diff --git a/packages/core.cmake b/packages/core.cmake index 023a32535..670fb136d 100644 --- a/packages/core.cmake +++ b/packages/core.cmake @@ -1,522 +1,525 @@ #=============================================================================== # @file core.cmake # # @author Guillaume Anciaux # @author Nicolas Richart # # @date creation: Mon Nov 21 2011 # @date last modification: Mon Jan 18 2016 # # @brief package description for core # # @section LICENSE # # Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de # Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des # Solides) # # Akantu is free software: you can redistribute it and/or modify it under the # terms of the GNU Lesser General Public License as published by the Free # Software Foundation, either version 3 of the License, or (at your option) any # later version. # # Akantu is distributed in the hope that it will be useful, but WITHOUT ANY # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR # A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public License # along with Akantu. If not, see . # #=============================================================================== package_declare(core NOT_OPTIONAL DESCRIPTION "core package for Akantu" FEATURES_PUBLIC cxx_strong_enums cxx_defaulted_functions cxx_deleted_functions cxx_auto_type cxx_decltype_auto FEATURES_PRIVATE cxx_lambdas cxx_nullptr cxx_range_for cxx_delegating_constructors DEPENDS INTERFACE Boost Eigen3) package_declare_sources(core common/aka_array.cc common/aka_array.hh common/aka_array_tmpl.hh common/aka_bbox.hh common/aka_blas_lapack.hh common/aka_circular_array.hh common/aka_circular_array_inline_impl.cc common/aka_common.cc common/aka_common.hh common/aka_common_inline_impl.cc common/aka_csr.hh common/aka_element_classes_info_inline_impl.cc common/aka_enum_macros.hh common/aka_error.cc common/aka_error.hh common/aka_event_handler_manager.hh common/aka_extern.cc common/aka_factory.hh common/aka_fwd.hh common/aka_grid_dynamic.hh common/aka_math.cc common/aka_math.hh common/aka_math_tmpl.hh common/aka_memory.cc common/aka_memory.hh common/aka_memory_inline_impl.cc common/aka_named_argument.hh common/aka_random_generator.hh common/aka_safe_enum.hh common/aka_static_memory.cc common/aka_static_memory.hh common/aka_static_memory_inline_impl.cc common/aka_static_memory_tmpl.hh common/aka_typelist.hh common/aka_types.hh + common/aka_types_eigen_matrix_plugin.hh + common/aka_types_eigen_matrix_base_plugin.hh + common/aka_types_eigen_plain_object_base_plugin.hh common/aka_view_iterators.hh common/aka_visitor.hh common/aka_voigthelper.hh common/aka_voigthelper_tmpl.hh common/aka_voigthelper.cc common/aka_warning.hh common/aka_warning_restore.hh common/aka_iterators.hh common/aka_static_if.hh common/aka_compatibilty_with_cpp_standard.hh fe_engine/element_class.hh fe_engine/element_class_tmpl.hh fe_engine/element_classes/element_class_hexahedron_8_inline_impl.cc fe_engine/element_classes/element_class_hexahedron_20_inline_impl.cc fe_engine/element_classes/element_class_pentahedron_6_inline_impl.cc fe_engine/element_classes/element_class_pentahedron_15_inline_impl.cc fe_engine/element_classes/element_class_point_1_inline_impl.cc fe_engine/element_classes/element_class_quadrangle_4_inline_impl.cc fe_engine/element_classes/element_class_quadrangle_8_inline_impl.cc fe_engine/element_classes/element_class_segment_2_inline_impl.cc fe_engine/element_classes/element_class_segment_3_inline_impl.cc fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.cc fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.cc fe_engine/element_classes/element_class_triangle_3_inline_impl.cc fe_engine/element_classes/element_class_triangle_6_inline_impl.cc fe_engine/element_type_conversion.hh fe_engine/fe_engine.cc fe_engine/fe_engine.hh fe_engine/fe_engine_inline_impl.cc fe_engine/fe_engine_template.hh fe_engine/fe_engine_template_tmpl_field.hh fe_engine/fe_engine_template_tmpl.hh fe_engine/geometrical_element_property.hh fe_engine/geometrical_element_property.cc fe_engine/gauss_integration.cc fe_engine/gauss_integration_tmpl.hh fe_engine/integrator.hh fe_engine/integrator_gauss.hh fe_engine/integrator_gauss_inline_impl.cc fe_engine/interpolation_element_tmpl.hh fe_engine/integration_point.hh fe_engine/shape_functions.hh fe_engine/shape_functions.cc fe_engine/shape_functions_inline_impl.cc fe_engine/shape_lagrange_base.cc fe_engine/shape_lagrange_base.hh fe_engine/shape_lagrange_base_inline_impl.cc fe_engine/shape_lagrange.hh fe_engine/shape_lagrange_inline_impl.cc fe_engine/element.hh io/dumper/dumpable.hh io/dumper/dumpable.cc io/dumper/dumpable_dummy.hh io/dumper/dumpable_inline_impl.hh io/dumper/dumper_field.hh io/dumper/dumper_material_padders.hh io/dumper/dumper_filtered_connectivity.hh io/dumper/dumper_element_partition.hh io/mesh_io.cc io/mesh_io.hh io/mesh_io/mesh_io_diana.cc io/mesh_io/mesh_io_diana.hh io/mesh_io/mesh_io_msh.cc io/mesh_io/mesh_io_msh.hh #io/model_io.cc #io/model_io.hh io/parser/algebraic_parser.hh io/parser/input_file_parser.hh io/parser/parsable.cc io/parser/parsable.hh io/parser/parser.cc io/parser/parser_real.cc io/parser/parser_random.cc io/parser/parser_types.cc io/parser/parser_input_files.cc io/parser/parser.hh io/parser/parser_tmpl.hh io/parser/parser_grammar_tmpl.hh io/parser/cppargparse/cppargparse.hh io/parser/cppargparse/cppargparse.cc io/parser/cppargparse/cppargparse_tmpl.hh io/parser/parameter_registry.cc io/parser/parameter_registry.hh io/parser/parameter_registry_tmpl.hh mesh/element_group.cc mesh/element_group.hh mesh/element_group_inline_impl.cc mesh/element_type_map.cc mesh/element_type_map.hh mesh/element_type_map_tmpl.hh mesh/element_type_map_filter.hh mesh/group_manager.cc mesh/group_manager.hh mesh/group_manager_inline_impl.cc mesh/mesh.cc mesh/mesh.hh mesh/mesh_periodic.cc mesh/mesh_accessor.hh mesh/mesh_events.hh mesh/mesh_filter.hh mesh/mesh_global_data_updater.hh mesh/mesh_data.cc mesh/mesh_data.hh mesh/mesh_data_tmpl.hh mesh/mesh_inline_impl.cc mesh/node_group.cc mesh/node_group.hh mesh/node_group_inline_impl.cc mesh/mesh_iterators.hh mesh_utils/mesh_partition.cc mesh_utils/mesh_partition.hh mesh_utils/mesh_partition/mesh_partition_mesh_data.cc mesh_utils/mesh_partition/mesh_partition_mesh_data.hh mesh_utils/mesh_partition/mesh_partition_scotch.hh mesh_utils/mesh_utils_pbc.cc mesh_utils/mesh_utils.cc mesh_utils/mesh_utils.hh mesh_utils/mesh_utils_distribution.cc mesh_utils/mesh_utils_distribution.hh mesh_utils/mesh_utils.hh mesh_utils/mesh_utils_inline_impl.cc mesh_utils/global_ids_updater.hh mesh_utils/global_ids_updater.cc mesh_utils/global_ids_updater_inline_impl.cc model/boundary_condition.hh model/boundary_condition_functor.hh model/boundary_condition_functor_inline_impl.cc model/boundary_condition_tmpl.hh model/common/neighborhood_base.hh model/common/neighborhood_base.cc model/common/neighborhood_base_inline_impl.cc model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.cc model/common/non_local_toolbox/non_local_manager.hh model/common/non_local_toolbox/non_local_manager.cc model/common/non_local_toolbox/non_local_manager_inline_impl.cc model/common/non_local_toolbox/non_local_manager_callback.hh model/common/non_local_toolbox/non_local_neighborhood_base.hh model/common/non_local_toolbox/non_local_neighborhood_base.cc model/common/non_local_toolbox/non_local_neighborhood.hh model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc model/common/non_local_toolbox/base_weight_function.hh model/common/non_local_toolbox/base_weight_function_inline_impl.cc model/dof_manager.cc model/dof_manager.hh model/dof_manager_default.cc model/dof_manager_default.hh model/dof_manager_default_inline_impl.cc model/dof_manager_inline_impl.cc model/model_solver.cc model/model_solver.hh model/non_linear_solver.cc model/non_linear_solver.hh model/non_linear_solver_default.hh model/non_linear_solver_lumped.cc model/non_linear_solver_lumped.hh model/solver_callback.hh model/solver_callback.cc model/time_step_solver.hh model/time_step_solvers/time_step_solver.cc model/time_step_solvers/time_step_solver_default.cc model/time_step_solvers/time_step_solver_default.hh model/time_step_solvers/time_step_solver_default_explicit.hh model/non_linear_solver_callback.hh model/time_step_solvers/time_step_solver_default_solver_callback.hh model/integration_scheme/generalized_trapezoidal.cc model/integration_scheme/generalized_trapezoidal.hh model/integration_scheme/integration_scheme.cc model/integration_scheme/integration_scheme.hh model/integration_scheme/integration_scheme_1st_order.cc model/integration_scheme/integration_scheme_1st_order.hh model/integration_scheme/integration_scheme_2nd_order.cc model/integration_scheme/integration_scheme_2nd_order.hh model/integration_scheme/newmark-beta.cc model/integration_scheme/newmark-beta.hh model/integration_scheme/pseudo_time.cc model/integration_scheme/pseudo_time.hh model/model.cc model/model.hh model/model_inline_impl.cc model/model_options.hh solver/sparse_solver.cc solver/sparse_solver.hh solver/sparse_solver_inline_impl.cc solver/sparse_matrix.cc solver/sparse_matrix.hh solver/sparse_matrix_inline_impl.cc solver/sparse_matrix_aij.cc solver/sparse_matrix_aij.hh solver/sparse_matrix_aij_inline_impl.cc solver/terms_to_assemble.hh synchronizer/communication_buffer_inline_impl.cc synchronizer/communication_descriptor.hh synchronizer/communication_descriptor_tmpl.hh synchronizer/communication_request.hh synchronizer/communication_tag.hh synchronizer/communications.hh synchronizer/communications_tmpl.hh synchronizer/communicator.cc synchronizer/communicator.hh synchronizer/communicator_dummy_inline_impl.cc synchronizer/communicator_event_handler.hh synchronizer/communicator_inline_impl.hh synchronizer/data_accessor.cc synchronizer/data_accessor.hh synchronizer/dof_synchronizer.cc synchronizer/dof_synchronizer.hh synchronizer/dof_synchronizer_inline_impl.cc synchronizer/element_info_per_processor.cc synchronizer/element_info_per_processor.hh synchronizer/element_info_per_processor_tmpl.hh synchronizer/element_synchronizer.cc synchronizer/element_synchronizer.hh synchronizer/facet_synchronizer.cc synchronizer/facet_synchronizer.hh synchronizer/facet_synchronizer_inline_impl.cc synchronizer/grid_synchronizer.cc synchronizer/grid_synchronizer.hh synchronizer/grid_synchronizer_tmpl.hh synchronizer/master_element_info_per_processor.cc synchronizer/node_info_per_processor.cc synchronizer/node_info_per_processor.hh synchronizer/node_synchronizer.cc synchronizer/node_synchronizer.hh synchronizer/periodic_node_synchronizer.cc synchronizer/periodic_node_synchronizer.hh synchronizer/slave_element_info_per_processor.cc synchronizer/synchronizer.cc synchronizer/synchronizer.hh synchronizer/synchronizer_impl.hh synchronizer/synchronizer_impl_tmpl.hh synchronizer/synchronizer_registry.cc synchronizer/synchronizer_registry.hh synchronizer/synchronizer_tmpl.hh synchronizer/communication_buffer.hh ) set(AKANTU_SPIRIT_SOURCES io/mesh_io/mesh_io_abaqus.cc io/parser/parser_real.cc io/parser/parser_random.cc io/parser/parser_types.cc io/parser/parser_input_files.cc PARENT_SCOPE ) package_declare_elements(core ELEMENT_TYPES _point_1 _segment_2 _segment_3 _triangle_3 _triangle_6 _quadrangle_4 _quadrangle_8 _tetrahedron_4 _tetrahedron_10 _pentahedron_6 _pentahedron_15 _hexahedron_8 _hexahedron_20 KIND regular GEOMETRICAL_TYPES _gt_point _gt_segment_2 _gt_segment_3 _gt_triangle_3 _gt_triangle_6 _gt_quadrangle_4 _gt_quadrangle_8 _gt_tetrahedron_4 _gt_tetrahedron_10 _gt_hexahedron_8 _gt_hexahedron_20 _gt_pentahedron_6 _gt_pentahedron_15 INTERPOLATION_TYPES _itp_lagrange_point_1 _itp_lagrange_segment_2 _itp_lagrange_segment_3 _itp_lagrange_triangle_3 _itp_lagrange_triangle_6 _itp_lagrange_quadrangle_4 _itp_serendip_quadrangle_8 _itp_lagrange_tetrahedron_4 _itp_lagrange_tetrahedron_10 _itp_lagrange_hexahedron_8 _itp_serendip_hexahedron_20 _itp_lagrange_pentahedron_6 _itp_lagrange_pentahedron_15 GEOMETRICAL_SHAPES _gst_point _gst_triangle _gst_square _gst_prism GAUSS_INTEGRATION_TYPES _git_point _git_segment _git_triangle _git_tetrahedron _git_pentahedron INTERPOLATION_KIND _itk_lagrangian FE_ENGINE_LISTS gradient_on_integration_points interpolate_on_integration_points interpolate compute_normals_on_integration_points inverse_map contains compute_shapes compute_shapes_derivatives get_shapes_derivatives lagrange_base ) package_declare_documentation_files(core manual.sty manual.cls manual.tex manual-macros.sty manual-titlepages.tex manual-authors.tex manual-changelog.tex manual-introduction.tex manual-gettingstarted.tex manual-io.tex manual-feengine.tex manual-elements.tex manual-appendix-elements.tex manual-appendix-packages.tex manual-backmatter.tex manual-bibliography.bib manual-bibliographystyle.bst figures/bc_and_ic_example.pdf figures/boundary.pdf figures/boundary.svg figures/dirichlet.pdf figures/dirichlet.svg # figures/doc_wheel.pdf # figures/doc_wheel.svg figures/hot-point-1.png figures/hot-point-2.png figures/insertion.pdf figures/interpolate.pdf figures/interpolate.svg figures/vectors.pdf figures/vectors.svg figures/elements/hexahedron_8.pdf figures/elements/hexahedron_8.svg figures/elements/quadrangle_4.pdf figures/elements/quadrangle_4.svg figures/elements/quadrangle_8.pdf figures/elements/quadrangle_8.svg figures/elements/segment_2.pdf figures/elements/segment_2.svg figures/elements/segment_3.pdf figures/elements/segment_3.svg figures/elements/tetrahedron_10.pdf figures/elements/tetrahedron_10.svg figures/elements/tetrahedron_4.pdf figures/elements/tetrahedron_4.svg figures/elements/triangle_3.pdf figures/elements/triangle_3.svg figures/elements/triangle_6.pdf figures/elements/triangle_6.svg figures/elements/xtemp.pdf ) package_declare_documentation(core "This package is the core engine of \\akantu. It depends on:" "\\begin{itemize}" "\\item A C++ compiler (\\href{http://gcc.gnu.org/}{GCC} >= 4, or \\href{https://software.intel.com/en-us/intel-compilers}{Intel})." "\\item The cross-platform, open-source \\href{http://www.cmake.org/}{CMake} build system." "\\item The \\href{http://www.boost.org/}{Boost} C++ portable libraries." "\\item The \\href{http://www.zlib.net/}{zlib} compression library." "\\end{itemize}" "" "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:" "\\begin{command}" " > sudo apt-get install cmake libboost-dev zlib1g-dev g++" "\\end{command}" "" "Under Mac OS X the installation requires the following steps:" "\\begin{itemize}" "\\item Install Xcode" "\\item Install the command line tools." "\\item Install the MacPorts project which allows to automatically" "download and install opensource packages." "\\end{itemize}" "Then the following commands should be typed in a terminal:" "\\begin{command}" " > sudo port install cmake gcc48 boost" "\\end{command}" ) find_program(READLINK_COMMAND readlink) find_program(ADDR2LINE_COMMAND addr2line) find_program(PATCH_COMMAND patch) mark_as_advanced(READLINK_COMMAND) mark_as_advanced(ADDR2LINE_COMMAND) package_declare_extra_files_to_package(core SOURCES common/aka_element_classes_info.hh.in common/aka_config.hh.in ) if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang" AND (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.9)) package_set_compile_flags(core CXX "-Wno-undefined-var-template") endif() if(DEFINED AKANTU_CXX11_FLAGS) package_declare(core_cxx11 NOT_OPTIONAL DESCRIPTION "C++ 11 additions for Akantu core" COMPILE_FLAGS CXX "${AKANTU_CXX11_FLAGS}") if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.6") set(AKANTU_CORE_CXX11 OFF CACHE BOOL "C++ 11 additions for Akantu core - not supported by the selected compiler" FORCE) endif() endif() package_declare_documentation(core_cxx11 "This option activates some features of the C++11 standard. This is usable with GCC>=4.7 or Intel>=13.") else() if(CMAKE_VERSION VERSION_LESS 3.1) message(FATAL_ERROR "Since version 3.0 Akantu requires at least c++11 capable compiler") endif() endif() diff --git a/packages/eigen.cmake b/packages/eigen.cmake index 3b21afccd..841c85a63 100644 --- a/packages/eigen.cmake +++ b/packages/eigen.cmake @@ -1,6 +1,8 @@ package_declare(Eigen3 EXTERNAL DESCRIPTION "Add Eigen3 dependency to akantu" EXTRA_PACKAGE_OPTIONS ARGS 3.3 + COMPILE_FLAGS CXX -DEIGEN_MAX_CPP_VER=14 + COMPILE_FLAGS CXX -DEIGEN_DEFAULT_DENSE_INDEX_TYPE=akantu::Idx ) mark_as_advanced(Eigen3_DIR) diff --git a/src/common/aka_array.hh b/src/common/aka_array.hh index 829a4679e..f587d4584 100644 --- a/src/common/aka_array.hh +++ b/src/common/aka_array.hh @@ -1,417 +1,416 @@ /** * @file aka_array.hh * * @author Till Junge * @author Nicolas Richart * * @date creation: Fri Jun 18 2010 * @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 (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides) * * Akantu is free software: you can redistribute it and/or modify it under the * terms of the GNU Lesser General Public License as published by the Free * Software Foundation, either version 3 of the License, or (at your option) any * later version. * * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more * details. * * You should have received a copy of the GNU Lesser General Public License * along with Akantu. If not, see . * */ /* -------------------------------------------------------------------------- */ #ifndef __AKANTU_VECTOR_HH__ #define __AKANTU_VECTOR_HH__ /* -------------------------------------------------------------------------- */ #include "aka_common.hh" #include "aka_view_iterators.hh" #include "aka_types.hh" /* -------------------------------------------------------------------------- */ #include #include /* -------------------------------------------------------------------------- */ namespace akantu { /// class that afford to store vectors in static memory class ArrayBase { /* ------------------------------------------------------------------------ */ /* Constructors/Destructors */ /* ------------------------------------------------------------------------ */ public: explicit ArrayBase(ID id = "") : id(std::move(id)) {} ArrayBase(const ArrayBase & other, const ID & id = "") { this->id = (id == "") ? other.id : id; } ArrayBase(ArrayBase && other) = default; ArrayBase & operator=(const ArrayBase & other) = default; // ArrayBase & operator=(ArrayBase && other) = default; virtual ~ArrayBase() = default; /* ------------------------------------------------------------------------ */ /* Methods */ /* ------------------------------------------------------------------------ */ public: /// get the amount of space allocated in bytes virtual UInt getMemorySize() const = 0; /// 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 = 0; /* ------------------------------------------------------------------------ */ /* Accessors */ /* ------------------------------------------------------------------------ */ public: /// Get the Size of the Array UInt size() const { return size_; } /// Get the number of components AKANTU_GET_MACRO(NbComponent, nb_component, UInt); /// Get the name of th array AKANTU_GET_MACRO(ID, id, const ID &); /// Set the name of th array AKANTU_SET_MACRO(ID, id, const ID &); /* ------------------------------------------------------------------------ */ /* Class Members */ /* ------------------------------------------------------------------------ */ protected: /// id of the vector ID id{""}; /// the size used UInt size_{0}; /// number of components UInt nb_component{1}; }; /* -------------------------------------------------------------------------- */ /* Memory handling layer */ /* -------------------------------------------------------------------------- */ enum class ArrayAllocationType { _default, _pod, }; template struct ArrayAllocationTrait : public std::conditional_t< std::is_scalar::value, std::integral_constant, std::integral_constant> {}; /* -------------------------------------------------------------------------- */ template ::value> class ArrayDataLayer : public ArrayBase { public: using value_type = T; using reference = value_type &; using pointer_type = value_type *; using const_reference = const value_type &; public: virtual ~ArrayDataLayer() = default; /// Allocation of a new vector explicit ArrayDataLayer(UInt size = 0, UInt nb_component = 1, const ID & id = ""); /// Allocation of a new vector with a default value ArrayDataLayer(UInt size, UInt nb_component, const_reference value, const ID & id = ""); /// Copy constructor (deep copy) ArrayDataLayer(const ArrayDataLayer & vect, const ID & id = ""); #ifndef SWIG /// Copy constructor (deep copy) explicit ArrayDataLayer(const std::vector & vect); #endif // copy operator ArrayDataLayer & operator=(const ArrayDataLayer & other); // move constructor ArrayDataLayer(ArrayDataLayer && other); // move assign ArrayDataLayer & operator=(ArrayDataLayer && other); protected: // deallocate the memory virtual void deallocate() {} // allocate the memory virtual void allocate(UInt size, UInt nb_component); // allocate and initialize the memory virtual void allocate(UInt size, UInt nb_component, const T & value); public: /// append a tuple of size nb_component containing value inline void push_back(const_reference value); /// append a vector // inline void push_back(const value_type new_elem[]); #ifndef SWIG /// append a Vector or a Matrix template