngine")
.interpolateOnIntegrationPoints(position, quad_facets);
/// compute elements quadrature point positions and build
/// element-facet quadrature points data structure
ElementTypeMapArray<Real> elements_quad_facets("elements_quad_facets", id);
elements_quad_facets.initialize(
mesh, _nb_component = Model::spatial_dimension,
_spatial_dimension = Model::spatial_dimension);
// mesh.initElementTypeMapArray(elements_quad_facets,
// Model::spatial_dimension,
// Model::spatial_dimension);
for (auto elem_gt : ghost_types) {
for (auto & type : mesh.elementTypes(Model::spatial_dimension, elem_gt)) {
UInt nb_element = mesh.getNbElement(type, elem_gt);
if (nb_element == 0)
continue;
/// compute elements' quadrature points and list of facet
/// quadrature points positions by element
const auto & facet_to_element =
mesh_facets.getSubelementToElement(type, elem_gt);
auto & el_q_facet = elements_quad_facets(type, elem_gt);
auto facet_type = Mesh::getFacetType(type);
auto nb_quad_per_facet =
getFEEngine("FacetsFEEngine").getNbIntegrationPoints(facet_type);
auto nb_facet_per_elem = facet_to_element.getNbComponent();
// small hack in the loop to skip boundary elements, they are silently
// initialized to NaN to see if this causes problems
el_q_facet.resize(nb_element * nb_facet_per_elem * nb_quad_per_facet,
std::numeric_limits<Real>::quiet_NaN());
for (auto && data :
zip(make_view(facet_to_element),
make_view(el_q_facet, spatial_dimension, nb_quad_per_facet))) {
const auto & global_facet = std::get<0>(data);
auto & el_q = std::get<1>(data);
if (global_facet == ElementNull)
continue;
Matrix<Real> quad_f =
make_view(quad_facets(global_facet.type, global_facet.ghost_type),
spatial_dimension, nb_quad_per_facet)
.begin()[global_facet.element];
el_q = quad_f;
// for (UInt q = 0; q < nb_quad_per_facet; ++q) {
// for (UInt s = 0; s < Model::spatial_dimension; ++s) {
// el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
// f * nb_quad_per_facet + q,
// s) = quad_f(global_facet * nb_quad_per_facet + q,
// s);
// }
// }
//}
}
}
}
/// loop over non cohesive materials
for (auto && material : materials) {
if (dynamic_cast<MaterialCohesive *>(material.get()))
continue;
/// initialize the interpolation function
material->initElementalFieldInterpolation(elements_quad_facets);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::assembleInternalForces() {
AKANTU_DEBUG_IN();
// f_int += f_int_cohe
for (auto & material : this->materials) {
try {
auto & mat = dynamic_cast<MaterialCohesive &>(*material);
mat.computeTraction(_not_ghost);
} catch (std::bad_cast & bce) {
}
}
SolidMechanicsModel::assembleInternalForces();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::computeNormals() {
AKANTU_DEBUG_IN();
Mesh & mesh_facets = this->inserter->getMeshFacets();
this->getFEEngine("FacetsFEEngine")
.computeNormalsOnIntegrationPoints(_not_ghost);
/**
* @todo store tangents while computing normals instead of
* recomputing them as follows:
*/
/* ------------------------------------------------------------------------ */
UInt tangent_components =
Model::spatial_dimension * (Model::spatial_dimension - 1);
tangents.initialize(mesh_facets, _nb_component = tangent_components,
_spatial_dimension = Model::spatial_dimension - 1);
// mesh_facets.initElementTypeMapArray(tangents, tangent_components,
// Model::spatial_dimension - 1);
for (auto facet_type :
mesh_facets.elementTypes(Model::spatial_dimension - 1)) {
const Array<Real> & normals =
this->getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(facet_type);
Array<Real> & tangents = this->tangents(facet_type);
Math::compute_tangents(normals, tangents);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::interpolateStress() {
ElementTypeMapArray<Real> by_elem_result("temporary_stress_by_facets", id);
for (auto & material : materials) {
auto * mat = dynamic_cast<MaterialCohesive *>(material.get());
if (mat == nullptr)
/// interpolate stress on facet quadrature points positions
material->interpolateStressOnFacets(facet_stress, by_elem_result);
}
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(
debug::_dm_model_cohesive, "Interpolated stresses before", facet_stress);
#endif
this->synchronize(_gst_smmc_facets_stress);
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_model_cohesive,
"Interpolated stresses", facet_stress);
#endif
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::checkCohesiveStress() {
AKANTU_DEBUG_IN();
interpolateStress();
for (auto & mat : materials) {
auto * mat_cohesive = dynamic_cast<MaterialCohesive *>(mat.get());
if (mat_cohesive) {
/// check which not ghost cohesive elements are to be created
mat_cohesive->checkInsertion();
}
}
/// communicate data among processors
this->synchronize(_gst_smmc_facets);
/// insert cohesive elements
UInt nb_new_elements = inserter->insertElements();
// if (nb_new_elements > 0) {
// this->reinitializeSolver();
// }
AKANTU_DEBUG_OUT();
return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onElementsAdded(
const Array<Element> & element_list, const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
updateCohesiveSynchronizers();
SolidMechanicsModel::onElementsAdded(element_list, event);
if (cohesive_synchronizer != nullptr)
cohesive_synchronizer->computeAllBufferSizes(*this);
if (is_extrinsic)
resizeFacetStress();
/// if (method != _explicit_lumped_mass) {
/// this->initSolver();
/// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onNodesAdded(const Array<UInt> & new_nodes,
const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
// 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(new_nodes, event);
UInt new_node, old_node;
try {
const auto & cohesive_event =
dynamic_cast<const CohesiveNewNodesEvent &>(event);
const auto & old_nodes = cohesive_event.getOldNodesList();
auto copy = [this, &new_node, &old_node](auto & arr) {
for (UInt s = 0; s < spatial_dimension; ++s) {
arr(new_node, s) = arr(old_node, s);
}
};
for (auto && pair : zip(new_nodes, old_nodes)) {
std::tie(new_node, old_node) = pair;
copy(*displacement);
copy(*blocked_dofs);
if (velocity)
copy(*velocity);
if (acceleration)
copy(*acceleration);
if (current_position)
copy(*current_position);
if (previous_displacement)
copy(*previous_displacement);
}
// if (this->getDOFManager().hasMatrix("M")) {
// this->assembleMass(old_nodes);
// }
// if (this->getDOFManager().hasLumpedMatrix("M")) {
// this->assembleMassLumped(old_nodes);
// }
} catch (std::bad_cast &) {
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onEndSolveStep(const AnalysisMethod &) {
AKANTU_DEBUG_IN();
/*
* This is required because the Cauchy stress is the stress measure that
* is used to check the insertion of cohesive elements
*/
for (auto & mat : materials) {
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();
this->facet_stress.initialize(getFEEngine("FacetsFEEngine"),
_nb_component =
2 * spatial_dimension * spatial_dimension,
_spatial_dimension = spatial_dimension - 1);
// for (auto && ghost_type : ghost_types) {
// for (const auto & type :
// mesh_facets.elementTypes(spatial_dimension - 1, ghost_type)) {
// UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);
// UInt nb_quadrature_points = getFEEngine("FacetsFEEngine")
// .getNbIntegrationPoints(type,
// ghost_type);
// UInt new_size = nb_facet * nb_quadrature_points;
// facet_stress(type, ghost_type).resize(new_size);
// }
// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::addDumpGroupFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
const std::string & group_name, const ElementKind & element_kind,
bool padding_flag) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = Model::spatial_dimension;
ElementKind _element_kind = element_kind;
if (dumper_name == "cohesive elements") {
_element_kind = _ek_cohesive;
} else if (dumper_name == "facets") {
spatial_dimension = Model::spatial_dimension - 1;
}
SolidMechanicsModel::addDumpGroupFieldToDumper(dumper_name, field_id,
group_name, spatial_dimension,
_element_kind, padding_flag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onDump() {
this->flattenAllRegisteredInternals(_ek_cohesive);
SolidMechanicsModel::onDump();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
index cf149d7b2..49abaabff 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
@@ -1,320 +1,320 @@
/**
* @file solid_mechanics_model_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
- * @date last modification: Mon Dec 14 2015
+ * @date last modification: Mon Feb 05 2018
*
* @brief Solid mechanics model for cohesive elements
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
#include "material_selector_cohesive.hh"
#include "random_internal_field.hh" // included to have the specialization of
#include "solid_mechanics_model.hh"
#include "solid_mechanics_model_event_handler.hh"
// ParameterTyped::operator Real()
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class FacetSynchronizer;
class FacetStressSynchronizer;
class ElementSynchronizer;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
struct FacetsCohesiveIntegrationOrderFunctor {
template <ElementType type,
ElementType cohesive_type =
CohesiveFacetProperty<type>::cohesive_type>
struct _helper {
static constexpr int get() {
return ElementClassProperty<cohesive_type>::polynomial_degree;
}
};
template <ElementType type> struct _helper<type, _not_defined> {
static constexpr int get() {
return ElementClassProperty<type>::polynomial_degree;
}
};
template <ElementType type> static inline constexpr int getOrder() {
return _helper<type>::get();
}
};
/* -------------------------------------------------------------------------- */
/* Solid Mechanics Model for Cohesive elements */
/* -------------------------------------------------------------------------- */
class SolidMechanicsModelCohesive : public SolidMechanicsModel,
public SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
class NewCohesiveNodesEvent : public NewNodesEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(OldNodesList, old_nodes, Array<UInt> &);
AKANTU_GET_MACRO(OldNodesList, old_nodes, const Array<UInt> &);
protected:
Array<UInt> old_nodes;
};
using MyFEEngineCohesiveType =
FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive>;
using MyFEEngineFacetType =
FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular,
FacetsCohesiveIntegrationOrderFunctor>;
SolidMechanicsModelCohesive(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model_cohesive",
const MemoryID & memory_id = 0);
~SolidMechanicsModelCohesive() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize the cohesive model
void initFullImpl(const ModelOptions & options) override;
public:
/// set the value of the time step
void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// assemble the residual for the explicit scheme
void assembleInternalForces() override;
/// function to perform a stress check on each facet and insert
/// cohesive elements if needed (returns the number of new cohesive
/// elements)
UInt checkCohesiveStress();
/// interpolate stress on facets
void interpolateStress();
/// update automatic insertion after a change in the element inserter
void updateAutomaticInsertion();
/// insert intrinsic cohesive elements
void insertIntrinsicElements();
// template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria
// criteria> bool solveStepCohesive(Real tolerance, Real & error, UInt
// max_iteration = 100,
// bool load_reduction = false,
// Real tol_increase_factor = 1.0,
// bool do_not_factorize = false);
protected:
/// initialize stress interpolation
void initStressInterpolation();
/// initialize the model
void initModel() override;
/// initialize cohesive material
void initMaterials() override;
/// init facet filters for cohesive materials
void initFacetFilter();
// synchronize facets physical data before insertion along physical surfaces
void synchronizeInsertionData();
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
private:
/// initialize cohesive material with extrinsic insertion
void initExtrinsicMaterials();
/// initialize cohesive material with intrinsic insertion
void initIntrinsicMaterials();
/// insert cohesive elements along a given physical surface of the mesh
void insertElementsFromMeshData(const std::string & physical_name);
/// initialize completely the model for extrinsic elements
void initAutomaticInsertion();
/// compute facets' normals
void computeNormals();
/// resize facet stress
void resizeFacetStress();
/// init facets_check array
void initFacetsCheck();
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
void onElementsAdded(const Array<Element> & nodes_list,
const NewElementsEvent & event) override;
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
void onEndSolveStep(const AnalysisMethod & method) override;
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
void onDump() override;
void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind,
bool padding_flag) override;
public:
/// register the tags associated with the parallel synchronizer for
/// cohesive elements
// void initParallel(MeshPartition * partition,
// DataAccessor * data_accessor = NULL,
// bool extrinsic = false);
protected:
void synchronizeGhostFacetsConnectivity();
void updateCohesiveSynchronizers();
void updateFacetStressSynchronizer();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override;
protected:
UInt getNbQuadsForFacetCheck(const Array<Element> & elements) const;
template <typename T>
void packFacetStressDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements) const;
template <typename T>
void unpackFacetStressDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements) const;
template <typename T, bool pack_helper>
void packUnpackFacetStressDataHelper(ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & element) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get facet mesh
AKANTU_GET_MACRO(MeshFacets, mesh.getMeshFacets(), const Mesh &);
/// get stress on facets vector
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(StressOnFacets, facet_stress, Real);
/// get facet material
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(FacetMaterial, facet_material, UInt);
/// get facet material
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(FacetMaterial, facet_material, UInt);
/// get facet material
AKANTU_GET_MACRO(FacetMaterial, facet_material,
const ElementTypeMapArray<UInt> &);
/// @todo THIS HAS TO BE CHANGED
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Tangents, tangents, Real);
/// get element inserter
AKANTU_GET_MACRO_NOT_CONST(ElementInserter, *inserter,
CohesiveElementInserter &);
/// get is_extrinsic boolean
AKANTU_GET_MACRO(IsExtrinsic, is_extrinsic, bool);
/// get cohesive elements synchronizer
AKANTU_GET_MACRO(CohesiveSynchronizer, *cohesive_synchronizer,
const ElementSynchronizer &);
/* ------------------------------------------------------------------------ */
/* 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
std::unique_ptr<CohesiveElementInserter> inserter;
/// facet stress synchronizer
std::unique_ptr<ElementSynchronizer> facet_stress_synchronizer;
/// cohesive elements synchronizer
std::unique_ptr<ElementSynchronizer> cohesive_synchronizer;
/// global connectivity
ElementTypeMapArray<UInt> * global_connectivity;
};
} // namespace akantu
#include "solid_mechanics_model_cohesive_inline_impl.cc"
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.cc
index bf3a809e3..43403bf43 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.cc
@@ -1,305 +1,306 @@
/**
* @file solid_mechanics_model_cohesive_inline_impl.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jan 18 2013
- * @date last modification: Thu Jan 14 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of inline functions for the Cohesive element model
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_CC__
#define __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
// template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
// bool SolidMechanicsModelCohesive::solveStepCohesive(
// Real tolerance, Real & error, UInt max_iteration, bool load_reduction,
// Real tol_increase_factor, bool do_not_factorize) {
// // EventManager::sendEvent(
// // SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
// // this->implicitPred();
// // bool insertion_new_element = true;
// // bool converged = false;
// // Array<Real> * displacement_tmp = NULL;
// // Array<Real> * velocity_tmp = NULL;
// // Array<Real> * acceleration_tmp = NULL;
// // StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
// // Int prank = comm.whoAmI();
// // /// Loop for the insertion of new cohesive elements
// // while (insertion_new_element) {
// // if (is_extrinsic) {
// // /**
// // * If in extrinsic the solution of the previous incremental step
// // * is saved in temporary arrays created for displacements,
// // * velocities and accelerations. Such arrays are used to find
// // * the solution with the Newton-Raphson scheme (this is done by
// // * pointing the pointer "displacement" to displacement_tmp). In
// // * this way, inside the array "displacement" is kept the
// // * solution of the previous incremental step, and in
// // * "displacement_tmp" is saved the current solution.
// // */
// // if (!displacement_tmp)
// // displacement_tmp = new Array<Real>(0, spatial_dimension);
// // displacement_tmp->copy(*(this->displacement));
// // if (!velocity_tmp)
// // velocity_tmp = new Array<Real>(0, spatial_dimension);
// // velocity_tmp->copy(*(this->velocity));
// // if (!acceleration_tmp) {
// // acceleration_tmp = new Array<Real>(0, spatial_dimension);
// // }
// // acceleration_tmp->copy(*(this->acceleration));
// // std::swap(displacement, displacement_tmp);
// // std::swap(velocity, velocity_tmp);
// // std::swap(acceleration, acceleration_tmp);
// // }
// // this->updateResidual();
// // AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
// // "You should first initialize the implicit solver and
// "
// // "assemble the stiffness matrix");
// // bool need_factorize = !do_not_factorize;
// // if (method == _implicit_dynamic) {
// // AKANTU_DEBUG_ASSERT(mass_matrix != NULL, "You should first initialize
// "
// // "the implicit solver and "
// // "assemble the mass matrix");
// // }
// // switch (cmethod) {
// // case _scm_newton_raphson_tangent:
// // case _scm_newton_raphson_tangent_not_computed:
// // break;
// // case _scm_newton_raphson_tangent_modified:
// // this->assembleStiffnessMatrix();
// // break;
// // default:
// // AKANTU_ERROR("The resolution method "
// // << cmethod << " has not been implemented!");
// // }
// // UInt iter = 0;
// // converged = false;
// // error = 0.;
// // if (criteria == _scc_residual) {
// // converged = this->testConvergence<criteria>(tolerance, error);
// // if (converged)
// // return converged;
// // }
// // /// Loop to solve the nonlinear system
// // do {
// // if (cmethod == _scm_newton_raphson_tangent)
// // this->assembleStiffnessMatrix();
// // solve<NewmarkBeta::_displacement_corrector>(*increment, 1.,
// // need_factorize);
// // this->implicitCorr();
// // this->updateResidual();
// // converged = this->testConvergence<criteria>(tolerance, error);
// // iter++;
// // AKANTU_DEBUG_INFO("[" << criteria << "] Convergence iteration "
// // << std::setw(std::log10(max_iteration)) << iter
// // << ": error " << error
// // << (converged ? " < " : " > ") << tolerance);
// // switch (cmethod) {
// // case _scm_newton_raphson_tangent:
// // need_factorize = true;
// // break;
// // case _scm_newton_raphson_tangent_not_computed:
// // case _scm_newton_raphson_tangent_modified:
// // need_factorize = false;
// // break;
// // default:
// // AKANTU_ERROR("The resolution method "
// // << cmethod << " has not been implemented!");
// // }
// // } while (!converged && iter < max_iteration);
// // /**
// // * This is to save the obtained result and proceed with the
// // * simulation even if the error is higher than the pre-fixed
// // * tolerance. This is done only after loading reduction
// // * (load_reduction = true).
// // */
// // // if (load_reduction && (error < tolerance * tol_increase_factor))
// // // converged = true;
// // if ((error < tolerance * tol_increase_factor))
// // converged = true;
// // if (converged) {
// // } else if (iter == max_iteration) {
// // if (prank == 0) {
// // AKANTU_DEBUG_WARNING(
// // "[" << criteria << "] Convergence not reached after "
// // << std::setw(std::log10(max_iteration)) << iter << "
// iteration"
// // << (iter == 1 ? "" : "s") << "!" << std::endl);
// // }
// // }
// // if (is_extrinsic) {
// // /**
// // * If is extrinsic the pointer "displacement" is moved back to
// // * the array displacement. In this way, the array displacement is
// // * correctly resized during the checkCohesiveStress function (in
// // * case new cohesive elements are added). This is possible
// // * because the procedure called by checkCohesiveStress does not
// // * use the displacement field (the correct one is now stored in
// // * displacement_tmp), but directly the stress field that is
// // * already computed.
// // */
// // Array<Real> * tmp_swap;
// // tmp_swap = displacement_tmp;
// // displacement_tmp = this->displacement;
// // this->displacement = tmp_swap;
// // tmp_swap = velocity_tmp;
// // velocity_tmp = this->velocity;
// // this->velocity = tmp_swap;
// // tmp_swap = acceleration_tmp;
// // acceleration_tmp = this->acceleration;
// // this->acceleration = tmp_swap;
// // /// If convergence is reached, call checkCohesiveStress in order
// // /// to check if cohesive elements have to be introduced
// // if (converged) {
// // UInt new_cohesive_elements = checkCohesiveStress();
// // if (new_cohesive_elements == 0) {
// // insertion_new_element = false;
// // } else {
// // insertion_new_element = true;
// // }
// // }
// // }
// // if (!converged && load_reduction)
// // insertion_new_element = false;
// // /**
// // * If convergence is not reached, there is the possibility to
// // * return back to the main file and reduce the load. Before doing
// // * this, a pre-fixed value as to be defined for the parameter
// // * delta_max of the cohesive elements introduced in the current
// // * incremental step. This is done by calling the function
// // * checkDeltaMax.
// // */
// // if (!converged) {
// // insertion_new_element = false;
// // for (UInt m = 0; m < materials.size(); ++m) {
// // try {
// // MaterialCohesive & mat =
// // dynamic_cast<MaterialCohesive &>(*materials[m]);
// // mat.checkDeltaMax(_not_ghost);
// // } catch (std::bad_cast &) {
// // }
// // }
// // }
// // } // end loop for the insertion of new cohesive elements
// // /**
// // * When the solution to the current incremental step is computed (no
// // * more cohesive elements have to be introduced), call the function
// // * to compute the energies.
// // */
// // if ((is_extrinsic && converged)) {
// // for (UInt m = 0; m < materials.size(); ++m) {
// // try {
// // MaterialCohesive & mat =
// // dynamic_cast<MaterialCohesive &>(*materials[m]);
// // mat.computeEnergies();
// // } catch (std::bad_cast & bce) {
// // }
// // }
// // EventManager::sendEvent(
// // SolidMechanicsModelEvent::AfterSolveStepEvent(method));
// // /**
// // * The function resetVariables is necessary to correctly set a
// // * variable that permit to decrease locally the penalty parameter
// // * for compression.
// // */
// // for (UInt m = 0; m < materials.size(); ++m) {
// // try {
// // MaterialCohesive & mat =
// // dynamic_cast<MaterialCohesive &>(*materials[m]);
// // mat.resetVariables(_not_ghost);
// // } catch (std::bad_cast &) {
// // }
// // }
// // /// The correct solution is saved
// // this->displacement->copy(*displacement_tmp);
// // this->velocity->copy(*velocity_tmp);
// // this->acceleration->copy(*acceleration_tmp);
// // }
// // delete displacement_tmp;
// // delete velocity_tmp;
// // delete acceleration_tmp;
// // return insertion_new_element;
//}
} // akantu
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
index da79875ba..7735e5e55 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
@@ -1,488 +1,505 @@
/**
* @file solid_mechanics_model_cohesive_parallel.cc
*
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
+ * @date creation: Wed Nov 05 2014
+ * @date last modification: Tue Feb 20 2018
*
* @brief Functions for parallel cohesive elements
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
*/
+
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "solid_mechanics_model_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::synchronizeGhostFacetsConnectivity() {
AKANTU_DEBUG_IN();
const Communicator & comm = mesh.getCommunicator();
Int psize = comm.getNbProc();
if (psize > 1) {
/// get global connectivity for not ghost facets
global_connectivity =
new ElementTypeMapArray<UInt>("global_connectivity", id);
auto & mesh_facets = inserter->getMeshFacets();
global_connectivity->initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _with_nb_nodes_per_element = true,
_element_kind = _ek_regular);
mesh_facets.getGlobalConnectivity(*global_connectivity);
/// communicate
synchronize(_gst_smmc_facets_conn);
/// flip facets
MeshUtils::flipFacets(mesh_facets, *global_connectivity, _ghost);
delete global_connectivity;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateCohesiveSynchronizers() {
/// update synchronizers if needed
if (not mesh.isDistributed())
return;
auto & mesh_facets = inserter->getMeshFacets();
auto & facet_synchronizer = mesh_facets.getElementSynchronizer();
const auto & cfacet_synchronizer = facet_synchronizer;
// update the cohesive element synchronizer
cohesive_synchronizer->updateSchemes([&](auto && scheme, auto && proc,
auto && direction) {
auto & facet_scheme =
cfacet_synchronizer.getCommunications().getScheme(proc, direction);
for (auto && facet : facet_scheme) {
const auto & connected_elements = mesh_facets.getElementToSubelement(
facet.type,
facet.ghost_type)(facet.element); // slow access here
const auto & cohesive_element = connected_elements[1];
if (cohesive_element == ElementNull or
cohesive_element.kind() == _ek_cohesive)
continue;
auto && cohesive_type = FEEngine::getCohesiveElementType(facet.type);
auto old_nb_cohesive_elements =
mesh.getNbElement(cohesive_type, facet.ghost_type);
old_nb_cohesive_elements -=
mesh_facets
.getData<UInt>("facet_to_double", facet.type, facet.ghost_type)
.size();
if (cohesive_element.element >= old_nb_cohesive_elements) {
scheme.push_back(cohesive_element);
}
}
});
const auto & comm = mesh.getCommunicator();
auto && my_rank = comm.whoAmI();
// update the facet stress synchronizer
if (facet_stress_synchronizer)
facet_stress_synchronizer->updateSchemes([&](auto && scheme, auto && proc,
auto && /*direction*/) {
auto it_element = scheme.begin();
for (auto && element : scheme) {
auto && facet_check = inserter->getCheckFacets(
element.type, element.ghost_type)(element.element); // slow access
// here
if (facet_check) {
auto && connected_elements = mesh_facets.getElementToSubelement(
element.type, element.ghost_type)(element.element); // slow access
// here
auto && rank_left = facet_synchronizer.getRank(connected_elements[0]);
auto && rank_right =
facet_synchronizer.getRank(connected_elements[1]);
// keep element if the element is still a boundary element between two
// processors
if ((rank_left == Int(proc) and rank_right == my_rank) or
(rank_left == my_rank and rank_right == Int(proc))) {
*it_element = element;
++it_element;
}
}
}
scheme.resize(it_element - scheme.begin());
});
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateFacetStressSynchronizer() {
if (facet_stress_synchronizer != nullptr) {
const auto & rank_to_element =
mesh.getElementSynchronizer().getElementToRank();
const auto & facet_checks = inserter->getCheckFacets();
const auto & mesh_facets = inserter->getMeshFacets();
const auto & element_to_facet = mesh_facets.getElementToSubelement();
UInt rank = mesh.getCommunicator().whoAmI();
facet_stress_synchronizer->updateSchemes(
[&](auto & scheme, auto & proc, auto & /*direction*/) {
UInt el = 0;
for (auto && element : scheme) {
if (not facet_checks(element))
continue;
const auto & next_el = element_to_facet(element);
UInt rank_left = rank_to_element(next_el[0]);
UInt rank_right = rank_to_element(next_el[1]);
if ((rank_left == rank and rank_right == proc) or
(rank_left == proc and rank_right == rank)) {
scheme[el] = element;
++el;
}
}
scheme.resize(el);
});
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SolidMechanicsModelCohesive::packFacetStressDataHelper(
const ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
packUnpackFacetStressDataHelper<T, true>(
const_cast<ElementTypeMapArray<T> &>(data_to_pack), buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SolidMechanicsModelCohesive::unpackFacetStressDataHelper(
ElementTypeMapArray<T> & data_to_unpack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
packUnpackFacetStressDataHelper<T, false>(data_to_unpack, buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void SolidMechanicsModelCohesive::packUnpackFacetStressDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt nb_quad_per_elem = 0;
UInt sp2 = spatial_dimension * spatial_dimension;
UInt nb_component = sp2 * 2;
bool element_rank = false;
Mesh & mesh_facets = inserter->getMeshFacets();
Array<T> * vect = nullptr;
Array<std::vector<Element>> * element_to_facet = nullptr;
auto & fe_engine = this->getFEEngine("FacetsFEEngine");
for (auto && el : elements) {
if (el.type == _not_defined)
AKANTU_EXCEPTION(
"packUnpackFacetStressDataHelper called with wrong inputs");
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect = &data_to_pack(el.type, el.ghost_type);
element_to_facet =
&(mesh_facets.getElementToSubelement(el.type, el.ghost_type));
nb_quad_per_elem =
fe_engine.getNbIntegrationPoints(el.type, el.ghost_type);
}
if (pack_helper)
element_rank =
(*element_to_facet)(el.element)[0].ghost_type != _not_ghost;
else
element_rank =
(*element_to_facet)(el.element)[0].ghost_type == _not_ghost;
for (UInt q = 0; q < nb_quad_per_elem; ++q) {
Vector<T> data(vect->storage() +
(el.element * nb_quad_per_elem + q) * nb_component +
element_rank * sp2,
sp2);
if (pack_helper)
buffer << data;
else
buffer >> data;
}
}
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::getNbQuadsForFacetCheck(
const Array<Element> & elements) const {
UInt nb_quads = 0;
UInt nb_quad_per_facet = 0;
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
auto & fe_engine = this->getFEEngine("FacetsFEEngine");
for (auto & el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
nb_quad_per_facet =
fe_engine.getNbIntegrationPoints(el.type, el.ghost_type);
}
nb_quads += nb_quad_per_facet;
}
return nb_quads;
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (elements.size() == 0)
return 0;
/// regular element case
if (elements(0).kind() == _ek_regular) {
switch (tag) {
case _gst_smmc_facets: {
size += elements.size() * sizeof(bool);
break;
}
case _gst_smmc_facets_conn: {
UInt nb_nodes = Mesh::getNbNodesPerElementList(elements);
size += nb_nodes * sizeof(UInt);
break;
}
case _gst_smmc_facets_stress: {
UInt nb_quads = getNbQuadsForFacetCheck(elements);
size += nb_quads * spatial_dimension * spatial_dimension * sizeof(Real);
break;
}
case _gst_material_id: {
for (auto && element : elements) {
if (Mesh::getSpatialDimension(element.type) == (spatial_dimension - 1))
size += sizeof(UInt);
}
size += SolidMechanicsModel::getNbData(elements, tag);
break;
}
default: { size += SolidMechanicsModel::getNbData(elements, tag); }
}
}
/// cohesive element case
else if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case _gst_material_id: {
size += elements.size() * sizeof(UInt);
break;
}
case _gst_smm_boundary: {
UInt nb_nodes_per_element = 0;
for (auto && el : elements) {
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
// force, displacement, boundary
size += nb_nodes_per_element * spatial_dimension *
(2 * sizeof(Real) + sizeof(bool));
break;
}
default:
break;
}
if (tag != _gst_material_id && tag != _gst_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
size += mat.getNbData(elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (elements.size() == 0)
return;
if (elements(0).kind() == _ek_regular) {
switch (tag) {
case _gst_smmc_facets: {
packElementalDataHelper(inserter->getInsertionFacetsByElement(), buffer,
elements, false, getFEEngine());
break;
}
case _gst_smmc_facets_conn: {
packElementalDataHelper(*global_connectivity, buffer, elements, false,
getFEEngine());
break;
}
case _gst_smmc_facets_stress: {
packFacetStressDataHelper(facet_stress, buffer, elements);
break;
}
case _gst_material_id: {
for (auto && element : elements) {
if (Mesh::getSpatialDimension(element.type) != (spatial_dimension - 1))
continue;
buffer << material_index(element);
}
SolidMechanicsModel::packData(buffer, elements, tag);
break;
}
default: { SolidMechanicsModel::packData(buffer, elements, tag); }
}
AKANTU_DEBUG_OUT();
return;
}
if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case _gst_material_id: {
packElementalDataHelper(material_index, buffer, elements, false,
getFEEngine("CohesiveFEEngine"));
break;
}
case _gst_smm_boundary: {
packNodalDataHelper(*internal_force, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {}
}
if (tag != _gst_material_id && tag != _gst_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.packData(buffer, elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (elements.size() == 0)
return;
if (elements(0).kind() == _ek_regular) {
switch (tag) {
case _gst_smmc_facets: {
unpackElementalDataHelper(inserter->getInsertionFacetsByElement(), buffer,
elements, false, getFEEngine());
break;
}
case _gst_smmc_facets_conn: {
unpackElementalDataHelper(*global_connectivity, buffer, elements, false,
getFEEngine());
break;
}
case _gst_smmc_facets_stress: {
unpackFacetStressDataHelper(facet_stress, buffer, elements);
break;
}
case _gst_material_id: {
for (auto && element : elements) {
if (Mesh::getSpatialDimension(element.type) != (spatial_dimension - 1))
continue;
UInt recv_mat_index;
buffer >> recv_mat_index;
UInt & mat_index = material_index(element);
if (mat_index != UInt(-1))
continue;
// add ghosts element to the correct material
mat_index = recv_mat_index;
auto & mat = dynamic_cast<MaterialCohesive &>(*materials[mat_index]);
mat.addFacet(element);
facet_material(element) = recv_mat_index;
}
SolidMechanicsModel::unpackData(buffer, elements, tag);
break;
}
default: { SolidMechanicsModel::unpackData(buffer, elements, tag); }
}
AKANTU_DEBUG_OUT();
return;
}
if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case _gst_material_id: {
unpackElementalDataHelper(material_index, buffer, elements, false,
getFEEngine("CohesiveFEEngine"));
break;
}
case _gst_smm_boundary: {
unpackNodalDataHelper(*internal_force, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {}
}
if (tag != _gst_material_id && tag != _gst_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.unpackData(buffer, elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
index f961c7a7c..a422e9b0d 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
@@ -1,179 +1,179 @@
/**
* @file embedded_interface_intersector.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri May 01 2015
- * @date last modification: Mon Jan 04 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Class that loads the interface from mesh and computes intersections
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "embedded_interface_intersector.hh"
#include "mesh_segment_intersector.hh"
/// Helper macro for types in the mesh. Creates an intersector and computes
/// intersection queries
#define INTERFACE_INTERSECTOR_CASE(dim, type) \
do { \
MeshSegmentIntersector<dim, type> intersector(this->mesh, interface_mesh); \
name_to_primitives_it = name_to_primitives_map.begin(); \
for (; name_to_primitives_it != name_to_primitives_end; \
++name_to_primitives_it) { \
intersector.setPhysicalName(name_to_primitives_it->first); \
intersector.buildResultFromQueryList(name_to_primitives_it->second); \
} \
} while (0)
#define INTERFACE_INTERSECTOR_CASE_2D(type) INTERFACE_INTERSECTOR_CASE(2, type)
#define INTERFACE_INTERSECTOR_CASE_3D(type) INTERFACE_INTERSECTOR_CASE(3, type)
namespace akantu {
EmbeddedInterfaceIntersector::EmbeddedInterfaceIntersector(
Mesh & mesh, const Mesh & primitive_mesh)
: MeshGeomAbstract(mesh),
interface_mesh(mesh.getSpatialDimension(), "interface_mesh"),
primitive_mesh(primitive_mesh) {
// Initiating mesh connectivity and data
interface_mesh.addConnectivityType(_segment_2, _not_ghost);
interface_mesh.addConnectivityType(_segment_2, _ghost);
interface_mesh.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(GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
const UInt dim = this->mesh.getSpatialDimension();
if (dim == 1)
AKANTU_ERROR(
"No embedded model in 1D. Deactivate intersection initialization");
Array<std::string> * physical_names = NULL;
try {
physical_names = &const_cast<Array<std::string> &>(
this->primitive_mesh.getData<std::string>("physical_names",
_segment_2));
} catch (debug::Exception & e) {
AKANTU_ERROR("You must define physical names to reinforcements in "
"order to use the embedded model");
throw e;
}
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_segment_2);
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;
// Loop over the physical names and register segment lists in
// name_to_primitives_map
for (; names_it != names_end; ++names_it) {
UInt element_id = names_it - physical_names->begin();
const Vector<UInt> el_connectivity = connectivity[element_id];
K::Segment_3 segment = this->createSegment(el_connectivity);
name_to_primitives_map[*names_it].push_back(segment);
}
// Loop over the background types of the mesh
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) {
// Used in AKANTU_BOOST_ELEMENT_SWITCH
ElementType type = *type_it;
AKANTU_DEBUG_INFO("Computing intersections with background element type "
<< type);
switch (dim) {
case 1:
break;
case 2:
// Compute intersections for supported 2D elements
AKANTU_BOOST_ELEMENT_SWITCH(INTERFACE_INTERSECTOR_CASE_2D,
(_triangle_3)(_triangle_6));
break;
case 3:
// Compute intersections for supported 3D elements
AKANTU_BOOST_ELEMENT_SWITCH(INTERFACE_INTERSECTOR_CASE_3D,
(_tetrahedron_4));
break;
}
}
AKANTU_DEBUG_OUT();
}
K::Segment_3
EmbeddedInterfaceIntersector::createSegment(const Vector<UInt> & connectivity) {
AKANTU_DEBUG_IN();
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;
}
} // namespace akantu
#undef INTERFACE_INTERSECTOR_CASE
#undef INTERFACE_INTERSECTOR_CASE_2D
#undef INTERFACE_INTERSECTOR_CASE_3D
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
index 03bf41fb0..9552e178b 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
@@ -1,98 +1,98 @@
/**
* @file embedded_interface_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri May 01 2015
- * @date last modification: Mon Dec 14 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Class that loads the interface from mesh and computes intersections
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
#define __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_geom_abstract.hh"
#include "mesh_geom_common.hh"
#include "mesh_segment_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace {
using K = cgal::Cartesian;
}
/**
* @brief Computes the intersections of the reinforcements defined in the
* primitive mesh
*
* The purpose of this class is to look for reinforcements in the primitive
* mesh, which
* should be defined by physical groups with the same names as the reinforcement
* materials
* in the model.
*
* It then constructs the CGAL primitives from the elements of those
* reinforcements
* and computes the intersections with the background mesh, to create an
* `interface_mesh`,
* which is in turn used by the EmbeddedInterfaceModel.
*
* @see MeshSegmentIntersector, MeshGeomAbstract
* @see EmbeddedInterfaceModel
*/
class EmbeddedInterfaceIntersector : public MeshGeomAbstract {
public:
/// Construct from mesh and a reinforcement mesh
explicit EmbeddedInterfaceIntersector(Mesh & mesh,
const Mesh & primitive_mesh);
/// Destructor
virtual ~EmbeddedInterfaceIntersector();
public:
/// Generate the interface mesh
virtual void constructData(GhostType ghost_type = _not_ghost);
/// 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;
};
} // akantu
#endif // __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
index c951110c8..4c260b2df 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
@@ -1,173 +1,173 @@
/**
* @file embedded_interface_model.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
- * @date last modification: Mon Dec 14 2015
+ * @date last modification: Wed Feb 14 2018
*
* @brief Model of Solid Mechanics with embedded interfaces
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "embedded_interface_model.hh"
#include "integrator_gauss.hh"
#include "material_elastic.hh"
#include "material_reinforcement.hh"
#include "mesh_iterators.hh"
#include "shape_lagrange.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumpable_inline_impl.hh"
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
EmbeddedInterfaceModel::EmbeddedInterfaceModel(Mesh & mesh,
Mesh & primitive_mesh,
UInt spatial_dimension,
const ID & id,
const MemoryID & memory_id)
: SolidMechanicsModel(mesh, spatial_dimension, id, memory_id),
intersector(mesh, primitive_mesh), interface_mesh(nullptr),
primitive_mesh(primitive_mesh), interface_material_selector(nullptr) {
this->model_type = ModelType::_embedded_model;
// This pointer should be deleted by ~SolidMechanicsModel()
auto mat_sel_pointer =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
*this);
this->setMaterialSelector(mat_sel_pointer);
interface_mesh = &(intersector.getInterfaceMesh());
// Create 1D FEEngine on the interface mesh
registerFEEngineObject<MyFEEngineType>("EmbeddedInterfaceFEEngine",
*interface_mesh, 1);
// Registering allocator for material reinforcement
MaterialFactory::getInstance().registerAllocator(
"reinforcement",
[&](UInt dim, const ID & constitutive, SolidMechanicsModel &,
const ID & id) -> std::unique_ptr<Material> {
if (constitutive == "elastic") {
using mat = MaterialElastic<1>;
switch (dim) {
case 2:
return std::make_unique<MaterialReinforcement<mat, 2>>(*this, id);
case 3:
return std::make_unique<MaterialReinforcement<mat, 3>>(*this, id);
default:
AKANTU_EXCEPTION("Dimension 1 is invalid for reinforcements");
}
} else {
AKANTU_EXCEPTION("Reinforcement type" << constitutive
<< " is not recognized");
}
});
}
/* -------------------------------------------------------------------------- */
EmbeddedInterfaceModel::~EmbeddedInterfaceModel() {
delete interface_material_selector;
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::initFullImpl(const ModelOptions & options) {
const auto & eim_options =
dynamic_cast<const EmbeddedInterfaceModelOptions &>(options);
// Do no initialize interface_mesh if told so
if (eim_options.has_intersections)
intersector.constructData();
SolidMechanicsModel::initFullImpl(options);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("reinforcement", id);
this->mesh.addDumpMeshToDumper("reinforcement", *interface_mesh, 1,
_not_ghost, _ek_regular);
#endif
}
void EmbeddedInterfaceModel::initModel() {
// Initialize interface FEEngine
SolidMechanicsModel::initModel();
FEEngine & engine = getFEEngine("EmbeddedInterfaceFEEngine");
engine.initShapeFunctions(_not_ghost);
engine.initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::assignMaterialToElements(
const ElementTypeMapArray<UInt> * filter) {
delete interface_material_selector;
interface_material_selector =
new InterfaceMeshDataMaterialSelector<std::string>("physical_names",
*this);
for_each_element(getInterfaceMesh(),
[&](auto && element) {
auto mat_index = (*interface_material_selector)(element);
// material_index(element) = mat_index;
materials[mat_index]->addElement(element);
// this->material_local_numbering(element) = index;
},
_element_filter = filter, _spatial_dimension = 1);
SolidMechanicsModel::assignMaterialToElements(filter);
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::addDumpGroupFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
const std::string & group_name, const ElementKind & element_kind,
bool padding_flag) {
#ifdef AKANTU_USE_IOHELPER
dumper::Field * field = NULL;
// If dumper is reinforcement, create a 1D elemental field
if (dumper_name == "reinforcement")
field = this->createElementalField(field_id, group_name, padding_flag, 1,
element_kind);
else {
try {
SolidMechanicsModel::addDumpGroupFieldToDumper(
dumper_name, field_id, group_name, element_kind, padding_flag);
} catch (...) {
}
}
if (field) {
DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name, group_name);
Model::addDumpGroupFieldToDumper(field_id, field, dumper);
}
#endif
}
} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
index 836661b31..42db35d34 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
@@ -1,154 +1,153 @@
/**
* @file embedded_interface_model.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Dec 14 2015
+ * @date last modification: Wed Jan 31 2018
*
* @brief Model of Solid Mechanics with embedded interfaces
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
#define __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
#include "aka_common.hh"
#include "mesh.hh"
#include "solid_mechanics_model.hh"
#include "embedded_interface_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Solid mechanics model using the embedded model.
*
* This SolidMechanicsModel subclass implements the embedded model,
* a method used to represent 1D elements in a finite elements model
* (eg. reinforcements in concrete).
*
* In addition to the SolidMechanicsModel properties, this model has
* a mesh of the 1D elements embedded in the model, and an instance of the
* EmbeddedInterfaceIntersector class for the computation of the intersections
* of the
* 1D elements with the background (bulk) mesh.
*
* @see MaterialReinforcement
*/
class EmbeddedInterfaceModel : public SolidMechanicsModel {
using MyFEEngineType = SolidMechanicsModel::MyFEEngineType;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief Constructor
*
* @param mesh main mesh (concrete)
* @param primitive_mesh mesh of the embedded reinforcement
*/
EmbeddedInterfaceModel(Mesh & mesh, Mesh & primitive_mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "embedded_interface_model",
const MemoryID & memory_id = 0);
/// Destructor
~EmbeddedInterfaceModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Initialise the model
void initFullImpl(
const ModelOptions & options = EmbeddedInterfaceModelOptions()) override;
/// Initialise the materials
void
assignMaterialToElements(const ElementTypeMapArray<UInt> * filter) override;
/// Initialize the embedded shape functions
void initModel() override;
/// Allows filtering of dump fields which need to be dumpes on interface mesh
void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind,
bool padding_flag) override;
// virtual ElementTypeMap<UInt> getInternalDataPerElem(const std::string &
// field_name,
// const ElementKind &
// kind);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get interface mesh
AKANTU_GET_MACRO(InterfaceMesh, *interface_mesh, Mesh &);
/// Get associated elements
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(
InterfaceAssociatedElements,
interface_mesh->getData<Element>("associated_element"), Element);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Intersector object to build the interface mesh
EmbeddedInterfaceIntersector intersector;
/// Interface mesh (weak reference)
Mesh * interface_mesh;
/// Mesh used to create the CGAL primitives for intersections
Mesh & primitive_mesh;
/// Material selector for interface
MaterialSelector * interface_material_selector;
};
/// Material selector based on mesh data for interface elements
template <typename T>
class InterfaceMeshDataMaterialSelector
: public ElementDataMaterialSelector<T> {
public:
InterfaceMeshDataMaterialSelector(const std::string & name,
const EmbeddedInterfaceModel & model,
UInt first_index = 1)
: ElementDataMaterialSelector<T>(
model.getInterfaceMesh().getData<T>(name), model, first_index) {}
};
} // akantu
#endif // __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
diff --git a/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh b/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
index ff5d8538c..6f1214c96 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
@@ -1,127 +1,126 @@
/**
* @file solid_mechanics_model_event_handler.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Dec 18 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief EventHandler implementation for SolidMechanicsEvents
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH__
namespace akantu {
/// akantu::SolidMechanicsModelEvent is the base event for model
namespace SolidMechanicsModelEvent {
struct BeforeSolveStepEvent {
BeforeSolveStepEvent(AnalysisMethod & method) : method(method) {}
AnalysisMethod method;
};
struct AfterSolveStepEvent {
AfterSolveStepEvent(AnalysisMethod & method) : method(method) {}
AnalysisMethod method;
};
struct BeforeDumpEvent {
BeforeDumpEvent() = default;
};
struct BeginningOfDamageIterationEvent {
BeginningOfDamageIterationEvent() = default;
};
struct AfterDamageEvent {
AfterDamageEvent() = default;
};
}
/// akantu::SolidMechanicsModelEvent
class SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
virtual ~SolidMechanicsModelEventHandler() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// Send what is before the solve step to the beginning of solve step through
/// EventManager
inline void
sendEvent(const SolidMechanicsModelEvent::BeforeSolveStepEvent & event) {
onBeginningSolveStep(event.method);
}
/// Send what is after the solve step to the end of solve step through
/// EventManager
inline void
sendEvent(const SolidMechanicsModelEvent::AfterSolveStepEvent & event) {
onEndSolveStep(event.method);
}
/// Send what is before dump to current dump through EventManager
inline void
sendEvent(__attribute__((unused))
const SolidMechanicsModelEvent::BeforeDumpEvent & event) {
onDump();
}
/// Send what is at the beginning of damage iteration to Damage iteration
/// through EventManager
inline void sendEvent(
__attribute__((unused))
const SolidMechanicsModelEvent::BeginningOfDamageIterationEvent & event) {
onDamageIteration();
}
/// Send what is after damage for the damage update through EventManager
inline void
sendEvent(__attribute__((unused))
const SolidMechanicsModelEvent::AfterDamageEvent & event) {
onDamageUpdate();
}
template <class EventHandler> friend class EventHandlerManager;
/* ------------------------------------------------------------------------ */
/* Interface */
/* ------------------------------------------------------------------------ */
public:
/// function to implement to react on akantu::BeforeSolveStepEvent
virtual void onBeginningSolveStep(__attribute__((unused))
const AnalysisMethod & method) {}
/// function to implement to react on akantu::AfterSolveStepEvent
virtual void onEndSolveStep(__attribute__((unused))
const AnalysisMethod & method) {}
/// function to implement to react on akantu::BeforeDumpEvent
virtual void onDump() {}
/// function to implement to react on akantu::BeginningOfDamageIterationEvent
virtual void onDamageIteration() {}
/// function to implement to react on akantu::AfterDamageEvent
virtual void onDamageUpdate() {}
};
} // akantu
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH__ */
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 322a480da..1ae4784cc 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
@@ -1,102 +1,102 @@
/**
* @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: Wed Nov 18 2015
+ * @date last modification: Tue Dec 05 2017
*
* @brief Implementation of the inline functions of the SolidMechanicsModel
* class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "material_selector.hh"
#include "material_selector_tmpl.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_CC__
#define __AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
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();
auto 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();
auto 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];
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_io.cc b/src/model/solid_mechanics/solid_mechanics_model_io.cc
index 71d9ff521..ba29a79ca 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_io.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_io.cc
@@ -1,324 +1,326 @@
/**
* @file solid_mechanics_model_io.cc
*
- * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Fri Jul 07 2017
+ * @date creation: Sun Jul 09 2017
+ * @date last modification: Sun Dec 03 2017
*
- * @brief Dumpable part of the SolidMechnicsModel
+ * @brief Dumpable part of the SolidMechnicsModel
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "group_manager_inline_impl.cc"
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_element_partition.hh"
#include "dumper_elemental_field.hh"
#include "dumper_field.hh"
#include "dumper_homogenizing_field.hh"
#include "dumper_internal_material_field.hh"
#include "dumper_iohelper.hh"
#include "dumper_material_padders.hh"
#include "dumper_paraview.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::isInternal(const std::string & field_name,
const ElementKind & element_kind) {
/// check if at least one material contains field_id as an internal
for (auto & material : materials) {
bool is_internal = material->isInternal<Real>(field_name, element_kind);
if (is_internal)
return true;
}
return false;
}
/* -------------------------------------------------------------------------- */
ElementTypeMap<UInt>
SolidMechanicsModel::getInternalDataPerElem(const std::string & field_name,
const ElementKind & element_kind) {
if (!(this->isInternal(field_name, element_kind)))
AKANTU_EXCEPTION("unknown internal " << field_name);
for (auto & material : materials) {
if (material->isInternal<Real>(field_name, element_kind))
return material->getInternalDataPerElem<Real>(field_name, element_kind);
}
return ElementTypeMap<UInt>();
}
/* -------------------------------------------------------------------------- */
ElementTypeMapArray<Real> &
SolidMechanicsModel::flattenInternal(const std::string & field_name,
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, this->memory_id);
}
ElementTypeMapArray<Real> * internal_flat = this->registered_internals[key];
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, kind)) {
if (internal_flat->exists(type, ghost_type)) {
auto & internal = (*internal_flat)(type, ghost_type);
// internal.clear();
internal.resize(0);
}
}
for (auto & material : materials) {
if (material->isInternal<Real>(field_name, kind))
material->flattenInternal(field_name, *internal_flat, ghost_type, kind);
}
return *internal_flat;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::flattenAllRegisteredInternals(
const ElementKind & kind) {
ElementKind _kind;
ID _id;
for (auto & internal : this->registered_internals) {
std::tie(_id, _kind) = internal.first;
if (kind == _kind)
this->flattenInternal(_id, kind);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onDump() {
this->flattenAllRegisteredInternals(_ek_regular);
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
dumper::Field * SolidMechanicsModel::createElementalField(
const std::string & field_name, const std::string & group_name,
bool padding_flag, const UInt & spatial_dimension,
const ElementKind & kind) {
dumper::Field * field = nullptr;
if (field_name == "partitions")
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, 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);
ElementTypeMapArray<Real> & internal_flat =
this->flattenInternal(field_name_copy, kind);
field = mesh.createElementalField<Real, dumper::InternalMaterialField>(
internal_flat, group_name, spatial_dimension, kind, nb_data_per_elem);
if (field_name == "strain") {
auto * foo = new dumper::ComputeStrain<false>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "Von Mises stress") {
auto * foo = new dumper::ComputeVonMisesStress(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "Green strain") {
auto * foo = new dumper::ComputeStrain<true>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "principal strain") {
auto * foo = new dumper::ComputePrincipalStrain<false>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "principal Green strain") {
auto * foo = new dumper::ComputePrincipalStrain<true>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
}
// treat the paddings
if (padding_flag) {
if (field_name == "stress") {
if (spatial_dimension == 2) {
auto * foo = new dumper::StressPadder<2>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
}
} else if (field_name == "strain" || field_name == "Green strain") {
if (spatial_dimension == 2) {
auto * 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"] = this->displacement;
real_nodal_fields["mass"] = this->mass;
real_nodal_fields["velocity"] = this->velocity;
real_nodal_fields["acceleration"] = this->acceleration;
real_nodal_fields["external_force"] = this->external_force;
real_nodal_fields["internal_force"] = this->internal_force;
real_nodal_fields["increment"] = this->displacement_increment;
if (field_name == "force") {
AKANTU_EXCEPTION("The 'force' field has been renamed in 'external_force'");
} else if (field_name == "residual") {
AKANTU_EXCEPTION(
"The 'residual' field has been replaced by 'internal_force'");
}
dumper::Field * field = nullptr;
if (padding_flag)
field = this->mesh.createNodalField(real_nodal_fields[field_name],
group_name, 3);
else
field =
this->mesh.createNodalField(real_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs;
dumper::Field * field = nullptr;
field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel::createElementalField(const std::string &,
const std::string &,
bool, const UInt &,
const ElementKind &) {
return nullptr;
}
/* --------------------------------------------------------------------------
*/
dumper::Field * SolidMechanicsModel::createNodalFieldReal(const std::string &,
const std::string &,
bool) {
return nullptr;
}
/* --------------------------------------------------------------------------
*/
dumper::Field * SolidMechanicsModel::createNodalFieldBool(const std::string &,
const std::string &,
bool) {
return nullptr;
}
#endif
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(const std::string & dumper_name) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name);
}
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(const std::string & dumper_name, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name, step);
}
/* -------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(const std::string & dumper_name, Real time,
UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name, time, step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump() {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(Real time, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(time, step);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_mass.cc b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
index e0f5392a6..66ddd6ac6 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_mass.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
@@ -1,159 +1,158 @@
/**
* @file solid_mechanics_model_mass.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 05 2010
- * @date last modification: Fri Oct 16 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief function handling mass computation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "material.hh"
#include "model_solver.hh"
#include "shape_lagrange.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ComputeRhoFunctor {
public:
explicit ComputeRhoFunctor(const SolidMechanicsModel & model)
: model(model){};
void operator()(Matrix<Real> & rho, const Element & element) const {
const Array<UInt> & mat_indexes =
model.getMaterialByElement(element.type, element.ghost_type);
Real mat_rho =
model.getMaterial(mat_indexes(element.element)).getParam("rho");
rho.set(mat_rho);
}
private:
const SolidMechanicsModel & model;
};
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped() {
AKANTU_DEBUG_IN();
if (not need_to_reassemble_lumped_mass)
return;
UInt nb_nodes = mesh.getNbNodes();
if (this->mass == nullptr) {
std::stringstream sstr_mass;
sstr_mass << id << ":mass";
mass =
&(alloc<Real>(sstr_mass.str(), nb_nodes, Model::spatial_dimension, 0));
} else {
mass->clear();
}
if (!this->getDOFManager().hasLumpedMatrix("M")) {
this->getDOFManager().getNewLumpedMatrix("M");
}
this->getDOFManager().clearLumpedMatrix("M");
assembleMassLumped(_not_ghost);
assembleMassLumped(_ghost);
this->getDOFManager().getLumpedMatrixPerDOFs("displacement", "M",
*(this->mass));
/// for not connected nodes put mass to one in order to avoid
#if !defined(AKANTU_NDEBUG)
bool has_unconnected_nodes = false;
auto mass_it = mass->begin_reinterpret(mass->size() * mass->getNbComponent());
auto mass_end = mass->end_reinterpret(mass->size() * mass->getNbComponent());
for (; mass_it != mass_end; ++mass_it) {
if (std::abs(*mass_it) < std::numeric_limits<Real>::epsilon() ||
Math::isnan(*mass_it)) {
has_unconnected_nodes = true;
break;
}
}
if (has_unconnected_nodes)
AKANTU_DEBUG_WARNING("There are nodes that seem to not be connected to any "
"elements, beware that they have lumped mass of 0.");
#endif
this->synchronize(_gst_smm_mass);
need_to_reassemble_lumped_mass = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMass() {
AKANTU_DEBUG_IN();
if (not need_to_reassemble_mass)
return;
this->getDOFManager().clearMatrix("M");
assembleMass(_not_ghost);
need_to_reassemble_mass = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped(GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor compute_rho(*this);
for (auto type : mesh.elementTypes(Model::spatial_dimension, ghost_type)) {
fem.assembleFieldLumped(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMass(GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor compute_rho(*this);
for (auto type : mesh.elementTypes(Model::spatial_dimension, ghost_type)) {
fem.assembleFieldMatrix(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_material.cc b/src/model/solid_mechanics/solid_mechanics_model_material.cc
index 74ce922a9..d21eb55e3 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_material.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_material.cc
@@ -1,254 +1,253 @@
/**
* @file solid_mechanics_model_material.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Nov 26 2010
- * @date last modification: Mon Nov 16 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief instatiation of materials
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "aka_math.hh"
#include "material_non_local.hh"
#include "mesh_iterators.hh"
#include "non_local_manager.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Material &
SolidMechanicsModel::registerNewMaterial(const ParserSection & section) {
std::string mat_name;
std::string mat_type = section.getName();
std::string opt_param = section.getOption();
try {
std::string tmp = section.getParameter("name");
mat_name = tmp; /** this can seam weird, but there is an ambiguous operator
* overload that i couldn't solve. @todo remove the
* weirdness of this code
*/
} catch (debug::Exception &) {
AKANTU_ERROR("A material of type \'"
<< mat_type
<< "\' in the input file has been defined without a name!");
}
Material & mat = this->registerNewMaterial(mat_name, mat_type, opt_param);
mat.parseSection(section);
return mat;
}
/* -------------------------------------------------------------------------- */
Material & SolidMechanicsModel::registerNewMaterial(const ID & mat_name,
const ID & mat_type,
const ID & opt_param) {
AKANTU_DEBUG_ASSERT(materials_names_to_id.find(mat_name) ==
materials_names_to_id.end(),
"A material with this name '"
<< mat_name << "' has already been registered. "
<< "Please use unique names for materials");
UInt mat_count = materials.size();
materials_names_to_id[mat_name] = mat_count;
std::stringstream sstr_mat;
sstr_mat << this->id << ":" << mat_count << ":" << mat_type;
ID mat_id = sstr_mat.str();
std::unique_ptr<Material> material = MaterialFactory::getInstance().allocate(
mat_type, spatial_dimension, opt_param, *this, mat_id);
materials.push_back(std::move(material));
return *(materials.back());
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::instantiateMaterials() {
ParserSection model_section;
bool is_empty;
std::tie(model_section, is_empty) = this->getParserSection();
if (not is_empty) {
auto model_materials = model_section.getSubSections(ParserType::_material);
for (const auto & section : model_materials) {
this->registerNewMaterial(section);
}
}
auto sub_sections = this->parser.getSubSections(ParserType::_material);
for (const auto & section : sub_sections) {
this->registerNewMaterial(section);
}
#ifdef AKANTU_DAMAGE_NON_LOCAL
for (auto & material : materials) {
if (dynamic_cast<MaterialNonLocalInterface *>(material.get()) == nullptr)
continue;
this->non_local_manager = std::make_unique<NonLocalManager>(
*this, *this, id + ":non_local_manager", memory_id);
break;
}
#endif
if (materials.empty())
AKANTU_EXCEPTION("No materials where instantiated for the model"
<< getID());
are_materials_instantiated = true;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assignMaterialToElements(
const ElementTypeMapArray<UInt> * filter) {
for_each_element(
mesh,
[&](auto && element) {
UInt mat_index = (*material_selector)(element);
AKANTU_DEBUG_ASSERT(
mat_index < materials.size(),
"The material selector returned an index that does not exists");
material_index(element) = mat_index;
},
_element_filter = filter, _ghost_type = _not_ghost);
if (non_local_manager)
non_local_manager->synchronize(*this, _gst_material_id);
for_each_element(mesh,
[&](auto && element) {
auto mat_index = material_index(element);
auto index = materials[mat_index]->addElement(element);
material_local_numbering(element) = index;
},
_element_filter = filter, _ghost_type = _not_ghost);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initMaterials() {
AKANTU_DEBUG_ASSERT(materials.size() != 0, "No material to initialize !");
if (!are_materials_instantiated)
instantiateMaterials();
this->assignMaterialToElements();
// synchronize the element material arrays
this->synchronize(_gst_material_id);
for (auto & material : materials) {
/// init internals properties
material->initMaterial();
}
this->synchronize(_gst_smm_init_mat);
if (this->non_local_manager) {
this->non_local_manager->initialize();
}
}
/* -------------------------------------------------------------------------- */
Int SolidMechanicsModel::getInternalIndexFromID(const ID & id) const {
AKANTU_DEBUG_IN();
auto it = materials.begin();
auto end = materials.end();
for (; it != end; ++it)
if ((*it)->getID() == id) {
AKANTU_DEBUG_OUT();
return (it - materials.begin());
}
AKANTU_DEBUG_OUT();
return -1;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::reassignMaterial() {
AKANTU_DEBUG_IN();
std::vector<Array<Element>> element_to_add(materials.size());
std::vector<Array<Element>> element_to_remove(materials.size());
Element element;
for (auto ghost_type : ghost_types) {
element.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
element.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<UInt> & mat_indexes = material_index(type, ghost_type);
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
UInt old_material = mat_indexes(el);
UInt new_material = (*material_selector)(element);
if (old_material != new_material) {
element_to_add[new_material].push_back(element);
element_to_remove[old_material].push_back(element);
}
}
}
}
UInt mat_index = 0;
for (auto mat_it = materials.begin(); mat_it != materials.end();
++mat_it, ++mat_index) {
(*mat_it)->removeElements(element_to_remove[mat_index]);
(*mat_it)->addElements(element_to_add[mat_index]);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::applyEigenGradU(
const Matrix<Real> & prescribed_eigen_grad_u, const ID & material_name,
const GhostType ghost_type) {
AKANTU_DEBUG_ASSERT(prescribed_eigen_grad_u.size() ==
spatial_dimension * spatial_dimension,
"The prescribed grad_u is not of the good size");
for (auto & material : materials) {
if (material->getName() == material_name)
material->applyEigenGradU(prescribed_eigen_grad_u, ghost_type);
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh b/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh
index afb0de79a..c749da2dd 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh
@@ -1,62 +1,62 @@
/**
* @file solid_mechanics_model_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Nov 13 2015
+ * @date last modification: Tue Nov 07 2017
*
* @brief template part of solid mechanics model
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH__
namespace akantu {
#define FWD(...) ::std::forward<decltype(__VA_ARGS__)>(__VA_ARGS__)
/* -------------------------------------------------------------------------- */
template <typename Operation>
void SolidMechanicsModel::splitByMaterial(const Array<Element> & elements,
Operation && op) const {
std::vector<Array<Element>> elements_per_mat(materials.size());
this->splitElementByMaterial(elements, elements_per_mat);
for (auto && mat : zip(materials, elements_per_mat)) {
FWD(op)(FWD(*std::get<0>(mat)), FWD(std::get<1>(mat)));
}
}
#undef FWD
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH__ */
diff --git a/src/model/solver_callback.cc b/src/model/solver_callback.cc
index 82b50e404..92728eb9d 100644
--- a/src/model/solver_callback.cc
+++ b/src/model/solver_callback.cc
@@ -1,53 +1,54 @@
/**
* @file solver_callback.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Mar 2 12:47:17 2016
+ * @date creation: Tue Jul 20 2010
+ * @date last modification: Wed Jan 31 2018
*
* @brief Default behavior of solver_callbacks
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solver_callback.hh"
#include "dof_manager.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
SolverCallback::SolverCallback(DOFManager & dof_manager)
: sc_dof_manager(&dof_manager) {}
/* -------------------------------------------------------------------------- */
SolverCallback::SolverCallback() = default;
/* -------------------------------------------------------------------------- */
SolverCallback::~SolverCallback() = default;
/* -------------------------------------------------------------------------- */
void SolverCallback::setDOFManager(DOFManager & dof_manager) {
this->sc_dof_manager = &dof_manager;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solver_callback.hh b/src/model/solver_callback.hh
index f986d9908..c282dcec2 100644
--- a/src/model/solver_callback.hh
+++ b/src/model/solver_callback.hh
@@ -1,108 +1,109 @@
/**
* @file solver_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Sep 15 22:45:27 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Feb 21 2018
*
* @brief Class defining the interface for non_linear_solver callbacks
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLVER_CALLBACK_HH__
#define __AKANTU_SOLVER_CALLBACK_HH__
namespace akantu {
class DOFManager;
}
namespace akantu {
class SolverCallback {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit SolverCallback(DOFManager & dof_manager);
explicit SolverCallback();
/* ------------------------------------------------------------------------ */
virtual ~SolverCallback();
protected:
void setDOFManager(DOFManager & dof_manager);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the type of matrix needed
virtual MatrixType getMatrixType(const ID &) = 0;
/// callback to assemble a Matrix
virtual void assembleMatrix(const ID &) = 0;
/// callback to assemble a lumped Matrix
virtual void assembleLumpedMatrix(const ID &) = 0;
/// callback to assemble the residual (rhs)
virtual void assembleResidual() = 0;
/// callback to assemble the rhs parts, (e.g. internal_forces +
/// external_forces)
virtual void assembleResidual(const ID & /*residual_part*/) {}
/* ------------------------------------------------------------------------ */
/* Dynamic simulations part */
/* ------------------------------------------------------------------------ */
/// callback for the predictor (in case of dynamic simulation)
virtual void predictor() {}
/// callback for the corrector (in case of dynamic simulation)
virtual void corrector() {}
/// tells if the residual can be computed in separated parts
virtual bool canSplitResidual() { return false; }
/* ------------------------------------------------------------------------ */
/* management callbacks */
/* ------------------------------------------------------------------------ */
virtual void beforeSolveStep(){};
virtual void afterSolveStep(){};
protected:
/// DOFManager prefixed to avoid collision in multiple inheritance cases
DOFManager * sc_dof_manager{nullptr};
};
namespace debug {
class SolverCallbackResidualPartUnknown : public Exception {
public:
SolverCallbackResidualPartUnknown(const ID & residual_part)
: Exception(residual_part + " is not known here.") {}
};
}
} // namespace akantu
#endif /* __AKANTU_SOLVER_CALLBACK_HH__ */
diff --git a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
index d59f608e5..53300ae7e 100644
--- a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
+++ b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
@@ -1,134 +1,137 @@
/**
* @file structural_element_bernoulli_beam_2.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Sep 19 2017
+ * @date creation: Wed Oct 11 2017
+ * @date last modification: Wed Jan 10 2018
*
- * @brief Specific functions for bernoulli beam 2d
+ * @brief Specific functions for bernoulli beam 2d
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH__
#define __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline void StructuralMechanicsModel::assembleMass<_bernoulli_beam_2>() {
AKANTU_DEBUG_IN();
constexpr ElementType type = _bernoulli_beam_2;
auto & fem = getFEEngineClass<MyFEEngineType>();
auto nb_element = mesh.getNbElement(type);
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type);
auto nb_fields_to_interpolate = ElementClass<type>::getNbStressComponents();
auto nt_n_field_size = nb_degree_of_freedom * nb_nodes_per_element;
Array<Real> n(nb_element * nb_quadrature_points,
nb_fields_to_interpolate * nt_n_field_size, "N");
Array<Real> * rho_field =
new Array<Real>(nb_element * nb_quadrature_points, 1, "Rho");
rho_field->clear();
computeRho(*rho_field, type, _not_ghost);
#if 0
bool sign = true;
for (auto && ghost_type : ghost_types) {
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
0, 0, 0, sign, ghost_type); // Ni ui -> u
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
1, 1, 1, sign, ghost_type); // Mi vi -> v
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
2, 2, 1, sign, ghost_type); // Li Theta_i -> v
fem.assembleFieldMatrix(*rho_field, nb_degree_of_freedom, *mass_matrix, n,
rotation_matrix, type, ghost_type);
}
#endif
delete rho_field;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeRotationMatrix<_bernoulli_beam_2>(
Array<Real> & rotations) {
auto type = _bernoulli_beam_2;
auto nodes_it = mesh.getNodes().begin(this->spatial_dimension);
for (auto && tuple :
zip(make_view(mesh.getConnectivity(type), 2),
make_view(rotations, nb_degree_of_freedom, nb_degree_of_freedom))) {
auto & connec = std::get<0>(tuple);
auto & R = std::get<1>(tuple);
Vector<Real> x2 = nodes_it[connec(1)]; // X2
Vector<Real> x1 = nodes_it[connec(0)]; // X1
auto le = x1.distance(x2);
auto c = (x2(0) - x1(0)) / le;
auto s = (x2(1) - x1(1)) / le;
/// Definition of the rotation matrix
R = {{c, s, 0.}, {-s, c, 0.}, {0., 0., 1.}};
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<_bernoulli_beam_2>(
Array<Real> & tangent_moduli) {
// auto nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_2);
auto nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_2);
auto tangent_size = 2;
tangent_moduli.clear();
auto D_it = tangent_moduli.begin(tangent_size, tangent_size);
auto el_mat = element_material(_bernoulli_beam_2, _not_ghost).begin();
for (auto & mat : element_material(_bernoulli_beam_2, _not_ghost)) {
auto E = materials[mat].E;
auto A = materials[mat].A;
auto I = materials[mat].I;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it) {
auto & D = *D_it;
D(0, 0) = E * A;
D(1, 1) = E * I;
}
}
}
} // namespace akantu
#endif /* __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH__ */
diff --git a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
index 16616689c..b00cbd1cd 100644
--- a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
+++ b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
@@ -1,187 +1,190 @@
/**
* @file structural_element_bernoulli_beam_3.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
- * @date creation Tue Sep 19 2017
+ * @date creation: Wed Oct 11 2017
+ * @date last modification: Tue Feb 20 2018
*
- * @brief Specific functions for bernoulli beam 3d
+ * @brief Specific functions for bernoulli beam 3d
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH__
#define __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH__
#include "structural_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline void StructuralMechanicsModel::assembleMass<_bernoulli_beam_3>() {
AKANTU_DEBUG_IN();
#if 0
GhostType ghost_type = _not_ghost;
ElementType type = _bernoulli_beam_3;
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
UInt nb_element = getFEEngine().getMesh().getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
UInt nb_fields_to_interpolate =
getTangentStiffnessVoigtSize<_bernoulli_beam_3>();
UInt nt_n_field_size = nb_degree_of_freedom * nb_nodes_per_element;
Array<Real> * n =
new Array<Real>(nb_element * nb_quadrature_points,
nb_fields_to_interpolate * nt_n_field_size, "N");
n->clear();
Array<Real> * rho_field =
new Array<Real>(nb_element * nb_quadrature_points, "Rho");
rho_field->clear();
computeRho(*rho_field, type, _not_ghost);
/* --------------------------------------------------------------------------
*/
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
0, 0, 0, true, ghost_type); // Ni ui -> u
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
1, 1, 1, true, ghost_type); // Mi vi -> v
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
2, 5, 1, true, ghost_type); // Li Theta_z_i -> v
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
1, 2, 2, true, ghost_type); // Mi wi -> w
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
2, 4, 2, false, ghost_type); // -Li Theta_y_i -> w
fem.computeShapesMatrix(type, nb_degree_of_freedom, nb_nodes_per_element, n,
0, 3, 3, true, ghost_type); // Ni Theta_x_i->Theta_x
/* --------------------------------------------------------------------------
*/
fem.assembleFieldMatrix(*rho_field, nb_degree_of_freedom, *mass_matrix, n,
rotation_matrix, type, ghost_type);
delete n;
delete rho_field;
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
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);
auto n_it = mesh.getNormals(type).begin(spatial_dimension);
Array<UInt>::iterator<Vector<UInt>> connec_it =
mesh.getConnectivity(type).begin(2);
auto 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::computeTangentModuli<_bernoulli_beam_3>(
Array<Real> & tangent_moduli) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_3);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_3);
UInt tangent_size = 4;
tangent_moduli.clear();
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;
}
}
}
} // akantu
#endif /* __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH__ */
diff --git a/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh b/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
index 30a4d44b4..e5559a345 100644
--- a/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
+++ b/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
@@ -1,77 +1,80 @@
/**
- * @file structural_element_bernoulli_kirchhoff_shell.hh
+ * @file structural_element_kirchhoff_shell.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
- * @date creation Tue Sep 19 2017
+ * @date creation: Wed Oct 11 2017
+ * @date last modification: Wed Feb 21 2018
*
- * @brief Specific functions for bernoulli kirchhoff shell
+ * @brief Specific functions for bernoulli kirchhoff shell
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_KIRCHHOFF_SHELL_HH__
#define __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_KIRCHHOFF_SHELL_HH__
#include "structural_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline void
StructuralMechanicsModel::assembleMass<_discrete_kirchhoff_triangle_18>() {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<
_discrete_kirchhoff_triangle_18>(Array<Real> & tangent_moduli) {
auto tangent_size =
ElementClass<_discrete_kirchhoff_triangle_18>::getNbStressComponents();
auto nb_quad =
getFEEngine().getNbIntegrationPoints(_discrete_kirchhoff_triangle_18);
auto H_it = tangent_moduli.begin(tangent_size, tangent_size);
for (UInt mat :
element_material(_discrete_kirchhoff_triangle_18, _not_ghost)) {
auto & m = materials[mat];
for (UInt q = 0; q < nb_quad; ++q, ++H_it) {
auto & H = *H_it;
H.clear();
Matrix<Real> D = {{1, m.nu, 0}, {m.nu, 1, 0}, {0, 0, (1 - m.nu) / 2}};
D *= m.E * m.t / (1 - m.nu * m.nu);
H.block(D, 0, 0); // in plane membrane behavior
H.block(D * Math::pow<3>(m.t) / 12., 3, 3); // bending behavior
}
}
}
} // akantu
#endif /* __AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_DISCRETE_KIRCHHOFF_TRIANGLE_18_HH__ \
*/
diff --git a/src/model/structural_mechanics/structural_mechanics_model.cc b/src/model/structural_mechanics/structural_mechanics_model.cc
index f1ea3fff0..29392c28c 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model.cc
@@ -1,483 +1,483 @@
/**
* @file structural_mechanics_model.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Model implementation for StucturalMechanics elements
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model.hh"
#include "dof_manager.hh"
#include "integrator_gauss.hh"
#include "mesh.hh"
#include "shape_structural.hh"
#include "sparse_matrix.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumpable_inline_impl.hh"
#include "dumper_elemental_field.hh"
#include "dumper_iohelper_paraview.hh"
#include "group_manager_inline_impl.cc"
#endif
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model_inline_impl.cc"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::StructuralMechanicsModel(Mesh & mesh, UInt dim,
const ID & id,
const MemoryID & memory_id)
: Model(mesh, ModelType::_structural_mechanics_model, 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),
rotation_matrix("rotation_matices", id, memory_id) {
AKANTU_DEBUG_IN();
registerFEEngineObject<MyFEEngineType>("StructuralMechanicsFEEngine", mesh,
spatial_dimension);
if (spatial_dimension == 2)
nb_degree_of_freedom = 3;
else if (spatial_dimension == 3)
nb_degree_of_freedom = 6;
else {
AKANTU_TO_IMPLEMENT();
}
#ifdef AKANTU_USE_IOHELPER
this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
#endif
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_structural);
this->initDOFManager();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::~StructuralMechanicsModel() = default;
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initFullImpl(const ModelOptions & options) {
// <<<< This is the SolidMechanicsModel implementation for future ref >>>>
// material_index.initialize(mesh, _element_kind = _ek_not_defined,
// _default_value = UInt(-1), _with_nb_element =
// true);
// material_local_numbering.initialize(mesh, _element_kind = _ek_not_defined,
// _with_nb_element = true);
// Model::initFullImpl(options);
// // initialize pbc
// if (this->pbc_pair.size() != 0)
// this->initPBC();
// // initialize the materials
// if (this->parser.getLastParsedFile() != "") {
// this->instantiateMaterials();
// }
// this->initMaterials();
// this->initBC(*this, *displacement, *displacement_increment,
// *external_force);
// <<<< END >>>>
Model::initFullImpl(options);
// Initializing stresses
ElementTypeMap<UInt> stress_components;
/// TODO this is ugly af, maybe add a function to FEEngine
for (auto & type : mesh.elementTypes(_spatial_dimension = _all_dimensions,
_element_kind = _ek_structural)) {
UInt nb_components = 0;
// Getting number of components for each element type
#define GET_(type) nb_components = ElementClass<type>::getNbStressComponents()
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(GET_);
#undef GET_
stress_components(nb_components, type);
}
stress.initialize(getFEEngine(), _spatial_dimension = _all_dimensions,
_element_kind = _ek_structural, _all_ghost_types = true,
_nb_component = [&stress_components](
const ElementType & type, const GhostType &) -> UInt {
return stress_components(type);
});
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initFEEngineBoundary() {
/// TODO: this function should not be reimplemented
/// we're just avoiding a call to Model::initFEEngineBoundary()
}
/* -------------------------------------------------------------------------- */
// void StructuralMechanicsModel::setTimeStep(Real time_step) {
// this->time_step = time_step;
// #if defined(AKANTU_USE_IOHELPER)
// this->mesh.getDumper().setTimeStep(time_step);
// #endif
// }
/* -------------------------------------------------------------------------- */
/* Initialisation */
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initSolver(
TimeStepSolverType time_step_solver_type, NonLinearSolverType) {
AKANTU_DEBUG_IN();
this->allocNodalField(displacement_rotation, nb_degree_of_freedom,
"displacement");
this->allocNodalField(external_force, nb_degree_of_freedom, "external_force");
this->allocNodalField(internal_force, nb_degree_of_freedom, "internal_force");
this->allocNodalField(blocked_dofs, nb_degree_of_freedom, "blocked_dofs");
auto & dof_manager = this->getDOFManager();
if (!dof_manager.hasDOFs("displacement")) {
dof_manager.registerDOFs("displacement", *displacement_rotation,
_dst_nodal);
dof_manager.registerBlockedDOFs("displacement", *this->blocked_dofs);
}
if (time_step_solver_type == _tsst_dynamic ||
time_step_solver_type == _tsst_dynamic_lumped) {
this->allocNodalField(velocity, spatial_dimension, "velocity");
this->allocNodalField(acceleration, spatial_dimension, "acceleration");
if (!dof_manager.hasDOFsDerivatives("displacement", 1)) {
dof_manager.registerDOFsDerivative("displacement", 1, *this->velocity);
dof_manager.registerDOFsDerivative("displacement", 2,
*this->acceleration);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initModel() {
for (auto && type : mesh.elementTypes(_element_kind = _ek_structural)) {
// computeRotationMatrix(type);
element_material.alloc(mesh.getNbElement(type), 1, type);
}
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
getDOFManager().getMatrix("K").clear();
for (auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_structural)) {
#define ASSEMBLE_STIFFNESS_MATRIX(type) assembleStiffnessMatrix<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(ASSEMBLE_STIFFNESS_MATRIX);
#undef ASSEMBLE_STIFFNESS_MATRIX
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeStresses() {
AKANTU_DEBUG_IN();
for (auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_structural)) {
#define COMPUTE_STRESS_ON_QUAD(type) computeStressOnQuad<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(COMPUTE_STRESS_ON_QUAD);
#undef COMPUTE_STRESS_ON_QUAD
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
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
auto R_it = rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
auto 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) {
auto & T = *T_it;
auto & R = *R_it;
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);
}
}
}
/* -------------------------------------------------------------------------- */
dumper::Field * StructuralMechanicsModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs;
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;
}
if (field_name == "displacement") {
return mesh.createStridedNodalField(displacement_rotation, group_name, n, 0,
padding_flag);
}
if (field_name == "rotation") {
return mesh.createStridedNodalField(displacement_rotation, group_name,
nb_degree_of_freedom - n, n,
padding_flag);
}
if (field_name == "force") {
return mesh.createStridedNodalField(external_force, group_name, n, 0,
padding_flag);
}
if (field_name == "momentum") {
return mesh.createStridedNodalField(
external_force, group_name, nb_degree_of_freedom - n, n, padding_flag);
}
if (field_name == "internal_force") {
return mesh.createStridedNodalField(internal_force, group_name, n, 0,
padding_flag);
}
if (field_name == "internal_momentum") {
return mesh.createStridedNodalField(
internal_force, group_name, nb_degree_of_freedom - n, n, padding_flag);
}
return nullptr;
}
/* -------------------------------------------------------------------------- */
dumper::Field * StructuralMechanicsModel::createElementalField(
const std::string & field_name, const std::string & group_name, bool,
const ElementKind & kind, const std::string &) {
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;
}
/* -------------------------------------------------------------------------- */
/* Virtual methods from SolverCallback */
/* -------------------------------------------------------------------------- */
/// get the type of matrix needed
MatrixType StructuralMechanicsModel::getMatrixType(const ID & /*id*/) {
return _symmetric;
}
/// callback to assemble a Matrix
void StructuralMechanicsModel::assembleMatrix(const ID & id) {
if (id == "K")
assembleStiffnessMatrix();
}
/// callback to assemble a lumped Matrix
void StructuralMechanicsModel::assembleLumpedMatrix(const ID & /*id*/) {}
/// callback to assemble the residual StructuralMechanicsModel::(rhs)
void StructuralMechanicsModel::assembleResidual() {
AKANTU_DEBUG_IN();
auto & dof_manager = getDOFManager();
internal_force->clear();
computeStresses();
assembleInternalForce();
dof_manager.assembleToResidual("displacement", *internal_force, -1);
dof_manager.assembleToResidual("displacement", *external_force, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Virtual methods from MeshEventHandler */
/* -------------------------------------------------------------------------- */
/// function to implement to react on akantu::NewNodesEvent
void StructuralMechanicsModel::onNodesAdded(const Array<UInt> & /*nodes_list*/,
const NewNodesEvent & /*event*/) {}
/// function to implement to react on akantu::RemovedNodesEvent
void StructuralMechanicsModel::onNodesRemoved(
const Array<UInt> & /*nodes_list*/, const Array<UInt> & /*new_numbering*/,
const RemovedNodesEvent & /*event*/) {}
/// function to implement to react on akantu::NewElementsEvent
void StructuralMechanicsModel::onElementsAdded(
const Array<Element> & /*elements_list*/,
const NewElementsEvent & /*event*/) {}
/// function to implement to react on akantu::RemovedElementsEvent
void StructuralMechanicsModel::onElementsRemoved(
const Array<Element> & /*elements_list*/,
const ElementTypeMapArray<UInt> & /*new_numbering*/,
const RemovedElementsEvent & /*event*/) {}
/// function to implement to react on akantu::ChangedElementsEvent
void StructuralMechanicsModel::onElementsChanged(
const Array<Element> & /*old_elements_list*/,
const Array<Element> & /*new_elements_list*/,
const ElementTypeMapArray<UInt> & /*new_numbering*/,
const ChangedElementsEvent & /*event*/) {}
/* -------------------------------------------------------------------------- */
/* Virtual methods from Model */
/* -------------------------------------------------------------------------- */
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
StructuralMechanicsModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _static: {
return std::make_tuple("static", _tsst_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", _tsst_dynamic);
}
default:
return std::make_tuple("unknown", _tsst_not_defined);
}
}
/* ------------------------------------------------------------------------ */
ModelSolverOptions StructuralMechanicsModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case _tsst_static: {
options.non_linear_solver_type = _nls_linear;
options.integration_scheme_type["displacement"] = _ist_pseudo_time;
options.solution_type["displacement"] = IntegrationScheme::_not_defined;
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleInternalForce() {
for (auto type : mesh.elementTypes(_spatial_dimension = _all_dimensions,
_element_kind = _ek_structural)) {
assembleInternalForce(type, _not_ghost);
// assembleInternalForce(type, _ghost);
}
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleInternalForce(const ElementType & type,
GhostType gt) {
auto & fem = getFEEngine();
auto & sigma = stress(type, gt);
auto ndof = getNbDegreeOfFreedom(type);
auto nb_nodes = mesh.getNbNodesPerElement(type);
auto ndof_per_elem = ndof * nb_nodes;
Array<Real> BtSigma(fem.getNbIntegrationPoints(type) *
mesh.getNbElement(type),
ndof_per_elem, "BtSigma");
fem.computeBtD(sigma, BtSigma, type, gt);
Array<Real> intBtSigma(0, ndof_per_elem, "intBtSigma");
fem.integrate(BtSigma, intBtSigma, ndof_per_elem, type, gt);
BtSigma.resize(0);
getDOFManager().assembleElementalArrayLocalArray(intBtSigma, *internal_force,
type, gt, 1);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/structural_mechanics/structural_mechanics_model.hh b/src/model/structural_mechanics/structural_mechanics_model.hh
index baa53daa2..e0ef8f284 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.hh
+++ b/src/model/structural_mechanics/structural_mechanics_model.hh
@@ -1,332 +1,333 @@
/**
* @file structural_mechanics_model.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
- * @date last modification: Thu Jan 21 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Particular implementation of the structural elements in the
* StructuralMechanicsModel
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "boundary_condition.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__
#define __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class Material;
class MaterialSelector;
class DumperIOHelper;
class NonLocalManager;
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeStructural;
} // namespace akantu
namespace akantu {
struct StructuralMaterial {
Real E{0};
Real A{1};
Real I{0};
Real Iz{0};
Real Iy{0};
Real GJ{0};
Real rho{0};
Real t{0};
Real nu{0};
};
class StructuralMechanicsModel : public Model {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MyFEEngineType =
FEEngineTemplate<IntegratorGauss, ShapeStructural, _ek_structural>;
StructuralMechanicsModel(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "structural_mechanics_model",
const MemoryID & memory_id = 0);
virtual ~StructuralMechanicsModel();
/// Init full model
void initFullImpl(const ModelOptions & options) override;
/// Init boundary FEEngine
void initFEEngineBoundary() override;
/* ------------------------------------------------------------------------ */
/* Virtual methods from SolverCallback */
/* ------------------------------------------------------------------------ */
/// get the type of matrix needed
MatrixType getMatrixType(const ID &) override;
/// callback to assemble a Matrix
void assembleMatrix(const ID &) override;
/// callback to assemble a lumped Matrix
void assembleLumpedMatrix(const ID &) override;
/// callback to assemble the residual (rhs)
void assembleResidual() override;
/* ------------------------------------------------------------------------ */
/* Virtual methods from MeshEventHandler */
/* ------------------------------------------------------------------------ */
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
/// function to implement to react on akantu::RemovedNodesEvent
void onNodesRemoved(const Array<UInt> & nodes_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) override;
/// function to implement to react on akantu::NewElementsEvent
void onElementsAdded(const Array<Element> & elements_list,
const NewElementsEvent & event) override;
/// function to implement to react on akantu::RemovedElementsEvent
void onElementsRemoved(const Array<Element> & elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
/// function to implement to react on akantu::ChangedElementsEvent
void onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) override;
/* ------------------------------------------------------------------------ */
/* Virtual methods from Model */
/* ------------------------------------------------------------------------ */
protected:
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
UInt getNbDegreeOfFreedom(const ElementType & type) const;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
void initSolver(TimeStepSolverType, NonLinearSolverType) override;
/// initialize the model
void initModel() override;
/// compute the stresses per elements
void computeStresses();
/// compute the nodal forces
void assembleInternalForce();
/// compute the nodal forces for an element type
void assembleInternalForce(const ElementType & type, GhostType gt);
/// assemble the stiffness matrix
void assembleStiffnessMatrix();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
/// TODO remove
void computeRotationMatrix(const ElementType & type);
protected:
/// compute Rotation Matrices
template <const ElementType type>
void computeRotationMatrix(__attribute__((unused)) Array<Real> & rotations) {}
/* ------------------------------------------------------------------------ */
/* 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> void assembleStiffnessMatrix();
template <ElementType type> void assembleMass();
template <ElementType type> void computeStressOnQuad();
template <ElementType type>
void computeTangentModuli(Array<Real> & tangent_moduli);
/* ------------------------------------------------------------------------ */
/* 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 std::string & fe_engine_id = "");
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// set the value of the time step
// void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// 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::external_force vector
AKANTU_GET_MACRO(ExternalForce, *external_force, Array<Real> &);
/// get the StructuralMechanicsModel::internal_force vector (boundary forces)
AKANTU_GET_MACRO(InternalForce, *internal_force, Array<Real> &);
/// get the StructuralMechanicsModel::boundary vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(RotationMatrix, rotation_matrix, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Stress, stress, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(ElementMaterial, element_material, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Set_ID, set_ID, UInt);
void addMaterial(StructuralMaterial & material) {
materials.push_back(material);
}
const StructuralMaterial & getMaterial(const Element & element) const {
return materials[element_material(element)];
}
/* ------------------------------------------------------------------------ */
/* 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);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// time step
Real time_step;
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
Array<Real> * displacement_rotation{nullptr};
/// velocities array
Array<Real> * velocity{nullptr};
/// accelerations array
Array<Real> * acceleration{nullptr};
/// forces array
Array<Real> * internal_force{nullptr};
/// forces array
Array<Real> * external_force{nullptr};
/// lumped mass array
Array<Real> * mass{nullptr};
/// boundaries array
Array<bool> * blocked_dofs{nullptr};
/// stress array
ElementTypeMapArray<Real> stress;
ElementTypeMapArray<UInt> element_material;
// Define sets of beams
ElementTypeMapArray<UInt> set_ID;
/// number of degre of freedom
UInt nb_degree_of_freedom;
// Rotation matrix
ElementTypeMapArray<Real> rotation_matrix;
// /// analysis method check the list in akantu::AnalysisMethod
// AnalysisMethod method;
/// flag defining if the increment must be computed or not
bool increment_flag;
/* ------------------------------------------------------------------------ */
std::vector<StructuralMaterial> materials;
};
} // namespace akantu
#endif /* __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__ */
diff --git a/src/model/structural_mechanics/structural_mechanics_model_boundary.cc b/src/model/structural_mechanics/structural_mechanics_model_boundary.cc
index 10f0b31f2..8ed826ad6 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_boundary.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model_boundary.cc
@@ -1,47 +1,46 @@
/**
* @file structural_mechanics_model_boundary.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Fri Oct 13 2017
*
* @brief Implementation of the boundary conditions for
* StructuralMechanicsModel
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "model.hh"
#include "shape_structural.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/model/structural_mechanics/structural_mechanics_model_inline_impl.cc b/src/model/structural_mechanics/structural_mechanics_model_inline_impl.cc
index 0a4bd6679..ebf76f302 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_inline_impl.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model_inline_impl.cc
@@ -1,370 +1,371 @@
/**
* @file structural_mechanics_model_inline_impl.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of inline functions of StructuralMechanicsModel
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_CC__
#define __AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt
StructuralMechanicsModel::getNbDegreeOfFreedom(const ElementType & type) const {
UInt ndof = 0;
#define GET_(type) ndof = ElementClass<type>::getNbDegreeOfFreedom()
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_, _ek_structural);
#undef GET_
return ndof;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeTangentModuli(
Array<Real> & /*tangent_moduli*/) {
AKANTU_TO_IMPLEMENT();
}
} // namespace akantu
#include "structural_element_bernoulli_beam_2.hh"
#include "structural_element_bernoulli_beam_3.hh"
#include "structural_element_kirchhoff_shell.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
auto nb_element = getFEEngine().getMesh().getNbElement(type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
auto tangent_size = ElementClass<type>::getNbStressComponents();
auto tangent_moduli = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points, tangent_size * tangent_size,
"tangent_stiffness_matrix");
computeTangentModuli<type>(*tangent_moduli);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = nb_degree_of_freedom * nb_nodes_per_element;
auto bt_d_b = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points, bt_d_b_size * bt_d_b_size, "B^t*D*B");
const auto & b = getFEEngine().getShapesDerivatives(type);
Matrix<Real> BtD(bt_d_b_size, tangent_size);
for (auto && tuple :
zip(make_view(b, tangent_size, bt_d_b_size),
make_view(*tangent_moduli, tangent_size, tangent_size),
make_view(*bt_d_b, bt_d_b_size, bt_d_b_size))) {
auto & B = std::get<0>(tuple);
auto & D = std::get<1>(tuple);
auto & BtDB = std::get<2>(tuple);
BtD.mul<true, false>(B, D);
BtDB.template mul<false, false>(BtD, B);
}
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto int_bt_d_b = std::make_unique<Array<Real>>(
nb_element, bt_d_b_size * bt_d_b_size, "int_B^t*D*B");
getFEEngine().integrate(*bt_d_b, *int_bt_d_b, bt_d_b_size * bt_d_b_size,
type);
getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *int_bt_d_b, type, _not_ghost, _symmetric);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeStressOnQuad() {
AKANTU_DEBUG_IN();
Array<Real> & sigma = stress(type, _not_ghost);
auto nb_element = mesh.getNbElement(type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
auto tangent_size = ElementClass<type>::getNbStressComponents();
auto tangent_moduli = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points, tangent_size * tangent_size,
"tangent_stiffness_matrix");
computeTangentModuli<type>(*tangent_moduli);
/// compute DB
auto d_b_size = nb_degree_of_freedom * nb_nodes_per_element;
auto d_b = std::make_unique<Array<Real>>(nb_element * nb_quadrature_points,
d_b_size * tangent_size, "D*B");
const auto & b = getFEEngine().getShapesDerivatives(type);
auto B = b.begin(tangent_size, d_b_size);
auto D = tangent_moduli->begin(tangent_size, tangent_size);
auto D_B = d_b->begin(tangent_size, d_b_size);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q, ++B, ++D, ++D_B) {
D_B->template mul<false, false>(*D, *B);
}
}
/// compute DBu
D_B = d_b->begin(tangent_size, d_b_size);
auto DBu = sigma.begin(tangent_size);
Array<Real> u_el(0, d_b_size);
FEEngine::extractNodalToElementField(mesh, *displacement_rotation, u_el,
type);
auto ug = u_el.begin(d_b_size);
// No need to rotate because B is post-multiplied
for (UInt e = 0; e < nb_element; ++e, ++ug) {
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_B, ++DBu) {
DBu->template mul<false>(*D_B, *ug);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeForcesByLocalTractionArray(
const Array<Real> & tractions) {
AKANTU_DEBUG_IN();
#if 0
UInt nb_element = getFEEngine().getMesh().getNbElement(type);
UInt nb_nodes_per_element =
getFEEngine().getMesh().getNbNodesPerElement(type);
UInt nb_quad = getFEEngine().getNbIntegrationPoints(type);
// check dimension match
AKANTU_DEBUG_ASSERT(
Mesh::getSpatialDimension(type) == getFEEngine().getElementDimension(),
"element type dimension does not match the dimension of boundaries : "
<< getFEEngine().getElementDimension()
<< " != " << Mesh::getSpatialDimension(type));
// check size of the vector
AKANTU_DEBUG_ASSERT(
tractions.size() == nb_quad * nb_element,
"the size of the vector should be the total number of quadrature points");
// check number of components
AKANTU_DEBUG_ASSERT(tractions.getNbComponent() == nb_degree_of_freedom,
"the number of components should be the spatial "
"dimension of the problem");
Array<Real> Nvoigt(nb_element * nb_quad, nb_degree_of_freedom *
nb_degree_of_freedom *
nb_nodes_per_element);
transferNMatrixToSymVoigtNMatrix<type>(Nvoigt);
Array<Real>::const_matrix_iterator N_it = Nvoigt.begin(
nb_degree_of_freedom, nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::const_matrix_iterator T_it =
rotation_matrix(type).begin(nb_degree_of_freedom * nb_nodes_per_element,
nb_degree_of_freedom * nb_nodes_per_element);
auto te_it =
tractions.begin(nb_degree_of_freedom);
Array<Real> funct(nb_element * nb_quad,
nb_degree_of_freedom * nb_nodes_per_element, 0.);
Array<Real>::iterator<Vector<Real>> Fe_it =
funct.begin(nb_degree_of_freedom * nb_nodes_per_element);
Vector<Real> fe(nb_degree_of_freedom * nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e, ++T_it) {
const Matrix<Real> & T = *T_it;
for (UInt q = 0; q < nb_quad; ++q, ++N_it, ++te_it, ++Fe_it) {
const Matrix<Real> & N = *N_it;
const Vector<Real> & te = *te_it;
Vector<Real> & Fe = *Fe_it;
// compute N^t tl
fe.mul<true>(N, te);
// turn N^t tl back in the global referential
Fe.mul<true>(T, fe);
}
}
// allocate the vector that will contain the integrated values
std::stringstream name;
name << id << type << ":integral_boundary";
Array<Real> int_funct(nb_element, nb_degree_of_freedom * nb_nodes_per_element,
name.str());
// do the integration
getFEEngine().integrate(funct, int_funct,
nb_degree_of_freedom * nb_nodes_per_element, type);
// assemble the result into force vector
getFEEngine().assembleArray(int_funct, *force_momentum,
dof_synchronizer->getLocalDOFEquationNumbers(),
nb_degree_of_freedom, type);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeForcesByGlobalTractionArray(
const Array<Real> & traction_global) {
AKANTU_DEBUG_IN();
#if 0
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad = getFEEngine().getNbIntegrationPoints(type);
UInt nb_nodes_per_element =
getFEEngine().getMesh().getNbNodesPerElement(type);
std::stringstream name;
name << id << ":structuralmechanics:imposed_linear_load";
Array<Real> traction_local(nb_element * nb_quad, nb_degree_of_freedom,
name.str());
Array<Real>::const_matrix_iterator T_it =
rotation_matrix(type).begin(nb_degree_of_freedom * nb_nodes_per_element,
nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::const_iterator<Vector<Real>> Te_it =
traction_global.begin(nb_degree_of_freedom);
Array<Real>::iterator<Vector<Real>> te_it =
traction_local.begin(nb_degree_of_freedom);
Matrix<Real> R(nb_degree_of_freedom, nb_degree_of_freedom);
for (UInt e = 0; e < nb_element; ++e, ++T_it) {
const Matrix<Real> & T = *T_it;
for (UInt i = 0; i < nb_degree_of_freedom; ++i)
for (UInt j = 0; j < nb_degree_of_freedom; ++j)
R(i, j) = T(i, j);
for (UInt q = 0; q < nb_quad; ++q, ++Te_it, ++te_it) {
const Vector<Real> & Te = *Te_it;
Vector<Real> & te = *te_it;
// turn the traction in the local referential
te.mul<false>(R, Te);
}
}
computeForcesByLocalTractionArray<type>(traction_local);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @param myf pointer to a function that fills a vector/tensor with respect to
* passed coordinates
*/
#if 0
template <ElementType type>
inline void StructuralMechanicsModel::computeForcesFromFunction(
BoundaryFunction myf, BoundaryFunctionType function_type) {
/** function type is
** _bft_forces : linear load is given
** _bft_stress : stress function is given -> Not already done for this kind
*of model
*/
std::stringstream name;
name << id << ":structuralmechanics:imposed_linear_load";
Array<Real> lin_load(0, nb_degree_of_freedom, name.str());
name.clear();
UInt offset = nb_degree_of_freedom;
// prepare the loop over element types
UInt nb_quad = getFEEngine().getNbIntegrationPoints(type);
UInt nb_element = getFEEngine().getMesh().getNbElement(type);
name.clear();
name << id << ":structuralmechanics:quad_coords";
Array<Real> quad_coords(nb_element * nb_quad, spatial_dimension,
"quad_coords");
getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.interpolateOnIntegrationPoints<type>(getFEEngine().getMesh().getNodes(),
quad_coords, spatial_dimension);
getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.interpolateOnIntegrationPoints<type>(
getFEEngine().getMesh().getNodes(), quad_coords, spatial_dimension,
_not_ghost, empty_filter, true, 0, 1, 1);
if (spatial_dimension == 3)
getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.interpolateOnIntegrationPoints<type>(
getFEEngine().getMesh().getNodes(), quad_coords, spatial_dimension,
_not_ghost, empty_filter, true, 0, 2, 2);
lin_load.resize(nb_element * nb_quad);
Real * imposed_val = lin_load.storage();
/// sigma/load on each quadrature points
Real * qcoord = quad_coords.storage();
for (UInt el = 0; el < nb_element; ++el) {
for (UInt q = 0; q < nb_quad; ++q) {
myf(qcoord, imposed_val, NULL, 0);
imposed_val += offset;
qcoord += spatial_dimension;
}
}
switch (function_type) {
case _bft_traction_local:
computeForcesByLocalTractionArray<type>(lin_load);
break;
case _bft_traction:
computeForcesByGlobalTractionArray<type>(lin_load);
break;
default:
break;
}
}
#endif
} // namespace akantu
#endif /* __AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_CC__ */
diff --git a/src/model/structural_mechanics/structural_mechanics_model_mass.cc b/src/model/structural_mechanics/structural_mechanics_model_mass.cc
index b24eeb0d2..d26224be8 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_mass.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model_mass.cc
@@ -1,76 +1,79 @@
/**
* @file structural_mechanics_model_mass.cc
*
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 07 2014
- * @date last modification: Thu Oct 15 2015
+ * @date last modification: Fri Dec 15 2017
*
* @brief function handling mass computation
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "material.hh"
#include "shape_structural.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ComputeRhoFunctorStruct {
public:
explicit ComputeRhoFunctorStruct(const StructuralMechanicsModel & model)
: model(model){};
void operator()(Matrix<Real> & rho, const Element & element) const {
Real mat_rho = model.getMaterial(element).rho;
rho.set(mat_rho);
}
private:
const StructuralMechanicsModel & model;
};
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleMass() {
AKANTU_DEBUG_IN();
assembleMass(_not_ghost);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleMass(GhostType ghost_type) {
AKANTU_DEBUG_IN();
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctorStruct compute_rho(*this);
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_structural)) {
fem.assembleFieldMatrix(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
} // akantu
diff --git a/src/model/time_step_solver.hh b/src/model/time_step_solver.hh
index dfef977ca..4437296ea 100644
--- a/src/model/time_step_solver.hh
+++ b/src/model/time_step_solver.hh
@@ -1,137 +1,138 @@
/**
* @file time_step_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Aug 24 12:42:04 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Feb 21 2018
*
* @brief This corresponding to the time step evolution solver
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_memory.hh"
#include "integration_scheme.hh"
#include "parameter_registry.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TIME_STEP_SOLVER_HH__
#define __AKANTU_TIME_STEP_SOLVER_HH__
namespace akantu {
class DOFManager;
class NonLinearSolver;
}
namespace akantu {
class TimeStepSolver : public Memory,
public ParameterRegistry,
public SolverCallback {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolver(DOFManager & dof_manager, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, const ID & id,
UInt memory_id);
~TimeStepSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solves on step
virtual void solveStep(SolverCallback & solver_callback) = 0;
/// register an integration scheme for a given dof
virtual void
setIntegrationScheme(const ID & dof_id, const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined) = 0;
/// replies if a integration scheme has been set
virtual bool hasIntegrationScheme(const ID & dof_id) const = 0;
/* ------------------------------------------------------------------------ */
/* Solver Callback interface */
/* ------------------------------------------------------------------------ */
public:
/// implementation of the SolverCallback::getMatrixType()
MatrixType getMatrixType(const ID &) final { return _mt_not_defined; }
/// implementation of the SolverCallback::predictor()
void predictor() override;
/// implementation of the SolverCallback::corrector()
void corrector() override;
/// implementation of the SolverCallback::assembleJacobian()
void assembleMatrix(const ID & matrix_id) override;
/// implementation of the SolverCallback::assembleJacobian()
void assembleLumpedMatrix(const ID & matrix_id) final;
/// implementation of the SolverCallback::assembleResidual()
void assembleResidual() override;
/// implementation of the SolverCallback::assembleResidual()
void assembleResidual(const ID & residual_part) override;
void beforeSolveStep() override;
void afterSolveStep() override;
bool canSplitResidual() { return solver_callback->canSplitResidual(); }
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(TimeStep, time_step, Real);
AKANTU_SET_MACRO(TimeStep, time_step, Real);
AKANTU_GET_MACRO(NonLinearSolver, non_linear_solver, const NonLinearSolver &);
AKANTU_GET_MACRO_NOT_CONST(NonLinearSolver, non_linear_solver,
NonLinearSolver &);
protected:
MatrixType getCommonMatrixType();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Underlying dof manager containing the dof to treat
DOFManager & _dof_manager;
/// Type of solver
TimeStepSolverType type;
/// The time step for this solver
Real time_step;
/// Temporary storage for solver callback
SolverCallback * solver_callback;
/// NonLinearSolver used by this tome step solver
NonLinearSolver & non_linear_solver;
/// List of required matrices
std::map<std::string, MatrixType> needed_matrices;
};
} // akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_HH__ */
diff --git a/src/model/time_step_solvers/time_step_solver.cc b/src/model/time_step_solvers/time_step_solver.cc
index d936db10b..04bb9f871 100644
--- a/src/model/time_step_solvers/time_step_solver.cc
+++ b/src/model/time_step_solvers/time_step_solver.cc
@@ -1,177 +1,177 @@
/**
* @file time_step_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Oct 12 16:56:43 2015
+ * @date creation: Tue Aug 18 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Implementation of common part of TimeStepSolvers
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "time_step_solver.hh"
#include "dof_manager.hh"
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
TimeStepSolver::TimeStepSolver(DOFManager & dof_manager,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
const ID & id, UInt memory_id)
: Memory(id, memory_id), SolverCallback(dof_manager),
_dof_manager(dof_manager), type(type), time_step(0.),
solver_callback(nullptr), non_linear_solver(non_linear_solver) {
this->registerSubRegistry("non_linear_solver", non_linear_solver);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver::~TimeStepSolver() = default;
/* -------------------------------------------------------------------------- */
MatrixType TimeStepSolver::getCommonMatrixType() {
MatrixType common_type = _mt_not_defined;
for (auto & pair : needed_matrices) {
auto & type = pair.second;
if (type == _mt_not_defined) {
type = this->solver_callback->getMatrixType(pair.first);
}
common_type = std::min(common_type, type);
}
AKANTU_DEBUG_ASSERT(common_type != _mt_not_defined,
"No type defined for the matrices");
return common_type;
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::predictor() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->predictor();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::corrector() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->corrector();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::beforeSolveStep() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->beforeSolveStep();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::afterSolveStep() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->afterSolveStep();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleLumpedMatrix(const ID & matrix_id) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
if (not _dof_manager.hasLumpedMatrix(matrix_id))
_dof_manager.getNewLumpedMatrix(matrix_id);
this->solver_callback->assembleLumpedMatrix(matrix_id);
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleMatrix(const ID & matrix_id) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
auto common_type = this->getCommonMatrixType();
if (matrix_id != "J") {
auto type = needed_matrices[matrix_id];
if (type == _mt_not_defined)
return;
if (not _dof_manager.hasMatrix(matrix_id)) {
_dof_manager.getNewMatrix(matrix_id, type);
}
this->solver_callback->assembleMatrix(matrix_id);
return;
}
if (not _dof_manager.hasMatrix("J"))
_dof_manager.getNewMatrix("J", common_type);
for (auto & pair : needed_matrices) {
auto type = pair.second;
if (type == _mt_not_defined)
continue;
auto name = pair.first;
if (not _dof_manager.hasMatrix(name))
_dof_manager.getNewMatrix(name, type);
this->solver_callback->assembleMatrix(name);
}
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleResidual() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->_dof_manager.clearResidual();
this->solver_callback->assembleResidual();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->assembleResidual(residual_part);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/time_step_solvers/time_step_solver_default.cc b/src/model/time_step_solvers/time_step_solver_default.cc
index 371050e61..cec055b5a 100644
--- a/src/model/time_step_solvers/time_step_solver_default.cc
+++ b/src/model/time_step_solvers/time_step_solver_default.cc
@@ -1,309 +1,310 @@
/**
* @file time_step_solver_default.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Sep 16 10:20:55 2015
+ * @date creation: Tue Sep 15 2015
+ * @date last modification: Wed Feb 21 2018
*
* @brief Default implementation of the time step solver
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "time_step_solver_default.hh"
#include "dof_manager_default.hh"
#include "integration_scheme_1st_order.hh"
#include "integration_scheme_2nd_order.hh"
#include "mesh.hh"
#include "non_linear_solver.hh"
#include "pseudo_time.hh"
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
TimeStepSolverDefault::TimeStepSolverDefault(
DOFManagerDefault & dof_manager, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, const ID & id, UInt memory_id)
: TimeStepSolver(dof_manager, type, non_linear_solver, id, memory_id),
dof_manager(dof_manager), is_mass_lumped(false) {
switch (type) {
case _tsst_dynamic:
break;
case _tsst_dynamic_lumped:
this->is_mass_lumped = true;
break;
case _tsst_static:
/// initialize a static time solver for callback dofs
break;
default:
AKANTU_TO_IMPLEMENT();
}
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::setIntegrationScheme(
const ID & dof_id, const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type) {
if (this->integration_schemes.find(dof_id) !=
this->integration_schemes.end()) {
AKANTU_EXCEPTION("Their DOFs "
<< dof_id
<< " have already an integration scheme associated");
}
std::unique_ptr<IntegrationScheme> integration_scheme;
if (this->is_mass_lumped) {
switch (type) {
case _ist_forward_euler: {
integration_scheme = std::make_unique<ForwardEuler>(dof_manager, dof_id);
break;
}
case _ist_central_difference: {
integration_scheme =
std::make_unique<CentralDifference>(dof_manager, dof_id);
break;
}
default:
AKANTU_EXCEPTION(
"This integration scheme cannot be used in lumped dynamic");
}
} else {
switch (type) {
case _ist_pseudo_time: {
integration_scheme = std::make_unique<PseudoTime>(dof_manager, dof_id);
break;
}
case _ist_forward_euler: {
integration_scheme = std::make_unique<ForwardEuler>(dof_manager, dof_id);
break;
}
case _ist_trapezoidal_rule_1: {
integration_scheme =
std::make_unique<TrapezoidalRule1>(dof_manager, dof_id);
break;
}
case _ist_backward_euler: {
integration_scheme = std::make_unique<BackwardEuler>(dof_manager, dof_id);
break;
}
case _ist_central_difference: {
integration_scheme =
std::make_unique<CentralDifference>(dof_manager, dof_id);
break;
}
case _ist_fox_goodwin: {
integration_scheme = std::make_unique<FoxGoodwin>(dof_manager, dof_id);
break;
}
case _ist_trapezoidal_rule_2: {
integration_scheme =
std::make_unique<TrapezoidalRule2>(dof_manager, dof_id);
break;
}
case _ist_linear_acceleration: {
integration_scheme =
std::make_unique<LinearAceleration>(dof_manager, dof_id);
break;
}
case _ist_generalized_trapezoidal: {
integration_scheme =
std::make_unique<GeneralizedTrapezoidal>(dof_manager, dof_id);
break;
}
case _ist_newmark_beta:
integration_scheme = std::make_unique<NewmarkBeta>(dof_manager, dof_id);
break;
}
}
AKANTU_DEBUG_ASSERT(integration_scheme,
"No integration scheme was found for the provided types");
auto && matrices_names = integration_scheme->getNeededMatrixList();
for (auto && name : matrices_names) {
needed_matrices.insert({name, _mt_not_defined});
}
this->integration_schemes[dof_id] = std::move(integration_scheme);
this->solution_types[dof_id] = solution_type;
this->integration_schemes_owner.insert(dof_id);
}
/* -------------------------------------------------------------------------- */
bool TimeStepSolverDefault::hasIntegrationScheme(const ID & dof_id) const {
return this->integration_schemes.find(dof_id) !=
this->integration_schemes.end();
}
/* -------------------------------------------------------------------------- */
TimeStepSolverDefault::~TimeStepSolverDefault() = default;
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::solveStep(SolverCallback & solver_callback) {
this->solver_callback = &solver_callback;
this->solver_callback->beforeSolveStep();
this->non_linear_solver.solve(*this);
this->solver_callback->afterSolveStep();
this->solver_callback = nullptr;
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::predictor() {
AKANTU_DEBUG_IN();
TimeStepSolver::predictor();
for (auto & pair : this->integration_schemes) {
auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
if (this->dof_manager.hasPreviousDOFs(dof_id)) {
this->dof_manager.savePreviousDOFs(dof_id);
}
/// integrator predictor
integration_scheme->predictor(this->time_step);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::corrector() {
AKANTU_DEBUG_IN();
TimeStepSolver::corrector();
for (auto & pair : this->integration_schemes) {
auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
const auto & solution_type = this->solution_types[dof_id];
integration_scheme->corrector(solution_type, this->time_step);
/// computing the increment of dof if needed
if (this->dof_manager.hasDOFsIncrement(dof_id)) {
if (!this->dof_manager.hasPreviousDOFs(dof_id)) {
AKANTU_DEBUG_WARNING("In order to compute the increment of "
<< dof_id << " a 'previous' has to be registered");
continue;
}
Array<Real> & increment = this->dof_manager.getDOFsIncrement(dof_id);
Array<Real> & previous = this->dof_manager.getPreviousDOFs(dof_id);
UInt dof_array_comp = this->dof_manager.getDOFs(dof_id).getNbComponent();
auto prev_dof_it = previous.begin(dof_array_comp);
auto incr_it = increment.begin(dof_array_comp);
auto incr_end = increment.end(dof_array_comp);
increment.copy(this->dof_manager.getDOFs(dof_id));
for (; incr_it != incr_end; ++incr_it, ++prev_dof_it) {
*incr_it -= *prev_dof_it;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleMatrix(const ID & matrix_id) {
AKANTU_DEBUG_IN();
TimeStepSolver::assembleMatrix(matrix_id);
if (matrix_id != "J")
return;
for (auto & pair : this->integration_schemes) {
auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
const auto & solution_type = this->solution_types[dof_id];
integration_scheme->assembleJacobian(solution_type, this->time_step);
}
this->dof_manager.applyBoundary("J");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleResidual() {
AKANTU_DEBUG_IN();
if (this->needed_matrices.find("M") != needed_matrices.end()) {
if (this->is_mass_lumped) {
this->assembleLumpedMatrix("M");
} else {
this->assembleMatrix("M");
}
}
TimeStepSolver::assembleResidual();
for (auto & pair : this->integration_schemes) {
auto & integration_scheme = pair.second;
integration_scheme->assembleResidual(this->is_mass_lumped);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_IN();
if (this->needed_matrices.find("M") != needed_matrices.end()) {
if (this->is_mass_lumped) {
this->assembleLumpedMatrix("M");
} else {
this->assembleMatrix("M");
}
}
if (residual_part != "inertial") {
TimeStepSolver::assembleResidual(residual_part);
}
if (residual_part == "inertial") {
for (auto & pair : this->integration_schemes) {
auto & integration_scheme = pair.second;
integration_scheme->assembleResidual(this->is_mass_lumped);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/time_step_solvers/time_step_solver_default.hh b/src/model/time_step_solvers/time_step_solver_default.hh
index 9996f657f..8dd17fbea 100644
--- a/src/model/time_step_solvers/time_step_solver_default.hh
+++ b/src/model/time_step_solvers/time_step_solver_default.hh
@@ -1,112 +1,113 @@
/**
* @file time_step_solver_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Aug 24 17:10:29 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Feb 21 2018
*
* @brief Default implementation for the time stepper
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__
#define __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class TimeStepSolverDefault : public TimeStepSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolverDefault(DOFManagerDefault & dof_manager,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, const ID & id,
UInt memory_id);
~TimeStepSolverDefault() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// registers an integration scheme for a given dof
void setIntegrationScheme(const ID & dof_id,
const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined) override;
bool hasIntegrationScheme(const ID & dof_id) const override;
/// implementation of the TimeStepSolver::predictor()
void predictor() override;
/// implementation of the TimeStepSolver::corrector()
void corrector() override;
/// implementation of the TimeStepSolver::assembleMatrix()
void assembleMatrix(const ID & matrix_id) override;
/// implementation of the TimeStepSolver::assembleResidual()
void assembleResidual() override;
void assembleResidual(const ID & residual_part) override;
/// implementation of the generic TimeStepSolver::solveStep()
void solveStep(SolverCallback & solver_callback) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using DOFsIntegrationSchemes =
std::map<ID, std::unique_ptr<IntegrationScheme>>;
using DOFsIntegrationSchemesSolutionTypes =
std::map<ID, IntegrationScheme::SolutionType>;
using DOFsIntegrationSchemesOwner = std::set<ID>;
/// DOFManager with its real type
DOFManagerDefault & dof_manager;
/// Underlying integration scheme per dof, \todo check what happens in dynamic
/// in case of coupled equations
DOFsIntegrationSchemes integration_schemes;
/// defines if the solver is owner of the memory or not
DOFsIntegrationSchemesOwner integration_schemes_owner;
/// Type of corrector to use
DOFsIntegrationSchemesSolutionTypes solution_types;
/// define if the mass matrix is lumped or not
bool is_mass_lumped;
};
} // namespace akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__ */
diff --git a/src/model/time_step_solvers/time_step_solver_default_explicit.hh b/src/model/time_step_solvers/time_step_solver_default_explicit.hh
index d23c30d3b..633730538 100644
--- a/src/model/time_step_solvers/time_step_solver_default_explicit.hh
+++ b/src/model/time_step_solvers/time_step_solver_default_explicit.hh
@@ -1,77 +1,78 @@
/**
* @file time_step_solver_default_explicit.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Aug 24 14:21:44 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
* @brief Default solver for explicit resolution
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH__
#define __AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH__
namespace akantu {
class TimeStepSolverDefaultExplicit : public TimeStepSolverDefault {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolverDefaultExplicit();
virtual ~TimeStepSolverDefaultExplicit();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void solveStep();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "time_step_solver_default_explicit_inline_impl.cc"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const TimeStepSolverDefaultExplicit & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH__ */
diff --git a/src/model/time_step_solvers/time_step_solver_default_solver_callback.hh b/src/model/time_step_solvers/time_step_solver_default_solver_callback.hh
index 9e0552b82..5d4c1d73d 100644
--- a/src/model/time_step_solvers/time_step_solver_default_solver_callback.hh
+++ b/src/model/time_step_solvers/time_step_solver_default_solver_callback.hh
@@ -1,63 +1,64 @@
/**
* @file time_step_solver_default_solver_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Sep 28 18:58:07 2015
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the NonLinearSolverCallback for the time step
* solver
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_callback.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TIME_STEP_SOLVER_DEFAULT_SOLVER_CALLBACK_HH__
#define __AKANTU_TIME_STEP_SOLVER_DEFAULT_SOLVER_CALLBACK_HH__
namespace akantu {
class TimeStepSolverCallback : public NonLinearSolverCallback {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// callback to assemble the Jacobian Matrix
virtual void assembleJacobian();
/// callback to assemble the residual (rhs)
virtual void assembleResidual();
/* ------------------------------------------------------------------------ */
/* Dynamic simulations part */
/* ------------------------------------------------------------------------ */
/// callback for the predictor (in case of dynamic simulation)
virtual void predictor();
/// callback for the corrector (in case of dynamic simulation)
virtual void corrector();
};
} // akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_DEFAULT_SOLVER_CALLBACK_HH__ */
diff --git a/src/python/python_functor.cc b/src/python/python_functor.cc
index 15986dcf1..d4c524ca0 100644
--- a/src/python/python_functor.cc
+++ b/src/python/python_functor.cc
@@ -1,80 +1,80 @@
/**
* @file python_functor.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Fri Nov 13 2015
+ * @date last modification: Tue Feb 06 2018
*
* @brief Python functor interface
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "python_functor.hh"
#include "aka_common.hh"
#include "internal_field.hh"
#include <vector>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
PythonFunctor::PythonFunctor(PyObject * obj) : python_obj(obj) {}
/* -------------------------------------------------------------------------- */
PyObject * PythonFunctor::callFunctor(PyObject * functor, PyObject * args,
PyObject * kwargs) const {
if (!PyCallable_Check(functor))
AKANTU_EXCEPTION("Provided functor is not a function");
PyObject * pValue = PyObject_Call(functor, args, kwargs);
PyObject * exception_type = PyErr_Occurred();
if (exception_type) {
PyObject * exception;
PyObject * traceback;
PyErr_Fetch(&exception_type, &exception, &traceback);
PyObject_Print(exception_type, stdout, Py_PRINT_RAW);
PyObject_Print(exception, stdout, Py_PRINT_RAW);
std::stringstream sstr;
sstr << "Exception occured while calling the functor: ";
PyObject * exception_mesg = PyObject_GetAttrString(exception, "message");
#if PY_MAJOR_VERSION >= 3
if (exception_mesg && PyUnicode_Check(exception_mesg))
#else
if (exception_mesg && PyString_Check(exception_mesg))
#endif
sstr << this->convertToAkantu<std::string>(exception_mesg);
else
sstr << this->convertToAkantu<std::string>(exception);
AKANTU_EXCEPTION(sstr.str());
}
return pValue;
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/python/python_functor.hh b/src/python/python_functor.hh
index effa1fc8f..ffda267b9 100644
--- a/src/python/python_functor.hh
+++ b/src/python/python_functor.hh
@@ -1,146 +1,146 @@
/**
* @file python_functor.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Nov 15 2015
+ * @date last modification: Wed Feb 07 2018
*
* @brief Python Functor interface
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_group.hh"
#include "internal_field.hh"
/* -------------------------------------------------------------------------- */
#include <Python.h>
#include <map>
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PYTHON_FUNCTOR_HH__
#define __AKANTU_PYTHON_FUNCTOR_HH__
namespace akantu {
class PythonFunctor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PythonFunctor(PyObject * obj);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
/// call the python functor
PyObject * callFunctor(PyObject * functor, PyObject * args,
PyObject * kwargs) const;
/// call the python functor from variadic types
template <typename return_type, typename... Params>
return_type callFunctor(const std::string & functor_name,
Params &... parameters) const;
/// empty function to cose the recursive template loop
static inline void packArguments(std::vector<PyObject *> & pArgs);
/// get the python function object
inline PyObject * getPythonFunction(const std::string & functor_name) const;
/// variadic template for unknown number of arguments to unpack
template <typename T, typename... Args>
static inline void packArguments(std::vector<PyObject *> & pArgs, T & p,
Args &... params);
/// convert an akantu object to python
template <typename T>
static inline PyObject * convertToPython(const T & akantu_obj);
/// convert a stl vector to python
template <typename T>
static inline PyObject * convertToPython(const std::vector<T> & akantu_obj);
/// convert a stl vector to python
template <typename T>
static inline PyObject *
convertToPython(const std::vector<Array<T> *> & akantu_obj);
/// convert a stl vector to python
template <typename T>
static inline PyObject *
convertToPython(const std::unique_ptr<T> & akantu_obj);
/// convert a stl vector to python
template <typename T1, typename T2>
static inline PyObject * convertToPython(const std::map<T1, T2> & akantu_obj);
/// convert an akantu vector to python
template <typename T>
static inline PyObject * convertToPython(const Vector<T> & akantu_obj);
/// convert an akantu internal to python
template <typename T>
static inline PyObject * convertToPython(const InternalField<T> & akantu_obj);
/// convert an akantu vector to python
template <typename T>
static inline PyObject *
convertToPython(const ElementTypeMapArray<T> & akantu_obj);
/// convert an akantu vector to python
template <typename T>
static inline PyObject * convertToPython(const Array<T> & akantu_obj);
/// convert an akantu vector to python
template <typename T>
static inline PyObject * convertToPython(Array<T> * akantu_obj);
/// convert a akantu matrix to python
template <typename T>
static inline PyObject * convertToPython(const Matrix<T> & akantu_obj);
/// convert a python object to an akantu object
template <typename return_type>
static inline return_type convertToAkantu(PyObject * python_obj);
/// convert a python object to an akantu object
template <typename T>
static inline std::vector<T> convertListToAkantu(PyObject * python_obj);
/// returns the numpy data type code
template <typename T> static inline int getPythonDataTypeCode();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
PyObject * python_obj;
};
} // akantu
#endif /* __AKANTU_PYTHON_FUNCTOR_HH__ */
#include "python_functor_inline_impl.cc"
diff --git a/src/python/python_functor_inline_impl.cc b/src/python/python_functor_inline_impl.cc
index e573bdabe..38ccd09da 100644
--- a/src/python/python_functor_inline_impl.cc
+++ b/src/python/python_functor_inline_impl.cc
@@ -1,462 +1,463 @@
/**
* @file python_functor_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Nov 13 2015
- * @date last modification: Wed Nov 18 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Python functor interface
*
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "integration_point.hh"
#include "internal_field.hh"
/* -------------------------------------------------------------------------- */
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <Python.h>
#include <numpy/arrayobject.h>
#include <typeinfo>
#if PY_MAJOR_VERSION >= 3
#include <codecvt>
#endif
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PYTHON_FUNCTOR_INLINE_IMPL_CC__
#define __AKANTU_PYTHON_FUNCTOR_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> inline int PythonFunctor::getPythonDataTypeCode() {
AKANTU_EXCEPTION("undefined type: " << debug::demangle(typeid(T).name()));
}
/* -------------------------------------------------------------------------- */
template <> inline int PythonFunctor::getPythonDataTypeCode<bool>() {
int data_typecode = NPY_NOTYPE;
size_t s = sizeof(bool);
switch (s) {
case 1:
data_typecode = NPY_BOOL;
break;
case 2:
data_typecode = NPY_UINT16;
break;
case 4:
data_typecode = NPY_UINT32;
break;
case 8:
data_typecode = NPY_UINT64;
break;
}
return data_typecode;
}
/* -------------------------------------------------------------------------- */
template <> inline int PythonFunctor::getPythonDataTypeCode<double>() {
return NPY_DOUBLE;
}
/* -------------------------------------------------------------------------- */
template <> inline int PythonFunctor::getPythonDataTypeCode<UInt>() {
return NPY_UINT;
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<double>(const double & akantu_object) {
return PyFloat_FromDouble(akantu_object);
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<UInt>(const UInt & akantu_object) {
#if PY_MAJOR_VERSION >= 3
return PyLong_FromLong(akantu_object);
#else
return PyInt_FromLong(akantu_object);
#endif
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<int>(const int & akantu_object) {
#if PY_MAJOR_VERSION >= 3
return PyLong_FromLong(akantu_object);
#else
return PyInt_FromLong(akantu_object);
#endif
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<bool>(const bool & akantu_object) {
return PyBool_FromLong(long(akantu_object));
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<std::string>(const std::string & str) {
#if PY_MAJOR_VERSION >= 3
return PyUnicode_FromString(str.c_str());
#else
return PyString_FromString(str.c_str());
#endif
}
/* --------------------------------------------------------------------------
*/
template <>
inline PyObject *
PythonFunctor::convertToPython<NodeGroup>(const NodeGroup & group) {
return PythonFunctor::convertToPython(group.getNodes());
}
/* --------------------------------------------------------------------------
*/
template <>
inline PyObject *
PythonFunctor::convertToPython<ElementGroup>(const ElementGroup & group) {
PyObject * res = PyDict_New();
PyDict_SetItem(res,
PythonFunctor::convertToPython(std::string("element_group")),
PythonFunctor::convertToPython(group.getElements()));
PyDict_SetItem(res, PythonFunctor::convertToPython(std::string("node_group")),
PythonFunctor::convertToPython(group.getNodeGroup()));
return res;
}
/* --------------------------------------------------------------------------
*/
template <>
inline PyObject *
PythonFunctor::convertToPython<ElementGroup *>(ElementGroup * const & group) {
return PythonFunctor::convertToPython(*group);
}
/* --------------------------------------------------------------------------
*/
template <>
inline PyObject *
PythonFunctor::convertToPython<ElementType>(const ElementType & type) {
// std::stringstream sstr;
// sstr << type;
// return PythonFunctor::convertToPython(sstr.str());
return PythonFunctor::convertToPython(int(type));
}
/* --------------------------------------------------------------------------
*/
template <typename T>
inline PyObject *
PythonFunctor::convertToPython(const ElementTypeMapArray<T> & map) {
std::map<std::string, Array<T> *> res;
for (const auto & type : map.elementTypes()) {
std::stringstream sstr;
sstr << type;
res[sstr.str()] = const_cast<Array<T> *>(&map(type));
}
return PythonFunctor::convertToPython(res);
}
/* --------------------------------------------------------------------------
*/
template <typename T> PyObject * PythonFunctor::convertToPython(const T &) {
AKANTU_EXCEPTION(__PRETTY_FUNCTION__ << " : not implemented yet !"
<< std::endl
<< debug::demangle(typeid(T).name()));
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline PyObject * PythonFunctor::convertToPython(const std::vector<T> & array) {
int data_typecode = getPythonDataTypeCode<T>();
npy_intp dims[1] = {int(array.size())};
PyObject * obj = PyArray_SimpleNewFromData(1, dims, data_typecode,
const_cast<T *>(&array[0]));
auto * res = (PyArrayObject *)obj;
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline PyObject *
PythonFunctor::convertToPython(const std::vector<Array<T> *> & array) {
PyObject * res = PyDict_New();
for (auto a : array) {
PyObject * obj = PythonFunctor::convertToPython(*a);
PyObject * name = PythonFunctor::convertToPython(a->getID());
PyDict_SetItem(res, name, obj);
}
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <typename T1, typename T2>
inline PyObject * PythonFunctor::convertToPython(const std::map<T1, T2> & map) {
PyObject * res = PyDict_New();
for (auto && a : map) {
PyObject * key = PythonFunctor::convertToPython(a.first);
PyObject * value = PythonFunctor::convertToPython(a.second);
PyDict_SetItem(res, key, value);
}
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
PyObject * PythonFunctor::convertToPython(const Vector<T> & array) {
int data_typecode = getPythonDataTypeCode<T>();
npy_intp dims[1] = {array.size()};
PyObject * obj =
PyArray_SimpleNewFromData(1, dims, data_typecode, array.storage());
auto * res = (PyArrayObject *)obj;
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline PyObject *
PythonFunctor::convertToPython(const InternalField<T> & internals) {
return convertToPython(
static_cast<const ElementTypeMapArray<T> &>(internals));
}
/* --------------------------------------------------------------------- */
template <typename T>
inline PyObject * PythonFunctor::convertToPython(const std::unique_ptr<T> & u) {
return convertToPython(*u);
}
/* --------------------------------------------------------------------- */
template <typename T>
PyObject * PythonFunctor::convertToPython(const Array<T> & array) {
int data_typecode = getPythonDataTypeCode<T>();
npy_intp dims[2] = {array.size(), array.getNbComponent()};
PyObject * obj =
PyArray_SimpleNewFromData(2, dims, data_typecode, array.storage());
auto * res = (PyArrayObject *)obj;
return (PyObject *)res;
}
/* ---------------------------------------------------------------------- */
template <typename T>
PyObject * PythonFunctor::convertToPython(Array<T> * array) {
return PythonFunctor::convertToPython(*array);
}
/* ---------------------------------------------------------------------- */
template <typename T>
PyObject * PythonFunctor::convertToPython(const Matrix<T> & mat) {
int data_typecode = getPythonDataTypeCode<T>();
npy_intp dims[2] = {mat.size(0), mat.size(1)};
PyObject * obj =
PyArray_SimpleNewFromData(2, dims, data_typecode, mat.storage());
auto * res = (PyArrayObject *)obj;
return (PyObject *)res;
}
/* ---------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<IntegrationPoint>(const IntegrationPoint & qp) {
PyObject * input = PyDict_New();
PyObject * num_point = PythonFunctor::convertToPython(qp.num_point);
PyObject * global_num = PythonFunctor::convertToPython(qp.global_num);
PyObject * material_id = PythonFunctor::convertToPython(qp.material_id);
PyObject * position = PythonFunctor::convertToPython(qp.getPosition());
PyDict_SetItemString(input, "num_point", num_point);
PyDict_SetItemString(input, "global_num", global_num);
PyDict_SetItemString(input, "material_id", material_id);
PyDict_SetItemString(input, "position", position);
return input;
}
/* --------------------------------------------------------------------------
*/
inline PyObject *
PythonFunctor::getPythonFunction(const std::string & functor_name) const {
#if PY_MAJOR_VERSION < 3
if (!PyInstance_Check(this->python_obj))
AKANTU_EXCEPTION("Python object is not an instance");
#else
// does not make sense to check everything is an instance of object in python 3
#endif
if (not PyObject_HasAttrString(this->python_obj, functor_name.c_str()))
AKANTU_EXCEPTION("Python dictionary has no " << functor_name << " entry");
PyObject * pFunctor =
PyObject_GetAttrString(this->python_obj, functor_name.c_str());
return pFunctor;
}
/* --------------------------------------------------------------------------
*/
inline void PythonFunctor::packArguments(__attribute__((unused))
std::vector<PyObject *> & p_args) {}
/* --------------------------------------------------------------------------
*/
template <typename T, typename... Args>
inline void PythonFunctor::packArguments(std::vector<PyObject *> & p_args,
T & p, Args &... params) {
p_args.push_back(PythonFunctor::convertToPython(p));
if (sizeof...(params) != 0)
PythonFunctor::packArguments(p_args, params...);
}
/* --------------------------------------------------------------------------
*/
template <typename return_type, typename... Params>
return_type PythonFunctor::callFunctor(const std::string & functor_name,
Params &... parameters) const {
_import_array();
std::vector<PyObject *> arg_vector;
this->packArguments(arg_vector, parameters...);
PyObject * pArgs = PyTuple_New(arg_vector.size());
for (UInt i = 0; i < arg_vector.size(); ++i) {
PyTuple_SetItem(pArgs, i, arg_vector[i]);
}
PyObject * kwargs = PyDict_New();
PyObject * pFunctor = this->getPythonFunction(functor_name);
PyObject * res = this->callFunctor(pFunctor, pArgs, kwargs);
Py_XDECREF(pArgs);
Py_XDECREF(kwargs);
return this->convertToAkantu<return_type>(res);
}
/* --------------------------------------------------------------------------
*/
template <typename return_type>
inline return_type PythonFunctor::convertToAkantu(PyObject * python_obj) {
if (PyList_Check(python_obj)) {
return PythonFunctor::convertListToAkantu<typename return_type::value_type>(
python_obj);
}
AKANTU_TO_IMPLEMENT();
}
/* --------------------------------------------------------------------------
*/
template <>
inline void PythonFunctor::convertToAkantu<void>(PyObject * python_obj) {
if (python_obj != Py_None)
AKANTU_DEBUG_WARNING(
"functor return a value while none was expected: ignored");
}
/* --------------------------------------------------------------------------
*/
template <>
inline std::string
PythonFunctor::convertToAkantu<std::string>(PyObject * python_obj) {
#if PY_MAJOR_VERSION >= 3
if (!PyUnicode_Check(python_obj))
AKANTU_EXCEPTION("cannot convert object to string");
std::wstring unicode_str(PyUnicode_AsWideCharString(python_obj, NULL));
std::wstring_convert<std::codecvt_utf8<wchar_t>, wchar_t> converter;
return converter.to_bytes(unicode_str);
#else
if (!PyString_Check(python_obj))
AKANTU_EXCEPTION("cannot convert object to string");
return PyString_AsString(python_obj);
#endif
}
/* --------------------------------------------------------------------------
*/
template <>
inline Real PythonFunctor::convertToAkantu<Real>(PyObject * python_obj) {
if (!PyFloat_Check(python_obj))
AKANTU_EXCEPTION("cannot convert object to float");
return PyFloat_AsDouble(python_obj);
}
/* --------------------------------------------------------------------------
*/
template <>
inline UInt PythonFunctor::convertToAkantu<UInt>(PyObject * python_obj) {
#if PY_MAJOR_VERSION >= 3
if (!PyLong_Check(python_obj))
AKANTU_EXCEPTION("cannot convert object to integer");
return PyLong_AsLong(python_obj);
#else
if (!PyInt_Check(python_obj))
AKANTU_EXCEPTION("cannot convert object to integer");
return PyInt_AsLong(python_obj);
#endif
}
/* --------------------------------------------------------------------------
*/
template <typename T>
inline std::vector<T>
PythonFunctor::convertListToAkantu(PyObject * python_obj) {
std::vector<T> res;
UInt size = PyList_Size(python_obj);
for (UInt i = 0; i < size; ++i) {
PyObject * item = PyList_GET_ITEM(python_obj, i);
res.push_back(PythonFunctor::convertToAkantu<T>(item));
}
return res;
}
/* --------------------------------------------------------------------------
*/
} // akantu
#endif /* __AKANTU_PYTHON_FUNCTOR_INLINE_IMPL_CC__ */
diff --git a/src/solver/petsc_wrapper.hh b/src/solver/petsc_wrapper.hh
index dab92ca0d..e49a50350 100644
--- a/src/solver/petsc_wrapper.hh
+++ b/src/solver/petsc_wrapper.hh
@@ -1,79 +1,79 @@
/**
* @file petsc_wrapper.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Wed Oct 07 2015
+ * @date last modification: Sat Feb 03 2018
*
* @brief Wrapper of PETSc structures
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PETSC_WRAPPER_HH__
#define __AKANTU_PETSC_WRAPPER_HH__
/* -------------------------------------------------------------------------- */
#include <mpi.h>
#include <petscao.h>
#include <petscis.h>
#include <petscksp.h>
#include <petscmat.h>
#include <petscvec.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
struct PETScMatrixWrapper {
Mat mat;
AO ao;
ISLocalToGlobalMapping mapping;
/// MPI communicator for PETSc commands
MPI_Comm communicator;
};
/* -------------------------------------------------------------------------- */
struct PETScSolverWrapper {
KSP ksp;
Vec solution;
Vec rhs;
// MPI communicator for PETSc commands
MPI_Comm communicator;
};
#if not defined(PETSC_CLANGUAGE_CXX)
extern int aka_PETScError(int ierr);
#define CHKERRXX(x) \
do { \
int error = aka_PETScError(x); \
if (error != 0) { \
AKANTU_EXCEPTION("Error in PETSC"); \
} \
} while (0)
#endif
} // akantu
#endif /* __AKANTU_PETSC_WRAPPER_HH__ */
diff --git a/src/solver/solver_petsc.cc b/src/solver/solver_petsc.cc
index b32a28b4c..7742143c7 100644
--- a/src/solver/solver_petsc.cc
+++ b/src/solver/solver_petsc.cc
@@ -1,1106 +1,1106 @@
/**
* @file solver_petsc.cc
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 13 2014
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Sun Aug 13 2017
*
* @brief Solver class implementation for the petsc solver
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solver_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_type_wrapper.hh"
#include "sparse_matrix_petsc.hh"
/* -------------------------------------------------------------------------- */
#include <petscksp.h>
//#include <petscsys.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SolverPETSc::SolverPETSc(DOFManagerPETSc & dof_manager, const ID & matrix_id,
const ID & id, const MemoryID & memory_id)
: SparseSolver(dof_manager, matrix_id, id, memory_id),
dof_manager(dof_manager), matrix(dof_manager.getMatrix(matrix_id)),
is_petsc_data_initialized(false) {
PetscErrorCode ierr;
/// create a solver context
ierr = KSPCreate(PETSC_COMM_WORLD, &this->ksp);
CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
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->ksp));
CHKERRXX(ierr);
this->is_petsc_data_initialized = false;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::initialize() {
AKANTU_DEBUG_IN();
this->is_petsc_data_initialized = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::solve() {
AKANTU_DEBUG_IN();
Vec & rhs = this->dof_manager.getResidual();
Vec & solution = this->dof_manager.getGlobalSolution();
PetscErrorCode ierr;
ierr = KSPSolve(this->ksp, rhs, 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.size();
// 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)
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
ierr = KSPSetOperators(this->ksp, this->matrix.getPETScMat(),
this->matrix.getPETScMat());
CHKERRXX(ierr);
#else
ierr = KSPSetOperators(this->ksp, this->matrix.getPETScMat(),
this->matrix.getPETScMat(), SAME_NONZERO_PATTERN);
CHKERRXX(ierr);
#endif
/// If this is not called the solution vector is zeroed in the call to
/// KSPSolve().
ierr = KSPSetInitialGuessNonzero(this->ksp, PETSC_TRUE);
KSPSetFromOptions(this->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->size();
// //
// // 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();
// //}
} // akantu
diff --git a/src/solver/solver_petsc.hh b/src/solver/solver_petsc.hh
index 241884da4..76837b321 100644
--- a/src/solver/solver_petsc.hh
+++ b/src/solver/solver_petsc.hh
@@ -1,183 +1,185 @@
/**
* @file solver_petsc.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 13 2014
- * @date last modification: Wed Oct 07 2015
+ * @date last modification: Mon Jun 19 2017
*
* @brief Solver class interface for the petsc solver
*
* @section LICENSE
*
- * Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_solver.hh"
/* -------------------------------------------------------------------------- */
#include <petscksp.h>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLVER_PETSC_HH__
#define __AKANTU_SOLVER_PETSC_HH__
namespace akantu {
class SparseMatrixPETSc;
class DOFManagerPETSc;
}
namespace akantu {
class SolverPETSc : public SparseSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SolverPETSc(DOFManagerPETSc & dof_manager, const ID & matrix_id,
const ID & id = "solver_petsc", const MemoryID & memory_id = 0);
virtual ~SolverPETSc();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create the solver context and set the matrices
virtual void initialize();
virtual void setOperators();
virtual void setRHS(Array<Real> & rhs);
virtual void solve();
virtual void solve(Array<Real> & solution);
private:
/// clean the petsc data
virtual void destroyInternalData();
private:
/// DOFManager correctly typed
DOFManagerPETSc & dof_manager;
/// PETSc linear solver
KSP ksp;
/// Matrix defining the system of equations
SparseMatrixPETSc & matrix;
/// specify if the petsc_data is initialized or not
bool is_petsc_data_initialized;
};
// SolverPETSc(int argc, char *argv[]) : allocated_(false) {
// /*
// Set linear solver defaults for this problem (optional).
// - By extracting the KSP and PC contexts from the KSP context,
// we can then directly call any KSP and PC routines to set
// various options.
// - The following four statements are optional; all of these
// parameters could alternatively be specified at runtime via
// KSPSetFromOptions();
// */
// // ierr = KSPGetPC(ksp_,&pc);CHKERRCONTINUE(ierr);
// // ierr = PCSetType(pc,PCILU);CHKERRCONTINUE(ierr);
// // ierr = PCSetType(pc,PCJACOBI);CHKERRCONTINUE(ierr);
// ierr =
// KSPSetTolerances(ksp_,1.e-5,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRCONTINUE(ierr);
// }
// //! Overload operator() to solve system of linear equations
// sparse_vector_type operator()(const sparse_matrix_type& AA, const
// sparse_vector_type& bb);
// //! Overload operator() to obtain reaction vector
// sparse_vector_type operator()(const sparse_matrix_type& Kpf, const
// sparse_matrix_type& Kpp, const sparse_vector_type& Up);
// //! Overload operator() to obtain the addition two vectors
// sparse_vector_type operator()(const sparse_vector_type& aa, const
// sparse_vector_type& bb);
// value_type norm(const sparse_matrix_type& aa, Element_insertion_type it =
// Add_t);
// value_type norm(const sparse_vector_type& aa, Element_insertion_type it =
// Add_t);
// // NOTE: the destructor will return an error if it is called after
// MPI_Finalize is
// // called because it uses collect communication to free-up allocated
// memory.
// ~SolverPETSc() {
// static bool exit = false;
// if (!exit) {
// // add finalize PETSc function at exit
// atexit(finalize);
// exit = true;
// }
// if (allocated_) {
// PetscErrorCode ierr = MatDestroy(&A_);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&x_);CHKERRCONTINUE(ierr);
// ierr = KSPDestroy(&ksp_);CHKERRCONTINUE(ierr);
// }
// }
// /* from the PETSc library, these are the options that can be passed
// to the command line
// Options Database Keys
// -options_table - Calls PetscOptionsView()
-// -options_left - Prints unused options that remain in the
+// -options_left - Prints unused options that remain in
+// the
// database
// -objects_left - Prints list of all objects that have not
// been freed
// -mpidump - Calls PetscMPIDump()
// -malloc_dump - Calls PetscMallocDump()
// -malloc_info - Prints total memory usage
// -malloc_log - Prints summary of memory usage
// Options Database Keys for Profiling
// -log_summary [filename] - Prints summary of flop and timing
// information to screen.
// If the filename is specified the summary is written to the file. See
// PetscLogView().
// -log_summary_python [filename] - Prints data on of flop and timing
// usage
// to a file or screen.
-// -log_all [filename] - Logs extensive profiling information See
+// -log_all [filename] - Logs extensive profiling information
+// See
// PetscLogDump().
// -log [filename] - Logs basic profiline information See
// PetscLogDump().
// -log_sync - Log the synchronization in scatters,
// inner products and norms
// -log_mpe [filename] - Creates a logfile viewable by the utility
// Upshot/Nupshot (in MPICH distribution)
// }
// }
// };
} // akantu
#endif /* __AKANTU_SOLVER_PETSC_HH__ */
diff --git a/src/solver/sparse_matrix.cc b/src/solver/sparse_matrix.cc
index 593016ef0..607399442 100644
--- a/src/solver/sparse_matrix.cc
+++ b/src/solver/sparse_matrix.cc
@@ -1,80 +1,79 @@
/**
* @file sparse_matrix.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Mon Nov 16 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief implementation of the SparseMatrix class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(DOFManager & dof_manager,
const MatrixType & matrix_type, const ID & id)
: id(id), _dof_manager(dof_manager), matrix_type(matrix_type),
size_(dof_manager.getSystemSize()), nb_non_zero(0) {
AKANTU_DEBUG_IN();
const auto & comm = _dof_manager.getCommunicator();
this->nb_proc = comm.getNbProc();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(const SparseMatrix & matrix, const ID & id)
: SparseMatrix(matrix._dof_manager, matrix.matrix_type, id) {
nb_non_zero = matrix.nb_non_zero;
}
/* -------------------------------------------------------------------------- */
SparseMatrix::~SparseMatrix() = default;
/* -------------------------------------------------------------------------- */
Array<Real> & operator*=(Array<Real> & vect, const SparseMatrix & mat) {
Array<Real> tmp(vect.size(), vect.getNbComponent(), 0.);
mat.matVecMul(vect, tmp);
vect.copy(tmp);
return vect;
}
/* -------------------------------------------------------------------------- */
void SparseMatrix::add(const SparseMatrix & B, Real alpha) {
B.addMeTo(*this, alpha);
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/solver/sparse_matrix.hh b/src/solver/sparse_matrix.hh
index 9dc5de8b3..08fe2c837 100644
--- a/src/solver/sparse_matrix.hh
+++ b/src/solver/sparse_matrix.hh
@@ -1,162 +1,160 @@
-
/**
* @file sparse_matrix.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Fri Oct 16 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief sparse matrix storage class (distributed assembled matrix)
* This is a COO format (Coordinate List)
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SPARSE_MATRIX_HH__
#define __AKANTU_SPARSE_MATRIX_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManager;
class TermsToAssemble;
}
namespace akantu {
class SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrix(DOFManager & dof_manager, const MatrixType & matrix_type,
const ID & id = "sparse_matrix");
SparseMatrix(const SparseMatrix & matrix, const ID & id = "sparse_matrix");
virtual ~SparseMatrix();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
virtual void clearProfile();
/// set the matrix to 0
virtual void clear() = 0;
/// add a non-zero element to the profile
virtual UInt add(UInt i, UInt j) = 0;
/// assemble a local matrix in the sparse one
virtual void add(UInt i, UInt j, Real value) = 0;
/// save the profil in a file using the MatrixMarket file format
virtual void saveProfile(__attribute__((unused)) const std::string &) const {
AKANTU_TO_IMPLEMENT();
}
/// save the matrix in a file using the MatrixMarket file format
virtual void saveMatrix(__attribute__((unused)) const std::string &) const {
AKANTU_TO_IMPLEMENT();
};
/// multiply the matrix by a coefficient
virtual void mul(Real alpha) = 0;
/// add matrices
virtual void add(const SparseMatrix & matrix, Real alpha = 1.);
/// Equivalent of *gemv in blas
virtual void matVecMul(const Array<Real> & x, Array<Real> & y,
Real alpha = 1., Real beta = 0.) const = 0;
/// modify the matrix to "remove" the blocked dof
virtual void applyBoundary(Real block_val = 1.) = 0;
/// operator *=
SparseMatrix & operator*=(Real alpha) {
this->mul(alpha);
return *this;
}
protected:
/// This is the revert of add B += \alpha * *this;
virtual void addMeTo(SparseMatrix & B, Real alpha) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the values at potition i, j
virtual inline Real operator()(__attribute__((unused)) UInt i,
__attribute__((unused)) UInt j) const {
AKANTU_TO_IMPLEMENT();
}
/// return the values at potition i, j
virtual inline Real & operator()(__attribute__((unused)) UInt i,
__attribute__((unused)) UInt j) {
AKANTU_TO_IMPLEMENT();
}
AKANTU_GET_MACRO(NbNonZero, nb_non_zero, UInt);
UInt size() const { return size_; }
AKANTU_GET_MACRO(MatrixType, matrix_type, const MatrixType &);
virtual UInt getRelease() const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ID id;
/// Underlying dof manager
DOFManager & _dof_manager;
/// sparce matrix type
MatrixType matrix_type;
/// Size of the matrix
UInt size_;
/// number of processors
UInt nb_proc;
/// number of non zero element
UInt nb_non_zero;
};
Array<Real> & operator*=(Array<Real> & vect, const SparseMatrix & mat);
} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_inline_impl.cc"
#endif /* __AKANTU_SPARSE_MATRIX_HH__ */
diff --git a/src/solver/sparse_matrix_aij.cc b/src/solver/sparse_matrix_aij.cc
index acf516e85..cb10f23ae 100644
--- a/src/solver/sparse_matrix_aij.cc
+++ b/src/solver/sparse_matrix_aij.cc
@@ -1,215 +1,216 @@
/**
* @file sparse_matrix_aij.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 18 16:31:23 2015
+ * @date creation: Fri Aug 21 2015
+ * @date last modification: Mon Dec 04 2017
*
* @brief Implementation of the AIJ sparse matrix
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij.hh"
#include "aka_iterators.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "terms_to_assemble.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::SparseMatrixAIJ(DOFManagerDefault & dof_manager,
const MatrixType & matrix_type, const ID & id)
: SparseMatrix(dof_manager, matrix_type, id), dof_manager(dof_manager),
irn(0, 1, id + ":irn"), jcn(0, 1, id + ":jcn"), a(0, 1, id + ":a") {}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::SparseMatrixAIJ(const SparseMatrixAIJ & matrix, const ID & id)
: SparseMatrix(matrix, id), dof_manager(matrix.dof_manager),
irn(matrix.irn, true, id + ":irn"), jcn(matrix.jcn, true, id + ":jcn"),
a(matrix.a, true, id + ":a") {}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::~SparseMatrixAIJ() = default;
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::applyBoundary(Real block_val) {
AKANTU_DEBUG_IN();
// clang-format off
const auto & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
for (auto && ij_a : zip(irn, jcn, a)) {
UInt ni = this->dof_manager.globalToLocalEquationNumber(std::get<0>(ij_a) - 1);
UInt nj = this->dof_manager.globalToLocalEquationNumber(std::get<1>(ij_a) - 1);
if (blocked_dofs(ni) || blocked_dofs(nj)) {
std::get<2>(ij_a) =
std::get<0>(ij_a) != std::get<1>(ij_a) ? 0.
: this->dof_manager.isLocalOrMasterDOF(ni) ? block_val
: 0.;
}
}
this->value_release++;
// clang-format on
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::saveProfile(const std::string & filename) const {
AKANTU_DEBUG_IN();
std::ofstream outfile;
outfile.open(filename.c_str());
UInt m = this->size_;
outfile << "%%MatrixMarket matrix coordinate pattern";
if (this->matrix_type == _symmetric)
outfile << " symmetric";
else
outfile << " general";
outfile << std::endl;
outfile << m << " " << m << " " << this->nb_non_zero << std::endl;
for (UInt i = 0; i < this->nb_non_zero; ++i) {
outfile << this->irn.storage()[i] << " " << this->jcn.storage()[i] << " 1"
<< std::endl;
}
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
// open and set the properties of the stream
std::ofstream outfile;
outfile.open(filename.c_str());
outfile.precision(std::numeric_limits<Real>::digits10);
// write header
outfile << "%%MatrixMarket matrix coordinate real";
if (this->matrix_type == _symmetric)
outfile << " symmetric";
else
outfile << " general";
outfile << std::endl;
outfile << this->size_ << " " << this->size_ << " " << this->nb_non_zero
<< std::endl;
// write content
for (UInt i = 0; i < this->nb_non_zero; ++i) {
outfile << this->irn(i) << " " << this->jcn(i) << " " << this->a(i)
<< std::endl;
}
// time to end
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::matVecMul(const Array<Real> & x, Array<Real> & y,
Real alpha, Real beta) const {
AKANTU_DEBUG_IN();
y *= beta;
auto i_it = this->irn.begin();
auto j_it = this->jcn.begin();
auto a_it = this->a.begin();
auto a_end = this->a.end();
auto x_it = x.begin_reinterpret(x.size() * x.getNbComponent());
auto y_it = y.begin_reinterpret(x.size() * x.getNbComponent());
for (; a_it != a_end; ++i_it, ++j_it, ++a_it) {
Int i = this->dof_manager.globalToLocalEquationNumber(*i_it - 1);
Int j = this->dof_manager.globalToLocalEquationNumber(*j_it - 1);
const Real & A = *a_it;
y_it[i] += alpha * A * x_it[j];
if ((this->matrix_type == _symmetric) && (i != j))
y_it[j] += alpha * A * x_it[i];
}
if (this->dof_manager.hasSynchronizer())
this->dof_manager.getSynchronizer().reduceSynchronize<AddOperation>(y);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::copyContent(const SparseMatrix & matrix) {
AKANTU_DEBUG_IN();
const auto & mat = dynamic_cast<const SparseMatrixAIJ &>(matrix);
AKANTU_DEBUG_ASSERT(nb_non_zero == mat.getNbNonZero(),
"The to matrix don't have the same profiles");
memcpy(a.storage(), mat.getA().storage(), nb_non_zero * sizeof(Real));
this->value_release++;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class MatrixType>
void SparseMatrixAIJ::addMeToTemplated(MatrixType & B, Real alpha) const {
UInt i, j;
Real A_ij;
for (auto && tuple : zip(irn, jcn, a)) {
std::tie(i, j, A_ij) = tuple;
B.add(i - 1, j - 1, alpha * A_ij);
}
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::addMeTo(SparseMatrix & B, Real alpha) const {
if (auto * B_aij = dynamic_cast<SparseMatrixAIJ *>(&B)) {
this->addMeToTemplated<SparseMatrixAIJ>(*B_aij, alpha);
} else {
// this->addMeToTemplated<SparseMatrix>(*this, alpha);
}
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::mul(Real alpha) {
this->a *= alpha;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::clear() {
a.set(0.);
this->value_release++;
}
} // namespace akantu
diff --git a/src/solver/sparse_matrix_aij.hh b/src/solver/sparse_matrix_aij.hh
index 9c067be24..668927be0 100644
--- a/src/solver/sparse_matrix_aij.hh
+++ b/src/solver/sparse_matrix_aij.hh
@@ -1,180 +1,182 @@
/**
* @file sparse_matrix_aij.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Mon Aug 17 21:22:57 2015
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Wed Nov 08 2017
*
- * @brief AIJ implementation of the SparseMatrix (this the format used by Mumps)
+ * @brief AIJ implementation of the SparseMatrix (this the format used by
+ * Mumps)
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SPARSE_MATRIX_AIJ_HH__
#define __AKANTU_SPARSE_MATRIX_AIJ_HH__
namespace akantu {
class DOFManagerDefault;
class TermsToAssemble;
}
namespace akantu {
class SparseMatrixAIJ : public SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrixAIJ(DOFManagerDefault & dof_manager,
const MatrixType & matrix_type,
const ID & id = "sparse_matrix_aij");
SparseMatrixAIJ(const SparseMatrixAIJ & matrix,
const ID & id = "sparse_matrix_aij");
~SparseMatrixAIJ() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
inline void clearProfile() override;
/// add a non-zero element
inline UInt add(UInt i, UInt j) override;
/// set the matrix to 0
void clear() override;
/// assemble a local matrix in the sparse one
inline void add(UInt i, UInt j, Real value) override;
/// set the size of the matrix
void resize(UInt size) { this->size_ = size; }
/// modify the matrix to "remove" the blocked dof
void applyBoundary(Real block_val = 1.) override;
/// save the profil in a file using the MatrixMarket file format
void saveProfile(const std::string & filename) const override;
/// save the matrix in a file using the MatrixMarket file format
void saveMatrix(const std::string & filename) const override;
/// copy assuming the profile are the same
virtual void copyContent(const SparseMatrix & matrix);
/// multiply the matrix by a scalar
void mul(Real alpha) override;
/// add matrix *this += B
// virtual void add(const SparseMatrix & matrix, Real alpha);
/// Equivalent of *gemv in blas
void matVecMul(const Array<Real> & x, Array<Real> & y, Real alpha = 1.,
Real beta = 0.) const override;
/* ------------------------------------------------------------------------ */
/// accessor to A_{ij} - if (i, j) not present it returns 0
inline Real operator()(UInt i, UInt j) const override;
/// accessor to A_{ij} - if (i, j) not present it fails, (i, j) should be
/// first added to the profile
inline Real & operator()(UInt i, UInt j) override;
protected:
/// This is the revert of add B += \alpha * *this;
void addMeTo(SparseMatrix & B, Real alpha) const override;
private:
/// This is just to inline the addToMatrix function
template <class MatrixType>
void addMeToTemplated(MatrixType & B, Real alpha) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(IRN, irn, const Array<Int> &);
AKANTU_GET_MACRO(JCN, jcn, const Array<Int> &);
AKANTU_GET_MACRO(A, a, const Array<Real> &);
/// The release changes at each call of a function that changes the profile,
/// it in increasing but could overflow so it should be checked as
/// (my_release != release) and not as (my_release < release)
AKANTU_GET_MACRO(ProfileRelease, profile_release, UInt);
AKANTU_GET_MACRO(ValueRelease, value_release, UInt);
UInt getRelease() const override { return value_release; }
protected:
using KeyCOO = std::pair<UInt, UInt>;
using coordinate_list_map = std::unordered_map<KeyCOO, UInt>;
/// get the pair corresponding to (i, j)
inline KeyCOO key(UInt i, UInt j) const {
if (this->matrix_type == _symmetric && (i > j))
return std::make_pair(j, i);
return std::make_pair(i, j);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// row indexes
Array<Int> irn;
/// column indexes
Array<Int> jcn;
/// values : A[k] = Matrix[irn[k]][jcn[k]]
Array<Real> a;
/// Profile release
UInt profile_release{1};
/// Value release
UInt value_release{1};
/// map for (i, j) -> k correspondence
coordinate_list_map irn_jcn_k;
};
} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij_inline_impl.cc"
#endif /* __AKANTU_SPARSE_MATRIX_AIJ_HH__ */
diff --git a/src/solver/sparse_matrix_aij_inline_impl.cc b/src/solver/sparse_matrix_aij_inline_impl.cc
index 2c6ee5081..d9d8f8774 100644
--- a/src/solver/sparse_matrix_aij_inline_impl.cc
+++ b/src/solver/sparse_matrix_aij_inline_impl.cc
@@ -1,116 +1,118 @@
/**
* @file sparse_matrix_aij_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Aug 18 00:42:45 2015
+ * @date creation: Fri Aug 21 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Implementation of inline functions of SparseMatrixAIJ
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_CC__
#define __AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_CC__
namespace akantu {
inline UInt SparseMatrixAIJ::add(UInt i, UInt j) {
KeyCOO jcn_irn = this->key(i, j);
auto it = this->irn_jcn_k.find(jcn_irn);
if (!(it == this->irn_jcn_k.end()))
return it->second;
if (i + 1 > this->size_)
this->size_ = i + 1;
if (j + 1 > this->size_)
this->size_ = j + 1;
this->irn.push_back(i + 1);
this->jcn.push_back(j + 1);
this->a.push_back(0.);
this->irn_jcn_k[jcn_irn] = this->nb_non_zero;
(this->nb_non_zero)++;
this->profile_release++;
this->value_release++;
return (this->nb_non_zero - 1);
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::clearProfile() {
SparseMatrix::clearProfile();
this->irn_jcn_k.clear();
this->irn.resize(0);
this->jcn.resize(0);
this->a.resize(0);
this->size_ = 0;
this->profile_release++;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::add(UInt i, UInt j, Real value) {
UInt idx = this->add(i, j);
this->a(idx) += value;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
inline Real SparseMatrixAIJ::operator()(UInt i, UInt j) const {
KeyCOO jcn_irn = this->key(i, j);
auto irn_jcn_k_it = this->irn_jcn_k.find(jcn_irn);
if (irn_jcn_k_it == this->irn_jcn_k.end())
return 0.;
return this->a(irn_jcn_k_it->second);
}
/* -------------------------------------------------------------------------- */
inline Real & SparseMatrixAIJ::operator()(UInt i, UInt j) {
KeyCOO jcn_irn = this->key(i, j);
auto irn_jcn_k_it = this->irn_jcn_k.find(jcn_irn);
AKANTU_DEBUG_ASSERT(irn_jcn_k_it != this->irn_jcn_k.end(),
"Couple (i,j) = (" << i << "," << j
<< ") does not exist in the profile");
// it may change the profile so it is considered as a change
this->value_release++;
return this->a(irn_jcn_k_it->second);
}
} // namespace akantu
#endif /* __AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_CC__ */
diff --git a/src/solver/sparse_matrix_inline_impl.cc b/src/solver/sparse_matrix_inline_impl.cc
index dc1a84948..8a90f0860 100644
--- a/src/solver/sparse_matrix_inline_impl.cc
+++ b/src/solver/sparse_matrix_inline_impl.cc
@@ -1,37 +1,36 @@
/**
* @file sparse_matrix_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Tue Aug 18 2015
+ * @date last modification: Mon Jun 19 2017
*
* @brief implementation of inline methods of the SparseMatrix class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
namespace akantu {
inline void SparseMatrix::clearProfile() { this->nb_non_zero = 0; }
} // akantu
diff --git a/src/solver/sparse_matrix_petsc.cc b/src/solver/sparse_matrix_petsc.cc
index 906c4056e..ab5c6dbad 100644
--- a/src/solver/sparse_matrix_petsc.cc
+++ b/src/solver/sparse_matrix_petsc.cc
@@ -1,402 +1,405 @@
/**
- * @file petsc_matrix.cc
- * @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
- * @date Mon Jul 21 17:40:41 2014
+ * @file sparse_matrix_petsc.cc
+ *
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ *
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Sat Feb 03 2018
*
* @brief Implementation of PETSc matrix class
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_type_wrapper.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#include <cstring>
#include <petscsys.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
#if not defined(PETSC_CLANGUAGE_CXX)
int aka_PETScError(int ierr) {
CHKERRQ(ierr);
return 0;
}
#endif
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::SparseMatrixPETSc(DOFManagerPETSc & dof_manager,
const MatrixType & sparse_matrix_type,
const ID & id, const MemoryID & memory_id)
: SparseMatrix(dof_manager, matrix_type, id, memory_id),
dof_manager(dof_manager), d_nnz(0, 1, "dnnz"), o_nnz(0, 1, "onnz"),
first_global_index(0) {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
// create the PETSc matrix object
ierr = MatCreate(PETSC_COMM_WORLD, &this->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->mat, MATAIJ);
CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::~SparseMatrixPETSc() {
AKANTU_DEBUG_IN();
/// destroy all the PETSc data structures used for this matrix
PetscErrorCode ierr;
ierr = MatDestroy(&this->mat);
CHKERRXX(ierr);
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 SparseMatrixPETSc::setSize() {
AKANTU_DEBUG_IN();
// PetscErrorCode ierr;
/// find the number of dofs corresponding to master or local nodes
UInt nb_dofs = this->dof_manager.getLocalSystemSize();
// 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();
throw;
/// 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 SparseMatrixPETSc::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(PETSC_COMM_WORLD, this->local_size, local_master_eq_nbs_ptr,
petsc_dofs.storage(), &(this->ao));
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 SparseMatrixPETSc::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
/// create Petsc viewer
PetscViewer viewer;
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD, 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->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 SparseMatrixPETSc::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) {
// 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),
// 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),
// 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 SparseMatrixPETSc::add(const SparseMatrixPETSc & matrix, Real alpha) {
PetscErrorCode ierr;
ierr = MatAXPY(this->mat, alpha, matrix.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 SparseMatrixPETSc::performAssembly() {
this->beginAssembly();
this->endAssembly();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::beginAssembly() {
PetscErrorCode ierr;
ierr = MatAssemblyBegin(this->mat, MAT_FINAL_ASSEMBLY);
CHKERRXX(ierr);
ierr = MatAssemblyEnd(this->mat, MAT_FINAL_ASSEMBLY);
CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::endAssembly() {
PetscErrorCode ierr;
ierr = MatAssemblyEnd(this->mat, MAT_FINAL_ASSEMBLY);
CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
/// access K(i, j). Works only for dofs on this processor!!!!
Real SparseMatrixPETSc::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;
return 0.;
}
/* -------------------------------------------------------------------------- */
/**
* 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 SparseMatrixPETSc::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
// UInt nb_component = boundary.getNbComponent();
// UInt size = boundary.size();
// 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);
// 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 SparseMatrixPETSc::clear() { MatZeroEntries(this->mat); }
} // akantu
diff --git a/src/solver/sparse_matrix_petsc.hh b/src/solver/sparse_matrix_petsc.hh
index fafa3b64c..89597ebd5 100644
--- a/src/solver/sparse_matrix_petsc.hh
+++ b/src/solver/sparse_matrix_petsc.hh
@@ -1,142 +1,141 @@
/**
- * @file petsc_matrix.hh
+ * @file sparse_matrix_petsc.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Aug 21 2015
+ * @date last modification: Tue Feb 06 2018
*
* @brief Interface for PETSc matrices
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PETSC_MATRIX_HH__
#define __AKANTU_PETSC_MATRIX_HH__
/* -------------------------------------------------------------------------- */
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <petscao.h>
#include <petscmat.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManagerPETSc;
}
namespace akantu {
class SparseMatrixPETSc : public SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrixPETSc(DOFManagerPETSc & dof_manager,
const MatrixType & matrix_type,
const ID & id = "sparse_matrix",
const MemoryID & memory_id = 0);
SparseMatrixPETSc(const SparseMatrix & matrix,
const ID & id = "sparse_matrix_petsc",
const MemoryID & memory_id = 0);
virtual ~SparseMatrixPETSc();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set the matrix to 0
virtual void clear();
/// modify the matrix to "remove" the blocked dof
virtual void applyBoundary(const Array<bool> & boundary, Real block_val = 1.);
/// save the matrix in a ASCII file format
virtual void saveMatrix(const std::string & filename) const;
/// add a sparse matrix assuming the profile are the same
virtual void add(const SparseMatrix & matrix, Real alpha);
/// add a petsc matrix assuming the profile are the same
virtual void add(const SparseMatrixPETSc & matrix, Real alpha);
Real operator()(UInt i, UInt j) const;
protected:
typedef std::pair<UInt, UInt> KeyCOO;
inline KeyCOO key(UInt i, UInt j) const { return std::make_pair(i, j); }
private:
virtual void destroyInternalData();
/// set the size of the PETSc matrix
void setSize();
void createGlobalAkantuToPETScMap(Int * local_master_eq_nbs_ptr);
void createLocalAkantuToPETScMap();
/// start to assemble the matrix
void beginAssembly();
/// finishes to assemble the matrix
void endAssembly();
/// perform the assembly stuff from petsc
void performAssembly();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(PETScMat, mat, const Mat &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
// DOFManagerPETSc that contains the numbering for petsc
DOFManagerPETSc & dof_manager;
/// store the PETSc matrix
Mat mat;
AO ao;
/// size of the diagonal part of the matrix partition
Int local_size;
/// number of nonzeros in every row of the diagonal part
Array<Int> d_nnz;
/// number of nonzeros in every row of the off-diagonal part
Array<Int> o_nnz;
/// the global index of the first local row
Int first_global_index;
/// bool to indicate if the matrix data has been initialized by calling
/// MatCreate
bool is_petsc_matrix_initialized;
};
} // akantu
#endif /* __AKANTU_PETSC_MATRIX_HH__ */
diff --git a/src/solver/sparse_solver.cc b/src/solver/sparse_solver.cc
index 81e6a18f8..9fe6be43a 100644
--- a/src/solver/sparse_solver.cc
+++ b/src/solver/sparse_solver.cc
@@ -1,85 +1,84 @@
/**
- * @file solver.cc
+ * @file sparse_solver.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Fri Dec 08 2017
*
* @brief Solver interface class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_solver.hh"
#include "communicator.hh"
#include "dof_manager.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseSolver::SparseSolver(DOFManager & dof_manager, const ID & matrix_id,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), Parsable(ParserType::_solver, id),
_dof_manager(dof_manager), matrix_id(matrix_id),
communicator(dof_manager.getCommunicator()) {
AKANTU_DEBUG_IN();
// OK this is fishy...
this->communicator.registerEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseSolver::~SparseSolver() {
AKANTU_DEBUG_IN();
// this->destroyInternalData();
this->communicator.unregisterEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolver::beforeStaticSolverDestroy() {
AKANTU_DEBUG_IN();
try {
this->destroyInternalData();
} catch (...) {
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolver::createSynchronizerRegistry() {
// this->synch_registry = new SynchronizerRegistry(this);
}
void SparseSolver::onCommunicatorFinalize() { this->destroyInternalData(); }
} // akantu
diff --git a/src/solver/sparse_solver.hh b/src/solver/sparse_solver.hh
index 7c79df5a1..5b042f3c3 100644
--- a/src/solver/sparse_solver.hh
+++ b/src/solver/sparse_solver.hh
@@ -1,130 +1,130 @@
/**
* @file sparse_solver.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Wed Jan 24 2018
*
* @brief interface for solvers
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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_memory.hh"
#include "communicator_event_handler.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLVER_HH__
#define __AKANTU_SOLVER_HH__
namespace akantu {
enum SolverParallelMethod {
_not_parallel,
_fully_distributed,
_master_slave_distributed
};
class DOFManager;
}
namespace akantu {
class SparseSolver : protected Memory,
public Parsable,
public CommunicatorEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseSolver(DOFManager & dof_manager, const ID & matrix_id,
const ID & id = "solver", const MemoryID & memory_id = 0);
~SparseSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the solver
virtual void initialize() = 0;
virtual void analysis(){};
virtual void factorize(){};
virtual void solve(){};
protected:
virtual void destroyInternalData(){};
public:
virtual void beforeStaticSolverDestroy();
void createSynchronizerRegistry();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
void onCommunicatorFinalize() override;
// inline virtual UInt getNbDataForDOFs(const Array<UInt> & dofs,
// SynchronizationTag tag) const;
// inline virtual void packDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag) const;
// inline virtual void unpackDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// manager handling the dofs for this SparseMatrix solver
DOFManager & _dof_manager;
/// The id of the associated matrix
ID matrix_id;
/// How to parallelize the solve
SolverParallelMethod parallel_method;
/// Communicator used by the solver
Communicator & communicator;
};
namespace debug {
class SingularMatrixException : public Exception {
public:
SingularMatrixException(const SparseMatrix & matrix)
: Exception("Solver encountered singular matrix"), matrix(matrix) {}
const SparseMatrix & matrix;
};
}
} // akantu
#endif /* __AKANTU_SOLVER_HH__ */
diff --git a/src/solver/sparse_solver_inline_impl.cc b/src/solver/sparse_solver_inline_impl.cc
index 98e3a7bc9..a2890274e 100644
--- a/src/solver/sparse_solver_inline_impl.cc
+++ b/src/solver/sparse_solver_inline_impl.cc
@@ -1,83 +1,87 @@
/**
- * @file solver_inline_impl.cc
- * @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
- * @date Thu Nov 13 14:43:41 2014
+ * @file sparse_solver_inline_impl.cc
+ *
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Sun Aug 13 2017
*
* @brief implementation of solver inline functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// inline UInt Solver::getNbDataForDOFs(const Array<UInt> & dofs,
// SynchronizationTag tag) const {
// AKANTU_DEBUG_IN();
// UInt size = 0;
// switch(tag) {
// case _gst_solver_solution: {
// size += dofs.size() * sizeof(Real);
// break;
// }
// default: { }
// }
// AKANTU_DEBUG_OUT();
// return size;
// }
// /* --------------------------------------------------------------------------
// */
// inline void Solver::packDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag) const {
// AKANTU_DEBUG_IN();
// switch(tag) {
// case _gst_solver_solution: {
// packDOFDataHelper(*solution, buffer, dofs);
// break;
// }
// default: {
// }
// }
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */
// inline void Solver::unpackDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag) {
// AKANTU_DEBUG_IN();
// switch(tag) {
// case _gst_solver_solution: {
// unpackDOFDataHelper(*solution, buffer, dofs);
// break;
// }
// default: {
// }
// }
// AKANTU_DEBUG_OUT();
// }
diff --git a/src/solver/sparse_solver_mumps.cc b/src/solver/sparse_solver_mumps.cc
index 918d89f09..63ea0148d 100644
--- a/src/solver/sparse_solver_mumps.cc
+++ b/src/solver/sparse_solver_mumps.cc
@@ -1,446 +1,445 @@
/**
* @file sparse_solver_mumps.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief implem of SparseSolverMumps class
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "sparse_matrix_aij.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
// static std::ostream & operator <<(std::ostream & stream, const DMUMPS_STRUC_C
// & _this) {
// stream << "DMUMPS Data [" << std::endl;
// stream << " + job : " << _this.job << std::endl;
// stream << " + par : " << _this.par << std::endl;
// stream << " + sym : " << _this.sym << std::endl;
// stream << " + comm_fortran : " << _this.comm_fortran << std::endl;
// stream << " + nz : " << _this.nz << std::endl;
// stream << " + irn : " << _this.irn << std::endl;
// stream << " + jcn : " << _this.jcn << std::endl;
// stream << " + nz_loc : " << _this.nz_loc << std::endl;
// stream << " + irn_loc : " << _this.irn_loc << std::endl;
// stream << " + jcn_loc : " << _this.jcn_loc << std::endl;
// stream << "]";
// return stream;
// }
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseSolverMumps::SparseSolverMumps(DOFManagerDefault & dof_manager,
const ID & matrix_id, const ID & id,
const MemoryID & memory_id)
: SparseSolver(dof_manager, matrix_id, id, memory_id),
dof_manager(dof_manager), master_rhs_solution(0, 1) {
AKANTU_DEBUG_IN();
this->prank = communicator.whoAmI();
#ifdef AKANTU_USE_MPI
this->parallel_method = _fully_distributed;
#else // AKANTU_USE_MPI
this->parallel_method = _not_parallel;
#endif // AKANTU_USE_MPI
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseSolverMumps::~SparseSolverMumps() {
AKANTU_DEBUG_IN();
mumpsDataDestroy();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::mumpsDataDestroy() {
if (this->is_initialized) {
this->mumps_data.job = _smj_destroy; // destroy
dmumps_c(&this->mumps_data);
this->is_initialized = false;
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::destroyInternalData() { mumpsDataDestroy(); }
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::checkInitialized() {
if (this->is_initialized)
return;
this->initialize();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::setOutputLevel() {
// Output setup
icntl(1) = 0; // error output
icntl(2) = 0; // diagnostics output
icntl(3) = 0; // information
icntl(4) = 0;
#if !defined(AKANTU_NDEBUG)
DebugLevel dbg_lvl = debug::debugger.getDebugLevel();
if (AKANTU_DEBUG_TEST(dblDump)) {
strcpy(this->mumps_data.write_problem, "mumps_matrix.mtx");
}
// clang-format off
icntl(1) = (dbg_lvl >= dblWarning) ? 6 : 0;
icntl(3) = (dbg_lvl >= dblInfo) ? 6 : 0;
icntl(2) = (dbg_lvl >= dblTrace) ? 6 : 0;
icntl(4) =
dbg_lvl >= dblDump ? 4 :
dbg_lvl >= dblTrace ? 3 :
dbg_lvl >= dblInfo ? 2 :
dbg_lvl >= dblWarning ? 1 :
0;
// clang-format on
#endif
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::initMumpsData() {
auto & A = dof_manager.getMatrix(matrix_id);
// Default Scaling
icntl(8) = 77;
// Assembled matrix
icntl(5) = 0;
/// Default centralized dense second member
icntl(20) = 0;
icntl(21) = 0;
// automatic choice for analysis
icntl(28) = 0;
UInt size = A.size();
if (prank == 0) {
this->master_rhs_solution.resize(size);
}
this->mumps_data.nz_alloc = 0;
this->mumps_data.n = size;
switch (this->parallel_method) {
case _fully_distributed:
icntl(18) = 3; // fully distributed
this->mumps_data.nz_loc = A.getNbNonZero();
this->mumps_data.irn_loc = A.getIRN().storage();
this->mumps_data.jcn_loc = A.getJCN().storage();
break;
case _not_parallel:
case _master_slave_distributed:
icntl(18) = 0; // centralized
if (prank == 0) {
this->mumps_data.nz = A.getNbNonZero();
this->mumps_data.irn = A.getIRN().storage();
this->mumps_data.jcn = A.getJCN().storage();
} else {
this->mumps_data.nz = 0;
this->mumps_data.irn = nullptr;
this->mumps_data.jcn = nullptr;
}
break;
default:
AKANTU_ERROR("This case should not happen!!");
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::initialize() {
AKANTU_DEBUG_IN();
this->mumps_data.par = 1; // The host is part of computations
switch (this->parallel_method) {
case _not_parallel:
break;
case _master_slave_distributed:
this->mumps_data.par = 0; // The host is not part of the computations
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it */
case _fully_distributed:
#ifdef AKANTU_USE_MPI
const auto & mpi_data = dynamic_cast<const MPICommunicatorData &>(
communicator.getCommunicatorData());
MPI_Comm mpi_comm = mpi_data.getMPICommunicator();
this->mumps_data.comm_fortran = MPI_Comm_c2f(mpi_comm);
#else
AKANTU_ERROR(
"You cannot use parallel method to solve without activating MPI");
#endif
break;
}
const auto & A = dof_manager.getMatrix(matrix_id);
this->mumps_data.sym = 2 * (A.getMatrixType() == _symmetric);
this->prank = communicator.whoAmI();
this->setOutputLevel();
this->mumps_data.job = _smj_initialize; // initialize
dmumps_c(&this->mumps_data);
this->setOutputLevel();
this->is_initialized = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::analysis() {
AKANTU_DEBUG_IN();
initMumpsData();
this->mumps_data.job = _smj_analyze; // analyze
dmumps_c(&this->mumps_data);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::factorize() {
AKANTU_DEBUG_IN();
auto & A = dof_manager.getMatrix(matrix_id);
if (parallel_method == _fully_distributed)
this->mumps_data.a_loc = A.getA().storage();
else {
if (prank == 0)
this->mumps_data.a = A.getA().storage();
}
this->mumps_data.job = _smj_factorize; // factorize
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solve(Array<Real> & x, const Array<Real> & b) {
auto & synch = this->dof_manager.getSynchronizer();
if (this->prank == 0) {
this->master_rhs_solution.resize(this->dof_manager.getSystemSize());
synch.gather(b, this->master_rhs_solution);
} else {
synch.gather(b);
}
this->solveInternal();
if (this->prank == 0) {
synch.scatter(x, this->master_rhs_solution);
} else {
synch.scatter(x);
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solve() {
this->master_rhs_solution.copy(this->dof_manager.getGlobalResidual());
this->solveInternal();
this->dof_manager.setGlobalSolution(this->master_rhs_solution);
this->dof_manager.splitSolutionPerDOFs();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solveInternal() {
AKANTU_DEBUG_IN();
this->checkInitialized();
const auto & A = dof_manager.getMatrix(matrix_id);
this->setOutputLevel();
if (this->last_profile_release != A.getProfileRelease()) {
this->analysis();
this->last_profile_release = A.getProfileRelease();
}
if (AKANTU_DEBUG_TEST(dblDump)) {
std::stringstream sstr;
sstr << prank << ".mtx";
A.saveMatrix("solver_mumps" + sstr.str());
}
if (this->last_value_release != A.getValueRelease()) {
this->factorize();
this->last_value_release = A.getValueRelease();
}
if (prank == 0) {
this->mumps_data.rhs = this->master_rhs_solution.storage();
}
this->mumps_data.job = _smj_solve; // solve
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::printError() {
Vector<Int> _info_v(2);
_info_v[0] = info(1); // to get errors
_info_v[1] = -info(1); // to get warnings
dof_manager.getCommunicator().allReduce(_info_v, SynchronizerOperation::_min);
_info_v[1] = -_info_v[1];
if (_info_v[0] < 0) { // < 0 is an error
switch (_info_v[0]) {
case -10:
AKANTU_CUSTOM_EXCEPTION(
debug::SingularMatrixException(dof_manager.getMatrix(matrix_id)));
break;
case -9: {
icntl(14) += 10;
if (icntl(14) != 90) {
// std::cout << "Dynamic memory increase of 10%" << std::endl;
AKANTU_DEBUG_WARNING("MUMPS dynamic memory is insufficient it will be "
"increased allowed to use 10% more");
// change releases to force a recompute
this->last_value_release--;
this->last_profile_release--;
this->solve();
} else {
AKANTU_ERROR("The MUMPS workarray is too small INFO(2)="
<< info(2) << "No further increase possible");
}
break;
}
default:
AKANTU_ERROR("Error in mumps during solve process, check mumps "
"user guide INFO(1) = "
<< _info_v[1]);
}
} else if (_info_v[1] > 0) {
AKANTU_DEBUG_WARNING("Warning in mumps during solve process, check mumps "
"user guide INFO(1) = "
<< _info_v[1]);
}
}
} // akantu
diff --git a/src/solver/sparse_solver_mumps.hh b/src/solver/sparse_solver_mumps.hh
index 23ec34a6b..af401c7e1 100644
--- a/src/solver/sparse_solver_mumps.hh
+++ b/src/solver/sparse_solver_mumps.hh
@@ -1,158 +1,157 @@
/**
* @file sparse_solver_mumps.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Sun Dec 03 2017
*
* @brief Solver class implementation for the mumps solver
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_solver.hh"
/* -------------------------------------------------------------------------- */
#include <dmumps_c.h>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLVER_MUMPS_HH__
#define __AKANTU_SOLVER_MUMPS_HH__
namespace akantu {
class DOFManagerDefault;
class SparseMatrixAIJ;
}
namespace akantu {
class SparseSolverMumps : public SparseSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseSolverMumps(DOFManagerDefault & dof_manager, const ID & matrix_id,
const ID & id = "sparse_solver_mumps",
const MemoryID & memory_id = 0);
~SparseSolverMumps() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build the profile and do the analysis part
void initialize() override;
/// analysis (symbolic facto + permutations)
void analysis() override;
/// factorize the matrix
void factorize() override;
/// solve the system
virtual void solve(Array<Real> & x, const Array<Real> & b);
/// solve using residual and solution from the dof_manager
void solve() override;
private:
/// print the error if any happened in mumps
void printError();
/// solve the system with master_rhs_solution as b and x
void solveInternal();
/// set internal values;
void initMumpsData();
/// set the level of verbosity of mumps based on the debug level of akantu
void setOutputLevel();
protected:
/// de-initialize the internal data
void destroyInternalData() override;
/// check if initialized and except if it is not the case
void checkInitialized();
private:
void mumpsDataDestroy();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
private:
/// access the control variable
inline Int & icntl(UInt i) { return mumps_data.icntl[i - 1]; }
/// access the results info
inline Int & info(UInt i) { return mumps_data.info[i - 1]; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// DOFManager used by the Mumps implementation of the SparseSolver
DOFManagerDefault & dof_manager;
/// Full right hand side on the master processors and solution after solve
Array<Real> master_rhs_solution;
/// mumps data
DMUMPS_STRUC_C mumps_data;
/// Rank of the current process
UInt prank;
/// matrix release at last solve
UInt last_profile_release{UInt(-1)};
/// matrix release at last solve
UInt last_value_release{UInt(-1)};
/// check if the solver data are initialized
bool is_initialized{false};
/* ------------------------------------------------------------------------ */
/* Local types */
/* ------------------------------------------------------------------------ */
private:
SolverParallelMethod parallel_method;
// bool rhs_is_local;
enum SolverMumpsJob {
_smj_initialize = -1,
_smj_analyze = 1,
_smj_factorize = 2,
_smj_solve = 3,
_smj_analyze_factorize = 4,
_smj_factorize_solve = 5,
_smj_complete = 6, // analyze, factorize, solve
_smj_destroy = -2
};
};
} // akantu
#endif /* __AKANTU_SOLVER_MUMPS_HH__ */
diff --git a/src/solver/terms_to_assemble.hh b/src/solver/terms_to_assemble.hh
index 375d30fe4..4b4d834ff 100644
--- a/src/solver/terms_to_assemble.hh
+++ b/src/solver/terms_to_assemble.hh
@@ -1,99 +1,100 @@
/**
* @file terms_to_assemble.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Dec 20 2016
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Nov 08 2017
*
- * @brief List of terms to assemble to a matrix
+ * @brief List of terms to assemble to a matrix
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TERMS_TO_ASSEMBLE_HH__
#define __AKANTU_TERMS_TO_ASSEMBLE_HH__
namespace akantu {
class TermsToAssemble {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TermsToAssemble() = default;
virtual ~TermsToAssemble() = default;
class TermToAssemble {
public:
TermToAssemble(UInt i, UInt j) : _i(i), _j(j), val(0.) {}
inline TermToAssemble & operator=(Real val) {
this->val = val;
return *this;
}
inline TermToAssemble operator+=(Real val) {
this->val += val;
return *this;
}
inline operator Real() const { return val; }
inline UInt i() const { return _i; }
inline UInt j() const { return _j; }
private:
UInt _i, _j;
Real val;
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline TermToAssemble & operator()(UInt i, UInt j) {
terms.emplace_back(i, j);
return terms.back();
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
private:
using TermsContainer = std::vector<TermToAssemble>;
public:
using const_terms_iterator = TermsContainer::const_iterator;
const_terms_iterator begin() const { return terms.begin(); }
const_terms_iterator end() const { return terms.end(); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
TermsContainer terms;
};
} // akantu
#endif /* __AKANTU_TERMS_TO_ASSEMBLE_HH__ */
diff --git a/src/synchronizer/communication_buffer.hh b/src/synchronizer/communication_buffer.hh
index 5cd056d1e..5e0b0da8d 100644
--- a/src/synchronizer/communication_buffer.hh
+++ b/src/synchronizer/communication_buffer.hh
@@ -1,183 +1,182 @@
/**
* @file communication_buffer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief Buffer for packing and unpacking data
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "element.hh"
#ifndef __AKANTU_COMMUNICATION_BUFFER_HH__
#define __AKANTU_COMMUNICATION_BUFFER_HH__
namespace akantu {
template <bool is_static = true> class CommunicationBufferTemplated {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit CommunicationBufferTemplated(UInt size) : buffer(size, 1) {
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
};
CommunicationBufferTemplated() : CommunicationBufferTemplated(0) {}
CommunicationBufferTemplated(const CommunicationBufferTemplated & other) {
buffer = other.buffer;
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
}
CommunicationBufferTemplated &
operator=(const CommunicationBufferTemplated & other) {
if (this != &other) {
buffer = other.buffer;
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
}
return *this;
}
virtual ~CommunicationBufferTemplated() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// reset to "empty"
inline void reset();
/// resize the internal buffer
inline void resize(UInt size);
/// clear buffer context
inline void clear();
private:
inline void packResize(UInt size);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline char * storage() { return buffer.storage(); };
inline const char * storage() const { return buffer.storage(); };
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
/// printing tool
template <typename T> inline std::string extractStream(UInt packet_size);
/// packing data
template <typename T>
inline CommunicationBufferTemplated & operator<<(const T & to_pack);
template <typename T>
inline CommunicationBufferTemplated & operator<<(const Vector<T> & to_pack);
template <typename T>
inline CommunicationBufferTemplated & operator<<(const Matrix<T> & to_pack);
template <typename T>
inline CommunicationBufferTemplated &
operator<<(const std::vector<T> & to_pack);
/// unpacking data
template <typename T>
inline CommunicationBufferTemplated & operator>>(T & to_unpack);
template <typename T>
inline CommunicationBufferTemplated & operator>>(Vector<T> & to_unpack);
template <typename T>
inline CommunicationBufferTemplated & operator>>(Matrix<T> & to_unpack);
template <typename T>
inline CommunicationBufferTemplated & operator>>(std::vector<T> & to_unpack);
inline CommunicationBufferTemplated & operator<<(const std::string & to_pack);
inline CommunicationBufferTemplated & operator>>(std::string & to_unpack);
private:
template <typename T> inline void packIterable(T & to_pack);
template <typename T> inline void unpackIterable(T & to_pack);
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
template <typename T> static inline UInt sizeInBuffer(const T & data);
template <typename T> static inline UInt sizeInBuffer(const Vector<T> & data);
template <typename T> static inline UInt sizeInBuffer(const Matrix<T> & data);
template <typename T>
static inline UInt sizeInBuffer(const std::vector<T> & data);
static inline UInt sizeInBuffer(const std::string & data);
/// return the size in bytes of the stored values
inline UInt getPackedSize() const { return ptr_pack - buffer.storage(); };
/// return the size in bytes of data left to be unpacked
inline UInt getLeftToUnpack() const {
return buffer.size() - (ptr_unpack - buffer.storage());
};
/// return the global size allocated
inline UInt size() const { return buffer.size(); };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// current position for packing
char * ptr_pack;
/// current position for unpacking
char * ptr_unpack;
/// storing buffer
Array<char> buffer;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "communication_buffer_inline_impl.cc"
#endif
using CommunicationBuffer = CommunicationBufferTemplated<true>;
using DynamicCommunicationBuffer = CommunicationBufferTemplated<false>;
} // namespace akantu
#endif /* __AKANTU_COMMUNICATION_BUFFER_HH__ */
diff --git a/src/synchronizer/communication_buffer_inline_impl.cc b/src/synchronizer/communication_buffer_inline_impl.cc
index 9e75736e8..d242a4b42 100644
--- a/src/synchronizer/communication_buffer_inline_impl.cc
+++ b/src/synchronizer/communication_buffer_inline_impl.cc
@@ -1,319 +1,318 @@
/**
* @file communication_buffer_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 14 2011
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief CommunicationBuffer inline implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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 <bool is_static>
template <typename T>
inline UInt CommunicationBufferTemplated<is_static>::sizeInBuffer(const T &) {
return sizeof(T);
}
template <bool is_static>
template <typename T>
inline UInt
CommunicationBufferTemplated<is_static>::sizeInBuffer(const Vector<T> & data) {
UInt size = data.size() * sizeof(T);
return size;
}
template <bool is_static>
template <typename T>
inline UInt
CommunicationBufferTemplated<is_static>::sizeInBuffer(const Matrix<T> & data) {
UInt size = data.size() * sizeof(T);
return size;
}
template <bool is_static>
template <typename T>
inline UInt CommunicationBufferTemplated<is_static>::sizeInBuffer(
const std::vector<T> & data) {
UInt size = data.size() * sizeof(T) + sizeof(size_t);
return size;
}
template <bool is_static>
inline UInt CommunicationBufferTemplated<is_static>::sizeInBuffer(
const std::string & data) {
UInt size = data.size() * sizeof(std::string::value_type) + sizeof(size_t);
return size;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::packResize(UInt size) {
if (!is_static) {
char * values = buffer.storage();
buffer.resize(buffer.size() + size);
ptr_pack = buffer.storage() + (ptr_pack - values);
ptr_unpack = buffer.storage() + (ptr_unpack - values);
}
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(const T & to_pack) {
UInt size = sizeInBuffer(to_pack);
packResize(size);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_pack + size),
"Packing too much data in the CommunicationBufferTemplated");
memcpy(ptr_pack, reinterpret_cast<const char *>(&to_pack), size);
ptr_pack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(T & to_unpack) {
UInt size = sizeInBuffer(to_unpack);
alignas(alignof(T)) std::array<char, sizeof(T)> aligned_ptr;
memcpy(aligned_ptr.data(), ptr_unpack, size);
auto * tmp = reinterpret_cast<T *>(aligned_ptr.data());
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_unpack + size),
"Unpacking too much data in the CommunicationBufferTemplated");
to_unpack = *tmp;
// memcpy(reinterpret_cast<char *>(&to_unpack), ptr_unpack, size);
ptr_unpack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
/* Specialization */
/* -------------------------------------------------------------------------- */
/**
* Vector
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(const Vector<T> & to_pack) {
UInt size = sizeInBuffer(to_pack);
packResize(size);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_pack + size),
"Packing too much data in the CommunicationBufferTemplated");
memcpy(ptr_pack, to_pack.storage(), size);
ptr_pack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(Vector<T> & to_unpack) {
UInt size = sizeInBuffer(to_unpack);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_unpack + size),
"Unpacking too much data in the CommunicationBufferTemplated");
memcpy(to_unpack.storage(), ptr_unpack, size);
ptr_unpack += size;
return *this;
}
/**
* Matrix
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(const Matrix<T> & to_pack) {
UInt size = sizeInBuffer(to_pack);
packResize(size);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_pack + size),
"Packing too much data in the CommunicationBufferTemplated");
memcpy(ptr_pack, to_pack.storage(), size);
ptr_pack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(Matrix<T> & to_unpack) {
UInt size = sizeInBuffer(to_unpack);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_unpack + size),
"Unpacking too much data in the CommunicationBufferTemplated");
memcpy(to_unpack.storage(), ptr_unpack, size);
ptr_unpack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline void CommunicationBufferTemplated<is_static>::packIterable(T & to_pack) {
operator<<(size_t(to_pack.size()));
auto it = to_pack.begin();
auto end = to_pack.end();
for (; it != end; ++it)
operator<<(*it);
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline void
CommunicationBufferTemplated<is_static>::unpackIterable(T & to_unpack) {
size_t size;
operator>>(size);
to_unpack.resize(size);
auto it = to_unpack.begin();
auto end = to_unpack.end();
for (; it != end; ++it)
operator>>(*it);
}
/**
* std::vector<T>
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::
operator<<(const std::vector<T> & to_pack) {
packIterable(to_pack);
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::
operator>>(std::vector<T> & to_unpack) {
unpackIterable(to_unpack);
return *this;
}
/**
* std::string
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::
operator<<(const std::string & to_pack) {
packIterable(to_pack);
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(std::string & to_unpack) {
unpackIterable(to_unpack);
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline std::string
CommunicationBufferTemplated<is_static>::extractStream(UInt block_size) {
std::stringstream str;
auto * ptr = reinterpret_cast<T *>(buffer.storage());
UInt sz = buffer.size() / sizeof(T);
UInt sz_block = block_size / sizeof(T);
UInt n_block = 0;
for (UInt i = 0; i < sz; ++i) {
if (i % sz_block == 0) {
str << std::endl << n_block << " ";
++n_block;
}
str << *ptr << " ";
++ptr;
}
return str.str();
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::resize(UInt size) {
if (!is_static) {
buffer.resize(0);
} else {
buffer.resize(size);
}
reset();
#ifndef AKANTU_NDEBUG
clear();
#endif
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::clear() {
buffer.clear();
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::reset() {
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
}
/* -------------------------------------------------------------------------- */
// template<bool is_static>
// inline CommunicationBufferTemplated<is_static> &
// CommunicationBufferTemplated<is_static>::packMeshData (const MeshData &
// to_pack, const ElementType & type) {
// UInt size = to_pack.size();
// operator<<(size);
// typename std::vector<T>::iterator it = to_pack.begin();
// typename std::vector<T>::iterator end = to_pack.end();
// for(;it != end; ++it) operator<<(*it);
// return *this;
//}
diff --git a/src/synchronizer/communication_descriptor.hh b/src/synchronizer/communication_descriptor.hh
index 373abd5b1..246422f47 100644
--- a/src/synchronizer/communication_descriptor.hh
+++ b/src/synchronizer/communication_descriptor.hh
@@ -1,153 +1,154 @@
/**
- * @file synchronizer_tmpl.hh
+ * @file communication_descriptor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 3 13:49:36 2016
+ * @date creation: Wed Sep 07 2016
+ * @date last modification: Thu Jan 25 2018
*
* @brief Implementation of the helper classes for the synchronizer
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "communication_request.hh"
#include "communication_tag.hh"
#include "data_accessor.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COMMUNICATION_DESCRIPTOR_HH__
#define __AKANTU_COMMUNICATION_DESCRIPTOR_HH__
namespace akantu {
/* ------------------------------------------------------------------------ */
enum CommunicationSendRecv { _send, _recv, _csr_not_defined };
/* -------------------------------------------------------------------------- */
struct CommunicationSRType {
using type = CommunicationSendRecv;
static const type _begin_ = _send;
static const type _end_ = _csr_not_defined;
};
using send_recv_t = safe_enum<CommunicationSRType>;
namespace {
send_recv_t iterate_send_recv{};
}
/* ------------------------------------------------------------------------ */
class Communication {
public:
explicit Communication(const CommunicationSendRecv & type = _csr_not_defined)
: _type(type) {}
Communication(const Communication &) = delete;
Communication & operator=(const Communication &) = delete;
void resize(UInt size) {
this->_size = size;
this->_buffer.resize(size);
}
inline const CommunicationSendRecv & type() const { return this->_type; }
inline const UInt & size() const { return this->_size; }
inline const CommunicationRequest & request() const { return this->_request; }
inline CommunicationRequest & request() { return this->_request; }
inline const CommunicationBuffer & buffer() const { return this->_buffer; }
inline CommunicationBuffer & buffer() { return this->_buffer; }
private:
UInt _size{0};
CommunicationBuffer _buffer;
CommunicationRequest _request;
CommunicationSendRecv _type;
};
template <class Entity> class Communications;
/* ------------------------------------------------------------------------ */
template <class Entity> class CommunicationDescriptor {
public:
CommunicationDescriptor(Communication & communication, Array<Entity> & scheme,
Communications<Entity> & communications,
const SynchronizationTag & tag, UInt proc);
CommunicationDescriptor(const CommunicationDescriptor &) = default;
CommunicationDescriptor &
operator=(const CommunicationDescriptor &) = default;
/// get the quantity of data in the buffer
UInt getNbData() { return communication.size(); }
/// set the quantity of data in the buffer
void setNbData(UInt size) { communication.resize(size); }
/// get the corresponding tag
const SynchronizationTag & getTag() const { return tag; }
/// get the data buffer
CommunicationBuffer & getBuffer();
/// get the corresponding request
CommunicationRequest & getRequest();
/// get the communication scheme
const Array<Entity> & getScheme();
/// reset the buffer before pack or after unpack
void resetBuffer();
/// pack data for entities in the buffer
void packData(const DataAccessor<Entity> & accessor);
/// unpack data for entities from the buffer
void unpackData(DataAccessor<Entity> & accessor);
/// posts asynchronous send requests
void postSend(int hash_id);
/// posts asynchronous receive requests
void postRecv(int hash_id);
/// free the request
void freeRequest();
UInt getProc() { return proc; }
protected:
Communication & communication;
const Array<Entity> & scheme;
Communications<Entity> & communications;
const SynchronizationTag & tag;
UInt proc;
UInt rank;
UInt counter;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "communication_descriptor_tmpl.hh"
#endif /* __AKANTU_COMMUNICATION_DESCRIPTOR_HH__ */
diff --git a/src/synchronizer/communication_descriptor_tmpl.hh b/src/synchronizer/communication_descriptor_tmpl.hh
index 8b61411ec..92044ef1a 100644
--- a/src/synchronizer/communication_descriptor_tmpl.hh
+++ b/src/synchronizer/communication_descriptor_tmpl.hh
@@ -1,151 +1,152 @@
/**
* @file communication_descriptor_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Sep 6 14:03:16 2016
+ * @date creation: Wed Sep 07 2016
+ * @date last modification: Thu Jan 25 2018
*
* @brief implementation of CommunicationDescriptor
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_descriptor.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH__
#define __AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Implementations */
/* -------------------------------------------------------------------------- */
template <class Entity>
CommunicationDescriptor<Entity>::CommunicationDescriptor(
Communication & communication, Array<Entity> & scheme,
Communications<Entity> & communications, const SynchronizationTag & tag,
UInt proc)
: communication(communication), scheme(scheme),
communications(communications), tag(tag), proc(proc),
rank(communications.getCommunicator().whoAmI()) {
counter = communications.getCounter(tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
CommunicationBuffer & CommunicationDescriptor<Entity>::getBuffer() {
return communication.buffer();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
CommunicationRequest & CommunicationDescriptor<Entity>::getRequest() {
return communication.request();
}
/* -------------------------------------------------------------------------- */
template <class Entity> void CommunicationDescriptor<Entity>::freeRequest() {
const auto & comm = communications.getCommunicator();
// comm.test(communication.request());
comm.freeCommunicationRequest(communication.request());
communications.decrementPending(tag, communication.type());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
const Array<Entity> & CommunicationDescriptor<Entity>::getScheme() {
return scheme;
}
template <class Entity> void CommunicationDescriptor<Entity>::resetBuffer() {
this->communication.buffer().reset();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::packData(
const DataAccessor<Entity> & accessor) {
AKANTU_DEBUG_ASSERT(
communication.type() == _send,
"Cannot pack data on communication that is not of type _send");
accessor.packData(communication.buffer(), scheme, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::unpackData(
DataAccessor<Entity> & accessor) {
AKANTU_DEBUG_ASSERT(
communication.type() == _recv,
"Cannot unpack data from communication that is not of type _recv");
accessor.unpackData(communication.buffer(), scheme, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::postSend(int hash_id) {
AKANTU_DEBUG_ASSERT(communication.type() == _send,
"Cannot send a communication that is not of type _send");
Tag comm_tag = Tag::genTag(rank, counter, tag, hash_id);
AKANTU_DEBUG_ASSERT(communication.buffer().getPackedSize() ==
communication.size(),
"a problem have been introduced with "
<< "false sent sizes declaration "
<< communication.buffer().getPackedSize()
<< " != " << communication.size());
AKANTU_DEBUG_INFO("Posting send to proc " << proc << " (tag: " << tag << " - "
<< communication.size()
<< " data to send) "
<< " [ " << comm_tag << " ]");
CommunicationRequest & request = communication.request();
request = communications.getCommunicator().asyncSend(communication.buffer(),
proc, comm_tag);
communications.incrementPending(tag, communication.type());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::postRecv(int hash_id) {
AKANTU_DEBUG_ASSERT(communication.type() == _recv,
"Cannot receive data for communication ("
<< communication.type()
<< ")that is not of type _recv");
Tag comm_tag = Tag::genTag(proc, counter, tag, hash_id);
AKANTU_DEBUG_INFO("Posting receive from proc "
<< proc << " (tag: " << tag << " - " << communication.size()
<< " data to receive) "
<< " [ " << comm_tag << " ]");
CommunicationRequest & request = communication.request();
request = communications.getCommunicator().asyncReceive(
communication.buffer(), proc, comm_tag);
communications.incrementPending(tag, communication.type());
}
} // akantu
#endif /* __AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH__ */
diff --git a/src/synchronizer/communication_request.hh b/src/synchronizer/communication_request.hh
index f93ba330c..73b83e0ec 100644
--- a/src/synchronizer/communication_request.hh
+++ b/src/synchronizer/communication_request.hh
@@ -1,113 +1,112 @@
/**
- * @file real_static_communicator.hh
+ * @file communication_request.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Wed Jan 13 2016
+ * @date last modification: Wed Nov 08 2017
*
* @brief empty class just for inheritance
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_REAL_STATIC_COMMUNICATOR_HH__
#define __AKANTU_REAL_STATIC_COMMUNICATOR_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
class InternalCommunicationRequest {
public:
InternalCommunicationRequest(UInt source, UInt dest);
virtual ~InternalCommunicationRequest();
virtual void printself(std::ostream & stream, int indent = 0) const;
AKANTU_GET_MACRO(Source, source, UInt);
AKANTU_GET_MACRO(Destination, destination, UInt);
private:
UInt source;
UInt destination;
UInt id;
static UInt counter;
};
/* -------------------------------------------------------------------------- */
class CommunicationRequest {
public:
CommunicationRequest(
std::shared_ptr<InternalCommunicationRequest> request = nullptr)
: request(std::move(request)) {}
virtual ~CommunicationRequest() = default;
virtual void free() { request.reset(); }
void printself(std::ostream & stream, int indent = 0) const {
request->printself(stream, indent);
};
UInt getSource() const { return request->getSource(); }
UInt getDestination() const { return request->getDestination(); }
bool isFreed() const { return request.get() == nullptr; }
InternalCommunicationRequest & getInternal() { return *request; }
private:
std::shared_ptr<InternalCommunicationRequest> request;
};
/* -------------------------------------------------------------------------- */
class CommunicationStatus {
public:
AKANTU_GET_MACRO(Source, source, Int);
UInt size() const { return size_; }
AKANTU_GET_MACRO(Tag, tag, Int);
AKANTU_SET_MACRO(Source, source, Int);
AKANTU_SET_MACRO(Size, size_, UInt);
AKANTU_SET_MACRO(Tag, tag, Int);
private:
Int source{0};
UInt size_{0};
Int tag{0};
};
/* -------------------------------------------------------------------------- */
/// Datatype to pack pairs for MPI_{MIN,MAX}LOC
template <typename T1, typename T2> struct SCMinMaxLoc {
T1 min_max;
T2 loc;
};
} // akantu
#endif /* __AKANTU_REAL_STATIC_COMMUNICATOR_HH__ */
diff --git a/src/synchronizer/communication_tag.hh b/src/synchronizer/communication_tag.hh
index e6fb54a82..f9c125ea1 100644
--- a/src/synchronizer/communication_tag.hh
+++ b/src/synchronizer/communication_tag.hh
@@ -1,116 +1,118 @@
/**
* @file communication_tag.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 24 12:40:55 2016
+ * @date creation: Wed Sep 07 2016
+ * @date last modification: Wed Nov 08 2017
*
* @brief Description of the communication tags
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* 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_COMMUNICATION_TAG_HH__
#define __AKANTU_COMMUNICATION_TAG_HH__
namespace akantu {
/**
* tag = |__________20_________|___8____|_4_|
* | proc | num mes| ct|
*/
class Tag {
public:
Tag() = default;
Tag(int val) : tag(val) {}
Tag(int val, int hash) : tag(val), hash(hash) {}
operator int() const {
return int(max_tag == 0 ? tag : (uint32_t(tag) % max_tag));
}
/// generates a tag
template <typename CommTag>
static inline Tag genTag(int proc, UInt msg_count, CommTag tag) {
int _tag = ((((proc & 0xFFFFF) << 12) + ((msg_count & 0xFF) << 4) +
((int)tag & 0xF)));
Tag t(_tag);
return t;
}
/// generates a tag and hashes it
template <typename CommTag>
static inline Tag genTag(int proc, UInt msg_count, CommTag tag, int hash) {
Tag t = genTag(proc, msg_count, tag);
t.tag = t.tag ^ hash;
t.hash = hash;
return t;
}
virtual void printself(std::ostream & stream, int) const {
int t = tag;
stream << "TAG(";
if (hash != 0)
t = t ^ hash;
stream << (t >> 12) << ":" << (t >> 4 & 0xFF) << ":" << (t & 0xF) << " -> "
<< std::hex << "0x" << int(*this);
if (hash != 0)
stream << " {hash: 0x" << hash << "}";
stream << " [0x" << this->max_tag << "]";
stream << ")";
}
enum CommTags : int {
_SIZES = 1,
_CONNECTIVITY = 2,
_DATA = 3,
_PARTITIONS = 4,
_NB_NODES = 5,
_NODES = 6,
_COORDINATES = 7,
_NODES_TYPE = 8,
_MESH_DATA = 9,
_ELEMENT_GROUP = 10,
_NODE_GROUP = 11,
_MODIFY_SCHEME = 12,
_GATHER_INITIALIZATION = 1,
_GATHER = 2,
_SCATTER = 3,
_SYNCHRONIZE = 15,
};
private:
static void setMaxTag(int _max_tag) { max_tag = _max_tag; }
friend void initialize(const std::string &, int &, char **&);
private:
int tag{0};
int hash{0};
static int max_tag;
};
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream, const Tag & _this) {
_this.printself(stream, 0);
return stream;
}
/* -------------------------------------------------------------------------- */
}
#endif /* __AKANTU_COMMUNICATION_TAG_HH__ */
diff --git a/src/synchronizer/communications.hh b/src/synchronizer/communications.hh
index 8190e94ed..f3968b4e3 100644
--- a/src/synchronizer/communications.hh
+++ b/src/synchronizer/communications.hh
@@ -1,272 +1,274 @@
/**
* @file communications.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 24 13:56:14 2016
+ * @date creation: Wed Sep 07 2016
+ * @date last modification: Tue Feb 20 2018
*
- * @brief
+ * @brief Class handling the pending communications and the communications
+ * schemes
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_descriptor.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COMMUNICATIONS_HH__
#define __AKANTU_COMMUNICATIONS_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications {
public:
using Scheme = Array<Entity>;
protected:
using CommunicationPerProcs = std::map<UInt, Communication>;
using CommunicationsPerTags =
std::map<SynchronizationTag, CommunicationPerProcs>;
using CommunicationSchemes = std::map<UInt, Scheme>;
using Request = std::map<UInt, std::vector<CommunicationRequest>>;
friend class CommunicationDescriptor<Entity>;
public:
using scheme_iterator = typename CommunicationSchemes::iterator;
using const_scheme_iterator = typename CommunicationSchemes::const_iterator;
/* ------------------------------------------------------------------------ */
class iterator;
class tag_iterator;
/* ------------------------------------------------------------------------ */
public:
CommunicationPerProcs & getCommunications(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
bool hasPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) const;
UInt getPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) const;
/* ------------------------------------------------------------------------ */
iterator begin(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
iterator end(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
iterator waitAny(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
void waitAll(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
void incrementPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
void decrementPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
void freeRequests(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
Scheme & createScheme(UInt proc, const CommunicationSendRecv & sr);
void resetSchemes(const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
void setCommunicationSize(const SynchronizationTag & tag, UInt proc,
UInt size, const CommunicationSendRecv & sr);
public:
explicit Communications(const Communicator & communicator);
explicit Communications(const Communications & communications);
/* ------------------------------------------------------------------------ */
class IterableCommunicationDesc {
public:
IterableCommunicationDesc(Communications & communications,
SynchronizationTag tag, CommunicationSendRecv sr)
: communications(communications), tag(std::move(tag)),
sr(std::move(sr)) {}
auto begin() { return communications.begin(tag, sr); }
auto end() { return communications.end(tag, sr); }
private:
Communications & communications;
SynchronizationTag tag;
CommunicationSendRecv sr;
};
auto iterateRecv(const SynchronizationTag & tag) {
return IterableCommunicationDesc(*this, tag, _recv);
}
auto iterateSend(const SynchronizationTag & tag) {
return IterableCommunicationDesc(*this, tag, _send);
}
/* ------------------------------------------------------------------------ */
// iterator begin_send(const SynchronizationTag & tag);
// iterator end_send(const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
// iterator begin_recv(const SynchronizationTag & tag);
// iterator end_recv(const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
class IterableTags {
public:
explicit IterableTags(Communications & communications)
: communications(communications) {}
decltype(auto) begin() { return communications.begin_tag(); }
decltype(auto) end() { return communications.end_tag(); }
private:
Communications & communications;
};
decltype(auto) iterateTags() { return IterableTags(*this); }
tag_iterator begin_tag();
tag_iterator end_tag();
/* ------------------------------------------------------------------------ */
bool hasCommunication(const SynchronizationTag & tag) const;
void incrementCounter(const SynchronizationTag & tag);
UInt getCounter(const SynchronizationTag & tag) const;
bool hasCommunicationSize(const SynchronizationTag & tag) const;
void invalidateSizes();
/* ------------------------------------------------------------------------ */
bool hasPendingRecv(const SynchronizationTag & tag) const;
bool hasPendingSend(const SynchronizationTag & tag) const;
const auto & getCommunicator() const;
/* ------------------------------------------------------------------------ */
iterator waitAnyRecv(const SynchronizationTag & tag);
iterator waitAnySend(const SynchronizationTag & tag);
void waitAllRecv(const SynchronizationTag & tag);
void waitAllSend(const SynchronizationTag & tag);
void freeSendRequests(const SynchronizationTag & tag);
void freeRecvRequests(const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
class IterableSchemes {
public:
IterableSchemes(Communications & communications, CommunicationSendRecv sr)
: communications(communications), sr(std::move(sr)) {}
decltype(auto) begin() { return communications.begin_scheme(sr); }
decltype(auto) end() { return communications.end_scheme(sr); }
private:
Communications & communications;
CommunicationSendRecv sr;
};
class ConstIterableSchemes {
public:
ConstIterableSchemes(const Communications & communications,
CommunicationSendRecv sr)
: communications(communications), sr(std::move(sr)) {}
decltype(auto) begin() const { return communications.begin_scheme(sr); }
decltype(auto) end() const { return communications.end_scheme(sr); }
private:
const Communications & communications;
CommunicationSendRecv sr;
};
decltype(auto) iterateSchemes(const CommunicationSendRecv & sr) {
return IterableSchemes(*this, sr);
}
decltype(auto) iterateSchemes(const CommunicationSendRecv & sr) const {
return ConstIterableSchemes(*this, sr);
}
decltype(auto) iterateSendSchemes() { return IterableSchemes(*this, _send); }
decltype(auto) iterateSendSchemes() const {
return ConstIterableSchemes(*this, _send);
}
decltype(auto) iterateRecvSchemes() { return IterableSchemes(*this, _recv); }
decltype(auto) iterateRecvSchemes() const {
return ConstIterableSchemes(*this, _recv);
}
scheme_iterator begin_scheme(const CommunicationSendRecv & sr);
scheme_iterator end_scheme(const CommunicationSendRecv & sr);
const_scheme_iterator begin_scheme(const CommunicationSendRecv & sr) const;
const_scheme_iterator end_scheme(const CommunicationSendRecv & sr) const;
/* ------------------------------------------------------------------------ */
scheme_iterator begin_send_scheme();
scheme_iterator end_send_scheme();
const_scheme_iterator begin_send_scheme() const;
const_scheme_iterator end_send_scheme() const;
/* ------------------------------------------------------------------------ */
scheme_iterator begin_recv_scheme();
scheme_iterator end_recv_scheme();
const_scheme_iterator begin_recv_scheme() const;
const_scheme_iterator end_recv_scheme() const;
/* ------------------------------------------------------------------------ */
Scheme & createSendScheme(UInt proc);
Scheme & createRecvScheme(UInt proc);
/* ------------------------------------------------------------------------ */
Scheme & getScheme(UInt proc, const CommunicationSendRecv & sr);
const Scheme & getScheme(UInt proc, const CommunicationSendRecv & sr) const;
/* ------------------------------------------------------------------------ */
void resetSchemes();
/* ------------------------------------------------------------------------ */
void setSendCommunicationSize(const SynchronizationTag & tag, UInt proc,
UInt size);
void setRecvCommunicationSize(const SynchronizationTag & tag, UInt proc,
UInt size);
void initializeCommunications(const SynchronizationTag & tag);
protected:
CommunicationSchemes schemes[2];
CommunicationsPerTags communications[2];
std::map<SynchronizationTag, UInt> comm_counter;
std::map<SynchronizationTag, UInt> pending_communications[2];
std::map<SynchronizationTag, bool> comm_size_computed;
const Communicator & communicator;
};
} // namespace akantu
#include "communications_tmpl.hh"
#endif /* __AKANTU_COMMUNICATIONS_HH__ */
diff --git a/src/synchronizer/communications_tmpl.hh b/src/synchronizer/communications_tmpl.hh
index 9b4f2aef9..71cb69298 100644
--- a/src/synchronizer/communications_tmpl.hh
+++ b/src/synchronizer/communications_tmpl.hh
@@ -1,550 +1,551 @@
/**
* @file communications_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Tue Sep 6 17:14:06 2016
+ * @date creation: Wed Sep 07 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of Communications
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communications.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COMMUNICATIONS_TMPL_HH__
#define __AKANTU_COMMUNICATIONS_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity>
Communications<Entity>::Communications(const Communicator & communicator)
: communicator(communicator) {}
/* -------------------------------------------------------------------------- */
template <class Entity>
Communications<Entity>::Communications(const Communications & other)
: communicator(other.communicator) {
for (auto sr : iterate_send_recv) {
for (const auto & scheme_pair : other.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & other_scheme = scheme_pair.second;
auto & scheme = this->createScheme(proc, sr);
scheme.copy(other_scheme);
}
}
this->invalidateSizes();
}
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications<Entity>::iterator {
using communication_iterator =
typename std::map<UInt, Communication>::iterator;
public:
iterator() : communications(nullptr) {}
iterator(scheme_iterator scheme_it, communication_iterator comm_it,
Communications<Entity> & communications,
const SynchronizationTag & tag)
: scheme_it(scheme_it), comm_it(comm_it), communications(&communications),
tag(tag) {}
iterator & operator=(const iterator & other) {
if (this != &other) {
this->scheme_it = other.scheme_it;
this->comm_it = other.comm_it;
this->communications = other.communications;
this->tag = other.tag;
}
return *this;
}
iterator & operator++() {
++scheme_it;
++comm_it;
return *this;
}
CommunicationDescriptor<Entity> operator*() {
AKANTU_DEBUG_ASSERT(
scheme_it->first == comm_it->first,
"The two iterators are not in phase, something wrong"
<< " happened, time to take out your favorite debugger ("
<< scheme_it->first << " != " << comm_it->first << ")");
return CommunicationDescriptor<Entity>(comm_it->second, scheme_it->second,
*communications, tag,
scheme_it->first);
}
bool operator==(const iterator & other) const {
return scheme_it == other.scheme_it && comm_it == other.comm_it;
}
bool operator!=(const iterator & other) const {
return scheme_it != other.scheme_it || comm_it != other.comm_it;
}
private:
scheme_iterator scheme_it;
communication_iterator comm_it;
Communications<Entity> * communications;
SynchronizationTag tag;
};
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications<Entity>::tag_iterator {
using internal_iterator = std::map<SynchronizationTag, UInt>::const_iterator;
public:
tag_iterator(const internal_iterator & it) : it(it) {}
tag_iterator & operator++() {
++it;
return *this;
}
SynchronizationTag operator*() { return it->first; }
bool operator==(const tag_iterator & other) const { return it == other.it; }
bool operator!=(const tag_iterator & other) const { return it != other.it; }
private:
internal_iterator it;
};
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::CommunicationPerProcs &
Communications<Entity>::getCommunications(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto comm_it = this->communications[sr].find(tag);
if (comm_it == this->communications[sr].end())
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No known communications for the tag: " << tag);
return comm_it->second;
}
/* ---------------------------------------------------------------------- */
template <class Entity>
UInt Communications<Entity>::getPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) const {
const std::map<SynchronizationTag, UInt> & pending =
pending_communications[sr];
auto it = pending.find(tag);
if (it == pending.end())
return 0;
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
bool Communications<Entity>::hasPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) const {
return this->hasCommunication(tag) && (this->getPending(tag, sr) != 0);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::begin(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
return iterator(this->schemes[sr].begin(), comms.begin(), *this, tag);
}
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::end(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
return iterator(this->schemes[sr].end(), comms.end(), *this, tag);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAny(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
auto it = comms.begin();
auto end = comms.end();
std::vector<CommunicationRequest> requests;
for (; it != end; ++it) {
auto & request = it->second.request();
if (!request.isFreed())
requests.push_back(request);
}
UInt req_id = communicator.waitAny(requests);
if (req_id != UInt(-1)) {
auto & request = requests[req_id];
UInt proc = sr == _recv ? request.getSource() : request.getDestination();
return iterator(this->schemes[sr].find(proc), comms.find(proc), *this, tag);
} else {
return this->end(tag, sr);
}
}
/* ---------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::waitAll(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
auto it = comms.begin();
auto end = comms.end();
std::vector<CommunicationRequest> requests;
for (; it != end; ++it) {
requests.push_back(it->second.request());
}
communicator.waitAll(requests);
}
template <class Entity>
void Communications<Entity>::incrementPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) {
++(pending_communications[sr][tag]);
}
template <class Entity>
void Communications<Entity>::decrementPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) {
--(pending_communications[sr][tag]);
}
template <class Entity>
void Communications<Entity>::freeRequests(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
iterator it = this->begin(tag, sr);
iterator end = this->end(tag, sr);
for (; it != end; ++it) {
(*it).freeRequest();
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createScheme(UInt proc,
const CommunicationSendRecv & sr) {
// scheme_iterator it = schemes[sr].find(proc);
// if (it != schemes[sr].end()) {
// AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
// "Communication scheme("
// << sr
// << ") already created for proc: " <<
// proc);
// }
return schemes[sr][proc];
}
template <class Entity>
void Communications<Entity>::resetSchemes(const CommunicationSendRecv & sr) {
auto it = this->schemes[sr].begin();
auto end = this->schemes[sr].end();
for (; it != end; ++it) {
it->second.resize(0);
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::setCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size,
const CommunicationSendRecv & sr) {
// accessor that fails if it does not exists
comm_size_computed[tag] = true; // TODO: need perhaps to be split based on sr
auto & comms = this->communications[sr];
auto & comms_per_tag = comms.at(tag);
comms_per_tag.at(proc).resize(size);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::initializeCommunications(
const SynchronizationTag & tag) {
for (auto t = send_recv_t::begin(); t != send_recv_t::end(); ++t) {
pending_communications[*t].insert(std::make_pair(tag, 0));
auto & comms = this->communications[*t];
auto & comms_per_tag =
comms.insert(std::make_pair(tag, CommunicationPerProcs()))
.first->second;
for (auto pair : this->schemes[*t]) {
comms_per_tag.emplace(std::piecewise_construct,
std::forward_as_tuple(pair.first),
std::forward_as_tuple(*t));
}
}
comm_counter.insert(std::make_pair(tag, 0));
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::tag_iterator
Communications<Entity>::begin_tag() {
return tag_iterator(comm_counter.begin());
}
template <class Entity>
typename Communications<Entity>::tag_iterator
Communications<Entity>::end_tag() {
return tag_iterator(comm_counter.end());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_scheme(const CommunicationSendRecv & sr) {
return this->schemes[sr].begin();
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_scheme(const CommunicationSendRecv & sr) {
return this->schemes[sr].end();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_scheme(const CommunicationSendRecv & sr) const {
return this->schemes[sr].begin();
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_scheme(const CommunicationSendRecv & sr) const {
return this->schemes[sr].end();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_send_scheme() {
return this->begin_scheme(_send);
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_send_scheme() {
return this->end_scheme(_send);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_send_scheme() const {
return this->begin_scheme(_send);
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_send_scheme() const {
return this->end_scheme(_send);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_recv_scheme() {
return this->begin_scheme(_recv);
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_recv_scheme() {
return this->end_scheme(_recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_recv_scheme() const {
return this->begin_scheme(_recv);
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_recv_scheme() const {
return this->end_scheme(_recv);
}
/* ------------------------------------------------------------------------ */
template <class Entity>
bool Communications<Entity>::hasCommunication(
const SynchronizationTag & tag) const {
return (communications[_send].find(tag) != communications[_send].end());
}
template <class Entity>
void Communications<Entity>::incrementCounter(const SynchronizationTag & tag) {
auto it = comm_counter.find(tag);
if (it == comm_counter.end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No counter initialized in communications for the tags: " << tag);
}
++(it->second);
}
template <class Entity>
UInt Communications<Entity>::getCounter(const SynchronizationTag & tag) const {
auto it = comm_counter.find(tag);
if (it == comm_counter.end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No counter initialized in communications for the tags: " << tag);
}
return it->second;
}
template <class Entity>
bool Communications<Entity>::hasCommunicationSize(
const SynchronizationTag & tag) const {
auto it = comm_size_computed.find(tag);
if (it == comm_size_computed.end()) {
return false;
}
return it->second;
}
template <class Entity> void Communications<Entity>::invalidateSizes() {
for (auto && pair : comm_size_computed) {
pair.second = true;
}
}
template <class Entity>
bool Communications<Entity>::hasPendingRecv(
const SynchronizationTag & tag) const {
return this->hasPending(tag, _recv);
}
template <class Entity>
bool Communications<Entity>::hasPendingSend(
const SynchronizationTag & tag) const {
return this->hasPending(tag, _send);
}
template <class Entity>
const auto & Communications<Entity>::getCommunicator() const {
return communicator;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAnyRecv(const SynchronizationTag & tag) {
return this->waitAny(tag, _recv);
}
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAnySend(const SynchronizationTag & tag) {
return this->waitAny(tag, _send);
}
template <class Entity>
void Communications<Entity>::waitAllRecv(const SynchronizationTag & tag) {
this->waitAll(tag, _recv);
}
template <class Entity>
void Communications<Entity>::waitAllSend(const SynchronizationTag & tag) {
this->waitAll(tag, _send);
}
template <class Entity>
void Communications<Entity>::freeSendRequests(const SynchronizationTag & tag) {
this->freeRequests(tag, _send);
}
template <class Entity>
void Communications<Entity>::freeRecvRequests(const SynchronizationTag & tag) {
this->freeRequests(tag, _recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createSendScheme(UInt proc) {
return createScheme(proc, _send);
}
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createRecvScheme(UInt proc) {
return createScheme(proc, _recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity> void Communications<Entity>::resetSchemes() {
resetSchemes(_send);
resetSchemes(_recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::getScheme(UInt proc, const CommunicationSendRecv & sr) {
return this->schemes[sr].find(proc)->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
const typename Communications<Entity>::Scheme &
Communications<Entity>::getScheme(UInt proc,
const CommunicationSendRecv & sr) const {
return this->schemes[sr].find(proc)->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::setSendCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size) {
this->setCommunicationSize(tag, proc, size, _send);
}
template <class Entity>
void Communications<Entity>::setRecvCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size) {
this->setCommunicationSize(tag, proc, size, _recv);
}
} // namespace akantu
#endif /* __AKANTU_COMMUNICATIONS_TMPL_HH__ */
diff --git a/src/synchronizer/communicator.cc b/src/synchronizer/communicator.cc
index ff8ae1f9a..fc925697c 100644
--- a/src/synchronizer/communicator.cc
+++ b/src/synchronizer/communicator.cc
@@ -1,182 +1,181 @@
/**
- * @file static_communicator.cc
+ * @file communicator.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Mon Feb 05 2018
*
* @brief implementation of the common part of the static communicator
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
#if defined(AKANTU_USE_MPI)
int MPICommunicatorData::is_externaly_initialized = 0;
#endif
UInt InternalCommunicationRequest::counter = 0;
/* -------------------------------------------------------------------------- */
InternalCommunicationRequest::InternalCommunicationRequest(UInt source,
UInt dest)
: source(source), destination(dest) {
this->id = counter++;
}
/* -------------------------------------------------------------------------- */
InternalCommunicationRequest::~InternalCommunicationRequest() = default;
/* -------------------------------------------------------------------------- */
void InternalCommunicationRequest::printself(std::ostream & stream,
int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "CommunicationRequest [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + source : " << source << std::endl;
stream << space << " + destination : " << destination << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
Communicator::~Communicator() {
auto * event = new FinalizeCommunicatorEvent(*this);
this->sendEvent(*event);
delete event;
}
/* -------------------------------------------------------------------------- */
Communicator & Communicator::getStaticCommunicator() {
AKANTU_DEBUG_IN();
if (!static_communicator) {
int nb_args = 0;
char ** null = nullptr;
static_communicator =
std::make_unique<Communicator>(nb_args, null, private_member{});
}
AKANTU_DEBUG_OUT();
return *static_communicator;
}
/* -------------------------------------------------------------------------- */
Communicator & Communicator::getStaticCommunicator(int & argc, char **& argv) {
if (!static_communicator)
static_communicator =
std::make_unique<Communicator>(argc, argv, private_member{});
return getStaticCommunicator();
}
} // namespace akantu
#ifdef AKANTU_USE_MPI
#include "communicator_mpi_inline_impl.cc"
#else
#include "communicator_dummy_inline_impl.cc"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Template instantiation */
/* -------------------------------------------------------------------------- */
#define AKANTU_COMM_INSTANTIATE(T) \
template void Communicator::probe<T>(Int sender, Int tag, \
CommunicationStatus & status) const; \
template bool Communicator::asyncProbe<T>( \
Int sender, Int tag, CommunicationStatus & status) const; \
template void Communicator::sendImpl<T>( \
const T * buffer, Int size, Int receiver, Int tag, \
const CommunicationMode & mode) const; \
template void Communicator::receiveImpl<T>(T * buffer, Int size, Int sender, \
Int tag) const; \
template CommunicationRequest Communicator::asyncSendImpl<T>( \
const T * buffer, Int size, Int receiver, Int tag, \
const CommunicationMode & mode) const; \
template CommunicationRequest Communicator::asyncReceiveImpl<T>( \
T * buffer, Int size, Int sender, Int tag) const; \
template void Communicator::allGatherImpl<T>(T * values, int nb_values) \
const; \
template void Communicator::allGatherVImpl<T>(T * values, int * nb_values) \
const; \
template void Communicator::gatherImpl<T>(T * values, int nb_values, \
int root) const; \
template void Communicator::gatherImpl<T>( \
T * values, int nb_values, T * gathered, int nb_gathered) const; \
template void Communicator::gatherVImpl<T>(T * values, int * nb_values, \
int root) const; \
template void Communicator::broadcastImpl<T>(T * values, int nb_values, \
int root) const; \
template void Communicator::allReduceImpl<T>( \
T * values, int nb_values, const SynchronizerOperation & op) const
#define MIN_MAX_REAL SCMinMaxLoc<Real, int>
AKANTU_COMM_INSTANTIATE(bool);
AKANTU_COMM_INSTANTIATE(Real);
AKANTU_COMM_INSTANTIATE(UInt);
AKANTU_COMM_INSTANTIATE(Int);
AKANTU_COMM_INSTANTIATE(char);
AKANTU_COMM_INSTANTIATE(NodeType);
AKANTU_COMM_INSTANTIATE(MIN_MAX_REAL);
#if AKANTU_INTEGER_SIZE > 4
AKANTU_COMM_INSTANTIATE(int);
#endif
// template void Communicator::send<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int receiver, Int tag);
// template void Communicator::receive<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int sender, Int tag);
// template CommunicationRequest
// Communicator::asyncSend<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int receiver, Int tag);
// template CommunicationRequest
// Communicator::asyncReceive<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int sender, Int tag);
// template void Communicator::probe<SCMinMaxLoc<Real, int>>(
// Int sender, Int tag, CommunicationStatus & status);
// template void Communicator::allGather<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values);
// template void Communicator::allGatherV<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int * nb_values);
// template void Communicator::gather<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values, int root);
// template void Communicator::gatherV<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int * nb_values, int root);
// template void Communicator::broadcast<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values, int root);
// template void Communicator::allReduce<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values,
// const SynchronizerOperation & op);
} // akantu
diff --git a/src/synchronizer/communicator.hh b/src/synchronizer/communicator.hh
index 045542321..d045722d3 100644
--- a/src/synchronizer/communicator.hh
+++ b/src/synchronizer/communicator.hh
@@ -1,437 +1,437 @@
/**
- * @file static_communicator.hh
+ * @file communicator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Jan 19 2016
+ * @date last modification: Wed Nov 15 2017
*
* @brief Class handling the parallel communications
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_event_handler_manager.hh"
#include "communication_buffer.hh"
#include "communication_request.hh"
#include "communicator_event_handler.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STATIC_COMMUNICATOR_HH__
#define __AKANTU_STATIC_COMMUNICATOR_HH__
namespace akantu {
namespace debug {
class CommunicationException : public Exception {
public:
CommunicationException()
: Exception("An exception happen during a communication process.") {}
};
} // namespace debug
/// @enum SynchronizerOperation reduce operation that the synchronizer can
/// perform
enum class SynchronizerOperation {
_sum,
_min,
_max,
_prod,
_land,
_band,
_lor,
_bor,
_lxor,
_bxor,
_min_loc,
_max_loc,
_null
};
enum class CommunicationMode { _auto, _synchronous, _ready };
namespace {
int _any_source = -1;
}
} // namespace akantu
namespace akantu {
struct CommunicatorInternalData {
virtual ~CommunicatorInternalData() = default;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class Communicator : public EventHandlerManager<CommunicatorEventHandler> {
struct private_member {};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Communicator(int & argc, char **& argv, const private_member &);
~Communicator() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Point to Point */
/* ------------------------------------------------------------------------ */
template <typename T>
inline void receive(Array<T> & values, Int sender, Int tag) const {
return this->receiveImpl(
values.storage(), values.size() * values.getNbComponent(), sender, tag);
}
template <typename Tensor>
inline void
receive(Tensor & values, Int sender, Int tag,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
template <bool is_static>
inline void receive(CommunicationBufferTemplated<is_static> & values,
Int sender, Int tag) const {
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
template <typename T>
inline void
receive(T & values, Int sender, Int tag,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
return this->receiveImpl(&values, 1, sender, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void
send(const Array<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.storage(),
values.size() * values.getNbComponent(), receiver,
tag, mode);
}
template <typename Tensor>
inline void
send(const Tensor & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
return this->sendImpl(values.storage(), values.size(), receiver, tag, mode);
}
template <bool is_static>
inline void
send(const CommunicationBufferTemplated<is_static> & values, Int receiver,
Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.storage(), values.size(), receiver, tag, mode);
}
template <typename T>
inline void
send(const T & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
return this->sendImpl(&values, 1, receiver, tag, mode);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest
asyncSend(const Array<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.storage(),
values.size() * values.getNbComponent(),
receiver, tag, mode);
}
template <typename T>
inline CommunicationRequest
asyncSend(const std::vector<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.data(), values.size(), receiver, tag,
mode);
}
template <typename Tensor>
inline CommunicationRequest
asyncSend(const Tensor & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
return this->asyncSendImpl(values.storage(), values.size(), receiver, tag,
mode);
}
template <bool is_static>
inline CommunicationRequest
asyncSend(const CommunicationBufferTemplated<is_static> & values,
Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.storage(), values.size(), receiver, tag,
mode);
}
template <typename T>
inline CommunicationRequest
asyncSend(const T & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
return this->asyncSendImpl(&values, 1, receiver, tag, mode);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest asyncReceive(Array<T> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(
values.storage(), values.size() * values.getNbComponent(), sender, tag);
}
template <typename T>
inline CommunicationRequest asyncReceive(std::vector<T> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.data(), values.size(), sender, tag);
}
template <typename Tensor,
typename = std::enable_if_t<is_tensor<Tensor>::value>>
inline CommunicationRequest asyncReceive(Tensor & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.storage(), values.size(), sender, tag);
}
template <bool is_static>
inline CommunicationRequest
asyncReceive(CommunicationBufferTemplated<is_static> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.storage(), values.size(), sender, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
void probe(Int sender, Int tag, CommunicationStatus & status) const;
template <typename T>
bool asyncProbe(Int sender, Int tag, CommunicationStatus & status) const;
/* ------------------------------------------------------------------------ */
/* Collectives */
/* ------------------------------------------------------------------------ */
template <typename T>
inline void allReduce(Array<T> & values,
const SynchronizerOperation & op) const {
this->allReduceImpl(values.storage(),
values.size() * values.getNbComponent(), op);
}
template <typename Tensor>
inline void
allReduce(Tensor & values, const SynchronizerOperation & op,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
this->allReduceImpl(values.storage(), values.size(), op);
}
template <typename T>
inline void
allReduce(T & values, const SynchronizerOperation & op,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
this->allReduceImpl(&values, 1, op);
}
/* ------------------------------------------------------------------------ */
template <typename T> inline void allGather(Array<T> & values) const {
AKANTU_DEBUG_ASSERT(UInt(psize) == values.size(),
"The array size is not correct");
this->allGatherImpl(values.storage(), values.getNbComponent());
}
template <typename Tensor,
typename = std::enable_if_t<is_tensor<Tensor>::value>>
inline void allGather(Tensor & values) const {
AKANTU_DEBUG_ASSERT(UInt(psize) == values.size(),
"The vector size is not correct");
this->allGatherImpl(values.storage(), 1);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void allGatherV(Array<T> & values, const Array<Int> & sizes) const {
this->allGatherVImpl(values.storage(), sizes.storage());
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void reduce(Array<T> & values, const SynchronizerOperation & op,
int root = 0) const {
this->reduceImpl(values.storage(), values.size() * values.getNbComponent(),
op, root);
}
/* ------------------------------------------------------------------------ */
template <typename Tensor>
inline void
gather(Tensor & values, int root = 0,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
this->gatherImpl(values.storage(), values.getNbComponent(), root);
}
template <typename T>
inline void
gather(T values, int root = 0,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
this->gatherImpl(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
template <typename Tensor, typename T>
inline void
gather(Tensor & values, Array<T> & gathered,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
AKANTU_DEBUG_ASSERT(values.size() == gathered.getNbComponent(),
"The array size is not correct");
gathered.resize(psize);
this->gatherImpl(values.data(), values.size(), gathered.storage(),
gathered.getNbComponent());
}
template <typename T>
inline void
gather(T values, Array<T> & gathered,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
this->gatherImpl(&values, 1, gathered.storage(), 1);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void gatherV(Array<T> & values, const Array<Int> & sizes,
int root = 0) const {
this->gatherVImpl(values.storage(), sizes.storage(), root);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void broadcast(Array<T> & values, int root = 0) const {
this->broadcastImpl(values.storage(),
values.size() * values.getNbComponent(), root);
}
template <bool is_static>
inline void broadcast(CommunicationBufferTemplated<is_static> & values,
int root = 0) const {
this->broadcastImpl(values.storage(), values.size(), root);
}
template <typename T> inline void broadcast(T & values, int root = 0) const {
this->broadcastImpl(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
void barrier() const;
CommunicationRequest asyncBarrier() const;
/* ------------------------------------------------------------------------ */
/* Request handling */
/* ------------------------------------------------------------------------ */
bool test(CommunicationRequest & request) const;
bool testAll(std::vector<CommunicationRequest> & request) const;
void wait(CommunicationRequest & request) const;
void waitAll(std::vector<CommunicationRequest> & requests) const;
UInt waitAny(std::vector<CommunicationRequest> & requests) const;
inline void freeCommunicationRequest(CommunicationRequest & request) const;
inline void
freeCommunicationRequest(std::vector<CommunicationRequest> & requests) const;
template <typename T, typename MsgProcessor, typename TagGen>
inline void
receiveAnyNumber(std::vector<CommunicationRequest> & send_requests,
Array<T> receive_buffer, MsgProcessor && processor,
TagGen && tag_gen) const;
protected:
template <typename T>
void
sendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const;
template <typename T>
void receiveImpl(T * buffer, Int size, Int sender, Int tag) const;
template <typename T>
CommunicationRequest asyncSendImpl(
const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const;
template <typename T>
CommunicationRequest asyncReceiveImpl(T * buffer, Int size, Int sender,
Int tag) const;
template <typename T>
void allReduceImpl(T * values, int nb_values,
const SynchronizerOperation & op) const;
template <typename T> void allGatherImpl(T * values, int nb_values) const;
template <typename T> void allGatherVImpl(T * values, int * nb_values) const;
template <typename T>
void reduceImpl(T * values, int nb_values, const SynchronizerOperation & op,
int root = 0) const;
template <typename T>
void gatherImpl(T * values, int nb_values, int root = 0) const;
template <typename T>
void gatherImpl(T * values, int nb_values, T * gathered,
int nb_gathered = 0) const;
template <typename T>
void gatherVImpl(T * values, int * nb_values, int root = 0) const;
template <typename T>
void broadcastImpl(T * values, int nb_values, int root = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
Int getNbProc() const { return psize; };
Int whoAmI() const { return prank; };
static Communicator & getStaticCommunicator();
static Communicator & getStaticCommunicator(int & argc, char **& argv);
int getMaxTag() const;
int getMinTag() const;
AKANTU_GET_MACRO(CommunicatorData, (*communicator_data), decltype(auto));
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
static std::unique_ptr<Communicator> static_communicator;
protected:
Int prank{0};
Int psize{1};
std::unique_ptr<CommunicatorInternalData> communicator_data;
};
inline std::ostream & operator<<(std::ostream & stream,
const CommunicationRequest & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "communicator_inline_impl.hh"
#endif /* __AKANTU_STATIC_COMMUNICATOR_HH__ */
diff --git a/src/synchronizer/communicator_dummy_inline_impl.cc b/src/synchronizer/communicator_dummy_inline_impl.cc
index 9b92a14fd..79aead7f4 100644
--- a/src/synchronizer/communicator_dummy_inline_impl.cc
+++ b/src/synchronizer/communicator_dummy_inline_impl.cc
@@ -1,118 +1,117 @@
/**
- * @file static_communicator_dummy.hh
+ * @file communicator_dummy_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jun 18 2010
- * @date last modification: Wed Jan 13 2016
+ * @date creation: Tue Nov 07 2017
+ * @date last modification: Fri Nov 10 2017
*
* @brief Dummy communicator to make everything work im sequential
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <cstring>
#include <type_traits>
#include <vector>
/* -------------------------------------------------------------------------- */
namespace akantu {
Communicator::Communicator(int & /*argc*/, char **& /*argv*/,
const private_member & /*unused*/) {}
template <typename T>
void Communicator::sendImpl(const T *, Int, Int, Int,
const CommunicationMode &) const {}
template <typename T>
void Communicator::receiveImpl(T *, Int, Int, Int) const {}
template <typename T>
CommunicationRequest
Communicator::asyncSendImpl(const T *, Int, Int, Int,
const CommunicationMode &) const {
return std::shared_ptr<InternalCommunicationRequest>(
new InternalCommunicationRequest(0, 0));
}
template <typename T>
CommunicationRequest Communicator::asyncReceiveImpl(T *, Int, Int, Int) const {
return std::shared_ptr<InternalCommunicationRequest>(
new InternalCommunicationRequest(0, 0));
}
template <typename T>
void Communicator::probe(Int, Int, CommunicationStatus &) const {}
template <typename T>
bool Communicator::asyncProbe(Int, Int, CommunicationStatus &) const {
return true;
}
bool Communicator::test(CommunicationRequest &) const { return true; }
bool Communicator::testAll(std::vector<CommunicationRequest> &) const {
return true;
}
void Communicator::wait(CommunicationRequest &) const {}
void Communicator::waitAll(std::vector<CommunicationRequest> &) const {}
UInt Communicator::waitAny(std::vector<CommunicationRequest> &) const {
return UInt(-1);
}
void Communicator::barrier() const {}
CommunicationRequest Communicator::asyncBarrier() const {
return std::shared_ptr<InternalCommunicationRequest>(
new InternalCommunicationRequest(0, 0));
}
template <typename T>
void Communicator::reduceImpl(T *, int, const SynchronizerOperation &,
int) const {}
template <typename T>
void Communicator::allReduceImpl(T *, int,
const SynchronizerOperation &) const {}
template <typename T> inline void Communicator::allGatherImpl(T *, int) const {}
template <typename T>
inline void Communicator::allGatherVImpl(T *, int *) const {}
template <typename T>
inline void Communicator::gatherImpl(T *, int, int) const {}
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, T * gathered,
int) const {
static_assert(std::is_trivially_copyable<T>{},
"Cannot send this type of data");
std::memcpy(gathered, values, nb_values);
}
template <typename T>
inline void Communicator::gatherVImpl(T *, int *, int) const {}
template <typename T>
inline void Communicator::broadcastImpl(T *, int, int) const {}
int Communicator::getMaxTag() const { return std::numeric_limits<int>::max(); }
int Communicator::getMinTag() const { return 0; }
} // namespace akantu
diff --git a/src/synchronizer/communicator_event_handler.hh b/src/synchronizer/communicator_event_handler.hh
index 9265521c7..f740ed40e 100644
--- a/src/synchronizer/communicator_event_handler.hh
+++ b/src/synchronizer/communicator_event_handler.hh
@@ -1,58 +1,61 @@
/**
* @file communicator_event_handler.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Wed Nov 15 2017
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Nov 15 2017
*
+ * @brief Event handler of the communicator
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COMMUNICATOR_EVENT_HANDLER_HH__
#define __AKANTU_COMMUNICATOR_EVENT_HANDLER_HH__
namespace akantu {
class Communicator;
struct FinalizeCommunicatorEvent {
explicit FinalizeCommunicatorEvent(const Communicator & comm)
: communicator(comm) {}
const Communicator & communicator;
};
class CommunicatorEventHandler {
public:
virtual ~CommunicatorEventHandler() = default;
virtual void onCommunicatorFinalize() = 0;
private:
inline void sendEvent(const FinalizeCommunicatorEvent &) {
this->onCommunicatorFinalize();
}
template <class EventHandler> friend class EventHandlerManager;
};
} // akantu
#endif /* __AKANTU_COMMUNICATOR_EVENT_HANDLER_HH__ */
diff --git a/src/synchronizer/communicator_inline_impl.hh b/src/synchronizer/communicator_inline_impl.hh
index 3d669332b..7021cb145 100644
--- a/src/synchronizer/communicator_inline_impl.hh
+++ b/src/synchronizer/communicator_inline_impl.hh
@@ -1,88 +1,88 @@
/**
- * @file static_communicator_inline_impl.hh
+ * @file communicator_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Sep 06 2010
- * @date last modification: Thu Dec 10 2015
+ * @date creation: Tue Feb 02 2016
+ * @date last modification: Tue Nov 07 2017
*
* @brief implementation of inline functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH__
#define __AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void
Communicator::freeCommunicationRequest(CommunicationRequest & request) const {
request.free();
}
/* -------------------------------------------------------------------------- */
inline void Communicator::freeCommunicationRequest(
std::vector<CommunicationRequest> & requests) const {
std::vector<CommunicationRequest>::iterator it;
for (it = requests.begin(); it != requests.end(); ++it) {
it->free();
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename MsgProcessor, typename TagGen>
inline void Communicator::receiveAnyNumber(
std::vector<CommunicationRequest> & send_requests, Array<T> receive_buffer,
MsgProcessor && processor, TagGen && tag_gen) const {
CommunicationRequest barrier_request;
bool got_all = false, are_send_finished = false;
while (not got_all) {
bool are_receives_ready = true;
while (are_receives_ready) {
auto && tag = std::forward<TagGen>(tag_gen)();
CommunicationStatus status;
are_receives_ready = asyncProbe<UInt>(_any_source, tag, status);
if (are_receives_ready) {
receive_buffer.resize(status.size());
receive(receive_buffer, status.getSource(), tag);
std::forward<MsgProcessor>(processor)(status.getSource(),
receive_buffer);
}
}
if (not are_send_finished) {
are_send_finished = testAll(send_requests);
if (are_send_finished)
barrier_request = asyncBarrier();
}
if (are_send_finished) {
got_all = test(barrier_request);
}
}
}
} // namespace akantu
#endif /* __AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH__ */
diff --git a/src/synchronizer/communicator_mpi_inline_impl.cc b/src/synchronizer/communicator_mpi_inline_impl.cc
index 9bd9fcf51..fda048047 100644
--- a/src/synchronizer/communicator_mpi_inline_impl.cc
+++ b/src/synchronizer/communicator_mpi_inline_impl.cc
@@ -1,460 +1,459 @@
/**
- * @file static_communicator_mpi.cc
+ * @file communicator_mpi_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Sun Sep 26 2010
- * @date last modification: Thu Jan 21 2016
+ * @date creation: Tue Nov 07 2017
+ * @date last modification: Mon Dec 18 2017
*
* @brief StaticCommunicatorMPI implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "mpi_communicator_data.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
#include <type_traits>
#include <unordered_map>
#include <vector>
/* -------------------------------------------------------------------------- */
#include <mpi.h>
/* -------------------------------------------------------------------------- */
#if (defined(__GNUC__) || defined(__GNUG__))
#if AKA_GCC_VERSION < 60000
namespace std {
template <> struct hash<akantu::SynchronizerOperation> {
using argument_type = akantu::SynchronizerOperation;
size_t operator()(const argument_type & e) const noexcept {
auto ue = underlying_type_t<argument_type>(e);
return uh(ue);
}
private:
const hash<underlying_type_t<argument_type>> uh{};
};
} // namespace std
#endif
#endif
namespace akantu {
class CommunicationRequestMPI : public InternalCommunicationRequest {
public:
CommunicationRequestMPI(UInt source, UInt dest)
: InternalCommunicationRequest(source, dest),
request(std::make_unique<MPI_Request>()) {}
MPI_Request & getMPIRequest() { return *request; };
private:
std::unique_ptr<MPI_Request> request;
};
namespace {
template <typename T> inline MPI_Datatype getMPIDatatype();
MPI_Op getMPISynchronizerOperation(const SynchronizerOperation & op) {
std::unordered_map<SynchronizerOperation, MPI_Op> _operations{
{SynchronizerOperation::_sum, MPI_SUM},
{SynchronizerOperation::_min, MPI_MIN},
{SynchronizerOperation::_max, MPI_MAX},
{SynchronizerOperation::_prod, MPI_PROD},
{SynchronizerOperation::_land, MPI_LAND},
{SynchronizerOperation::_band, MPI_BAND},
{SynchronizerOperation::_lor, MPI_LOR},
{SynchronizerOperation::_bor, MPI_BOR},
{SynchronizerOperation::_lxor, MPI_LXOR},
{SynchronizerOperation::_bxor, MPI_BXOR},
{SynchronizerOperation::_min_loc, MPI_MINLOC},
{SynchronizerOperation::_max_loc, MPI_MAXLOC},
{SynchronizerOperation::_null, MPI_OP_NULL}};
return _operations[op];
}
template <typename T> MPI_Datatype inline getMPIDatatype() {
return MPI_DATATYPE_NULL;
}
#define SPECIALIZE_MPI_DATATYPE(type, mpi_type) \
template <> MPI_Datatype inline getMPIDatatype<type>() { return mpi_type; }
#define COMMA ,
SPECIALIZE_MPI_DATATYPE(char, MPI_CHAR)
SPECIALIZE_MPI_DATATYPE(float, MPI_FLOAT)
SPECIALIZE_MPI_DATATYPE(double, MPI_DOUBLE)
SPECIALIZE_MPI_DATATYPE(long double, MPI_LONG_DOUBLE)
SPECIALIZE_MPI_DATATYPE(signed int, MPI_INT)
SPECIALIZE_MPI_DATATYPE(NodeType, getMPIDatatype<Int>())
SPECIALIZE_MPI_DATATYPE(unsigned int, MPI_UNSIGNED)
SPECIALIZE_MPI_DATATYPE(signed long int, MPI_LONG)
SPECIALIZE_MPI_DATATYPE(unsigned long int, MPI_UNSIGNED_LONG)
SPECIALIZE_MPI_DATATYPE(signed long long int, MPI_LONG_LONG)
SPECIALIZE_MPI_DATATYPE(unsigned long long int, MPI_UNSIGNED_LONG_LONG)
SPECIALIZE_MPI_DATATYPE(SCMinMaxLoc<double COMMA int>, MPI_DOUBLE_INT)
SPECIALIZE_MPI_DATATYPE(SCMinMaxLoc<float COMMA int>, MPI_FLOAT_INT)
SPECIALIZE_MPI_DATATYPE(bool, MPI_CXX_BOOL)
inline int getMPISource(int src) {
if (src == _any_source)
return MPI_ANY_SOURCE;
return src;
}
decltype(auto) convertRequests(std::vector<CommunicationRequest> & requests) {
std::vector<MPI_Request> mpi_requests(requests.size());
for (auto && request_pair : zip(requests, mpi_requests)) {
auto && req = std::get<0>(request_pair);
auto && mpi_req = std::get<1>(request_pair);
mpi_req = dynamic_cast<CommunicationRequestMPI &>(req.getInternal())
.getMPIRequest();
}
return mpi_requests;
}
} // namespace
// this is ugly but shorten the code a lot
#define MPIDATA \
(*reinterpret_cast<MPICommunicatorData *>(communicator_data.get()))
/* -------------------------------------------------------------------------- */
/* Implementation */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
Communicator::Communicator(int & /*argc*/, char **& /*argv*/,
const private_member & /*unused*/)
: communicator_data(std::make_unique<MPICommunicatorData>()) {
prank = MPIDATA.rank();
psize = MPIDATA.size();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::sendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
switch (mode) {
case CommunicationMode::_auto:
MPI_Send(buffer, size, type, receiver, tag, communicator);
break;
case CommunicationMode::_synchronous:
MPI_Ssend(buffer, size, type, receiver, tag, communicator);
break;
case CommunicationMode::_ready:
MPI_Rsend(buffer, size, type, receiver, tag, communicator);
break;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::receiveImpl(T * buffer, Int size, Int sender,
Int tag) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status status;
MPI_Datatype type = getMPIDatatype<T>();
MPI_Recv(buffer, size, type, getMPISource(sender), tag, communicator,
&status);
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest
Communicator::asyncSendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
auto * request = new CommunicationRequestMPI(prank, receiver);
MPI_Request & req = request->getMPIRequest();
MPI_Datatype type = getMPIDatatype<T>();
switch (mode) {
case CommunicationMode::_auto:
MPI_Isend(buffer, size, type, receiver, tag, communicator, &req);
break;
case CommunicationMode::_synchronous:
MPI_Issend(buffer, size, type, receiver, tag, communicator, &req);
break;
case CommunicationMode::_ready:
MPI_Irsend(buffer, size, type, receiver, tag, communicator, &req);
break;
}
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest Communicator::asyncReceiveImpl(T * buffer, Int size,
Int sender, Int tag) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
auto * request = new CommunicationRequestMPI(sender, prank);
MPI_Datatype type = getMPIDatatype<T>();
MPI_Request & req = request->getMPIRequest();
MPI_Irecv(buffer, size, type, getMPISource(sender), tag, communicator, &req);
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::probe(Int sender, Int tag,
CommunicationStatus & status) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status mpi_status;
MPI_Probe(getMPISource(sender), tag, communicator, &mpi_status);
MPI_Datatype type = getMPIDatatype<T>();
int count;
MPI_Get_count(&mpi_status, type, &count);
status.setSource(mpi_status.MPI_SOURCE);
status.setTag(mpi_status.MPI_TAG);
status.setSize(count);
}
/* -------------------------------------------------------------------------- */
template <typename T>
bool Communicator::asyncProbe(Int sender, Int tag,
CommunicationStatus & status) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status mpi_status;
int test;
MPI_Iprobe(getMPISource(sender), tag, communicator, &test, &mpi_status);
if (not test)
return false;
MPI_Datatype type = getMPIDatatype<T>();
int count;
MPI_Get_count(&mpi_status, type, &count);
status.setSource(mpi_status.MPI_SOURCE);
status.setTag(mpi_status.MPI_TAG);
status.setSize(count);
return true;
}
/* -------------------------------------------------------------------------- */
bool Communicator::test(CommunicationRequest & request) const {
MPI_Status status;
int flag;
auto & req_mpi =
dynamic_cast<CommunicationRequestMPI &>(request.getInternal());
MPI_Request & req = req_mpi.getMPIRequest();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Test(&req, &flag, &status);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Test.");
return (flag != 0);
}
/* -------------------------------------------------------------------------- */
bool Communicator::testAll(std::vector<CommunicationRequest> & requests) const {
int are_finished;
auto && mpi_requests = convertRequests(requests);
MPI_Testall(mpi_requests.size(), mpi_requests.data(), &are_finished,
MPI_STATUSES_IGNORE);
return are_finished != 0 ? true : false;
}
/* -------------------------------------------------------------------------- */
void Communicator::wait(CommunicationRequest & request) const {
MPI_Status status;
auto & req_mpi =
dynamic_cast<CommunicationRequestMPI &>(request.getInternal());
MPI_Request & req = req_mpi.getMPIRequest();
MPI_Wait(&req, &status);
}
/* -------------------------------------------------------------------------- */
void Communicator::waitAll(std::vector<CommunicationRequest> & requests) const {
auto && mpi_requests = convertRequests(requests);
MPI_Waitall(mpi_requests.size(), mpi_requests.data(), MPI_STATUSES_IGNORE);
}
/* -------------------------------------------------------------------------- */
UInt Communicator::waitAny(std::vector<CommunicationRequest> & requests) const {
auto && mpi_requests = convertRequests(requests);
int pos;
MPI_Waitany(mpi_requests.size(), mpi_requests.data(), &pos,
MPI_STATUSES_IGNORE);
if (pos != MPI_UNDEFINED) {
return pos;
} else {
return UInt(-1);
}
}
/* -------------------------------------------------------------------------- */
void Communicator::barrier() const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Barrier(communicator);
}
/* -------------------------------------------------------------------------- */
CommunicationRequest Communicator::asyncBarrier() const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
auto * request = new CommunicationRequestMPI(0, 0);
MPI_Request & req = request->getMPIRequest();
MPI_Ibarrier(communicator, &req);
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::reduceImpl(T * values, int nb_values,
const SynchronizerOperation & op,
int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Reduce(MPI_IN_PLACE, values, nb_values, type,
getMPISynchronizerOperation(op), root, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allReduceImpl(T * values, int nb_values,
const SynchronizerOperation & op) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allreduce(MPI_IN_PLACE, values, nb_values, type,
getMPISynchronizerOperation(op), communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allGatherImpl(T * values, int nb_values) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allgather(MPI_IN_PLACE, nb_values, type, values, nb_values, type,
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allGatherVImpl(T * values, int * nb_values) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
std::vector<int> displs(psize);
displs[0] = 0;
for (int i = 1; i < psize; ++i) {
displs[i] = displs[i - 1] + nb_values[i - 1];
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allgatherv(MPI_IN_PLACE, *nb_values, type, values, nb_values,
displs.data(), type, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
T *send_buf = nullptr, *recv_buf = nullptr;
if (prank == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
} else {
send_buf = values;
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_values, type, root,
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, T * gathered,
int nb_gathered) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
T * send_buf = values;
T * recv_buf = gathered;
if (nb_gathered == 0)
nb_gathered = nb_values;
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_gathered, type,
this->prank, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherVImpl(T * values, int * nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
int * displs = nullptr;
if (prank == root) {
displs = new int[psize];
displs[0] = 0;
for (int i = 1; i < psize; ++i) {
displs[i] = displs[i - 1] + nb_values[i - 1];
}
}
T *send_buf = nullptr, *recv_buf = nullptr;
if (prank == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
} else
send_buf = values;
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gatherv(send_buf, *nb_values, type, recv_buf, nb_values, displs, type,
root, communicator);
if (prank == root) {
delete[] displs;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::broadcastImpl(T * values, int nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Bcast(values, nb_values, type, root, communicator);
}
/* -------------------------------------------------------------------------- */
int Communicator::getMaxTag() const { return MPIDATA.getMaxTag(); }
int Communicator::getMinTag() const { return 0; }
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/data_accessor.cc b/src/synchronizer/data_accessor.cc
index 3a51a7016..e80b72ce3 100644
--- a/src/synchronizer/data_accessor.cc
+++ b/src/synchronizer/data_accessor.cc
@@ -1,155 +1,154 @@
/**
* @file data_accessor.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Oct 19 2014
+ * @date last modification: Tue Feb 20 2018
*
* @brief data accessors constructor functions
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "fe_engine.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void DataAccessor<Element>::packUnpackNodalDataHelper(
Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
UInt nb_component = data.getNbComponent();
UInt nb_nodes_per_element = 0;
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt * conn = nullptr;
for (auto & el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
conn = mesh.getConnectivity(el.type, el.ghost_type).storage();
nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
}
UInt el_offset = el.element * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt offset_conn = conn[el_offset + n];
Vector<T> data_vect(data.storage() + offset_conn * nb_component,
nb_component);
if (pack_helper)
buffer << data_vect;
else
buffer >> data_vect;
}
}
}
/* ------------------------------------------------------------------------ */
template <typename T, bool pack_helper>
void DataAccessor<Element>::packUnpackElementalDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & element, bool per_quadrature_point_data,
const FEEngine & fem) {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt nb_quad_per_elem = 0;
UInt nb_component = 0;
Array<T> * vect = nullptr;
for (auto & el : element) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect = &data_to_pack(el.type, el.ghost_type);
nb_quad_per_elem =
per_quadrature_point_data
? fem.getNbIntegrationPoints(el.type, el.ghost_type)
: 1;
nb_component = vect->getNbComponent();
}
Vector<T> data(vect->storage() +
el.element * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem);
if (pack_helper)
buffer << data;
else
buffer >> data;
}
}
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void DataAccessor<UInt>::packUnpackDOFDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
T * data_ptr = data.storage();
for (const auto & dof : dofs) {
if (pack_helper)
buffer << data_ptr[dof];
else
buffer >> data_ptr[dof];
}
}
/* -------------------------------------------------------------------------- */
#define DECLARE_HELPERS(T) \
template void DataAccessor<Element>::packUnpackNodalDataHelper<T, false>( \
Array<T> & data, CommunicationBuffer & buffer, \
const Array<Element> & elements, const Mesh & mesh); \
template void DataAccessor<Element>::packUnpackNodalDataHelper<T, true>( \
Array<T> & data, CommunicationBuffer & buffer, \
const Array<Element> & elements, const Mesh & mesh); \
template void \
DataAccessor<Element>::packUnpackElementalDataHelper<T, false>( \
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer, \
const Array<Element> & element, bool per_quadrature_point_data, \
const FEEngine & fem); \
template void DataAccessor<Element>::packUnpackElementalDataHelper<T, true>( \
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer, \
const Array<Element> & element, bool per_quadrature_point_data, \
const FEEngine & fem); \
template void DataAccessor<UInt>::packUnpackDOFDataHelper<T, true>( \
Array<T> & data, CommunicationBuffer & buffer, \
const Array<UInt> & dofs); \
template void DataAccessor<UInt>::packUnpackDOFDataHelper<T, false>( \
Array<T> & data, CommunicationBuffer & buffer, const Array<UInt> & dofs)
/* -------------------------------------------------------------------------- */
DECLARE_HELPERS(Real);
DECLARE_HELPERS(UInt);
DECLARE_HELPERS(bool);
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/synchronizer/data_accessor.hh b/src/synchronizer/data_accessor.hh
index cebcb66b3..78c956279 100644
--- a/src/synchronizer/data_accessor.hh
+++ b/src/synchronizer/data_accessor.hh
@@ -1,279 +1,278 @@
/**
* @file data_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Sun Feb 04 2018
*
* @brief Interface of accessors for pack_unpack system
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "communication_buffer.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DATA_ACCESSOR_HH__
#define __AKANTU_DATA_ACCESSOR_HH__
namespace akantu {
class FEEngine;
} // akantu
namespace akantu {
class DataAccessorBase {
public:
DataAccessorBase() = default;
virtual ~DataAccessorBase() = default;
};
template <class T> class DataAccessor : public virtual DataAccessorBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DataAccessor() = default;
~DataAccessor() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief get the number of data to exchange for a given array of T
* (elements or dofs) and a given akantu::SynchronizationTag
*/
virtual UInt getNbData(const Array<T> & elements,
const SynchronizationTag & tag) const = 0;
/**
* @brief pack the data for a given array of T (elements or dofs) and a given
* akantu::SynchronizationTag
*/
virtual void packData(CommunicationBuffer & buffer, const Array<T> & element,
const SynchronizationTag & tag) const = 0;
/**
* @brief unpack the data for a given array of T (elements or dofs) and a
* given akantu::SynchronizationTag
*/
virtual void unpackData(CommunicationBuffer & buffer,
const Array<T> & element,
const SynchronizationTag & tag) = 0;
};
/* -------------------------------------------------------------------------- */
/* Specialization */
/* -------------------------------------------------------------------------- */
template <> class DataAccessor<Element> : public virtual DataAccessorBase {
public:
DataAccessor() = default;
~DataAccessor() override = default;
virtual UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const = 0;
virtual void packData(CommunicationBuffer & buffer,
const Array<Element> & element,
const SynchronizationTag & tag) const = 0;
virtual void unpackData(CommunicationBuffer & buffer,
const Array<Element> & element,
const SynchronizationTag & tag) = 0;
/* ------------------------------------------------------------------------ */
public:
template <typename T, bool pack_helper>
static void
packUnpackNodalDataHelper(Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh);
/* ------------------------------------------------------------------------ */
template <typename T, bool pack_helper>
static void packUnpackElementalDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & element, bool per_quadrature_point_data,
const FEEngine & fem);
/* ------------------------------------------------------------------------ */
template <typename T>
static void
packNodalDataHelper(const Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
packUnpackNodalDataHelper<T, true>(const_cast<Array<T> &>(data), buffer,
elements, mesh);
}
template <typename T>
static inline void
unpackNodalDataHelper(Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
packUnpackNodalDataHelper<T, false>(data, buffer, elements, mesh);
}
/* ------------------------------------------------------------------------ */
template <typename T>
static inline void
packElementalDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point, const FEEngine & fem) {
packUnpackElementalDataHelper<T, true>(
const_cast<ElementTypeMapArray<T> &>(data_to_pack), buffer, elements,
per_quadrature_point, fem);
}
template <typename T>
static inline void
unpackElementalDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point, const FEEngine & fem) {
packUnpackElementalDataHelper<T, false>(data_to_unpack, buffer, elements,
per_quadrature_point, fem);
}
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <> class DataAccessor<UInt> : public virtual DataAccessorBase {
public:
DataAccessor() = default;
~DataAccessor() override = default;
virtual UInt getNbData(const Array<UInt> & elements,
const SynchronizationTag & tag) const = 0;
virtual void packData(CommunicationBuffer & buffer,
const Array<UInt> & element,
const SynchronizationTag & tag) const = 0;
virtual void unpackData(CommunicationBuffer & buffer,
const Array<UInt> & element,
const SynchronizationTag & tag) = 0;
/* ------------------------------------------------------------------------ */
public:
template <typename T, bool pack_helper>
static void packUnpackDOFDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<UInt> & dofs);
template <typename T>
static inline void packDOFDataHelper(const Array<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
packUnpackDOFDataHelper<T, true>(const_cast<Array<T> &>(data_to_pack),
buffer, dofs);
}
template <typename T>
static inline void unpackDOFDataHelper(Array<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
packUnpackDOFDataHelper<T, false>(data_to_unpack, buffer, dofs);
}
};
/* -------------------------------------------------------------------------- */
template <typename T> class AddOperation {
public:
inline T operator()(T & a, T & b) { return a + b; };
};
template <typename T> class IdentityOperation {
public:
inline T & operator()(T &, T & b) { return b; };
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <template <class> class Op, class T>
class ReduceUIntDataAccessor : public virtual DataAccessor<UInt> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ReduceUIntDataAccessor(Array<T> & data, const SynchronizationTag & tag)
: data(data), tag(tag) {}
~ReduceUIntDataAccessor() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<UInt> & elements,
const SynchronizationTag & tag) const override {
if (tag != this->tag)
return 0;
Vector<T> tmp(data.getNbComponent());
return elements.size() * CommunicationBuffer::sizeInBuffer(tmp);
}
/* ------------------------------------------------------------------------ */
void packData(CommunicationBuffer & buffer, const Array<UInt> & elements,
const SynchronizationTag & tag) const override {
if (tag != this->tag)
return;
auto data_it = data.begin(data.getNbComponent());
for (auto el : elements) {
buffer << Vector<T>(data_it[el]);
}
}
/* ------------------------------------------------------------------------ */
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & elements,
const SynchronizationTag & tag) override {
if (tag != this->tag)
return;
auto data_it = data.begin(data.getNbComponent());
for (auto el : elements) {
Vector<T> unpacked(data.getNbComponent());
Vector<T> vect(data_it[el]);
buffer >> unpacked;
vect = oper(vect, unpacked);
}
}
protected:
/// data to (un)pack
Array<T> & data;
/// Tag to consider
SynchronizationTag tag;
/// reduction operator
Op<Vector<T>> oper;
};
/* -------------------------------------------------------------------------- */
template <class T>
using SimpleUIntDataAccessor = ReduceUIntDataAccessor<IdentityOperation, T>;
} // akantu
#endif /* __AKANTU_DATA_ACCESSOR_HH__ */
diff --git a/src/synchronizer/dof_synchronizer.cc b/src/synchronizer/dof_synchronizer.cc
index 944332113..ed0a9bcf2 100644
--- a/src/synchronizer/dof_synchronizer.cc
+++ b/src/synchronizer/dof_synchronizer.cc
@@ -1,280 +1,279 @@
/**
* @file dof_synchronizer.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
- * @date last modification: Wed Oct 21 2015
+ * @date last modification: Tue Feb 06 2018
*
* @brief DOF synchronizing object implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_synchronizer.hh"
#include "aka_iterators.hh"
#include "dof_manager_default.hh"
#include "mesh.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* A DOFSynchronizer needs a mesh and the number of degrees of freedom
* per node to be created. In the constructor computes the local and global dof
* number for each dof. The member
* proc_informations (std vector) is resized with the number of mpi
* processes. Each entry in the vector is a PerProcInformations object
* that contains the interactions of the current mpi process (prank) with the
* mpi process corresponding to the position of that entry. Every
* ProcInformations object contains one array with the dofs that have
* to be sent to prank and a second one with dofs that willl be received form
* prank.
* This information is needed for the asychronous communications. The
* constructor sets up this information.
*/
DOFSynchronizer::DOFSynchronizer(DOFManagerDefault & dof_manager, const ID & id,
MemoryID memory_id)
: SynchronizerImpl<UInt>(dof_manager.getCommunicator(), id, memory_id),
root(0), dof_manager(dof_manager),
root_dofs(0, 1, "dofs-to-receive-from-master"), dof_changed(true) {
std::vector<ID> dof_ids = dof_manager.getDOFIDs();
// Transfers nodes to global equation numbers in new schemes
for (const ID & dof_id : dof_ids) {
registerDOFs(dof_id);
}
this->initScatterGatherCommunicationScheme();
}
/* -------------------------------------------------------------------------- */
DOFSynchronizer::~DOFSynchronizer() = default;
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::registerDOFs(const ID & dof_id) {
if (this->nb_proc == 1)
return;
if (dof_manager.getSupportType(dof_id) != _dst_nodal)
return;
using const_scheme_iterator = Communications<UInt>::const_scheme_iterator;
const auto equation_numbers = dof_manager.getLocalEquationNumbers(dof_id);
const auto & associated_nodes = dof_manager.getDOFsAssociatedNodes(dof_id);
const auto & node_synchronizer = dof_manager.getMesh().getNodeSynchronizer();
const auto & node_communications = node_synchronizer.getCommunications();
auto transcode_node_to_global_dof_scheme =
[this, &associated_nodes,
&equation_numbers](const_scheme_iterator it, const_scheme_iterator end,
const CommunicationSendRecv & sr) -> void {
for (; it != end; ++it) {
auto & scheme = communications.createScheme(it->first, sr);
const auto & node_scheme = it->second;
for (auto & node : node_scheme) {
auto an_begin = associated_nodes.begin();
auto an_it = an_begin;
auto an_end = associated_nodes.end();
std::vector<UInt> global_dofs_per_node;
while ((an_it = std::find(an_it, an_end, node)) != an_end) {
UInt pos = an_it - an_begin;
UInt local_eq_num = equation_numbers(pos);
UInt global_eq_num =
dof_manager.localToGlobalEquationNumber(local_eq_num);
global_dofs_per_node.push_back(global_eq_num);
++an_it;
}
std::sort(global_dofs_per_node.begin(), global_dofs_per_node.end());
std::transform(global_dofs_per_node.begin(), global_dofs_per_node.end(),
global_dofs_per_node.begin(), [this](UInt g) -> UInt {
UInt l = dof_manager.globalToLocalEquationNumber(g);
return l;
});
for (auto & leqnum : global_dofs_per_node) {
scheme.push_back(leqnum);
}
}
}
};
for (auto sr_it = send_recv_t::begin(); sr_it != send_recv_t::end();
++sr_it) {
auto ncs_it = node_communications.begin_scheme(*sr_it);
auto ncs_end = node_communications.end_scheme(*sr_it);
transcode_node_to_global_dof_scheme(ncs_it, ncs_end, *sr_it);
}
dof_changed = true;
}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::initScatterGatherCommunicationScheme() {
AKANTU_DEBUG_IN();
if (this->nb_proc == 1) {
dof_changed = false;
AKANTU_DEBUG_OUT();
return;
}
UInt nb_dofs = dof_manager.getLocalSystemSize();
this->root_dofs.clear();
this->master_receive_dofs.clear();
Array<UInt> dofs_to_send;
for (UInt n = 0; n < nb_dofs; ++n) {
if (dof_manager.isLocalOrMasterDOF(n)) {
auto & receive_per_proc = master_receive_dofs[this->root];
UInt global_dof = dof_manager.localToGlobalEquationNumber(n);
root_dofs.push_back(n);
receive_per_proc.push_back(global_dof);
dofs_to_send.push_back(global_dof);
}
}
if (this->rank == UInt(this->root)) {
Array<UInt> nb_dof_per_proc(this->nb_proc);
communicator.gather(dofs_to_send.size(), nb_dof_per_proc);
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == UInt(this->root))
continue;
auto & receive_per_proc = master_receive_dofs[p];
receive_per_proc.resize(nb_dof_per_proc(p));
if (nb_dof_per_proc(p) != 0)
requests.push_back(communicator.asyncReceive(
receive_per_proc, p,
Tag::genTag(p, 0, Tag::_GATHER_INITIALIZATION, this->hash_id)));
}
communicator.waitAll(requests);
communicator.freeCommunicationRequest(requests);
} else {
communicator.gather(dofs_to_send.size(), this->root);
AKANTU_DEBUG(dblDebug,
"I have " << nb_dofs << " dofs (" << dofs_to_send.size()
<< " to send to master proc");
if (dofs_to_send.size() != 0)
communicator.send(dofs_to_send, this->root,
Tag::genTag(this->rank, 0, Tag::_GATHER_INITIALIZATION,
this->hash_id));
}
dof_changed = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
bool DOFSynchronizer::hasChanged() {
communicator.allReduce(dof_changed, SynchronizerOperation::_lor);
return dof_changed;
}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::onNodesAdded(const Array<UInt> & nodes_list) {
auto dof_ids = dof_manager.getDOFIDs();
const auto & node_synchronizer = dof_manager.getMesh().getNodeSynchronizer();
const auto & node_communications = node_synchronizer.getCommunications();
std::set<UInt> relevant_nodes;
std::map<UInt, std::vector<UInt>> nodes_per_proc[2];
for (auto sr_it = send_recv_t::begin(); sr_it != send_recv_t::end();
++sr_it) {
auto sit = node_communications.begin_scheme(*sr_it);
auto send = node_communications.end_scheme(*sr_it);
for (; sit != send; ++sit) {
auto proc = sit->first;
const auto & scheme = sit->second;
for (auto node : nodes_list) {
if (scheme.find(node) == UInt(-1))
continue;
relevant_nodes.insert(node);
nodes_per_proc[*sr_it][proc].push_back(node);
}
}
}
std::map<UInt, std::vector<UInt>> dofs_per_proc[2];
for (auto & dof_id : dof_ids) {
const auto & associated_nodes = dof_manager.getDOFsAssociatedNodes(dof_id);
const auto & local_equation_numbers =
dof_manager.getEquationsNumbers(dof_id);
for (auto tuple : zip(associated_nodes, local_equation_numbers)) {
UInt assoc_node;
UInt local_eq_num;
std::tie(assoc_node, local_eq_num) = tuple;
for (auto sr_it = send_recv_t::begin(); sr_it != send_recv_t::end();
++sr_it) {
for (auto & pair : nodes_per_proc[*sr_it]) {
if (std::find(pair.second.end(), pair.second.end(), assoc_node) !=
pair.second.end()) {
dofs_per_proc[*sr_it][pair.first].push_back(local_eq_num);
}
}
}
}
}
for (auto sr_it = send_recv_t::begin(); sr_it != send_recv_t::end();
++sr_it) {
for (auto & pair : dofs_per_proc[*sr_it]) {
std::sort(pair.second.begin(), pair.second.end(),
[this](UInt la, UInt lb) -> bool {
UInt ga = dof_manager.localToGlobalEquationNumber(la);
UInt gb = dof_manager.localToGlobalEquationNumber(lb);
return ga < gb;
});
auto & scheme = communications.getScheme(pair.first, *sr_it);
for (auto leq : pair.second) {
scheme.push_back(leq);
}
}
}
dof_changed = true;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/dof_synchronizer.hh b/src/synchronizer/dof_synchronizer.hh
index 8fbd31a28..a5184a9e1 100644
--- a/src/synchronizer/dof_synchronizer.hh
+++ b/src/synchronizer/dof_synchronizer.hh
@@ -1,112 +1,111 @@
/**
* @file dof_synchronizer.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Synchronize Array of DOFs
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Mesh;
class DOFManagerDefault;
}
#ifndef __AKANTU_DOF_SYNCHRONIZER_HH__
#define __AKANTU_DOF_SYNCHRONIZER_HH__
namespace akantu {
class DOFSynchronizer : public SynchronizerImpl<UInt> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFSynchronizer(DOFManagerDefault & dof_manager,
const ID & id = "dof_synchronizer", MemoryID memory_id = 0);
~DOFSynchronizer() override;
virtual void registerDOFs(const ID & dof_id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename T>
/// Gather the DOF value on the root proccessor
void gather(const Array<T> & to_gather, Array<T> & gathered);
/// Gather the DOF value on the root proccessor
template <typename T> void gather(const Array<T> & to_gather);
/// Scatter a DOF Array form root to all processors
template <typename T>
void scatter(Array<T> & scattered, const Array<T> & to_scatter);
/// Scatter a DOF Array form root to all processors
template <typename T> void scatter(Array<T> & scattered);
template <typename T> void synchronize(Array<T> & vector) const;
template <template <class> class Op, typename T>
void reduceSynchronize(Array<T> & vector) const;
void onNodesAdded(const Array<UInt> & nodes);
protected:
/// check if dof changed set on at least one processor
bool hasChanged();
/// init the scheme for scatter and gather operation, need extra memory
void initScatterGatherCommunicationScheme();
Int getRank(const UInt & /*node*/) const final { AKANTU_TO_IMPLEMENT(); }
private:
/// Root processor for scatter/gather operations
Int root;
/// information on the dofs
DOFManagerDefault & dof_manager;
/// dofs from root
Array<UInt> root_dofs;
/// Dofs received from slaves proc (only on master)
std::map<UInt, Array<UInt>> master_receive_dofs;
bool dof_changed;
};
} // akantu
#include "dof_synchronizer_inline_impl.cc"
#endif /* __AKANTU_DOF_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/dof_synchronizer_inline_impl.cc b/src/synchronizer/dof_synchronizer_inline_impl.cc
index 9165512ca..1a6cd6d30 100644
--- a/src/synchronizer/dof_synchronizer_inline_impl.cc
+++ b/src/synchronizer/dof_synchronizer_inline_impl.cc
@@ -1,298 +1,297 @@
/**
* @file dof_synchronizer_inline_impl.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
- * @date last modification: Tue Dec 09 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief DOFSynchronizer inline implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
#include "data_accessor.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_CC__
#define __AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFSynchronizer::gather(const Array<T> & to_gather, Array<T> & gathered) {
if (this->hasChanged())
initScatterGatherCommunicationScheme();
AKANTU_DEBUG_ASSERT(this->rank == UInt(this->root),
"This function cannot be called on a slave processor");
AKANTU_DEBUG_ASSERT(to_gather.size() ==
this->dof_manager.getLocalSystemSize(),
"The array to gather does not have the correct size");
AKANTU_DEBUG_ASSERT(gathered.size() == this->dof_manager.getSystemSize(),
"The gathered array does not have the correct size");
if (this->nb_proc == 1) {
gathered.copy(to_gather, true);
AKANTU_DEBUG_OUT();
return;
}
std::map<UInt, CommunicationBuffer> buffers;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p == UInt(this->root))
continue;
auto receive_it = this->master_receive_dofs.find(p);
AKANTU_DEBUG_ASSERT(receive_it != this->master_receive_dofs.end(),
"Could not find the receive list for dofs of proc "
<< p);
const Array<UInt> & receive_dofs = receive_it->second;
if (receive_dofs.size() == 0)
continue;
CommunicationBuffer & buffer = buffers[p];
buffer.resize(receive_dofs.size() * to_gather.getNbComponent() * sizeof(T));
AKANTU_DEBUG_INFO(
"Preparing to receive data for "
<< receive_dofs.size() << " dofs from processor " << p << " "
<< Tag::genTag(p, this->root, Tag::_GATHER, this->hash_id));
requests.push_back(communicator.asyncReceive(
buffer, p, Tag::genTag(p, this->root, Tag::_GATHER, this->hash_id)));
}
auto data_gathered_it = gathered.begin(to_gather.getNbComponent());
{ // copy master data
auto data_to_gather_it = to_gather.begin(to_gather.getNbComponent());
for (auto local_dof : root_dofs) {
UInt global_dof = dof_manager.localToGlobalEquationNumber(local_dof);
Vector<T> dof_data_gathered = data_gathered_it[global_dof];
Vector<T> dof_data_to_gather = data_to_gather_it[local_dof];
dof_data_gathered = dof_data_to_gather;
}
}
auto rr = UInt(-1);
while ((rr = communicator.waitAny(requests)) != UInt(-1)) {
CommunicationRequest & request = requests[rr];
UInt sender = request.getSource();
AKANTU_DEBUG_ASSERT(this->master_receive_dofs.find(sender) !=
this->master_receive_dofs.end() &&
buffers.find(sender) != buffers.end(),
"Missing infos concerning proc " << sender);
const Array<UInt> & receive_dofs =
this->master_receive_dofs.find(sender)->second;
CommunicationBuffer & buffer = buffers[sender];
for (auto global_dof : receive_dofs) {
Vector<T> dof_data = data_gathered_it[global_dof];
buffer >> dof_data;
}
requests.erase(requests.begin() + rr);
}
}
/* -------------------------------------------------------------------------- */
template <typename T> void DOFSynchronizer::gather(const Array<T> & to_gather) {
AKANTU_DEBUG_IN();
if (this->hasChanged())
initScatterGatherCommunicationScheme();
AKANTU_DEBUG_ASSERT(this->rank != UInt(this->root),
"This function cannot be called on the root processor");
AKANTU_DEBUG_ASSERT(to_gather.size() ==
this->dof_manager.getLocalSystemSize(),
"The array to gather does not have the correct size");
if (this->root_dofs.size() == 0) {
AKANTU_DEBUG_OUT();
return;
}
CommunicationBuffer buffer(this->root_dofs.size() *
to_gather.getNbComponent() * sizeof(T));
auto data_it = to_gather.begin(to_gather.getNbComponent());
for (auto dof : this->root_dofs) {
Vector<T> data = data_it[dof];
buffer << data;
}
AKANTU_DEBUG_INFO("Gathering data for "
<< to_gather.size() << " dofs on processor " << this->root
<< " "
<< Tag::genTag(this->rank, 0, Tag::_GATHER, this->hash_id));
communicator.send(buffer, this->root,
Tag::genTag(this->rank, 0, Tag::_GATHER, this->hash_id));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFSynchronizer::scatter(Array<T> & scattered,
const Array<T> & to_scatter) {
AKANTU_DEBUG_IN();
if (this->hasChanged())
initScatterGatherCommunicationScheme();
AKANTU_DEBUG_ASSERT(this->rank == UInt(this->root),
"This function cannot be called on a slave processor");
AKANTU_DEBUG_ASSERT(scattered.size() ==
this->dof_manager.getLocalSystemSize(),
"The scattered array does not have the correct size");
AKANTU_DEBUG_ASSERT(to_scatter.size() == this->dof_manager.getSystemSize(),
"The array to scatter does not have the correct size");
if (this->nb_proc == 1) {
scattered.copy(to_scatter, true);
AKANTU_DEBUG_OUT();
return;
}
std::map<UInt, CommunicationBuffer> buffers;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
auto data_to_scatter_it = to_scatter.begin(to_scatter.getNbComponent());
if (p == this->rank) {
auto data_scattered_it = scattered.begin(to_scatter.getNbComponent());
// copy the data for the local processor
for (auto local_dof : root_dofs) {
auto global_dof = dof_manager.localToGlobalEquationNumber(local_dof);
Vector<T> dof_data_to_scatter = data_to_scatter_it[global_dof];
Vector<T> dof_data_scattered = data_scattered_it[local_dof];
dof_data_scattered = dof_data_to_scatter;
}
continue;
}
const Array<UInt> & receive_dofs =
this->master_receive_dofs.find(p)->second;
// prepare the send buffer
CommunicationBuffer & buffer = buffers[p];
buffer.resize(receive_dofs.size() * scattered.getNbComponent() * sizeof(T));
// pack the data
for (auto global_dof : receive_dofs) {
Vector<T> dof_data_to_scatter = data_to_scatter_it[global_dof];
buffer << dof_data_to_scatter;
}
// send the data
requests.push_back(communicator.asyncSend(
buffer, p, Tag::genTag(p, 0, Tag::_SCATTER, this->hash_id)));
}
// wait a clean communications
communicator.waitAll(requests);
communicator.freeCommunicationRequest(requests);
// synchronize slave and ghost nodes
synchronize(scattered);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T> void DOFSynchronizer::scatter(Array<T> & scattered) {
AKANTU_DEBUG_IN();
if (this->hasChanged())
this->initScatterGatherCommunicationScheme();
AKANTU_DEBUG_ASSERT(this->rank != UInt(this->root),
"This function cannot be called on the root processor");
AKANTU_DEBUG_ASSERT(scattered.size() ==
this->dof_manager.getLocalSystemSize(),
"The scattered array does not have the correct size");
// prepare the data
auto data_scattered_it = scattered.begin(scattered.getNbComponent());
CommunicationBuffer buffer(this->root_dofs.size() *
scattered.getNbComponent() * sizeof(T));
// receive the data
communicator.receive(
buffer, this->root,
Tag::genTag(this->rank, 0, Tag::_SCATTER, this->hash_id));
// unpack the data
for (auto local_dof : root_dofs) {
Vector<T> dof_data_scattered = data_scattered_it[local_dof];
buffer >> dof_data_scattered;
}
// synchronize the ghosts
synchronize(scattered);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFSynchronizer::synchronize(Array<T> & dof_values_to_synchronize) const {
AKANTU_DEBUG_IN();
SimpleUIntDataAccessor<T> data_accessor(dof_values_to_synchronize,
_gst_whatever);
this->synchronizeOnce(data_accessor, _gst_whatever);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <class> class Op, typename T>
void DOFSynchronizer::reduceSynchronize(Array<T> & dof_vector) const {
AKANTU_DEBUG_IN();
ReduceUIntDataAccessor<Op, T> data_accessor(dof_vector, _gst_whatever);
this->synchronizeOnce(data_accessor, _gst_whatever);
AKANTU_DEBUG_OUT();
}
} // akantu
#endif /* __AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_CC__ */
diff --git a/src/synchronizer/element_info_per_processor.cc b/src/synchronizer/element_info_per_processor.cc
index a1ae4e5a4..b39152c38 100644
--- a/src/synchronizer/element_info_per_processor.cc
+++ b/src/synchronizer/element_info_per_processor.cc
@@ -1,109 +1,110 @@
/**
* @file element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Mar 11 14:56:42 2016
+ * @date creation: Wed Mar 16 2016
+ * @date last modification: Tue Nov 07 2017
*
- * @brief
+ * @brief Helper class to distribute a mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_info_per_processor.hh"
#include "communicator.hh"
#include "element_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ElementInfoPerProc::ElementInfoPerProc(ElementSynchronizer & synchronizer,
UInt message_cnt, UInt root,
ElementType type)
: MeshAccessor(synchronizer.getMesh()), synchronizer(synchronizer),
rank(synchronizer.getCommunicator().whoAmI()),
nb_proc(synchronizer.getCommunicator().getNbProc()), root(root),
type(type), message_count(message_cnt), mesh(synchronizer.getMesh()),
comm(synchronizer.getCommunicator()) {}
/* -------------------------------------------------------------------------- */
void ElementInfoPerProc::fillCommunicationScheme(
const Array<UInt> & partition) {
AKANTU_DEBUG_IN();
Element element;
element.type = this->type;
auto & communications = this->synchronizer.getCommunications();
auto part = partition.begin();
std::map<UInt, Array<Element>> send_array_per_proc;
for (UInt lel = 0; lel < nb_local_element; ++lel) {
UInt nb_send = *part;
++part;
element.element = lel;
element.ghost_type = _not_ghost;
for (UInt p = 0; p < nb_send; ++p, ++part) {
UInt proc = *part;
AKANTU_DEBUG(dblAccessory,
"Must send : " << element << " to proc " << proc);
send_array_per_proc[proc].push_back(element);
}
}
for (auto & send_schemes : send_array_per_proc) {
if (send_schemes.second.size() == 0)
continue;
auto & scheme = communications.createSendScheme(send_schemes.first);
scheme.append(send_schemes.second);
}
std::map<UInt, Array<Element>> recv_array_per_proc;
for (UInt gel = 0; gel < nb_ghost_element; ++gel, ++part) {
UInt proc = *part;
element.element = gel;
element.ghost_type = _ghost;
AKANTU_DEBUG(dblAccessory,
"Must recv : " << element << " from proc " << proc);
recv_array_per_proc[proc].push_back(element);
}
for (auto & recv_schemes : recv_array_per_proc) {
if (recv_schemes.second.size() == 0)
continue;
auto & scheme = communications.createRecvScheme(recv_schemes.first);
scheme.append(recv_schemes.second);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/element_info_per_processor.hh b/src/synchronizer/element_info_per_processor.hh
index df7c8c21b..a31e70d41 100644
--- a/src/synchronizer/element_info_per_processor.hh
+++ b/src/synchronizer/element_info_per_processor.hh
@@ -1,144 +1,145 @@
/**
* @file element_info_per_processor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Mar 11 14:45:15 2016
+ * @date creation: Wed Mar 16 2016
+ * @date last modification: Tue Nov 07 2017
*
* @brief Helper classes to create the distributed synchronizer and distribute
- * a mesh
+ * a mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "communication_buffer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH__
#define __AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH__
namespace akantu {
class ElementSynchronizer;
class Communicator;
class MeshPartition;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementInfoPerProc : protected MeshAccessor {
public:
ElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root, ElementType type);
virtual void synchronizeConnectivities() = 0;
virtual void synchronizePartitions() = 0;
virtual void synchronizeTags() = 0;
virtual void synchronizeGroups() = 0;
protected:
void fillCommunicationScheme(const Array<UInt> & partition);
template <class CommunicationBuffer>
void fillElementGroupsFromBuffer(CommunicationBuffer & buffer);
template <typename T, typename BufferType>
void fillMeshDataTemplated(BufferType & buffer, const std::string & tag_name,
UInt nb_component);
template <typename BufferType>
void fillMeshData(BufferType & buffer, const std::string & tag_name,
const MeshDataTypeCode & type_code, UInt nb_component);
protected:
ElementSynchronizer & synchronizer;
UInt rank{0};
UInt nb_proc{1};
UInt root{0};
ElementType type{_not_defined};
UInt nb_tags{0};
UInt nb_nodes_per_element{0};
UInt nb_element{0};
UInt nb_local_element{0};
UInt nb_ghost_element{0};
UInt message_count{0};
Mesh & mesh;
const Communicator & comm;
};
/* -------------------------------------------------------------------------- */
class MasterElementInfoPerProc : protected ElementInfoPerProc {
public:
MasterElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root, ElementType type,
const MeshPartition & partition);
void synchronizeConnectivities() override;
void synchronizePartitions() override;
void synchronizeTags() override;
void synchronizeGroups() override;
protected:
template <typename T>
void fillTagBufferTemplated(std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name);
void fillTagBuffer(std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name);
private:
const MeshPartition & partition;
Vector<UInt> all_nb_local_element;
Vector<UInt> all_nb_ghost_element;
Vector<UInt> all_nb_element_to_send;
};
/* -------------------------------------------------------------------------- */
class SlaveElementInfoPerProc : protected ElementInfoPerProc {
public:
SlaveElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root);
void synchronizeConnectivities() override;
void synchronizePartitions() override;
void synchronizeTags() override;
void synchronizeGroups() override;
bool needSynchronize();
private:
UInt nb_element_to_receive{0};
};
} // akantu
#include "element_info_per_processor_tmpl.hh"
#endif /* __AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH__ */
diff --git a/src/synchronizer/element_info_per_processor_tmpl.hh b/src/synchronizer/element_info_per_processor_tmpl.hh
index 299a61f4a..3fb055721 100644
--- a/src/synchronizer/element_info_per_processor_tmpl.hh
+++ b/src/synchronizer/element_info_per_processor_tmpl.hh
@@ -1,145 +1,147 @@
/**
* @file element_info_per_processor_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Mar 11 15:03:12 2016
+ * @date creation: Wed Mar 16 2016
+ * @date last modification: Tue Feb 20 2018
*
- * @brief
+ * @brief Helper classes to create the distributed synchronizer and distribute
+ * a mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "element_info_per_processor.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH__
#define __AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, typename BufferType>
void ElementInfoPerProc::fillMeshDataTemplated(BufferType & buffer,
const std::string & tag_name,
UInt nb_component) {
AKANTU_DEBUG_ASSERT(this->mesh.getNbElement(this->type) == nb_local_element,
"Did not got enought informations for the tag "
<< tag_name << " and the element type " << this->type
<< ":"
<< "_not_ghost."
<< " Got " << nb_local_element << " values, expected "
<< mesh.getNbElement(this->type));
MeshData & mesh_data = this->getMeshData();
mesh_data.registerElementalData<T>(tag_name);
Array<T> & data = mesh_data.getElementalDataArrayAlloc<T>(
tag_name, this->type, _not_ghost, nb_component);
data.resize(nb_local_element);
/// unpacking the data, element by element
for (UInt i(0); i < nb_local_element; ++i) {
for (UInt j(0); j < nb_component; ++j) {
buffer >> data(i, j);
}
}
AKANTU_DEBUG_ASSERT(mesh.getNbElement(this->type, _ghost) == nb_ghost_element,
"Did not got enought informations for the tag "
<< tag_name << " and the element type " << this->type
<< ":"
<< "_ghost."
<< " Got " << nb_ghost_element << " values, expected "
<< mesh.getNbElement(this->type, _ghost));
Array<T> & data_ghost = mesh_data.getElementalDataArrayAlloc<T>(
tag_name, this->type, _ghost, nb_component);
data_ghost.resize(nb_ghost_element);
/// unpacking the ghost data, element by element
for (UInt j(0); j < nb_ghost_element; ++j) {
for (UInt k(0); k < nb_component; ++k) {
buffer >> data_ghost(j, k);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename BufferType>
void ElementInfoPerProc::fillMeshData(BufferType & buffer,
const std::string & tag_name,
const MeshDataTypeCode & type_code,
UInt nb_component) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
fillMeshDataTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(buffer, tag_name, \
nb_component); \
break; \
}
switch (type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not determine the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
template <class CommunicationBuffer>
void ElementInfoPerProc::fillElementGroupsFromBuffer(
CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
Element el;
el.type = type;
for (auto ghost_type : ghost_types) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
el.ghost_type = ghost_type;
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
std::vector<std::string> element_to_group;
buffer >> element_to_group;
AKANTU_DEBUG_ASSERT(e < mesh.getNbElement(type, ghost_type),
"The mesh does not have the element " << e);
for (auto && element : element_to_group) {
mesh.getElementGroup(element).add(el, false, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH__ */
diff --git a/src/synchronizer/element_synchronizer.cc b/src/synchronizer/element_synchronizer.cc
index 32698e302..a0e65e5cc 100644
--- a/src/synchronizer/element_synchronizer.cc
+++ b/src/synchronizer/element_synchronizer.cc
@@ -1,369 +1,368 @@
/**
* @file element_synchronizer.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Sep 01 2010
- * @date last modification: Fri Jan 22 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief implementation of a communicator using a static_communicator for
* real
* send/receive
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ElementSynchronizer::ElementSynchronizer(Mesh & mesh, const ID & id,
MemoryID memory_id,
bool register_to_event_manager,
EventHandlerPriority event_priority)
: SynchronizerImpl<Element>(mesh.getCommunicator(), id, memory_id),
mesh(mesh), element_to_prank("element_to_prank", id, memory_id) {
AKANTU_DEBUG_IN();
if (register_to_event_manager)
this->mesh.registerEventHandler(*this, event_priority);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementSynchronizer::ElementSynchronizer(const ElementSynchronizer & other,
const ID & id,
bool register_to_event_manager,
EventHandlerPriority event_priority)
: SynchronizerImpl<Element>(other, id), mesh(other.mesh),
element_to_prank("element_to_prank", id, other.memory_id) {
AKANTU_DEBUG_IN();
element_to_prank.copy(other.element_to_prank);
if (register_to_event_manager)
this->mesh.registerEventHandler(*this, event_priority);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementSynchronizer::~ElementSynchronizer() = default;
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::substituteElements(
const std::map<Element, Element> & old_to_new_elements) {
auto found_element_end = old_to_new_elements.end();
// substitute old elements with new ones
for (auto && sr : iterate_send_recv) {
for (auto && scheme_pair : communications.iterateSchemes(sr)) {
auto & list = scheme_pair.second;
for (auto & el : list) {
auto found_element_it = old_to_new_elements.find(el);
if (found_element_it != found_element_end)
el = found_element_it->second;
}
}
}
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::onElementsChanged(
const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list, const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) {
// create a map to link old elements to new ones
std::map<Element, Element> old_to_new_elements;
for (UInt el = 0; el < old_elements_list.size(); ++el) {
AKANTU_DEBUG_ASSERT(old_to_new_elements.find(old_elements_list(el)) ==
old_to_new_elements.end(),
"The same element cannot appear twice in the list");
old_to_new_elements[old_elements_list(el)] = new_elements_list(el);
}
substituteElements(old_to_new_elements);
communications.invalidateSizes();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::onElementsRemoved(
const Array<Element> & element_to_remove,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent &) {
AKANTU_DEBUG_IN();
this->removeElements(element_to_remove);
this->renumberElements(new_numbering);
communications.invalidateSizes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::buildElementToPrank() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
element_to_prank.initialize(mesh, _spatial_dimension = spatial_dimension,
_element_kind = _ek_not_defined,
_with_nb_element = true, _default_value = rank);
/// assign prank to all ghost elements
for (auto && scheme : communications.iterateSchemes(_recv)) {
auto & recv = scheme.second;
auto proc = scheme.first;
for (auto & element : recv) {
element_to_prank(element) = proc;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Int ElementSynchronizer::getRank(const Element & element) const {
if (not element_to_prank.exists(element.type, element.ghost_type)) {
// Nicolas: Ok This is nasty I know....
const_cast<ElementSynchronizer *>(this)->buildElementToPrank();
}
return element_to_prank(element);
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::reset() {
AKANTU_DEBUG_IN();
communications.resetSchemes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::removeElements(
const Array<Element> & element_to_remove) {
AKANTU_DEBUG_IN();
std::vector<CommunicationRequest> send_requests;
std::map<UInt, Array<UInt>> list_of_elements_per_proc;
auto filter_list = [](const Array<UInt> & keep, Array<Element> & list) {
Array<Element> new_list;
for (UInt e = 0; e < keep.size() - 1; ++e) {
Element & el = list(keep(e));
new_list.push_back(el);
}
list.copy(new_list);
};
// Handling ghost elements
for (auto && scheme_pair : communications.iterateSchemes(_recv)) {
auto proc = scheme_pair.first;
auto & recv = scheme_pair.second;
Array<UInt> & keep_list = list_of_elements_per_proc[proc];
auto rem_it = element_to_remove.begin();
auto rem_end = element_to_remove.end();
for (auto && pair : enumerate(recv)) {
const auto & el = std::get<1>(pair);
auto pos = std::find(rem_it, rem_end, el);
if (pos == rem_end) {
keep_list.push_back(std::get<0>(pair));
}
}
keep_list.push_back(UInt(-1)); // To no send empty arrays
auto && tag = Tag::genTag(proc, 0, Tag::_MODIFY_SCHEME, this->hash_id);
AKANTU_DEBUG_INFO("Sending a message of size "
<< keep_list.size() << " to proc " << proc << " TAG("
<< tag << ")");
send_requests.push_back(this->communicator.asyncSend(keep_list, proc, tag));
#ifndef AKANTU_NDEBUG
auto old_size = recv.size();
#endif
filter_list(keep_list, recv);
AKANTU_DEBUG_INFO("I had " << old_size << " elements to recv from proc "
<< proc << " and " << keep_list.size()
<< " elements to keep. I have " << recv.size()
<< " elements left.");
}
for (auto && scheme_pair : communications.iterateSchemes(_send)) {
auto proc = scheme_pair.first;
auto & send = scheme_pair.second;
CommunicationStatus status;
auto && tag = Tag::genTag(rank, 0, Tag::_MODIFY_SCHEME, this->hash_id);
AKANTU_DEBUG_INFO("Getting number of elements of proc "
<< proc << " to keep - TAG(" << tag << ")");
this->communicator.probe<UInt>(proc, tag, status);
Array<UInt> keep_list(status.size());
AKANTU_DEBUG_INFO("Receiving list of elements ("
<< keep_list.size() << " elements) to keep for proc "
<< proc << " TAG(" << tag << ")");
this->communicator.receive(keep_list, proc, tag);
#ifndef AKANTU_NDEBUG
auto old_size = send.size();
#endif
filter_list(keep_list, send);
AKANTU_DEBUG_INFO("I had " << old_size << " elements to send to proc "
<< proc << " and " << keep_list.size()
<< " elements to keep. I have " << send.size()
<< " elements left.");
}
this->communicator.waitAll(send_requests);
this->communicator.freeCommunicationRequest(send_requests);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::renumberElements(
const ElementTypeMapArray<UInt> & new_numbering) {
for (auto && sr : iterate_send_recv) {
for (auto && scheme_pair : communications.iterateSchemes(sr)) {
auto & list = scheme_pair.second;
for (auto && el : list) {
if (new_numbering.exists(el.type, el.ghost_type))
el.element = new_numbering(el);
}
}
}
}
/* -------------------------------------------------------------------------- */
UInt ElementSynchronizer::sanityCheckDataSize(
const Array<Element> & elements, const SynchronizationTag &) const {
UInt size = 0;
size += sizeof(SynchronizationTag); // tag
size += sizeof(UInt); // comm_desc.getNbData();
size += sizeof(UInt); // comm_desc.getProc();
size += sizeof(UInt); // mesh.getCommunicator().whoAmI();
// barycenters
size += (elements.size() * mesh.getSpatialDimension() * sizeof(Real));
return size;
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::packSanityCheckData(
CommunicationDescriptor<Element> & comm_desc) const {
auto & buffer = comm_desc.getBuffer();
buffer << comm_desc.getTag();
buffer << comm_desc.getNbData();
buffer << comm_desc.getProc();
buffer << mesh.getCommunicator().whoAmI();
auto & send_element = comm_desc.getScheme();
/// pack barycenters in debug mode
for (auto && element : send_element) {
Vector<Real> barycenter(mesh.getSpatialDimension());
mesh.getBarycenter(element, barycenter);
buffer << barycenter;
}
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::unpackSanityCheckData(
CommunicationDescriptor<Element> & comm_desc) const {
auto & buffer = comm_desc.getBuffer();
const auto & tag = comm_desc.getTag();
auto nb_data = comm_desc.getNbData();
auto proc = comm_desc.getProc();
auto rank = mesh.getCommunicator().whoAmI();
decltype(nb_data) recv_nb_data;
decltype(proc) recv_proc;
decltype(rank) recv_rank;
SynchronizationTag t;
buffer >> t;
buffer >> recv_nb_data;
buffer >> recv_proc;
buffer >> recv_rank;
AKANTU_DEBUG_ASSERT(
t == tag, "The tag received does not correspond to the tag expected");
AKANTU_DEBUG_ASSERT(
nb_data == recv_nb_data,
"The nb_data received does not correspond to the nb_data expected");
AKANTU_DEBUG_ASSERT(UInt(recv_rank) == proc,
"The rank received does not correspond to the proc");
AKANTU_DEBUG_ASSERT(recv_proc == UInt(rank),
"The proc received does not correspond to the rank");
auto & recv_element = comm_desc.getScheme();
auto spatial_dimension = mesh.getSpatialDimension();
for (auto && element : recv_element) {
Vector<Real> barycenter_loc(spatial_dimension);
mesh.getBarycenter(element, barycenter_loc);
Vector<Real> barycenter(spatial_dimension);
buffer >> barycenter;
auto dist = barycenter_loc.distance(barycenter);
if (not Math::are_float_equal(dist, 0.))
AKANTU_EXCEPTION("Unpacking an unknown value for the element "
<< element << "(barycenter " << barycenter_loc
<< " != buffer " << barycenter << ") [" << dist
<< "] - tag: " << tag << " comm from " << proc << " to "
<< rank);
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/element_synchronizer.hh b/src/synchronizer/element_synchronizer.hh
index 8764beb79..d72058515 100644
--- a/src/synchronizer/element_synchronizer.hh
+++ b/src/synchronizer/element_synchronizer.hh
@@ -1,216 +1,215 @@
/**
* @file element_synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Main element synchronizer
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_SYNCHRONIZER_HH__
#define __AKANTU_ELEMENT_SYNCHRONIZER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "mesh_partition.hh"
#include "synchronizer_impl.hh"
namespace akantu {
class Mesh;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer : public SynchronizerImpl<Element>,
public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementSynchronizer(Mesh & mesh, const ID & id = "element_synchronizer",
MemoryID memory_id = 0,
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
ElementSynchronizer(const ElementSynchronizer & other,
const ID & id = "element_synchronizer_copy",
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
public:
~ElementSynchronizer() override;
friend class ElementInfoPerProc;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/// mesh event handler onElementsChanged
void onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) override;
/// mesh event handler onRemovedElement
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
/// mesh event handler onNodesAdded
void onNodesAdded(const Array<UInt> & /* nodes_list*/,
const NewNodesEvent & /*event*/) override{};
/// mesh event handler onRemovedNodes
void onNodesRemoved(const Array<UInt> & /*nodes_list*/,
const Array<UInt> & /*new_numbering*/,
const RemovedNodesEvent & /*event*/) override{};
/// mesh event handler onElementsAdded
void onElementsAdded(const Array<Element> & /*elements_list*/,
const NewElementsEvent & /*event*/) override{};
protected:
/// reset send and recv element lists
void reset();
/// remove elements from the synchronizer without renumbering them
void removeElements(const Array<Element> & element_to_remove);
/// renumber the elements in the synchronizer
void renumberElements(const ElementTypeMapArray<UInt> & new_numbering);
/// build processor to element correspondence
void buildElementToPrank();
protected:
/// fill the nodes type vector
void fillNodesType(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name, const ElementType & el_type,
const Array<UInt> & partition_num);
template <typename T>
void fillTagBufferTemplated(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);
void 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);
/// function that handels the MeshData to be split (root side)
static void synchronizeTagsSend(ElementSynchronizer & 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);
/// function that handles the MeshData to be split (other nodes)
static void synchronizeTagsRecv(ElementSynchronizer & communicator, UInt root,
Mesh & mesh, UInt nb_tags,
const ElementType & type,
UInt nb_local_element, UInt nb_ghost_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(ElementSynchronizer & communicator,
UInt root, Mesh & mesh,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(ElementSynchronizer & communicator,
UInt root, Mesh & mesh,
const ElementType & type);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsMaster(ElementSynchronizer & communicator,
UInt root, Mesh & mesh);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsSlaves(ElementSynchronizer & communicator,
UInt root, Mesh & mesh);
template <class CommunicationBuffer>
static void fillNodeGroupsFromBuffer(ElementSynchronizer & communicator,
Mesh & mesh,
CommunicationBuffer & buffer);
/// substitute elements in the send and recv arrays
void
substituteElements(const std::map<Element, Element> & old_to_new_elements);
/* ------------------------------------------------------------------------ */
/* Sanity checks */
/* ------------------------------------------------------------------------ */
UInt sanityCheckDataSize(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
/* ------------------------------------------------------------------------ */
void packSanityCheckData(
CommunicationDescriptor<Element> & comm_desc) const override;
/* ------------------------------------------------------------------------ */
void unpackSanityCheckData(
CommunicationDescriptor<Element> & comm_desc) const override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Mesh, mesh, Mesh &);
AKANTU_GET_MACRO(ElementToRank, element_to_prank,
const ElementTypeMapArray<Int> &);
Int getRank(const Element & element) const final;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// reference to the underlying mesh
Mesh & mesh;
friend class FacetSynchronizer;
ElementTypeMapArray<Int> element_to_prank;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_ELEMENT_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/facet_synchronizer.cc b/src/synchronizer/facet_synchronizer.cc
index 9fef0f160..6c65293ee 100644
--- a/src/synchronizer/facet_synchronizer.cc
+++ b/src/synchronizer/facet_synchronizer.cc
@@ -1,514 +1,531 @@
/**
* @file facet_synchronizer.cc
*
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
+ * @date creation: Wed Nov 05 2014
+ * @date last modification: Fri Jan 26 2018
*
* @brief Facet synchronizer for parallel simulations with cohesive elments
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
*/
+
/* -------------------------------------------------------------------------- */
#include "facet_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
FacetSynchronizer::FacetSynchronizer(
Mesh & mesh, const ElementSynchronizer & element_synchronizer,
const ID & id, MemoryID memory_id)
: ElementSynchronizer(mesh, id, memory_id) {
const auto & comm = mesh.getCommunicator();
auto spatial_dimension = mesh.getSpatialDimension();
element_to_prank.initialize(mesh, _spatial_dimension = spatial_dimension - 1,
_ghost_type = _ghost, _with_nb_element = true,
_default_value = rank);
for (auto && scheme_pair :
element_synchronizer.communications.iterateSchemes(_recv)) {
auto proc = std::get<0>(scheme_pair);
const auto & scheme = std::get<1>(scheme_pair);
for (auto && elem : scheme) {
const auto & facet_to_element =
mesh.getSubelementToElement(elem.type, elem.ghost_type);
Vector<Element> facets = facet_to_element.begin(
facet_to_element.getNbComponent())[elem.element];
for (UInt f = 0; f < facets.size(); ++f) {
auto & facet = facets(f);
if (facet == ElementNull)
continue;
if (facet.ghost_type == _not_ghost)
continue;
auto & facet_rank = element_to_prank(facet);
if ((proc < UInt(facet_rank)) || (UInt(facet_rank) == rank))
facet_rank = proc;
}
}
}
ElementTypeMapArray<UInt> facet_global_connectivities(
"facet_global_connectivities", id, memory_id);
facet_global_connectivities.initialize(
mesh, _spatial_dimension = spatial_dimension - 1, _with_nb_element = true,
_with_nb_nodes_per_element = true);
mesh.getGlobalConnectivity(facet_global_connectivities);
/// init facet check tracking
ElementTypeMapArray<bool> facet_checked("facet_checked", id, memory_id);
std::vector<CommunicationRequest> send_requests;
std::map<UInt, ElementTypeMapArray<UInt>> send_facets;
std::map<UInt, ElementTypeMapArray<UInt>> connectivities;
for (auto && sr : iterate_send_recv) {
GhostType interesting_ghost_type = sr == _send ? _not_ghost : _ghost;
for (auto && scheme_pair :
element_synchronizer.communications.iterateSchemes(sr)) {
facet_checked.initialize(mesh, _spatial_dimension = spatial_dimension - 1,
_ghost_type = interesting_ghost_type,
_with_nb_element = true, _default_value = false);
auto && proc = scheme_pair.first;
auto & elements = scheme_pair.second;
auto & facet_scheme = communications.createScheme(proc, sr);
// this creates empty arrays...
auto & facet_send_elements = send_facets[proc];
auto & connectivities_for_proc = connectivities[proc];
if (sr == _send) {
connectivities_for_proc.setID(id + ":connectivities_for_proc:");
connectivities_for_proc.initialize(
mesh, _spatial_dimension = spatial_dimension - 1,
_with_nb_nodes_per_element = true);
facet_send_elements.setID(id + ":facet_send_elements");
facet_send_elements.initialize(
mesh, _spatial_dimension = spatial_dimension - 1);
}
for (auto && element : elements) {
const auto & facet_to_element =
mesh.getSubelementToElement(element.type, element.ghost_type);
Vector<Element> facets = facet_to_element.begin(
facet_to_element.getNbComponent())[element.element];
for (UInt f = 0; f < facets.size(); ++f) {
auto & facet = facets(f);
if (facet == ElementNull)
continue;
if (facet.ghost_type != interesting_ghost_type)
continue;
if (sr == _recv && UInt(element_to_prank(facet)) != proc)
continue;
auto & checked = facet_checked(facet);
if (checked)
continue;
checked = true;
if (sr == _recv) {
facet_scheme.push_back(facet);
} else {
facet_send_elements(facet.type, facet.ghost_type)
.push_back(facet.element);
}
auto & global_conn =
facet_global_connectivities(facet.type, facet.ghost_type);
Vector<UInt> conn =
global_conn.begin(global_conn.getNbComponent())[facet.element];
std::sort(conn.storage(), conn.storage() + conn.size());
connectivities_for_proc(facet.type, facet.ghost_type).push_back(conn);
}
}
}
}
/// do every communication by element type
for (auto && type : mesh.elementTypes(spatial_dimension - 1)) {
for (auto && pair : connectivities) {
auto proc = std::get<0>(pair);
const auto & connectivities_for_proc = std::get<1>(pair);
auto && tag = Tag::genTag(proc, proc, 1337);
send_requests.push_back(
comm.asyncSend(connectivities_for_proc(type, _ghost), proc, tag,
CommunicationMode::_synchronous));
}
auto nb_nodes_per_facet = Mesh::getNbNodesPerElement(type);
Array<UInt> buffer;
Element facet{type, 0, _not_ghost};
comm.receiveAnyNumber(
send_requests, buffer,
[&](auto && proc, auto && message) {
auto & local_connectivities = connectivities[proc](type, _not_ghost);
auto & list = send_facets[proc](type, _not_ghost);
auto & send_scheme = communications.getScheme(proc, _send);
std::vector<bool> checked(list.size(), false);
for (auto && c_to_match : make_view(message, nb_nodes_per_facet)) {
#if !defined(AKANTU_NDEBUG)
bool found = false;
#endif
for (auto && pair : enumerate(
make_view(local_connectivities, nb_nodes_per_facet))) {
UInt f;
Vector<UInt> local_conn;
std::tie(f, local_conn) = pair;
if (checked[f])
continue;
if (c_to_match == local_conn) {
#if !defined(AKANTU_NDEBUG)
found = true;
#endif
checked[f] = true;
facet.element = list(f);
send_scheme.push_back(facet);
break;
}
}
AKANTU_DEBUG_ASSERT(found, "facet not found");
}
},
[&]() { return Tag::genTag(rank, rank, 1337); });
}
}
// /* --------------------------------------------------------------------------
// */ void FacetSynchronizer::setupFacetSynchronization(
// ElementSynchronizer & distributed_synchronizer) {
// AKANTU_DEBUG_IN();
// Array<Element> * distrib_send_element =
// distributed_synchronizer.send_element; Array<Element> *
// distrib_recv_element = distributed_synchronizer.recv_element;
// /// build rank to facet correspondance
// ElementTypeMapArray<UInt> rank_to_facet("rank_to_facet", id);
// initRankToFacet(rank_to_facet);
// buildRankToFacet(rank_to_facet, distrib_recv_element);
// /// generate temp_send/recv element arrays with their connectivity
// Array<ElementTypeMapArray<UInt> *> temp_send_element(nb_proc);
// Array<ElementTypeMapArray<UInt> *> temp_recv_element(nb_proc);
// Array<ElementTypeMapArray<UInt> *> send_connectivity(nb_proc);
// Array<ElementTypeMapArray<UInt> *> recv_connectivity(nb_proc);
// UInt spatial_dimension = mesh.getSpatialDimension();
// for (UInt p = 0; p < nb_proc; ++p) {
// if (p == rank)
// continue;
// std::stringstream sstr;
// sstr << p;
// temp_send_element(p) = new ElementTypeMapArray<UInt>(
// "temp_send_element_proc_" + sstr.str(), id);
// mesh.initElementTypeMapArray(*temp_send_element(p), 1,
// spatial_dimension - 1);
// temp_recv_element(p) = new ElementTypeMapArray<UInt>(
// "temp_recv_element_proc_" + sstr.str(), id);
// mesh.initElementTypeMapArray(*temp_recv_element(p), 1,
// spatial_dimension - 1);
// send_connectivity(p) = new ElementTypeMapArray<UInt>(
// "send_connectivity_proc_" + sstr.str(), id);
// mesh.initElementTypeMapArray(*send_connectivity(p), 1,
// spatial_dimension - 1, true);
// recv_connectivity(p) = new ElementTypeMapArray<UInt>(
// "recv_connectivity_proc_" + sstr.str(), id);
// mesh.initElementTypeMapArray(*recv_connectivity(p), 1,
// spatial_dimension - 1, true);
// }
// /// build global connectivity arrays
// getFacetGlobalConnectivity<_not_ghost>(distributed_synchronizer,
// rank_to_facet, distrib_send_element,
// send_connectivity,
// temp_send_element);
// getFacetGlobalConnectivity<_ghost>(distributed_synchronizer, rank_to_facet,
// distrib_recv_element, recv_connectivity,
// temp_recv_element);
// /// build send/recv facet arrays
// buildSendElementList(send_connectivity, recv_connectivity,
// temp_send_element); buildRecvElementList(temp_recv_element);
// #ifndef AKANTU_NDEBUG
// /// count recv facets for each processor
// Array<UInt> nb_facets_recv(nb_proc);
// nb_facets_recv.clear();
// Mesh::type_iterator first = mesh.firstType(spatial_dimension - 1, _ghost);
// Mesh::type_iterator last = mesh.lastType(spatial_dimension - 1, _ghost);
// for (; first != last; ++first) {
// const Array<UInt> & r_to_f = rank_to_facet(*first, _ghost);
// UInt nb_facet = r_to_f.getSize();
// for (UInt f = 0; f < nb_facet; ++f) {
// UInt proc = r_to_f(f);
// if (proc != rank)
// ++nb_facets_recv(proc);
// }
// }
// for (UInt p = 0; p < nb_proc; ++p) {
// AKANTU_DEBUG_ASSERT(nb_facets_recv(p) == recv_element[p].getSize(),
// "Wrong number of recv facets");
// }
// #endif
// for (UInt p = 0; p < nb_proc; ++p) {
// delete temp_send_element(p);
// delete temp_recv_element(p);
// delete send_connectivity(p);
// delete recv_connectivity(p);
// }
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */ void FacetSynchronizer::buildSendElementList(
// const Array<ElementTypeMapArray<UInt> *> & send_connectivity,
// const Array<ElementTypeMapArray<UInt> *> & recv_connectivity,
// const Array<ElementTypeMapArray<UInt> *> & temp_send_element) {
// AKANTU_DEBUG_IN();
// StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
// UInt spatial_dimension = mesh.getSpatialDimension();
// GhostType ghost_type = _ghost;
// Mesh::type_iterator first = mesh.firstType(spatial_dimension - 1,
// ghost_type); Mesh::type_iterator last = mesh.lastType(spatial_dimension -
// 1, ghost_type);
// /// do every communication by element type
// for (; first != last; ++first) {
// ElementType facet_type = *first;
// std::vector<CommunicationRequest *> send_requests;
// UInt * send_size = new UInt[nb_proc];
// /// send asynchronous data
// for (UInt p = 0; p < nb_proc; ++p) {
// if (p == rank)
// continue;
// const Array<UInt> & recv_conn =
// (*recv_connectivity(p))(facet_type, _ghost);
// send_size[p] = recv_conn.getSize();
// /// send connectivity size
// send_requests.push_back(
// comm.asyncSend(send_size + p, 1, p, Tag::genTag(rank, p, 0)));
// /// send connectivity data
// send_requests.push_back(comm.asyncSend(
// recv_conn.storage(), recv_conn.getSize() *
// recv_conn.getNbComponent(), p, Tag::genTag(rank, p, 1)));
// }
// UInt * recv_size = new UInt[nb_proc];
// UInt nb_nodes_per_facet = Mesh::getNbNodesPerElement(facet_type);
// /// receive data
// for (UInt p = 0; p < nb_proc; ++p) {
// if (p == rank)
// continue;
// /// receive connectivity size
// comm.receive(recv_size + p, 1, p, Tag::genTag(p, rank, 0));
// Array<UInt> conn_to_match(recv_size[p], nb_nodes_per_facet);
// /// receive connectivity
// comm.receive(conn_to_match.storage(),
// conn_to_match.getSize() * conn_to_match.getNbComponent(),
// p, Tag::genTag(p, rank, 1));
// const Array<UInt> & send_conn =
// (*send_connectivity(p))(facet_type, _not_ghost);
// const Array<UInt> & list =
// (*temp_send_element(p))(facet_type, _not_ghost);
// UInt nb_local_facets = send_conn.getSize();
// AKANTU_DEBUG_ASSERT(nb_local_facets == list.getSize(),
// "connectivity and facet list have different
// sizes");
// Array<bool> checked(nb_local_facets);
// checked.clear();
// Element facet(facet_type, 0, _not_ghost, _ek_regular);
// Array<UInt>::iterator<Vector<UInt>> c_to_match_it =
// conn_to_match.begin(nb_nodes_per_facet);
// Array<UInt>::iterator<Vector<UInt>> c_to_match_end =
// conn_to_match.end(nb_nodes_per_facet);
// /// for every sent facet of other processors, find the
// /// corresponding one in the local send connectivity data in
// /// order to build the send_element arrays
// for (; c_to_match_it != c_to_match_end; ++c_to_match_it) {
// Array<UInt>::const_iterator<Vector<UInt>> c_local_it =
// send_conn.begin(nb_nodes_per_facet);
// Array<UInt>::const_iterator<Vector<UInt>> c_local_end =
// send_conn.end(nb_nodes_per_facet);
// for (UInt f = 0; f < nb_local_facets; ++f, ++c_local_it) {
// if (checked(f))
// continue;
// if ((*c_to_match_it) == (*c_local_it)) {
// checked(f) = true;
// facet.element = list(f);
// send_element[p].push_back(facet);
// break;
// }
// }
// AKANTU_DEBUG_ASSERT(c_local_it != c_local_end, "facet not found");
// }
// }
// /// wait for all communications to be done and free the
// /// communication request array
// comm.waitAll(send_requests);
// comm.freeCommunicationRequest(send_requests);
// delete[] send_size;
// delete[] recv_size;
// }
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */ void FacetSynchronizer::buildRecvElementList(
// const Array<ElementTypeMapArray<UInt> *> & temp_recv_element) {
// AKANTU_DEBUG_IN();
// UInt spatial_dimension = mesh.getSpatialDimension();
// for (UInt p = 0; p < nb_proc; ++p) {
// if (p == rank)
// continue;
// GhostType ghost_type = _ghost;
// Mesh::type_iterator first =
// mesh.firstType(spatial_dimension - 1, ghost_type);
// Mesh::type_iterator last = mesh.lastType(spatial_dimension - 1,
// ghost_type);
// for (; first != last; ++first) {
// ElementType facet_type = *first;
// const Array<UInt> & list =
// (*temp_recv_element(p))(facet_type, ghost_type);
// UInt nb_local_facets = list.getSize();
// Element facet(facet_type, 0, ghost_type, _ek_regular);
// for (UInt f = 0; f < nb_local_facets; ++f) {
// facet.element = list(f);
// recv_element[p].push_back(facet);
// }
// }
// }
// AKANTU_DEBUG_OUT();
// }
// void FacetSynchronizer::initRankToFacet(
// ElementTypeMapArray<UInt> & rank_to_facet) {
// AKANTU_DEBUG_IN();
// auto spatial_dimension = mesh.getSpatialDimension();
// for (; first != last; ++first) {
// ElementType type = *first;
// UInt nb_facet = mesh.getNbElement(type, ghost_type);
// Array<UInt> & rank_to_f = rank_to_facet(type, ghost_type);
// rank_to_f.resize(nb_facet);
// for (UInt f = 0; f < nb_facet; ++f)
// rank_to_f(f) = rank;
// }
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */ void FacetSynchronizer::buildRankToFacet(
// ElementTypeMapArray<UInt> & rank_to_facet,
// const Array<Element> * elements) {
// AKANTU_DEBUG_IN();
// for (UInt p = 0; p < nb_proc; ++p) {
// if (p == rank)
// continue;
// const Array<Element> & elem = elements[p];
// UInt nb_element = elem.getSize();
// for (UInt el = 0; el < nb_element; ++el) {
// ElementType type = elem(el).type;
// GhostType gt = elem(el).ghost_type;
// UInt el_index = elem(el).element;
// const Array<Element> & facet_to_element =
// mesh.getSubelementToElement(type, gt);
// UInt nb_facets_per_element = Mesh::getNbFacetsPerElement(type);
// ElementType facet_type = Mesh::getFacetType(type);
// for (UInt f = 0; f < nb_facets_per_element; ++f) {
// const Element & facet = facet_to_element(el_index, f);
// if (facet == ElementNull)
// continue;
// UInt facet_index = facet.element;
// GhostType facet_gt = facet.ghost_type;
// if (facet_gt == _not_ghost)
// continue;
// Array<UInt> & t_to_f = rank_to_facet(facet_type, facet_gt);
// if ((p < t_to_f(facet_index)) || (t_to_f(facet_index) == rank))
// t_to_f(facet_index) = p;
// }
// }
// }
// AKANTU_DEBUG_OUT();
// }
} // namespace akantu
diff --git a/src/synchronizer/facet_synchronizer_inline_impl.cc b/src/synchronizer/facet_synchronizer_inline_impl.cc
index 35656bd14..7d5c21329 100644
--- a/src/synchronizer/facet_synchronizer_inline_impl.cc
+++ b/src/synchronizer/facet_synchronizer_inline_impl.cc
@@ -1,127 +1,143 @@
/**
* @file facet_synchronizer_inline_impl.cc
*
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
+ * @date creation: Wed Nov 05 2014
+ * @date last modification: Tue Nov 07 2017
*
* @brief facet synchronizer inline implementation
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * 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<GhostType ghost_facets>
// inline void FacetSynchronizer::getFacetGlobalConnectivity(const
// DistributedSynchronizer & distributed_synchronizer,
// const
// ElementTypeMapArray<UInt>
// & rank_to_facet,
// const Array<Element> *
// elements,
// Array<ElementTypeMapArray<UInt>
// *> & connectivity,
// Array<ElementTypeMapArray<UInt>
// *> & facets) {
// AKANTU_DEBUG_IN();
// UInt spatial_dimension = mesh.getSpatialDimension();
// /// init facet check tracking
// ElementTypeMapArray<bool> facet_checked("facet_checked", id);
// mesh.initElementTypeMapArray(facet_checked, 1, spatial_dimension - 1);
// Mesh::type_iterator first = mesh.firstType(spatial_dimension - 1,
// ghost_facets);
// Mesh::type_iterator last = mesh.lastType(spatial_dimension - 1,
// ghost_facets);
// for (; first != last; ++first) {
// ElementType type = *first;
// Array<bool> & f_checked = facet_checked(type, ghost_facets);
// UInt nb_facet = mesh.getNbElement(type, ghost_facets);
// f_checked.resize(nb_facet);
// }
// const Array<UInt> & nodes_global_ids =
// distributed_synchronizer.mesh.getGlobalNodesIds();
// /// loop on every processor
// for (UInt p = 0; p < nb_proc; ++p) {
// if (p == rank) continue;
// /// reset facet check
// Mesh::type_iterator first = mesh.firstType(spatial_dimension - 1,
// ghost_facets);
// Mesh::type_iterator last = mesh.lastType(spatial_dimension - 1,
// ghost_facets);
// for (; first != last; ++first) {
// ElementType type = *first;
// Array<bool> & f_checked = facet_checked(type, ghost_facets);
// f_checked.clear();
// }
// ElementTypeMapArray<UInt> & global_conn = (*connectivity(p));
// const Array<Element> & elem = elements[p];
// ElementTypeMapArray<UInt> & facet_list = (*facets(p));
// UInt nb_element = elem.getSize();
// /// loop on every send/recv element
// for (UInt el = 0; el < nb_element; ++el) {
// ElementType type = elem(el).type;
// GhostType gt = elem(el).ghost_type;
// UInt el_index = elem(el).element;
// const Array<Element> & facet_to_element =
// mesh.getSubelementToElement(type, gt);
// UInt nb_facets_per_element = Mesh::getNbFacetsPerElement(type);
// ElementType facet_type = Mesh::getFacetType(type);
// UInt nb_nodes_per_facet = Mesh::getNbNodesPerElement(facet_type);
// Vector<UInt> conn_tmp(nb_nodes_per_facet);
// /// loop on every facet of the element
// for (UInt f = 0; f < nb_facets_per_element; ++f) {
// const Element & facet = facet_to_element(el_index, f);
// if (facet == ElementNull) continue;
// UInt facet_index = facet.element;
// GhostType facet_gt = facet.ghost_type;
// const Array<UInt> & t_to_f = rank_to_facet(facet_type, facet_gt);
// /// exclude not ghost facets, facets assigned to other
// /// processors
// if (facet_gt != ghost_facets) continue;
// if ((facet_gt == _ghost) && (t_to_f(facet_index) != p)) continue;
// /// exclude facets that have already been added
// Array<bool> & f_checked = facet_checked(facet_type, facet_gt);
// if (f_checked(facet_index)) continue;
// else f_checked(facet_index) = true;
// /// add facet index
// Array<UInt> & f_list = facet_list(facet_type, facet_gt);
// f_list.push_back(facet_index);
// /// add sorted facet global connectivity
// const Array<UInt> & conn = mesh.getConnectivity(facet_type, facet_gt);
// Array<UInt> & g_conn = global_conn(facet_type, facet_gt);
// for (UInt n = 0; n < nb_nodes_per_facet; ++n)
// conn_tmp(n) = nodes_global_ids(conn(facet_index, n));
// std::sort(conn_tmp.storage(), conn_tmp.storage() + nb_nodes_per_facet);
// g_conn.push_back(conn_tmp);
// }
// }
// }
// AKANTU_DEBUG_OUT();
// }
diff --git a/src/synchronizer/grid_synchronizer.cc b/src/synchronizer/grid_synchronizer.cc
index 2a2896e8f..1c4045304 100644
--- a/src/synchronizer/grid_synchronizer.cc
+++ b/src/synchronizer/grid_synchronizer.cc
@@ -1,543 +1,542 @@
/**
* @file grid_synchronizer.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Oct 03 2011
- * @date last modification: Fri Jan 22 2016
+ * @date last modification: Tue Nov 07 2017
*
* @brief implementation of the grid synchronizer
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "grid_synchronizer.hh"
#include "aka_grid_dynamic.hh"
#include "communicator.hh"
#include "fe_engine.hh"
#include "integration_point.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class E>
void GridSynchronizer::createGridSynchronizer(const SpatialGrid<E> & grid) {
AKANTU_DEBUG_IN();
const Communicator & comm = this->mesh.getCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
if (nb_proc == 1)
return;
UInt spatial_dimension = this->mesh.getSpatialDimension();
Tensor3<Real> bounding_boxes(spatial_dimension, 2, nb_proc);
Matrix<Real> my_bounding_box = bounding_boxes(my_rank);
const auto & lower = grid.getLowerBounds();
const auto & upper = grid.getUpperBounds();
const auto & spacing = grid.getSpacing();
Vector<Real>(my_bounding_box(0)) = lower - spacing;
Vector<Real>(my_bounding_box(1)) = upper + spacing;
AKANTU_DEBUG_INFO(
"Exchange of bounding box to detect the overlapping regions.");
comm.allGather(bounding_boxes);
std::vector<bool> intersects_proc(nb_proc);
std::fill(intersects_proc.begin(), intersects_proc.end(), true);
Matrix<Int> first_cells(spatial_dimension, nb_proc);
Matrix<Int> last_cells(spatial_dimension, nb_proc);
std::map<UInt, ElementTypeMapArray<UInt>> element_per_proc;
// check the overlapping between my box and the one from other processors
for (UInt p = 0; p < nb_proc; ++p) {
if (p == my_rank)
continue;
Matrix<Real> proc_bounding_box = bounding_boxes(p);
bool intersects = false;
Vector<Int> first_cell_p = first_cells(p);
Vector<Int> last_cell_p = last_cells(p);
for (UInt s = 0; s < spatial_dimension; ++s) {
// check overlapping of grid
intersects =
Math::intersects(my_bounding_box(s, 0), my_bounding_box(s, 1),
proc_bounding_box(s, 0), proc_bounding_box(s, 1));
intersects_proc[p] = intersects_proc[p] & intersects;
if (intersects) {
AKANTU_DEBUG_INFO("I intersects with processor "
<< p << " in direction " << s);
// is point 1 of proc p in the dimension s in the range ?
bool point1 =
Math::is_in_range(proc_bounding_box(s, 0), my_bounding_box(s, 0),
my_bounding_box(s, 1));
// is point 2 of proc p in the dimension s in the range ?
bool point2 =
Math::is_in_range(proc_bounding_box(s, 1), my_bounding_box(s, 0),
my_bounding_box(s, 1));
Real start = 0.;
Real end = 0.;
if (point1 && !point2) {
/* |-----------| my_bounding_box(i)
* |-----------| proc_bounding_box(i)
* 1 2
*/
start = proc_bounding_box(s, 0);
end = my_bounding_box(s, 1);
AKANTU_DEBUG_INFO("Intersection scheme 1 in direction "
<< s << " with processor " << p << " [" << start
<< ", " << end << "]");
} else if (point1 && point2) {
/* |-----------------| my_bounding_box(i)
* |-----------| proc_bounding_box(i)
* 1 2
*/
start = proc_bounding_box(s, 0);
end = proc_bounding_box(s, 1);
AKANTU_DEBUG_INFO("Intersection scheme 2 in direction "
<< s << " with processor " << p << " [" << start
<< ", " << end << "]");
} else if (!point1 && point2) {
/* |-----------| my_bounding_box(i)
* |-----------| proc_bounding_box(i)
* 1 2
*/
start = my_bounding_box(s, 0);
end = proc_bounding_box(s, 1);
AKANTU_DEBUG_INFO("Intersection scheme 3 in direction "
<< s << " with processor " << p << " [" << start
<< ", " << end << "]");
} else {
/* |-----------| my_bounding_box(i)
* |-----------------| proc_bounding_box(i)
* 1 2
*/
start = my_bounding_box(s, 0);
end = my_bounding_box(s, 1);
AKANTU_DEBUG_INFO("Intersection scheme 4 in direction "
<< s << " with processor " << p << " [" << start
<< ", " << end << "]");
}
first_cell_p(s) = grid.getCellID(start, s);
last_cell_p(s) = grid.getCellID(end, s);
}
}
// create the list of cells in the overlapping
using CellID = typename SpatialGrid<E>::CellID;
std::vector<CellID> cell_ids;
if (intersects_proc[p]) {
AKANTU_DEBUG_INFO("I intersects with processor " << p);
CellID cell_id(spatial_dimension);
// for (UInt i = 0; i < spatial_dimension; ++i) {
// if(first_cell_p[i] != 0) --first_cell_p[i];
// if(last_cell_p[i] != 0) ++last_cell_p[i];
// }
for (Int fd = first_cell_p(0); fd <= last_cell_p(0); ++fd) {
cell_id.setID(0, fd);
if (spatial_dimension == 1) {
cell_ids.push_back(cell_id);
} else {
for (Int sd = first_cell_p(1); sd <= last_cell_p(1); ++sd) {
cell_id.setID(1, sd);
if (spatial_dimension == 2) {
cell_ids.push_back(cell_id);
} else {
for (Int ld = first_cell_p(2); ld <= last_cell_p(2); ++ld) {
cell_id.setID(2, ld);
cell_ids.push_back(cell_id);
}
}
}
}
}
// get the list of elements in the cells of the overlapping
std::set<Element> to_send;
for (auto & cur_cell_id : cell_ids) {
auto & cell = grid.getCell(cur_cell_id);
for (auto & element : cell) {
to_send.insert(element);
}
}
AKANTU_DEBUG_INFO("I have prepared " << to_send.size()
<< " elements to send to processor "
<< p);
auto & scheme = this->getCommunications().createSendScheme(p);
std::stringstream sstr;
sstr << "element_per_proc_" << p;
element_per_proc.emplace(
std::piecewise_construct, std::forward_as_tuple(p),
std::forward_as_tuple(sstr.str(), id, memory_id));
ElementTypeMapArray<UInt> & elempproc = element_per_proc[p];
for (auto elem : to_send) {
ElementType type = elem.type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
// /!\ this part must be slow due to the access in the
// ElementTypeMapArray<UInt>
if (!elempproc.exists(type, _not_ghost))
elempproc.alloc(0, nb_nodes_per_element, type, _not_ghost);
Vector<UInt> global_connect(nb_nodes_per_element);
Vector<UInt> local_connect = mesh.getConnectivity(type).begin(
nb_nodes_per_element)[elem.element];
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
global_connect(i) = mesh.getNodeGlobalId(local_connect(i));
AKANTU_DEBUG_ASSERT(
global_connect(i) < mesh.getNbGlobalNodes(),
"This global node send in the connectivity does not seem correct "
<< global_connect(i) << " corresponding to "
<< local_connect(i) << " from element " << elem.element);
}
elempproc(type).push_back(global_connect);
scheme.push_back(elem);
}
}
}
AKANTU_DEBUG_INFO("I have finished to compute intersection,"
<< " no it's time to communicate with my neighbors");
/**
* Sending loop, sends the connectivity asynchronously to all concerned proc
*/
std::vector<CommunicationRequest> isend_requests;
Tensor3<UInt> space(2, _max_element_type, nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
if (p == my_rank)
continue;
if (not intersects_proc[p])
continue;
Matrix<UInt> info_proc = space(p);
auto & elempproc = element_per_proc[p];
UInt count = 0;
for (auto type : elempproc.elementTypes(_all_dimensions, _not_ghost)) {
Array<UInt> & conn = elempproc(type, _not_ghost);
Vector<UInt> info = info_proc((UInt)type);
info[0] = (UInt)type;
info[1] = conn.size() * conn.getNbComponent();
AKANTU_DEBUG_INFO(
"I have " << conn.size() << " elements of type " << type
<< " to send to processor " << p << " (communication tag : "
<< Tag::genTag(my_rank, count, DATA_TAG) << ")");
isend_requests.push_back(
comm.asyncSend(info, p, Tag::genTag(my_rank, count, SIZE_TAG)));
if (info[1] != 0)
isend_requests.push_back(comm.asyncSend<UInt>(
conn, p, Tag::genTag(my_rank, count, DATA_TAG)));
++count;
}
Vector<UInt> info = info_proc((UInt)_not_defined);
info[0] = (UInt)_not_defined;
info[1] = 0;
isend_requests.push_back(
comm.asyncSend(info, p, Tag::genTag(my_rank, count, SIZE_TAG)));
}
/**
* Receives the connectivity and store them in the ghosts elements
*/
MeshAccessor mesh_accessor(mesh);
auto & global_nodes_ids = mesh_accessor.getNodesGlobalIds();
auto & nodes_type = mesh_accessor.getNodesType();
std::vector<CommunicationRequest> isend_nodes_requests;
Vector<UInt> nb_nodes_to_recv(nb_proc);
UInt nb_total_nodes_to_recv = 0;
UInt nb_current_nodes = global_nodes_ids.size();
NewNodesEvent new_nodes;
NewElementsEvent new_elements;
std::map<UInt, std::vector<UInt>> ask_nodes_per_proc;
for (UInt p = 0; p < nb_proc; ++p) {
nb_nodes_to_recv(p) = 0;
if (p == my_rank)
continue;
if (!intersects_proc[p])
continue;
auto & scheme = this->getCommunications().createRecvScheme(p);
ask_nodes_per_proc.emplace(std::piecewise_construct,
std::forward_as_tuple(p),
std::forward_as_tuple(0));
auto & ask_nodes = ask_nodes_per_proc[p];
UInt count = 0;
ElementType type = _not_defined;
do {
Vector<UInt> info(2);
comm.receive(info, p, Tag::genTag(p, count, SIZE_TAG));
type = (ElementType)info[0];
if (type == _not_defined)
break;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt nb_element = info[1] / nb_nodes_per_element;
Array<UInt> tmp_conn(nb_element, nb_nodes_per_element);
tmp_conn.clear();
if (info[1] != 0)
comm.receive<UInt>(tmp_conn, p, Tag::genTag(p, count, DATA_TAG));
AKANTU_DEBUG_INFO("I will receive "
<< nb_element << " elements of type "
<< ElementType(info[0]) << " from processor " << p
<< " (communication tag : "
<< Tag::genTag(p, count, DATA_TAG) << ")");
auto & ghost_connectivity = mesh_accessor.getConnectivity(type, _ghost);
auto & ghost_counter = mesh_accessor.getGhostsCounters(type, _ghost);
UInt nb_ghost_element = ghost_connectivity.size();
Element element{type, 0, _ghost};
Vector<UInt> conn(nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el) {
UInt nb_node_to_ask_for_elem = 0;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt gn = tmp_conn(el, n);
UInt ln = global_nodes_ids.find(gn);
AKANTU_DEBUG_ASSERT(gn < mesh.getNbGlobalNodes(),
"This global node seems not correct "
<< gn << " from element " << el << " node "
<< n);
if (ln == UInt(-1)) {
global_nodes_ids.push_back(gn);
nodes_type.push_back(_nt_pure_gost); // pure ghost node
ln = nb_current_nodes;
new_nodes.getList().push_back(ln);
++nb_current_nodes;
ask_nodes.push_back(gn);
++nb_node_to_ask_for_elem;
}
conn[n] = ln;
}
// all the nodes are already known locally, the element should
// already exists
auto c = UInt(-1);
if (nb_node_to_ask_for_elem == 0) {
c = ghost_connectivity.find(conn);
element.element = c;
}
if (c == UInt(-1)) {
element.element = nb_ghost_element;
++nb_ghost_element;
ghost_connectivity.push_back(conn);
ghost_counter.push_back(1);
new_elements.getList().push_back(element);
} else {
++ghost_counter(c);
}
scheme.push_back(element);
}
count++;
} while (type != _not_defined);
AKANTU_DEBUG_INFO("I have "
<< ask_nodes.size()
<< " missing nodes for elements coming from processor "
<< p << " (communication tag : "
<< Tag::genTag(my_rank, 0, ASK_NODES_TAG) << ")");
ask_nodes.push_back(UInt(-1));
isend_nodes_requests.push_back(
comm.asyncSend(ask_nodes, p, Tag::genTag(my_rank, 0, ASK_NODES_TAG)));
nb_nodes_to_recv(p) = ask_nodes.size() - 1;
nb_total_nodes_to_recv += nb_nodes_to_recv(p);
}
comm.waitAll(isend_requests);
comm.freeCommunicationRequest(isend_requests);
/**
* Sends requested nodes to proc
*/
auto & nodes = const_cast<Array<Real> &>(mesh.getNodes());
UInt nb_nodes = nodes.size();
std::vector<CommunicationRequest> isend_coordinates_requests;
std::map<UInt, Array<Real>> nodes_to_send_per_proc;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == my_rank || !intersects_proc[p])
continue;
Array<UInt> asked_nodes;
CommunicationStatus status;
AKANTU_DEBUG_INFO("Waiting list of nodes to send to processor "
<< p << "(communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
comm.probe<UInt>(p, Tag::genTag(p, 0, ASK_NODES_TAG), status);
UInt nb_nodes_to_send = status.size();
asked_nodes.resize(nb_nodes_to_send);
AKANTU_DEBUG_INFO("I have " << nb_nodes_to_send - 1
<< " nodes to send to processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
AKANTU_DEBUG_INFO("Getting list of nodes to send to processor "
<< p << " (communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
comm.receive(asked_nodes, p, Tag::genTag(p, 0, ASK_NODES_TAG));
nb_nodes_to_send--;
asked_nodes.resize(nb_nodes_to_send);
nodes_to_send_per_proc.emplace(std::piecewise_construct,
std::forward_as_tuple(p),
std::forward_as_tuple(0, spatial_dimension));
auto & nodes_to_send = nodes_to_send_per_proc[p];
auto node_it = nodes.begin(spatial_dimension);
for (UInt n = 0; n < nb_nodes_to_send; ++n) {
UInt ln = global_nodes_ids.find(asked_nodes(n));
AKANTU_DEBUG_ASSERT(ln != UInt(-1),
"The node [" << asked_nodes(n)
<< "] requested by proc " << p
<< " was not found locally!");
nodes_to_send.push_back(node_it + ln);
}
if (nb_nodes_to_send != 0) {
AKANTU_DEBUG_INFO("Sending the "
<< nb_nodes_to_send << " nodes to processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, SEND_NODES_TAG) << ")");
isend_coordinates_requests.push_back(comm.asyncSend(
nodes_to_send, p, Tag::genTag(my_rank, 0, SEND_NODES_TAG)));
}
#if not defined(AKANTU_NDEBUG)
else {
AKANTU_DEBUG_INFO("No nodes to send to processor " << p);
}
#endif
}
comm.waitAll(isend_nodes_requests);
comm.freeCommunicationRequest(isend_nodes_requests);
nodes.resize(nb_total_nodes_to_recv + nb_nodes);
for (UInt p = 0; p < nb_proc; ++p) {
if ((p != my_rank) && (nb_nodes_to_recv(p) > 0)) {
AKANTU_DEBUG_INFO("Receiving the "
<< nb_nodes_to_recv(p) << " nodes from processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, SEND_NODES_TAG) << ")");
Vector<Real> nodes_to_recv(nodes.storage() + nb_nodes * spatial_dimension,
nb_nodes_to_recv(p) * spatial_dimension);
comm.receive(nodes_to_recv, p, Tag::genTag(p, 0, SEND_NODES_TAG));
nb_nodes += nb_nodes_to_recv(p);
}
#if not defined(AKANTU_NDEBUG)
else {
if (p != my_rank) {
AKANTU_DEBUG_INFO("No nodes to receive from processor " << p);
}
}
#endif
}
comm.waitAll(isend_coordinates_requests);
comm.freeCommunicationRequest(isend_coordinates_requests);
mesh.sendEvent(new_nodes);
mesh.sendEvent(new_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template void GridSynchronizer::createGridSynchronizer<IntegrationPoint>(
const SpatialGrid<IntegrationPoint> & grid);
template void GridSynchronizer::createGridSynchronizer<Element>(
const SpatialGrid<Element> & grid);
} // namespace akantu
diff --git a/src/synchronizer/grid_synchronizer.hh b/src/synchronizer/grid_synchronizer.hh
index 1005d0654..62b0b039c 100644
--- a/src/synchronizer/grid_synchronizer.hh
+++ b/src/synchronizer/grid_synchronizer.hh
@@ -1,103 +1,102 @@
/**
* @file grid_synchronizer.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 08 2015
+ * @date last modification: Wed Nov 08 2017
*
* @brief Synchronizer based on spatial grid
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_synchronizer.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GRID_SYNCHRONIZER_HH__
#define __AKANTU_GRID_SYNCHRONIZER_HH__
namespace akantu {
class Mesh;
template <class T> class SpatialGrid;
class GridSynchronizer : public ElementSynchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
template <typename E>
GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
const ID & id = "grid_synchronizer", MemoryID memory_id = 0,
const bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
template <typename E>
GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
SynchronizerRegistry & synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register,
const ID & id = "grid_synchronizer", MemoryID memory_id = 0,
const bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
~GridSynchronizer() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/**
*Create the Grid Synchronizer:
*Compute intersection and send info to neighbours that will be stored in
*ghosts elements
*/
template <typename E>
void createGridSynchronizer(const SpatialGrid<E> & grid);
protected:
/// Define the tags that will be used in the send and receive instructions
enum CommTags {
SIZE_TAG = 0,
DATA_TAG = 1,
ASK_NODES_TAG = 2,
SEND_NODES_TAG = 3
};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
#include "grid_synchronizer_tmpl.hh"
#endif /* __AKANTU_GRID_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/grid_synchronizer_tmpl.hh b/src/synchronizer/grid_synchronizer_tmpl.hh
index fc33da1fe..32500b7f4 100644
--- a/src/synchronizer/grid_synchronizer_tmpl.hh
+++ b/src/synchronizer/grid_synchronizer_tmpl.hh
@@ -1,73 +1,75 @@
/**
* @file grid_synchronizer_tmpl.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jun 20 2017
+ * @date creation: Thu Jul 06 2017
+ * @date last modification: Wed Aug 09 2017
*
- * @brief A Documented file.
+ * @brief implementation of the templated part of the grid syncrhonizers
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "grid_synchronizer.hh"
#ifndef __AKANTU_GRID_SYNCHRONIZER_TMPL_HH__
#define __AKANTU_GRID_SYNCHRONIZER_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename E>
GridSynchronizer::GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
const ID & id, MemoryID memory_id,
const bool register_to_event_manager,
EventHandlerPriority event_priority)
: ElementSynchronizer(mesh, id, memory_id, register_to_event_manager,
event_priority) {
AKANTU_DEBUG_IN();
this->createGridSynchronizer(grid);
AKANTU_DEBUG_OUT();
}
template <typename E>
GridSynchronizer::GridSynchronizer(
Mesh & mesh, const SpatialGrid<E> & grid,
SynchronizerRegistry & synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register, const ID & id,
MemoryID memory_id, const bool register_to_event_manager,
EventHandlerPriority event_priority)
: GridSynchronizer(mesh, grid, id, memory_id, register_to_event_manager,
event_priority) {
AKANTU_DEBUG_IN();
// Register the tags if any
for (auto & tag : tags_to_register) {
synchronizer_registry.registerSynchronizer(*this, tag);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* __AKANTU_GRID_SYNCHRONIZER_TMPL_HH__ */
diff --git a/src/synchronizer/master_element_info_per_processor.cc b/src/synchronizer/master_element_info_per_processor.cc
index b3b91967a..74053d36e 100644
--- a/src/synchronizer/master_element_info_per_processor.cc
+++ b/src/synchronizer/master_element_info_per_processor.cc
@@ -1,461 +1,463 @@
/**
* @file master_element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Mar 11 14:57:13 2016
+ * @date creation: Wed Mar 16 2016
+ * @date last modification: Tue Feb 20 2018
*
- * @brief
+ * @brief Helper class to distribute a mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
#include <tuple>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MasterElementInfoPerProc::MasterElementInfoPerProc(
ElementSynchronizer & synchronizer, UInt message_cnt, UInt root,
ElementType type, const MeshPartition & partition)
: ElementInfoPerProc(synchronizer, message_cnt, root, type),
partition(partition), all_nb_local_element(nb_proc, 0),
all_nb_ghost_element(nb_proc, 0), all_nb_element_to_send(nb_proc, 0) {
Vector<UInt> size(5);
size(0) = (UInt)type;
if (type != _not_defined) {
nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
nb_element = mesh.getNbElement(type);
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el) {
this->all_nb_local_element[partition_num(el)]++;
for (auto part = ghost_partition.begin(el);
part != ghost_partition.end(el); ++part) {
this->all_nb_ghost_element[*part]++;
}
this->all_nb_element_to_send[partition_num(el)] +=
ghost_partition.getNbCols(el) + 1;
}
/// tag info
std::vector<std::string> tag_names;
this->getMeshData().getTagNames(tag_names, type);
this->nb_tags = tag_names.size();
size(4) = nb_tags;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
size(1) = this->all_nb_local_element[p];
size(2) = this->all_nb_ghost_element[p];
size(3) = this->all_nb_element_to_send[p];
AKANTU_DEBUG_INFO(
"Sending connectivities informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_SIZES)
<< ")");
comm.send(size, p,
Tag::genTag(this->rank, this->message_count, Tag::_SIZES));
} else {
this->nb_local_element = this->all_nb_local_element[p];
this->nb_ghost_element = this->all_nb_ghost_element[p];
}
}
} else {
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p != this->root) {
AKANTU_DEBUG_INFO(
"Sending empty connectivities informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_SIZES)
<< ")");
comm.send(size, p,
Tag::genTag(this->rank, this->message_count, Tag::_SIZES));
}
}
}
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizeConnectivities() {
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->nb_proc);
const auto & connectivities =
this->mesh.getConnectivity(this->type, _not_ghost);
/// copying the local connectivity
for (auto && part_conn :
zip(partition_num,
make_view(connectivities, this->nb_nodes_per_element))) {
auto && part = std::get<0>(part_conn);
auto && conn = std::get<1>(part_conn);
for (UInt i = 0; i < conn.size(); ++i) {
buffers[part].push_back(conn[i]);
}
}
/// copying the connectivity of ghost element
for (auto && tuple :
enumerate(make_view(connectivities, this->nb_nodes_per_element))) {
auto && el = std::get<0>(tuple);
auto && conn = std::get<1>(tuple);
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part) {
UInt proc = *part;
for (UInt i = 0; i < conn.size(); ++i) {
buffers[proc].push_back(conn[i]);
}
}
}
#ifndef AKANTU_NDEBUG
for (auto p : arange(this->nb_proc)) {
UInt size = this->nb_nodes_per_element *
(this->all_nb_local_element[p] + this->all_nb_ghost_element[p]);
AKANTU_DEBUG_ASSERT(
buffers[p].size() == size,
"The connectivity data packed in the buffer are not correct");
}
#endif
/// send all connectivity and ghost information to all processors
std::vector<CommunicationRequest> requests;
for (auto p : arange(this->nb_proc)) {
if (p == this->root)
continue;
auto && tag =
Tag::genTag(this->rank, this->message_count, Tag::_CONNECTIVITY);
AKANTU_DEBUG_INFO("Sending connectivities to proc " << p << " TAG(" << tag
<< ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
Array<UInt> & old_nodes = this->getNodesGlobalIds();
/// create the renumbered connectivity
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh, buffers[root], all_nb_local_element[root],
all_nb_ghost_element[root], type, old_nodes);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizePartitions() {
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->partition.getNbPartition());
/// splitting the partition information to send them to processors
Vector<UInt> count_by_proc(nb_proc, 0);
for (UInt el = 0; el < nb_element; ++el) {
UInt proc = partition_num(el);
buffers[proc].push_back(ghost_partition.getNbCols(el));
UInt i(0);
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part, ++i) {
buffers[proc].push_back(*part);
}
}
for (UInt el = 0; el < nb_element; ++el) {
UInt i(0);
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part, ++i) {
buffers[*part].push_back(partition_num(el));
}
}
#ifndef AKANTU_NDEBUG
for (UInt p = 0; p < this->nb_proc; ++p) {
AKANTU_DEBUG_ASSERT(buffers[p].size() == (this->all_nb_ghost_element[p] +
this->all_nb_element_to_send[p]),
"Data stored in the buffer are most probably wrong");
}
#endif
std::vector<CommunicationRequest> requests;
/// last data to compute the communication scheme
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p == this->root)
continue;
auto && tag =
Tag::genTag(this->rank, this->message_count, Tag::_PARTITIONS);
AKANTU_DEBUG_INFO("Sending partition informations to proc " << p << " TAG("
<< tag << ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
if (Mesh::getSpatialDimension(this->type) ==
this->mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
this->fillCommunicationScheme(buffers[this->rank]);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeTags() {
AKANTU_DEBUG_IN();
if (this->nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
UInt mesh_data_sizes_buffer_length;
auto & mesh_data = this->getMeshData();
/// tag info
std::vector<std::string> tag_names;
mesh_data.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;
for (auto && tag_name : tag_names) {
mesh_data_sizes_buffer << tag_name;
mesh_data_sizes_buffer << mesh_data.getTypeCode(tag_name);
mesh_data_sizes_buffer << mesh_data.getNbComponent(tag_name, type);
}
mesh_data_sizes_buffer_length = mesh_data_sizes_buffer.size();
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, 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, root);
if (mesh_data_sizes_buffer_length != 0) {
// Sending the actual data to each processor
std::vector<DynamicCommunicationBuffer> buffers(nb_proc);
// Loop over each tag for the current type
for (auto && tag_name : tag_names) {
// Type code of the current tag (i.e. the tag named *names_it)
this->fillTagBuffer(buffers, tag_name);
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == root)
continue;
auto && tag =
Tag::genTag(this->rank, this->message_count, Tag::_MESH_DATA);
AKANTU_DEBUG_INFO("Sending " << buffers[p].size()
<< " bytes of mesh data to proc " << p
<< " TAG(" << tag << ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
// Loop over each tag for the current type
for (auto && tag_name : tag_names) {
// Reinitializing the mesh data on the master
this->fillMeshData(buffers[root], tag_name,
mesh_data.getTypeCode(tag_name),
mesh_data.getNbComponent(tag_name, type));
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void MasterElementInfoPerProc::fillTagBufferTemplated(
std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name) {
MeshData & mesh_data = this->getMeshData();
const auto & data = mesh_data.getElementalDataArray<T>(tag_name, type);
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
// Not possible to use the iterator because it potentially triggers the
// creation of complex
// type templates (such as akantu::Vector< std::vector<Element> > which don't
// implement the right interface
// (e.g. operator<< in that case).
// typename Array<T>::template const_iterator< Vector<T> > data_it =
// data.begin(data.getNbComponent());
// typename Array<T>::template const_iterator< Vector<T> > data_end =
// data.end(data.getNbComponent());
const T * data_it = data.storage();
const T * data_end = data.storage() + data.size() * data.getNbComponent();
const UInt * part = partition_num.storage();
/// copying the data, element by element
for (; data_it != data_end; ++part) {
for (UInt j(0); j < data.getNbComponent(); ++j, ++data_it) {
buffers[*part] << *data_it;
}
}
data_it = data.storage();
/// copying the data for the ghost element
for (UInt el(0); data_it != data_end;
data_it += data.getNbComponent(), ++el) {
auto it = ghost_partition.begin(el);
auto end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
for (UInt j(0); j < data.getNbComponent(); ++j) {
buffers[proc] << data_it[j];
}
}
}
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::fillTagBuffer(
std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name) {
MeshData & mesh_data = this->getMeshData();
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
this->fillTagBufferTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(buffers, \
tag_name); \
break; \
}
MeshDataTypeCode data_type_code = mesh_data.getTypeCode(tag_name);
switch (data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not obtain the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
std::vector<DynamicCommunicationBuffer> buffers(nb_proc);
using ElementToGroup = std::vector<std::vector<std::string>>;
ElementToGroup element_to_group(nb_element);
for (auto & eg : ElementGroupsIterable(mesh)) {
const auto & name = eg.getName();
for (const auto & element : eg.getElements(type, _not_ghost)) {
element_to_group[element].push_back(name);
}
auto eit = eg.begin(type, _not_ghost);
if (eit != eg.end(type, _not_ghost))
const_cast<Array<UInt> &>(eg.getElements(type)).empty();
}
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
/// copying the data, element by element
for (auto && pair : zip(partition_num, element_to_group)) {
buffers[std::get<0>(pair)] << std::get<1>(pair);
}
/// copying the data for the ghost element
for (auto && pair : enumerate(element_to_group)) {
auto && el = std::get<0>(pair);
auto it = ghost_partition.begin(el);
auto end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
buffers[proc] << std::get<1>(pair);
}
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p == this->rank)
continue;
auto && tag = Tag::genTag(this->rank, p, Tag::_ELEMENT_GROUP);
AKANTU_DEBUG_INFO("Sending element groups to proc " << p << " TAG(" << tag
<< ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
this->fillElementGroupsFromBuffer(buffers[this->rank]);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/mpi_communicator_data.hh b/src/synchronizer/mpi_communicator_data.hh
index be387e22b..f85d30c8b 100644
--- a/src/synchronizer/mpi_communicator_data.hh
+++ b/src/synchronizer/mpi_communicator_data.hh
@@ -1,135 +1,134 @@
/**
- * @file mpi_type_wrapper.hh
+ * @file mpi_communicator_data.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Wed Oct 07 2015
+ * @date last modification: Mon Feb 05 2018
*
* @brief Wrapper on MPI types to have a better separation between libraries
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#if __cplusplus > 199711L
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wliteral-suffix"
#endif
#endif
#include <mpi.h>
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#if __cplusplus > 199711L
#pragma GCC diagnostic pop
#endif
#endif
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MPI_TYPE_WRAPPER_HH__
#define __AKANTU_MPI_TYPE_WRAPPER_HH__
namespace akantu {
class MPICommunicatorData : public CommunicatorInternalData {
public:
MPICommunicatorData() {
MPI_Initialized(&is_externaly_initialized);
if (!is_externaly_initialized) {
MPI_Init(nullptr, nullptr); // valid according to the spec
}
MPI_Comm_create_errhandler(MPICommunicatorData::errorHandler,
&error_handler);
MPI_Comm_set_errhandler(MPI_COMM_WORLD, error_handler);
setMPICommunicator(MPI_COMM_WORLD);
}
~MPICommunicatorData() override {
if (not is_externaly_initialized) {
MPI_Finalize();
}
}
inline void setMPICommunicator(MPI_Comm comm) {
MPI_Comm_set_errhandler(communicator, save_error_handler);
communicator = comm;
MPI_Comm_get_errhandler(comm, &save_error_handler);
MPI_Comm_set_errhandler(comm, error_handler);
}
inline int rank() const {
int prank;
MPI_Comm_rank(communicator, &prank);
return prank;
}
inline int size() const {
int psize;
MPI_Comm_size(communicator, &psize);
return psize;
}
inline MPI_Comm getMPICommunicator() const { return communicator; }
inline int getMaxTag() const {
int flag;
int * value;
MPI_Comm_get_attr(communicator, MPI_TAG_UB, &value, &flag);
AKANTU_DEBUG_ASSERT(flag, "No attribute MPI_TAG_UB.");
return *value;
}
private:
MPI_Comm communicator{MPI_COMM_WORLD};
MPI_Errhandler save_error_handler{MPI_ERRORS_ARE_FATAL};
static int is_externaly_initialized;
/* ------------------------------------------------------------------------ */
MPI_Errhandler error_handler;
static void errorHandler(MPI_Comm * /*comm*/, int * error_code, ...) {
char error_string[MPI_MAX_ERROR_STRING];
int str_len;
MPI_Error_string(*error_code, error_string, &str_len);
AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
"MPI failed with the error code "
<< *error_code << ": \"" << error_string
<< "\"");
}
};
} // namespace akantu
#endif /* __AKANTU_MPI_TYPE_WRAPPER_HH__ */
diff --git a/src/synchronizer/node_info_per_processor.cc b/src/synchronizer/node_info_per_processor.cc
index 3b4a73b32..bed5332f1 100644
--- a/src/synchronizer/node_info_per_processor.cc
+++ b/src/synchronizer/node_info_per_processor.cc
@@ -1,497 +1,499 @@
/**
* @file node_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Mar 11 15:49:43 2016
+ * @date creation: Wed Mar 16 2016
+ * @date last modification: Wed Nov 08 2017
*
- * @brief
+ * @brief Please type the brief for file: Helper classes to create the
+ * distributed synchronizer and distribute a mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_info_per_processor.hh"
#include "communicator.hh"
#include "node_group.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeInfoPerProc::NodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: MeshAccessor(synchronizer.getMesh()), synchronizer(synchronizer),
comm(synchronizer.getCommunicator()), rank(comm.whoAmI()),
nb_proc(comm.getNbProc()), root(root), mesh(synchronizer.getMesh()),
spatial_dimension(synchronizer.getMesh().getSpatialDimension()),
message_count(message_cnt) {}
/* -------------------------------------------------------------------------- */
template <class CommunicationBuffer>
void NodeInfoPerProc::fillNodeGroupsFromBuffer(CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
std::vector<std::vector<std::string>> node_to_group;
buffer >> node_to_group;
AKANTU_DEBUG_ASSERT(node_to_group.size() == mesh.getNbGlobalNodes(),
"Not the good amount of nodes where transmitted");
const auto & global_nodes = mesh.getGlobalNodesIds();
auto nbegin = global_nodes.begin();
auto nit = global_nodes.begin();
auto nend = global_nodes.end();
for (; nit != nend; ++nit) {
auto it = node_to_group[*nit].begin();
auto 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 NodeInfoPerProc::fillNodesType() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
Array<NodeType> & nodes_type = this->getNodesType();
Array<UInt> nodes_set(nb_nodes);
nodes_set.set(0);
enum NodeSet {
NORMAL_SET = 1,
GHOST_SET = 2,
};
Array<bool> already_seen(nb_nodes, 1, false);
for (UInt g = _not_ghost; g <= _ghost; ++g) {
auto gt = (GhostType)g;
UInt set = NORMAL_SET;
if (gt == _ghost)
set = GHOST_SET;
already_seen.set(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>::const_vector_iterator conn_it =
mesh.getConnectivity(type, gt).begin(nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e, ++conn_it) {
const 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;
}
}
}
}
}
for (UInt i = 0; i < nb_nodes; ++i) {
if (nodes_set(i) == NORMAL_SET)
nodes_type(i) = _nt_normal;
else if (nodes_set(i) == GHOST_SET)
nodes_type(i) = _nt_pure_gost;
else if (nodes_set(i) == (GHOST_SET + NORMAL_SET))
nodes_type(i) = _nt_master;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillCommunicationScheme(const Array<UInt> & master_info) {
AKANTU_DEBUG_IN();
Communications<UInt> & communications =
this->synchronizer.getCommunications();
{ // send schemes
auto it = master_info.begin_reinterpret(2, master_info.size() / 2);
auto end = master_info.end_reinterpret(2, master_info.size() / 2);
std::map<UInt, Array<UInt>> send_array_per_proc;
for (; it != end; ++it) {
const Vector<UInt> & send_info = *it;
send_array_per_proc[send_info(0)].push_back(send_info(1));
}
for (auto & send_schemes : send_array_per_proc) {
auto & scheme = communications.createSendScheme(send_schemes.first);
auto & sends = send_schemes.second;
std::sort(sends.begin(), sends.end());
std::transform(sends.begin(), sends.end(), sends.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(sends);
}
}
{ // receive schemes
const Array<NodeType> & nodes_type = this->getNodesType();
std::map<UInt, Array<UInt>> recv_array_per_proc;
UInt node = 0;
for (auto & node_type : nodes_type) {
if (Int(node_type) >= 0) {
recv_array_per_proc[node_type].push_back(mesh.getNodeGlobalId(node));
}
++node;
}
for (auto & recv_schemes : recv_array_per_proc) {
auto & scheme = communications.createRecvScheme(recv_schemes.first);
auto & recvs = recv_schemes.second;
std::sort(recvs.begin(), recvs.end());
std::transform(recvs.begin(), recvs.end(), recvs.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(recvs);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
MasterNodeInfoPerProc::MasterNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root) {
UInt nb_global_nodes = this->mesh.getNbGlobalNodes();
this->comm.broadcast(nb_global_nodes, this->root);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeNodes() {
this->nodes_per_proc.resize(nb_proc);
this->nb_nodes_per_proc.resize(nb_proc);
Array<Real> local_nodes(0, spatial_dimension);
Array<Real> & nodes = this->getNodes();
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_nodes = 0;
// UInt * buffer;
Array<Real> * nodes_to_send;
Array<UInt> & nodespp = nodes_per_proc[p];
if (p != root) {
nodes_to_send = new Array<Real>(0, spatial_dimension);
AKANTU_DEBUG_INFO("Receiving number of nodes from proc "
<< p << " " << Tag::genTag(p, 0, Tag::_NB_NODES));
comm.receive(nb_nodes, p, Tag::genTag(p, 0, Tag::_NB_NODES));
nodespp.resize(nb_nodes);
this->nb_nodes_per_proc(p) = nb_nodes;
AKANTU_DEBUG_INFO("Receiving list of nodes from proc "
<< p << " " << Tag::genTag(p, 0, Tag::_NODES));
comm.receive(nodespp, p, Tag::genTag(p, 0, Tag::_NODES));
} else {
Array<UInt> & local_ids = this->getNodesGlobalIds();
this->nb_nodes_per_proc(p) = local_ids.size();
nodespp.copy(local_ids);
nodes_to_send = &local_nodes;
}
Array<UInt>::const_scalar_iterator it = nodespp.begin();
Array<UInt>::const_scalar_iterator end = nodespp.end();
/// get the coordinates for the selected nodes
for (; it != end; ++it) {
Vector<Real> coord(nodes.storage() + spatial_dimension * *it,
spatial_dimension);
nodes_to_send->push_back(coord);
}
if (p != root) { /// send them for distant processors
AKANTU_DEBUG_INFO("Sending coordinates to proc "
<< p << " "
<< Tag::genTag(this->rank, 0, Tag::_COORDINATES));
comm.send(*nodes_to_send, p,
Tag::genTag(this->rank, 0, Tag::_COORDINATES));
delete nodes_to_send;
}
}
/// construct the local nodes coordinates
nodes.copy(local_nodes);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeTypes() {
// <global_id, <proc, local_id> >
std::multimap<UInt, std::pair<UInt, UInt>> nodes_to_proc;
std::vector<Array<NodeType>> nodes_type_per_proc(nb_proc);
// arrays containing pairs of (proc, node)
std::vector<Array<UInt>> nodes_to_send_per_proc(nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
nodes_type_per_proc[p].resize(nb_nodes_per_proc(p));
}
this->fillNodesType();
for (UInt p = 0; p < nb_proc; ++p) {
auto & nodes_types = nodes_type_per_proc[p];
if (p != root) {
AKANTU_DEBUG_INFO(
"Receiving first nodes types from proc "
<< p << " "
<< Tag::genTag(this->rank, this->message_count, Tag::_NODES_TYPE));
comm.receive(nodes_types, p, Tag::genTag(p, 0, Tag::_NODES_TYPE));
} else {
nodes_types.copy(this->getNodesType());
}
// stack all processors claiming to be master for a node
for (UInt local_node = 0; local_node < nb_nodes_per_proc(p); ++local_node) {
if (nodes_types(local_node) == _nt_master) {
UInt global_node = nodes_per_proc[p](local_node);
nodes_to_proc.insert(
std::make_pair(global_node, std::make_pair(p, local_node)));
}
}
}
for (UInt i = 0; i < mesh.getNbGlobalNodes(); ++i) {
auto it_range = nodes_to_proc.equal_range(i);
if (it_range.first == nodes_to_proc.end() || it_range.first->first != i)
continue;
// pick the first processor out of the multi-map as the actual master
UInt master_proc = (it_range.first)->second.first;
for (auto 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 != master_proc) {
// store the info on all the slaves for a given master
nodes_type_per_proc[proc](node) = NodeType(master_proc);
nodes_to_send_per_proc[master_proc].push_back(proc);
nodes_to_send_per_proc[master_proc].push_back(i);
}
}
}
std::vector<CommunicationRequest> requests_send_type;
std::vector<CommunicationRequest> requests_send_master_info;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
AKANTU_DEBUG_INFO("Sending nodes types to proc "
<< p << " "
<< Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
requests_send_type.push_back(
comm.asyncSend(nodes_type_per_proc[p], p,
Tag::genTag(this->rank, 0, Tag::_NODES_TYPE)));
auto & nodes_to_send = nodes_to_send_per_proc[p];
/// push back an element to avoid a send of size 0
nodes_to_send.push_back(-1);
AKANTU_DEBUG_INFO("Sending nodes master info to proc "
<< p << " "
<< Tag::genTag(this->rank, 1, Tag::_NODES_TYPE));
requests_send_master_info.push_back(comm.asyncSend(
nodes_to_send, p, Tag::genTag(this->rank, 1, Tag::_NODES_TYPE)));
} else {
this->getNodesType().copy(nodes_type_per_proc[p]);
this->fillCommunicationScheme(nodes_to_send_per_proc[root]);
}
}
comm.waitAll(requests_send_type);
comm.freeCommunicationRequest(requests_send_type);
requests_send_type.clear();
comm.waitAll(requests_send_master_info);
comm.freeCommunicationRequest(requests_send_master_info);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
UInt nb_total_nodes = mesh.getNbGlobalNodes();
DynamicCommunicationBuffer buffer;
using NodeToGroup = std::vector<std::vector<std::string>>;
NodeToGroup node_to_group;
node_to_group.resize(nb_total_nodes);
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 == this->rank)
continue;
AKANTU_DEBUG_INFO("Sending node groups to proc "
<< p << " "
<< Tag::genTag(this->rank, p, Tag::_NODE_GROUP));
requests.push_back(comm.asyncSend(
buffer, p, Tag::genTag(this->rank, p, Tag::_NODE_GROUP)));
}
this->fillNodeGroupsFromBuffer(buffer);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
SlaveNodeInfoPerProc::SlaveNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root) {
UInt nb_global_nodes = 0;
comm.broadcast(nb_global_nodes, root);
this->setNbGlobalNodes(nb_global_nodes);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeNodes() {
AKANTU_DEBUG_INFO("Sending list of nodes to proc "
<< root << " " << Tag::genTag(this->rank, 0, Tag::_NB_NODES)
<< " " << Tag::genTag(this->rank, 0, Tag::_NODES));
Array<UInt> & local_ids = this->getNodesGlobalIds();
Array<Real> & nodes = this->getNodes();
UInt nb_nodes = local_ids.size();
comm.send(nb_nodes, root, Tag::genTag(this->rank, 0, Tag::_NB_NODES));
comm.send(local_ids, root, Tag::genTag(this->rank, 0, Tag::_NODES));
/* --------<<<<-COORDINATES---------------------------------------------- */
nodes.resize(nb_nodes);
AKANTU_DEBUG_INFO("Receiving coordinates from proc "
<< root << " " << Tag::genTag(root, 0, Tag::_COORDINATES));
comm.receive(nodes, root, Tag::genTag(root, 0, Tag::_COORDINATES));
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeTypes() {
this->fillNodesType();
Array<NodeType> & nodes_types = this->getNodesType();
AKANTU_DEBUG_INFO("Sending first nodes types to proc "
<< root << ""
<< Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
comm.send(nodes_types, root, Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
AKANTU_DEBUG_INFO("Receiving nodes types from proc "
<< root << " " << Tag::genTag(root, 0, Tag::_NODES_TYPE));
comm.receive(nodes_types, root, Tag::genTag(root, 0, Tag::_NODES_TYPE));
AKANTU_DEBUG_INFO("Receiving nodes master info from proc "
<< root << " " << Tag::genTag(root, 1, Tag::_NODES_TYPE));
CommunicationStatus status;
comm.probe<UInt>(root, Tag::genTag(root, 1, Tag::_NODES_TYPE), status);
Array<UInt> nodes_master_info(status.size());
comm.receive(nodes_master_info, root, Tag::genTag(root, 1, Tag::_NODES_TYPE));
nodes_master_info.resize(nodes_master_info.size() - 1);
this->fillCommunicationScheme(nodes_master_info);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Receiving node groups from proc "
<< root << " "
<< Tag::genTag(root, this->rank, Tag::_NODE_GROUP));
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, this->rank, Tag::_NODE_GROUP),
status);
CommunicationBuffer buffer(status.size());
comm.receive(buffer, root, Tag::genTag(root, this->rank, Tag::_NODE_GROUP));
this->fillNodeGroupsFromBuffer(buffer);
AKANTU_DEBUG_OUT();
}
} // akantu
diff --git a/src/synchronizer/node_info_per_processor.hh b/src/synchronizer/node_info_per_processor.hh
index da67e5479..1bb583524 100644
--- a/src/synchronizer/node_info_per_processor.hh
+++ b/src/synchronizer/node_info_per_processor.hh
@@ -1,107 +1,108 @@
/**
* @file node_info_per_processor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Mar 11 14:45:15 2016
+ * @date creation: Wed Mar 16 2016
+ * @date last modification: Wed Nov 08 2017
*
* @brief Helper classes to create the distributed synchronizer and distribute
- * a mesh
+ * a mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NODE_INFO_PER_PROCESSOR_HH__
#define __AKANTU_NODE_INFO_PER_PROCESSOR_HH__
namespace akantu {
class NodeSynchronizer;
class Communicator;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class NodeInfoPerProc : protected MeshAccessor {
public:
NodeInfoPerProc(NodeSynchronizer & synchronizer, UInt message_cnt, UInt root);
virtual void synchronizeNodes() = 0;
virtual void synchronizeTypes() = 0;
virtual void synchronizeGroups() = 0;
protected:
template <class CommunicationBuffer>
void fillNodeGroupsFromBuffer(CommunicationBuffer & buffer);
void fillNodesType();
void fillCommunicationScheme(const Array<UInt> &);
protected:
NodeSynchronizer & synchronizer;
const Communicator & comm;
UInt rank;
UInt nb_proc;
UInt root;
Mesh & mesh;
UInt spatial_dimension;
UInt message_count;
};
/* -------------------------------------------------------------------------- */
class MasterNodeInfoPerProc : protected NodeInfoPerProc {
public:
MasterNodeInfoPerProc(NodeSynchronizer & synchronizer, UInt message_cnt,
UInt root);
void synchronizeNodes() override;
void synchronizeTypes() override;
void synchronizeGroups() override;
private:
/// get the list of nodes to send and send them
std::vector<Array<UInt>> nodes_per_proc;
Array<UInt> nb_nodes_per_proc;
};
/* -------------------------------------------------------------------------- */
class SlaveNodeInfoPerProc : protected NodeInfoPerProc {
public:
SlaveNodeInfoPerProc(NodeSynchronizer & synchronizer, UInt message_cnt,
UInt root);
void synchronizeNodes() override;
void synchronizeTypes() override;
void synchronizeGroups() override;
private:
};
} // akantu
#endif /* __AKANTU_NODE_INFO_PER_PROCESSOR_HH__ */
diff --git a/src/synchronizer/node_synchronizer.cc b/src/synchronizer/node_synchronizer.cc
index 7610c7a3a..15c889ffb 100644
--- a/src/synchronizer/node_synchronizer.cc
+++ b/src/synchronizer/node_synchronizer.cc
@@ -1,121 +1,122 @@
/**
* @file node_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Sep 23 12:01:24 2016
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Nov 15 2017
*
* @brief Implementation of the node synchronizer
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_synchronizer.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeSynchronizer::NodeSynchronizer(Mesh & mesh, const ID & id,
MemoryID memory_id,
const bool register_to_event_manager,
EventHandlerPriority event_priority)
: SynchronizerImpl<UInt>(mesh.getCommunicator(), id, memory_id),
mesh(mesh) {
AKANTU_DEBUG_IN();
if (register_to_event_manager) {
this->mesh.registerEventHandler(*this, event_priority);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NodeSynchronizer::~NodeSynchronizer() = default;
/* -------------------------------------------------------------------------- */
void NodeSynchronizer::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent &) {
std::map<UInt, std::vector<UInt>> nodes_per_proc;
Array<UInt> sizes_per_proc(nb_proc, nb_proc, UInt(0));
Vector<UInt> local_sizes_per_proc = sizes_per_proc.begin(nb_proc)[rank];
for (auto & local_id : nodes_list) {
auto type = mesh.getNodeType(local_id);
if (type < 0)
continue; // local, master or pure ghost
auto global_id = mesh.getNodeGlobalId(local_id);
auto proc = UInt(type);
nodes_per_proc[proc].push_back(global_id);
++local_sizes_per_proc[proc];
auto & scheme = communications.getScheme(proc, _recv);
scheme.push_back(local_id);
}
communicator.allGather(sizes_per_proc);
std::vector<CommunicationRequest> send_request_per_proc,
recv_request_per_proc;
std::map<UInt, std::vector<UInt>> nodes_needed_by_proc;
for (UInt proc = 0; proc < nb_proc; ++proc) {
auto size = sizes_per_proc(proc, rank);
if (size == 0)
continue;
nodes_needed_by_proc[proc].resize(size);
recv_request_per_proc.push_back(communicator.asyncReceive(
nodes_needed_by_proc[proc], proc, Tag::genTag(rank, 0, 0)));
}
for (auto & pair : nodes_per_proc) {
auto proc = pair.first;
auto & nodes = pair.second;
send_request_per_proc.push_back(
communicator.asyncSend(nodes, proc, Tag::genTag(proc, 0, 0)));
}
UInt req_nb;
while ((req_nb = communicator.waitAny(recv_request_per_proc)) != UInt(-1)) {
auto & request = recv_request_per_proc[req_nb];
auto proc = request.getSource();
auto & nodes = nodes_needed_by_proc[proc];
auto & scheme = communications.getScheme(proc, _send);
for (auto global_id : nodes) {
auto local_id = mesh.getNodeLocalId(global_id);
AKANTU_DEBUG_ASSERT(local_id != UInt(-1),
"The global node "
<< global_id << "is not known on rank " << rank);
scheme.push_back(local_id);
}
recv_request_per_proc.erase(recv_request_per_proc.begin() + req_nb);
}
communicator.waitAll(send_request_per_proc);
communicator.freeCommunicationRequest(send_request_per_proc);
}
} // namespace akantu
diff --git a/src/synchronizer/node_synchronizer.hh b/src/synchronizer/node_synchronizer.hh
index cc600ca2b..5378ef648 100644
--- a/src/synchronizer/node_synchronizer.hh
+++ b/src/synchronizer/node_synchronizer.hh
@@ -1,86 +1,87 @@
/**
* @file node_synchronizer.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Sep 23 11:45:24 2016
+ * @date creation: Tue Nov 08 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Synchronizer for nodal information
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_events.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NODE_SYNCHRONIZER_HH__
#define __AKANTU_NODE_SYNCHRONIZER_HH__
namespace akantu {
class NodeSynchronizer : public MeshEventHandler,
public SynchronizerImpl<UInt> {
public:
NodeSynchronizer(Mesh & mesh, const ID & id = "element_synchronizer",
MemoryID memory_id = 0,
const bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
~NodeSynchronizer() override;
friend class NodeInfoPerProc;
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override;
/// function to implement to react on akantu::RemovedNodesEvent
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) override {}
/// function to implement to react on akantu::NewElementsEvent
void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) override {}
/// function to implement to react on akantu::RemovedElementsEvent
void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) override {}
/// function to implement to react on akantu::ChangedElementsEvent
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override {}
public:
AKANTU_GET_MACRO(Mesh, mesh, Mesh &);
protected:
Int getRank(const UInt & /*node*/) const final { AKANTU_TO_IMPLEMENT(); }
protected:
Mesh & mesh;
// std::unordered_map<UInt, Int> node_to_prank;
};
} // namespace akantu
#endif /* __AKANTU_NODE_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/slave_element_info_per_processor.cc b/src/synchronizer/slave_element_info_per_processor.cc
index 0d9415e1a..e38400012 100644
--- a/src/synchronizer/slave_element_info_per_processor.cc
+++ b/src/synchronizer/slave_element_info_per_processor.cc
@@ -1,197 +1,198 @@
/**
* @file slave_element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Fri Mar 11 14:59:21 2016
+ * @date creation: Wed Mar 16 2016
+ * @date last modification: Tue Nov 07 2017
*
- * @brief
+ * @brief Helper class to distribute a mesh
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SlaveElementInfoPerProc::SlaveElementInfoPerProc(
ElementSynchronizer & synchronizer, UInt message_cnt, UInt root)
: ElementInfoPerProc(synchronizer, message_cnt, root, _not_defined) {
Vector<UInt> size(5);
comm.receive(size, this->root,
Tag::genTag(this->root, this->message_count, Tag::_SIZES));
this->type = (ElementType)size[0];
this->nb_local_element = size[1];
this->nb_ghost_element = size[2];
this->nb_element_to_receive = size[3];
this->nb_tags = size[4];
if (this->type != _not_defined)
this->nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
}
/* -------------------------------------------------------------------------- */
bool SlaveElementInfoPerProc::needSynchronize() {
return this->type != _not_defined;
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeConnectivities() {
Array<UInt> local_connectivity(
(this->nb_local_element + this->nb_ghost_element) *
this->nb_nodes_per_element);
AKANTU_DEBUG_INFO("Receiving connectivities from proc " << root);
comm.receive(
local_connectivity, this->root,
Tag::genTag(this->root, this->message_count, Tag::_CONNECTIVITY));
auto & old_nodes = this->getNodesGlobalIds();
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(this->mesh, local_connectivity,
this->nb_local_element, this->nb_ghost_element,
this->type, old_nodes);
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizePartitions() {
Array<UInt> local_partitions(this->nb_element_to_receive +
this->nb_ghost_element * 2);
AKANTU_DEBUG_INFO("Receiving partition informations from proc " << root);
this->comm.receive(local_partitions, this->root,
Tag::genTag(root, this->message_count, Tag::_PARTITIONS));
if (Mesh::getSpatialDimension(this->type) ==
this->mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
this->fillCommunicationScheme(local_partitions);
}
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeTags() {
AKANTU_DEBUG_IN();
if (this->nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
/* --------<<<<-TAGS------------------------------------------------- */
UInt mesh_data_sizes_buffer_length = 0;
CommunicationBuffer mesh_data_sizes_buffer;
AKANTU_DEBUG_INFO(
"Receiving the size of the information about the mesh data tags.");
comm.broadcast(mesh_data_sizes_buffer_length, 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, 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, this->message_count, Tag::_MESH_DATA)
<< ")");
comm.probe<char>(root,
Tag::genTag(root, this->message_count, Tag::_MESH_DATA),
mesh_data_comm_status);
UInt mesh_data_buffer_size(mesh_data_comm_status.size());
AKANTU_DEBUG_INFO("Receiving "
<< mesh_data_buffer_size << " bytes of mesh data TAG("
<< Tag::genTag(root, this->message_count, Tag::_MESH_DATA)
<< ")");
mesh_data_buffer.resize(mesh_data_buffer_size);
comm.receive(mesh_data_buffer, root,
Tag::genTag(root, this->message_count, Tag::_MESH_DATA));
// Loop over each tag for the current type
UInt k(0);
for (; names_it != names_end; ++names_it, ++k) {
this->fillMeshData(mesh_data_buffer, *names_it, tag_type_codes[k],
tag_nb_component[k]);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
const Communicator & comm = mesh.getCommunicator();
UInt my_rank = comm.whoAmI();
AKANTU_DEBUG_INFO("Receiving element groups from proc "
<< root << " TAG("
<< Tag::genTag(root, my_rank, Tag::_ELEMENT_GROUP) << ")");
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, my_rank, Tag::_ELEMENT_GROUP),
status);
CommunicationBuffer buffer(status.size());
comm.receive(buffer, root, Tag::genTag(root, my_rank, Tag::_ELEMENT_GROUP));
this->fillElementGroupsFromBuffer(buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/synchronizer/synchronizer.cc b/src/synchronizer/synchronizer.cc
index cfc86b95c..4917daf4e 100644
--- a/src/synchronizer/synchronizer.cc
+++ b/src/synchronizer/synchronizer.cc
@@ -1,56 +1,55 @@
/**
* @file synchronizer.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
- * @date last modification: Tue Dec 09 2014
+ * @date last modification: Wed Nov 15 2017
*
* @brief implementation of the common part
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "synchronizer.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Synchronizer::Synchronizer(const Communicator & comm, const ID & id,
MemoryID memory_id)
: Memory(id, memory_id), communicator(comm) {
int max_tag = comm.getMaxTag();
this->hash_id = std::hash<std::string>()(this->getID());
if (max_tag != 0)
this->hash_id = this->hash_id % max_tag;
this->nb_proc = communicator.getNbProc();
this->rank = communicator.whoAmI();
}
} // namespace akantu
diff --git a/src/synchronizer/synchronizer.hh b/src/synchronizer/synchronizer.hh
index 8f3501158..1d1e4cbe4 100644
--- a/src/synchronizer/synchronizer.hh
+++ b/src/synchronizer/synchronizer.hh
@@ -1,125 +1,125 @@
/**
* @file synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Dec 10 2015
+ * @date last modification: Tue Feb 20 2018
*
* @brief Common interface for synchronizers
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You 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_memory.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SYNCHRONIZER_HH__
#define __AKANTU_SYNCHRONIZER_HH__
namespace akantu {
class Communicator;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Base class for synchronizers */
/* -------------------------------------------------------------------------- */
class Synchronizer : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Synchronizer(const Communicator & comm, const ID & id = "synchronizer",
MemoryID memory_id = 0);
Synchronizer(const Synchronizer & other) = default;
~Synchronizer() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronize ghosts without state
template <class DataAccessor>
void synchronizeOnce(DataAccessor & data_accessor,
const SynchronizationTag & tag) const;
/// synchronize ghosts
template <class DataAccessor>
void synchronize(DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// asynchronous synchronization of ghosts
template <class DataAccessor>
void asynchronousSynchronize(const DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// wait end of asynchronous synchronization of ghosts
template <class DataAccessor>
void waitEndSynchronize(DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// compute buffer size for a given tag and data accessor
template <class DataAccessor>
void computeBufferSize(const DataAccessor & data_accessor,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Communicator, communicator, const Communicator &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the synchronizer
ID id;
/// hashed version of the id
int hash_id;
/// message counter per tag
std::map<SynchronizationTag, UInt> tag_counter;
/// the static memory instance
const Communicator & communicator;
/// nb processors in the communicator
UInt nb_proc;
/// rank in the communicator
UInt rank;
};
} // namespace akantu
#include "synchronizer_tmpl.hh"
#endif /* __AKANTU_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/synchronizer_impl.hh b/src/synchronizer/synchronizer_impl.hh
index fcfedb3e8..1bb1eaf56 100644
--- a/src/synchronizer/synchronizer_impl.hh
+++ b/src/synchronizer/synchronizer_impl.hh
@@ -1,123 +1,124 @@
/**
* @file synchronizer_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 24 13:26:47 2016
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the generic part of synchronizers
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communications.hh"
#include "synchronizer.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SYNCHRONIZER_IMPL_HH__
#define __AKANTU_SYNCHRONIZER_IMPL_HH__
namespace akantu {
template <class Entity> class SynchronizerImpl : public Synchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SynchronizerImpl(const Communicator & communicator,
const ID & id = "synchronizer", MemoryID memory_id = 0);
SynchronizerImpl(const SynchronizerImpl & other, const ID & id);
~SynchronizerImpl() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronous synchronization without state
virtual void synchronizeOnceImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const;
/// asynchronous synchronization of ghosts
virtual void
asynchronousSynchronizeImpl(const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/// wait end of asynchronous synchronization of ghosts
virtual void waitEndSynchronizeImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/// compute all buffer sizes
virtual void
computeAllBufferSizes(const DataAccessor<Entity> & data_accessor);
/// compute buffer size for a given tag and data accessor
virtual void computeBufferSizeImpl(const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
virtual void synchronizeImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
this->asynchronousSynchronizeImpl(data_accessor, tag);
this->waitEndSynchronizeImpl(data_accessor, tag);
}
/* ------------------------------------------------------------------------ */
/// extract the elements that have a true predicate from in_synchronizer and
/// store them in the current synchronizer
template <typename Pred>
void split(SynchronizerImpl & in_synchronizer, Pred && pred);
/// update schemes in a synchronizer
template <typename Updater> void updateSchemes(Updater && scheme_updater);
/* ------------------------------------------------------------------------ */
virtual UInt sanityCheckDataSize(const Array<Entity> & elements,
const SynchronizationTag & tag) const;
virtual void
packSanityCheckData(CommunicationDescriptor<Entity> & comm_desc) const;
virtual void
unpackSanityCheckData(CommunicationDescriptor<Entity> & comm_desc) const;
public:
AKANTU_GET_MACRO(Communications, communications,
const Communications<Entity> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(Communications, communications,
Communications<Entity> &);
virtual Int getRank(const Entity & entity) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// information on the communications
Communications<Entity> communications;
};
} // namespace akantu
#include "synchronizer_impl_tmpl.hh"
#endif /* __AKANTU_SYNCHRONIZER_IMPL_HH__ */
diff --git a/src/synchronizer/synchronizer_impl_tmpl.hh b/src/synchronizer/synchronizer_impl_tmpl.hh
index 7831fbc79..1c919afbd 100644
--- a/src/synchronizer/synchronizer_impl_tmpl.hh
+++ b/src/synchronizer/synchronizer_impl_tmpl.hh
@@ -1,314 +1,315 @@
/**
* @file synchronizer_impl_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 24 13:29:47 2016
+ * @date creation: Wed Sep 07 2016
+ * @date last modification: Tue Feb 20 2018
*
* @brief Implementation of the SynchronizerImpl
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SYNCHRONIZER_IMPL_TMPL_HH__
#define __AKANTU_SYNCHRONIZER_IMPL_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity>
SynchronizerImpl<Entity>::SynchronizerImpl(const Communicator & comm,
const ID & id, MemoryID memory_id)
: Synchronizer(comm, id, memory_id), communications(comm) {}
/* -------------------------------------------------------------------------- */
template <class Entity>
SynchronizerImpl<Entity>::SynchronizerImpl(const SynchronizerImpl & other,
const ID & id)
: Synchronizer(other), communications(other.communications) {
this->id = id;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::synchronizeOnceImpl(
DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const {
// no need to synchronize
if (this->nb_proc == 1)
return;
using CommunicationRequests = std::vector<CommunicationRequest>;
using CommunicationBuffers = std::map<UInt, CommunicationBuffer>;
CommunicationRequests send_requests, recv_requests;
CommunicationBuffers send_buffers, recv_buffers;
auto postComm = [&](const CommunicationSendRecv & sr,
CommunicationBuffers & buffers,
CommunicationRequests & requests) -> void {
for (auto && pair : communications.iterateSchemes(sr)) {
auto & proc = pair.first;
const auto & scheme = pair.second;
auto & buffer = buffers[proc];
UInt buffer_size = data_accessor.getNbData(scheme, tag);
buffer.resize(buffer_size);
if (sr == _recv) {
requests.push_back(communicator.asyncReceive(
buffer, proc,
Tag::genTag(this->rank, 0, Tag::_SYNCHRONIZE, this->hash_id)));
} else {
data_accessor.packData(buffer, scheme, tag);
send_requests.push_back(communicator.asyncSend(
buffer, proc,
Tag::genTag(proc, 0, Tag::_SYNCHRONIZE, this->hash_id)));
}
}
};
// post the receive requests
postComm(_recv, recv_buffers, recv_requests);
// post the send data requests
postComm(_send, send_buffers, send_requests);
// treat the receive requests
UInt request_ready;
while ((request_ready = communicator.waitAny(recv_requests)) != UInt(-1)) {
CommunicationRequest & req = recv_requests[request_ready];
UInt proc = req.getSource();
CommunicationBuffer & buffer = recv_buffers[proc];
const auto & scheme = this->communications.getScheme(proc, _recv);
data_accessor.unpackData(buffer, scheme, tag);
req.free();
recv_requests.erase(recv_requests.begin() + request_ready);
}
communicator.waitAll(send_requests);
communicator.freeCommunicationRequest(send_requests);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::asynchronousSynchronizeImpl(
const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (not this->communications.hasCommunicationSize(tag))
this->computeBufferSize(data_accessor, tag);
this->communications.incrementCounter(tag);
// Posting the receive -------------------------------------------------------
if (this->communications.hasPendingRecv(tag)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"There must still be some pending receive communications."
<< " Tag is " << tag << " Cannot start new ones");
}
for (auto && comm_desc : this->communications.iterateRecv(tag)) {
comm_desc.postRecv(this->hash_id);
}
// Posting the sends -------------------------------------------------------
if (communications.hasPendingSend(tag)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"There must be some pending sending communications."
<< " Tag is " << tag);
}
for (auto && comm_desc : this->communications.iterateSend(tag)) {
comm_desc.resetBuffer();
#ifndef AKANTU_NDEBUG
this->packSanityCheckData(comm_desc);
#endif
comm_desc.packData(data_accessor);
comm_desc.postSend(this->hash_id);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::waitEndSynchronizeImpl(
DataAccessor<Entity> & data_accessor, const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
if (this->communications.begin(tag, _recv) !=
this->communications.end(tag, _recv) &&
!this->communications.hasPendingRecv(tag))
AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
"No pending communication with the tag \""
<< tag);
#endif
auto recv_end = this->communications.end(tag, _recv);
decltype(recv_end) recv_it;
while ((recv_it = this->communications.waitAnyRecv(tag)) != recv_end) {
auto && comm_desc = *recv_it;
#ifndef AKANTU_NDEBUG
this->unpackSanityCheckData(comm_desc);
#endif
comm_desc.unpackData(data_accessor);
comm_desc.resetBuffer();
comm_desc.freeRequest();
}
this->communications.waitAllSend(tag);
this->communications.freeSendRequests(tag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::computeAllBufferSizes(
const DataAccessor<Entity> & data_accessor) {
for (auto && tag : this->communications.iterateTags()) {
this->computeBufferSize(data_accessor, tag);
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::computeBufferSizeImpl(
const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (not this->communications.hasCommunication(tag)) {
this->communications.initializeCommunications(tag);
AKANTU_DEBUG_ASSERT(communications.hasCommunication(tag) == true,
"Communications where not properly initialized");
}
for (auto sr : iterate_send_recv) {
for (auto && pair : this->communications.iterateSchemes(sr)) {
auto proc = pair.first;
const auto & scheme = pair.second;
UInt size = 0;
#ifndef AKANTU_NDEBUG
size += this->sanityCheckDataSize(scheme, tag);
#endif
size += data_accessor.getNbData(scheme, tag);
AKANTU_DEBUG_INFO("I have "
<< size << "(" << printMemorySize<char>(size) << " - "
<< scheme.size() << " element(s)) data to "
<< std::string(sr == _recv ? "receive from" : "send to")
<< proc << " for tag " << tag);
this->communications.setCommunicationSize(tag, proc, size, sr);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Entity>
template <typename Pred>
void SynchronizerImpl<Entity>::split(SynchronizerImpl<Entity> & in_synchronizer,
Pred && pred) {
AKANTU_DEBUG_IN();
auto filter_list = [&](auto & list, auto & new_list) {
auto copy = list;
list.resize(0);
new_list.resize(0);
for (auto && entity : copy) {
if (std::forward<Pred>(pred)(entity)) {
new_list.push_back(entity);
} else {
list.push_back(entity);
}
}
};
for (auto sr : iterate_send_recv) {
for (auto & scheme_pair :
in_synchronizer.communications.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
auto & new_scheme = communications.createScheme(proc, sr);
filter_list(scheme, new_scheme);
}
}
in_synchronizer.communications.invalidateSizes();
communications.invalidateSizes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Entity>
template <typename Updater>
void SynchronizerImpl<Entity>::updateSchemes(Updater && scheme_updater) {
for (auto sr : iterate_send_recv) {
for (auto & scheme_pair : communications.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
std::forward<Updater>(scheme_updater)(scheme, proc, sr);
}
}
communications.invalidateSizes();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
UInt SynchronizerImpl<Entity>::sanityCheckDataSize(
const Array<Entity> &, const SynchronizationTag &) const {
return 0;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::packSanityCheckData(
CommunicationDescriptor<Entity> &) const {}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::unpackSanityCheckData(
CommunicationDescriptor<Entity> &) const {}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_SYNCHRONIZER_IMPL_TMPL_HH__ */
diff --git a/src/synchronizer/synchronizer_registry.cc b/src/synchronizer/synchronizer_registry.cc
index 3711fa3af..f99fac614 100644
--- a/src/synchronizer/synchronizer_registry.cc
+++ b/src/synchronizer/synchronizer_registry.cc
@@ -1,121 +1,120 @@
/**
* @file synchronizer_registry.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 16 2011
- * @date last modification: Thu Oct 08 2015
+ * @date last modification: Wed Nov 15 2017
*
* @brief Registry of synchronizers
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "synchronizer_registry.hh"
#include "synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SynchronizerRegistry::SynchronizerRegistry() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SynchronizerRegistry::~SynchronizerRegistry() {
AKANTU_DEBUG_IN();
synchronizers.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::registerDataAccessor(
DataAccessorBase & data_accessor) {
this->data_accessor = &data_accessor;
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::synchronize(SynchronizationTag tag) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(data_accessor != nullptr, "No data accessor set.");
std::pair<Tag2Sync::iterator, Tag2Sync::iterator> range =
synchronizers.equal_range(tag);
for (auto it = range.first; it != range.second; ++it) {
it->second->synchronize(*data_accessor, tag);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::asynchronousSynchronize(SynchronizationTag tag) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(data_accessor != nullptr, "No data accessor set.");
std::pair<Tag2Sync::iterator, Tag2Sync::iterator> range =
synchronizers.equal_range(tag);
for (auto it = range.first; it != range.second; ++it) {
(*it).second->asynchronousSynchronize(*data_accessor, tag);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::waitEndSynchronize(SynchronizationTag tag) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(data_accessor != nullptr, "No data accessor set.");
std::pair<Tag2Sync::iterator, Tag2Sync::iterator> range =
synchronizers.equal_range(tag);
for (auto it = range.first; it != range.second; ++it) {
(*it).second->waitEndSynchronize(*data_accessor, tag);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::registerSynchronizer(Synchronizer & synchronizer,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
synchronizers.insert(
std::pair<SynchronizationTag, Synchronizer *>(tag, &synchronizer));
AKANTU_DEBUG_OUT();
}
} // akantu
diff --git a/src/synchronizer/synchronizer_registry.hh b/src/synchronizer/synchronizer_registry.hh
index 1edf20b9a..54c2026ee 100644
--- a/src/synchronizer/synchronizer_registry.hh
+++ b/src/synchronizer/synchronizer_registry.hh
@@ -1,91 +1,90 @@
/**
* @file synchronizer_registry.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Dec 09 2014
+ * @date last modification: Sun Dec 03 2017
*
* @brief Registry of synchronizers
*
* @section LICENSE
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SYNCHRONIZER_REGISTRY_HH__
#define __AKANTU_SYNCHRONIZER_REGISTRY_HH__
namespace akantu {
class DataAccessorBase;
class Synchronizer;
}
namespace akantu {
class SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SynchronizerRegistry();
virtual ~SynchronizerRegistry();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronize operation
void synchronize(SynchronizationTag tag);
/// asynchronous synchronization
void asynchronousSynchronize(SynchronizationTag tag);
/// wait end of asynchronous synchronization
void waitEndSynchronize(SynchronizationTag tag);
/// register a new synchronization
void registerSynchronizer(Synchronizer & synchronizer,
SynchronizationTag tag);
/// Register a different data accessor.
void registerDataAccessor(DataAccessorBase & data_accessor);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using Tag2Sync = std::multimap<SynchronizationTag, Synchronizer *>;
/// list of registered synchronization
Tag2Sync synchronizers;
/// data accessor that will permit to do the pack/unpack things
DataAccessorBase * data_accessor{nullptr};
};
} // akantu
#endif /* __AKANTU_SYNCHRONIZER_REGISTRY_HH__ */
diff --git a/src/synchronizer/synchronizer_tmpl.hh b/src/synchronizer/synchronizer_tmpl.hh
index c7b76c4c7..763cb9070 100644
--- a/src/synchronizer/synchronizer_tmpl.hh
+++ b/src/synchronizer/synchronizer_tmpl.hh
@@ -1,120 +1,121 @@
/**
* @file synchronizer_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date Wed Aug 3 13:49:36 2016
+ * @date creation: Wed Sep 07 2016
+ * @date last modification: Thu May 11 2017
*
* @brief Implementation of the helper classes for the synchronizer
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "data_accessor.hh"
#include "synchronizer.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SYNCHRONIZER_TMPL_HH__
#define __AKANTU_SYNCHRONIZER_TMPL_HH__
namespace akantu {
template <class DataAccessorT>
void Synchronizer::synchronizeOnce(DataAccessorT & data_accessor,
const SynchronizationTag & tag) const {
if (const auto * synch_el =
dynamic_cast<const SynchronizerImpl<Element> *>(this)) {
synch_el->synchronizeOnceImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (const auto * synch_dof =
dynamic_cast<const SynchronizerImpl<UInt> *>(this)) {
synch_dof->synchronizeOnceImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/// synchronize ghosts
template <class DataAccessorT>
void Synchronizer::synchronize(DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->synchronizeImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->synchronizeImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/* -------------------------------------------------------------------------- */
template <class DataAccessorT>
void Synchronizer::asynchronousSynchronize(const DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->asynchronousSynchronizeImpl(
dynamic_cast<const DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->asynchronousSynchronizeImpl(
dynamic_cast<const DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/* -------------------------------------------------------------------------- */
template <class DataAccessorT>
void Synchronizer::waitEndSynchronize(DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->waitEndSynchronizeImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->waitEndSynchronizeImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/// compute buffer size for a given tag and data accessor
template <class DataAccessorT>
void Synchronizer::computeBufferSize(const DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->computeBufferSizeImpl(
dynamic_cast<const DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->computeBufferSizeImpl(
dynamic_cast<const DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
} // akantu
#endif /* __AKANTU_SYNCHRONIZER_TMPL_HH__ */