Merge branch 'master' into features/viscoel-damage
e4b9ab981754
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Authored by gallyamov on Jul 16 2019, 17:30.

Description

Merge branch 'master' into features/viscoel-damage

Details

Committed

gallyamov

Jul 16 2019, 17:30

Pushed

gitlab-richart

Jan 18 2021, 21:10

Parents

rAKA969790be627e: Was not updating Jacobian with cohesive elements
rAKA64b062ea67f5: Allowing to call the solver with a different solver callback

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Event Timeline

gallyamov committed rAKAe4b9ab981754: Merge branch 'master' into features/viscoel-damage (authored by gallyamov).Jul 16 2019, 17:30

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
64b062ea67f5	richart	Allowing to call the solver with a different solver callback	Jul 4 2019
1ac558c31da4	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Jul 3 2019
34b888c7b651	richart	Adding first version of anisotroptic damage law	Jul 3 2019
8a9c0bc03921	richart	Fixed compilations of examples	Jul 3 2019
9543100400f7	frerot	Fixed compile error in user guide	Jun 25 2019
05c872f48feb	richart	Bug fixed again after merge	Jun 16 2019
121f89dc006f	richart	Bug fix on static patch tests	Jun 16 2019
f387b399ae6e	richart	Small leak fix	Jun 16 2019
9fdb8de9cf68	richart	Bug fix in non linear tests	Jun 16 2019
5adfe4547377	richart	Bug fix in the python patch tests	Jun 16 2019
9ff675c44194	richart	Modified gitignore	Jun 16 2019
7d83cd218a34	richart	Bug fix in Dumper shared_ptr changes	Jun 16 2019
1dd86a07d392	richart	Bug fixing in the python interface	Jun 16 2019
59acc25aa216	richart	Merge branch 'features/pybind11' of c4science:/diffusion/AKAPRIV/akantu-private…	Jun 16 2019
0e4984f5a64d	richart	Merge branch 'master' into features/pybind11	Jun 15 2019
05ff840cd866	anciaux	remove a warning	Jun 14 2019
dacd1c6ce4d6	anciaux	added the possibility to build dumper::Field in python	Jun 14 2019
b8a8a46e2135	anciaux	Remove the raw pointers on dumper::Fields	Jun 14 2019
5d2dc82607de	richart	Bug fix in the createElementGroups function	Jun 13 2019
c7e89d5fc02b	richart	Version change	Jun 13 2019
788ec250fa23	richart	Fixing bugs in parallel:	Jun 12 2019
f2382b4ee542	richart	Make it compatible with the new versions of google-test	Jun 12 2019
36cb05800fb2	richart	Compiling with clang with -fsanitize=memory	Jun 12 2019
f6f78a8e1f57	richart	Bug fix in cohesive elements	Jun 5 2019
1308f870eb08	richart	Repairing some swig things	Jun 5 2019
69c3f4c90ff0	richart	Merge branch 'master' into features/petsc	Jun 5 2019
aa8c5c4077ce	richart	Minor bug fixes	Jun 5 2019
d77e9ccf0452	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Jun 4 2019
7a04471d3e4d	richart	Bug fix in the MSH reader version 4	Jun 2 2019
b1971f0dd3a7	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	May 31 2019
e8875aefc8da	anciaux/richart	correct the construction of the element filter with ek_regular	May 31 2019
e6acdd6c5042	gallyamov/richart	Correction of the default element types within element_type_map:	May 31 2019
8a8cbaa53817	richart	Few modifications	May 31 2019
df7dd4dc2abc	richart	Update on mesh_io_msh read and write	May 29 2019
fddfb5094d24	richart	Update for latest findcgal.cmake	May 21 2019
84880d975de9	richart	Modified MSH reader for version 4.1 of the files	May 21 2019
1db43774e5c0	anciaux	renaming a file	May 14 2019
93c1c85addbd	anciaux	adding a full example with eigen mode treatments	May 14 2019
46779f984fa4	anciaux	adding a few methods for solidmechanics model	May 14 2019
c992924e0405	richart	Reactivating anisotropic patch tests	May 14 2019
c42b7b3e4d52	richart	Bug fix in material anisotropic	May 14 2019
0dda5dcc1039	anciaux	heat transfer patch test working	May 10 2019
eaa9fd19df2a	anciaux	on my way to fix heattransfer tests	May 9 2019
28153145c446	anciaux	remove swig completely	May 9 2019
8b217bd84ecd	anciaux	removing python files useless now thanks to pybind	May 9 2019
5f01385313a8	anciaux	adding the heat transfert interface	May 9 2019
f26800db0de2	anciaux	revert the BC namespace	May 9 2019
4cfbb587ed7d	anciaux	sparse matrix example working in pybind	May 9 2019
576e37d3ad30	anciaux	towards sparsematrix	May 9 2019
cc57f6b6180a	anciaux	towards sparsematrix	May 9 2019

Changes (584)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
M		.gitignore
M		CMakeLists.txt
M		VERSION
M		cmake/AkantuExtraCompilationProfiles.cmake
M		cmake/AkantuInstall.cmake
M		cmake/AkantuMacros.cmake
M		cmake/AkantuTestsMacros.cmake
M		cmake/Modules/CMakePackagesSystem.cmake
D		cmake/Modules/CorrectWindowsPaths.cmake
M		cmake/Modules/FindPETSc.cmake
D		cmake/Modules/FindPackageMultipass.cmake
D		cmake/Modules/ResolveCompilerPaths.cmake
M		cmake/akantu_environement.sh.in
A		cmake/sanitize-blacklist.txt
M		doc/doxygen/CMakeLists.txt
M		doc/manual/manual-solidmechanicsmodel.tex
M		examples/cohesive_element/cohesive_extrinsic_implicit/cohesive_extrinsic_implicit.cc
M		examples/embedded/embedded.cc
M		examples/implicit/implicit_dynamic.cc
M		examples/io/dumper/dumpable_interface.cc
M		examples/io/dumper/dumper_low_level.cc
M		examples/new_material/local_material_damage.cc
M		examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc
M		examples/python/CMakeLists.txt
A	(dir)	examples/python/cohesive/
A		examples/python/cohesive/material.dat
A		examples/python/cohesive/plate.geo
A		examples/python/cohesive/plate.py
M		examples/python/custom-material/bi-material.py
M		examples/python/custom-material/custom-material.py
M		examples/python/dynamics/dynamics.py
A	(dir)	examples/python/eigen_modes/
A		examples/python/eigen_modes/eigen_modes.py
A		examples/python/eigen_modes/image_saver.py
A		examples/python/eigen_modes/material.dat
P		examples/python/plate-hole/plate-mpi.py Copied from examples/python/plate-hole/plate.py
P		examples/python/plate-hole/plate.py Copied to examples/python/plate-hole/plate-mpi.py
A	(dir)	examples/python/stiffness_matrix/
A		examples/python/stiffness_matrix/CMakeLists.txt
A		examples/python/stiffness_matrix/material.dat
A		examples/python/stiffness_matrix/plate.geo
A		examples/python/stiffness_matrix/plate.msh
A		examples/python/stiffness_matrix/stiffness_matrix.py
M		examples/static/static.cc
M		extra_packages/extra-materials/src/material_damage/material_damage_iterative_inline_impl.cc
M		extra_packages/extra-materials/test/test_material_damage/test_material_damage_iterative_non_local_parallel.cc
M		extra_packages/extra-materials/test/test_material_damage/test_material_damage_iterative_non_local_serial.cc
M		extra_packages/igfem/src/material_igfem/material_igfem_inline_impl.cc
M		extra_packages/igfem/src/non_local_manager_igfem.cc
M		extra_packages/igfem/test/patch_tests/test_igfem_triangle_4.cc
M		extra_packages/igfem/test/patch_tests/test_igfem_triangle_5.cc
M		extra_packages/igfem/test/patch_tests/test_interface_position.cc
M		extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_ASR_damage.cc
M		extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_material_igfem_iterative_stiffness_reduction.cc
M		extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_material_igfem_iterative_stiffness_reduction_damage_step_transfer.cc
M		extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_material_igfem_iterative_stiffness_reduction_parallel.cc
M		extra_packages/igfem/test/test_solid_mechanics_model_igfem/test_solid_mechanics_model_igfem.cc
M		extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.cc
M		extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact_inline_impl.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.cc
M		packages/cgal.cmake
M		packages/core.cmake
M		packages/implicit.cmake
M		packages/mpi.cmake
M		packages/mumps.cmake
M		packages/petsc.cmake
M		packages/python_interface.cmake
A		packages/python_interpreter.cmake
M		packages/pythonlibs.cmake
M		packages/solid_mechanics.cmake
M		python/CMakeLists.txt
A	(dir)	python/akantu/
A		python/akantu/__init__.py
A		python/py_aka_array.hh
A		python/py_aka_common.cc
A		python/py_aka_common.hh
A		python/py_aka_error.cc
A		python/py_aka_error.hh
A		python/py_akantu.cc
A		python/py_akantu.hh
A		python/py_boundary_conditions.cc
A		python/py_boundary_conditions.hh
A		python/py_dumpable.cc
A		python/py_dumpable.hh
A		python/py_fe_engine.cc
A		python/py_fe_engine.hh
A		python/py_group_manager.cc
A		python/py_group_manager.hh
A		python/py_heat_transfer_model.cc
A		python/py_heat_transfer_model.hh
A		python/py_material.cc
A		python/py_material.hh
A		python/py_mesh.cc
A		python/py_mesh.hh
A		python/py_model.cc
A		python/py_model.hh
A		python/py_parser.cc
A		python/py_parser.hh
A		python/py_solid_mechanics_model.cc
A		python/py_solid_mechanics_model.hh
A		python/py_solid_mechanics_model_cohesive.cc
A		python/py_solid_mechanics_model_cohesive.hh
D		python/setup.py.in
D		python/swig
D		python/swig/aka_array.i
D		python/swig/aka_common.i
D		python/swig/aka_csr.i
D		python/swig/akantu.i
D		python/swig/communicator.i
D		python/swig/fe_engine.i
D		python/swig/heat_transfer_model.i
D		python/swig/load_functions.i
D		python/swig/material.i
D		python/swig/mesh.i
D		python/swig/mesh_utils.i
D		python/swig/model.i
D		python/swig/numpy.i
V		{python/swig/parser.i → src/solver/solver_vector_default.cc}
D		python/swig/solid_mechanics_model.i
D		python/swig/solid_mechanics_model_cohesive.i
D		python/swig/sparse_matrix.i
D		python/swig/structural_mechanics_model.i
M		src/CMakeLists.txt
M		src/common/aka_array.hh
A		src/common/aka_array_printer.hh
M		src/common/aka_array_tmpl.hh
M		src/common/aka_common.cc
M		src/common/aka_common.hh
M		src/common/aka_common_inline_impl.cc
M		src/common/aka_csr.hh
M		src/common/aka_element_classes_info.hh.in
M		src/common/aka_element_classes_info_inline_impl.cc
M		src/common/aka_enum_macros.hh
M		src/common/aka_error.cc
M		src/common/aka_error.hh
M		src/common/aka_extern.cc
M		src/common/aka_fwd.hh
M		src/common/aka_iterators.hh
M		src/common/aka_types.hh
M		src/fe_engine/fe_engine.cc
M		src/fe_engine/fe_engine.hh
M		src/fe_engine/fe_engine_template_tmpl.hh
M		src/fe_engine/shape_lagrange_base.cc
M		src/io/dumper/dumpable.cc
M		src/io/dumper/dumpable_dummy.hh
M		src/io/dumper/dumpable_inline_impl.hh
M		src/io/dumper/dumpable_iohelper.hh
M		src/io/dumper/dumper_compute.hh
M		src/io/dumper/dumper_field.hh
M		src/io/dumper/dumper_generic_elemental_field.hh
M		src/io/dumper/dumper_homogenizing_field.hh
M		src/io/dumper/dumper_iohelper.cc
M		src/io/dumper/dumper_iohelper.hh
M		src/io/dumper/dumper_iohelper_paraview.cc
M		src/io/dumper/dumper_nodal_field.hh
M		src/io/dumper/dumper_text.cc
M		src/io/mesh_io.cc
M		src/io/mesh_io.hh
M		src/io/mesh_io/mesh_io_msh.cc
M		src/io/mesh_io/mesh_io_msh.hh
M		src/io/parser/cppargparse/cppargparse.cc
M		src/io/parser/cppargparse/cppargparse.hh
M		src/io/parser/parameter_registry.cc
M		src/io/parser/parameter_registry_tmpl.hh
M		src/io/parser/parser.cc
M		src/io/parser/parser.hh
M		src/mesh/element_group.cc
M		src/mesh/element_group.hh
M		src/mesh/element_type_map.hh
M		src/mesh/element_type_map_tmpl.hh
M		src/mesh/group_manager.cc
M		src/mesh/group_manager.hh
M		src/mesh/group_manager_inline_impl.cc
M		src/mesh/mesh.cc
M		src/mesh/mesh.hh
M		src/mesh/mesh_data.hh
M		src/mesh/mesh_data_tmpl.hh
M		src/mesh/mesh_iterators.hh
M		src/mesh/node_group.cc
M		src/mesh/node_group.hh
M		src/mesh_utils/cohesive_element_inserter.cc
M		src/mesh_utils/cohesive_element_inserter_inline_impl.cc
M		src/mesh_utils/global_ids_updater.cc
M		src/mesh_utils/global_ids_updater_inline_impl.cc
M		src/mesh_utils/mesh_partition.cc
M		src/mesh_utils/mesh_partition.hh
M		src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
M		src/mesh_utils/mesh_utils.cc
V		src/model/{ → common/boundary_condition}/boundary_condition.hh
V		src/model/{ → common/boundary_condition}/boundary_condition_functor.hh
V		src/model/{ → common/boundary_condition}/boundary_condition_functor_inline_impl.cc
D		src/model/boundary_condition_python_functor.cc
D		src/model/boundary_condition_python_functor.hh
V		src/model/{ → common/boundary_condition}/boundary_condition_tmpl.hh
A	(dir)	src/model/common/boundary_condition/
V		src/model/{common/boundary_condition ← }/boundary_condition.hh
V		src/model/{common/boundary_condition ← }/boundary_condition_functor.hh
V		src/model/{common/boundary_condition ← }/boundary_condition_functor_inline_impl.cc
V		src/model/{common/boundary_condition ← }/boundary_condition_tmpl.hh
A	(dir)	src/model/common/dof_manager/
V		src/model/{common/dof_manager ← }/dof_manager.cc
V		src/model/{common/dof_manager ← }/dof_manager.hh
A		src/model/common/dof_manager/dof_manager_default.cc
V		src/model/{common/dof_manager ← }/dof_manager_default.hh
P		src/model/common/dof_manager/dof_manager_default_inline_impl.cc Copied from src/model/non_linear_solver_default.hh
A		src/model/common/dof_manager/dof_manager_inline_impl.cc
A		src/model/common/dof_manager/dof_manager_petsc.cc
A		src/model/common/dof_manager/dof_manager_petsc.hh
A	(dir)	src/model/common/integration_scheme/
V		src/model/{common ← }/integration_scheme/generalized_trapezoidal.cc
V		src/model/{common ← }/integration_scheme/generalized_trapezoidal.hh
V		src/model/{common ← }/integration_scheme/integration_scheme.cc
V		src/model/{common ← }/integration_scheme/integration_scheme.hh
V		src/model/{common ← }/integration_scheme/integration_scheme_1st_order.cc
V		src/model/{common ← }/integration_scheme/integration_scheme_1st_order.hh
V		src/model/{common ← }/integration_scheme/integration_scheme_2nd_order.cc
V		src/model/{common ← }/integration_scheme/integration_scheme_2nd_order.hh
V		src/model/{common ← }/integration_scheme/newmark-beta.cc
V		src/model/{common ← }/integration_scheme/newmark-beta.hh
V		src/model/{common ← }/integration_scheme/pseudo_time.cc
V		src/model/{common ← }/integration_scheme/pseudo_time.hh
V		src/model/{common ← }/model_solver.cc
V		src/model/{common ← }/model_solver.hh
V		src/model/common/{ → non_local_toolbox}/neighborhood_base.cc
V		src/model/common/{ → non_local_toolbox}/neighborhood_base.hh
V		src/model/common/{ → non_local_toolbox}/neighborhood_base_inline_impl.cc
D		src/model/common/neighborhoods_criterion_evaluation
V		src/model/common/{ → non_local_toolbox}/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
V		src/model/common/{ → non_local_toolbox}/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
V		src/model/common/{ → non_local_toolbox}/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.cc
A	(dir)	src/model/common/non_linear_solver/
V		src/model/{common/non_linear_solver ← }/non_linear_solver.cc
P		src/model/common/non_linear_solver/non_linear_solver.hh Copied from src/model/non_linear_solver.hh
V		src/model/{common/non_linear_solver ← }/non_linear_solver_default.hh
V		src/model/{common/non_linear_solver ← }/non_linear_solver_linear.cc
V		src/model/{common/non_linear_solver ← }/non_linear_solver_linear.hh
V		src/model/{common/non_linear_solver ← }/non_linear_solver_lumped.cc
V		src/model/{common/non_linear_solver ← }/non_linear_solver_lumped.hh
V		src/model/{common/non_linear_solver ← }/non_linear_solver_newton_raphson.cc
V		src/model/{common/non_linear_solver ← }/non_linear_solver_newton_raphson.hh
A		src/model/common/non_linear_solver/non_linear_solver_petsc.cc
V		src/model/{common/non_linear_solver/non_linear_solver_petsc.hh ← non_linear_solver.hh}
V		src/model/common/{non_local_toolbox ← }/neighborhood_base.cc
V		src/model/common/{non_local_toolbox ← }/neighborhood_base.hh
V		src/model/common/{non_local_toolbox ← }/neighborhood_base_inline_impl.cc
A	(dir)	src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/
V		src/model/common/{non_local_toolbox ← }/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
V		src/model/common/{non_local_toolbox ← }/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
V		src/model/common/{non_local_toolbox ← }/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.cc
M		src/model/common/non_local_toolbox/non_local_manager.cc
M		src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
M		src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc
M		src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
V		src/model/{common ← }/solver_callback.cc
V		src/model/{common ← }/solver_callback.hh
A	(dir)	src/model/common/time_step_solvers/
V		src/model/{common ← }/time_step_solvers/time_step_solver.cc
V		src/model/{common/time_step_solvers ← }/time_step_solver.hh
V		src/model/{common ← }/time_step_solvers/time_step_solver_default.cc
V		src/model/{common ← }/time_step_solvers/time_step_solver_default.hh
V		src/model/{common ← }/time_step_solvers/time_step_solver_default_explicit.hh
V		src/model/{ → common/dof_manager}/dof_manager.cc
V		src/model/{ → common/dof_manager}/dof_manager.hh
D		src/model/dof_manager_default.cc
V		src/model/{ → common/dof_manager}/dof_manager_default.hh
D		src/model/dof_manager_default_inline_impl.cc
D		src/model/dof_manager_inline_impl.cc
D		src/model/dof_manager_petsc.cc
D		src/model/dof_manager_petsc.hh
M		src/model/heat_transfer/heat_transfer_model.cc
M		src/model/heat_transfer/heat_transfer_model.hh
D		src/model/integration_scheme
V		src/model/{ → common}/integration_scheme/generalized_trapezoidal.cc
V		src/model/{ → common}/integration_scheme/generalized_trapezoidal.hh
V		src/model/{ → common}/integration_scheme/integration_scheme.cc
V		src/model/{ → common}/integration_scheme/integration_scheme.hh
V		src/model/{ → common}/integration_scheme/integration_scheme_1st_order.cc
V		src/model/{ → common}/integration_scheme/integration_scheme_1st_order.hh
V		src/model/{ → common}/integration_scheme/integration_scheme_2nd_order.cc
V		src/model/{ → common}/integration_scheme/integration_scheme_2nd_order.hh
V		src/model/{ → common}/integration_scheme/newmark-beta.cc
V		src/model/{ → common}/integration_scheme/newmark-beta.hh
V		src/model/{ → common}/integration_scheme/pseudo_time.cc
V		src/model/{ → common}/integration_scheme/pseudo_time.hh
M		src/model/model.cc
M		src/model/model.hh
M		src/model/model_inline_impl.cc
V		src/model/{ → common}/model_solver.cc
V		src/model/{ → common}/model_solver.hh
V		src/model/{ → common/non_linear_solver}/non_linear_solver.cc
P		src/model/non_linear_solver.hh Deleted after being copied to multiple locations: src/model/common/non_linear_solver/non_linear_solver.hh src/model/common/non_linear_solver/non_linear_solver_petsc.hh
D		src/model/non_linear_solver_callback.hh
P		src/model/non_linear_solver_default.hh Deleted after being copied to multiple locations: src/model/common/dof_manager/dof_manager_default_inline_impl.cc src/model/common/non_linear_solver/non_linear_solver_default.hh
V		src/model/{ → common/non_linear_solver}/non_linear_solver_linear.cc
V		src/model/{ → common/non_linear_solver}/non_linear_solver_linear.hh
V		src/model/{ → common/non_linear_solver}/non_linear_solver_lumped.cc
V		src/model/{ → common/non_linear_solver}/non_linear_solver_lumped.hh
V		src/model/{ → common/non_linear_solver}/non_linear_solver_newton_raphson.cc
V		src/model/{ → common/non_linear_solver}/non_linear_solver_newton_raphson.hh
M		src/model/solid_mechanics/material.cc
M		src/model/solid_mechanics/material.hh
M		src/model/solid_mechanics/material_inline_impl.cc
A		src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc
A		src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh
A		src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh
M		src/model/solid_mechanics/materials/material_damage/material_damage.hh
M		src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
M		src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.cc
M		src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.cc
M		src/model/solid_mechanics/materials/material_elastic.cc
M		src/model/solid_mechanics/materials/material_elastic.hh
M		src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
M		src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
M		src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
M		src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
M		src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
M		src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
M		src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
M		src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
D		src/model/solid_mechanics/materials/material_python
D		src/model/solid_mechanics/materials/material_python/material_python.cc
D		src/model/solid_mechanics/materials/material_python/material_python.hh
M		src/model/solid_mechanics/materials/material_thermal.cc
M		src/model/solid_mechanics/materials/material_thermal.hh
M		src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc
M		src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.cc
M		src/model/solid_mechanics/solid_mechanics_model.cc
M		src/model/solid_mechanics/solid_mechanics_model.hh
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.cc
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.cc
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
M		src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
M		src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
M		src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
M		src/model/solid_mechanics/solid_mechanics_model_io.cc
M		src/model/solid_mechanics/solid_mechanics_model_mass.cc
M		src/model/solid_mechanics/solid_mechanics_model_material.cc
V		src/model/{ → common}/solver_callback.cc
V		src/model/{ → common}/solver_callback.hh
M		src/model/structural_mechanics/structural_mechanics_model.cc
M		src/model/structural_mechanics/structural_mechanics_model.hh
V		src/model/{ → common/time_step_solvers}/time_step_solver.hh
D		src/model/time_step_solvers
V		src/model/{ → common}/time_step_solvers/time_step_solver.cc
V		src/model/{ → common}/time_step_solvers/time_step_solver_default.cc
V		src/model/{ → common}/time_step_solvers/time_step_solver_default.hh
V		src/model/{ → common}/time_step_solvers/time_step_solver_default_explicit.hh
D		src/model/time_step_solvers/time_step_solver_default_solver_callback.hh
D		src/python
D		src/python/python_functor.cc
D		src/python/python_functor.hh
D		src/python/python_functor_inline_impl.cc
M		src/solver/petsc_wrapper.hh
M		src/solver/solver_petsc.cc
M		src/solver/solver_petsc.hh
A		src/solver/solver_vector.hh
V		{src/solver/solver_vector_default.cc ← python/swig/parser.i}
A		src/solver/solver_vector_default.hh
A		src/solver/solver_vector_default_tmpl.hh
A		src/solver/solver_vector_distributed.cc
A		src/solver/solver_vector_distributed.hh
A		src/solver/solver_vector_petsc.cc
A		src/solver/solver_vector_petsc.hh
M		src/solver/sparse_matrix.cc
P		src/solver/sparse_matrix.hh Copied to src/solver/sparse_matrix_petsc.hh
M		src/solver/sparse_matrix_aij.cc
M		src/solver/sparse_matrix_aij.hh
M		src/solver/sparse_matrix_aij_inline_impl.cc
M		src/solver/sparse_matrix_petsc.cc
P		src/solver/sparse_matrix_petsc.hh Copied from src/solver/sparse_matrix.hh
M		src/solver/sparse_solver_inline_impl.cc
M		src/solver/sparse_solver_mumps.cc
M		src/synchronizer/communicator.cc
M		src/synchronizer/communicator.hh
M		src/synchronizer/communicator_dummy_inline_impl.cc
M		src/synchronizer/communicator_inline_impl.hh
M		src/synchronizer/communicator_mpi_inline_impl.cc
M		src/synchronizer/dof_synchronizer.cc
M		src/synchronizer/dof_synchronizer_inline_impl.cc
M		src/synchronizer/element_info_per_processor_tmpl.hh
M		src/synchronizer/element_synchronizer.cc
M		src/synchronizer/master_element_info_per_processor.cc
M		src/synchronizer/mpi_communicator_data.hh
M		src/synchronizer/node_info_per_processor.cc
M		src/synchronizer/node_synchronizer.cc
M		src/synchronizer/node_synchronizer.hh
M		src/synchronizer/periodic_node_synchronizer.hh
M		src/synchronizer/synchronizer_impl_tmpl.hh
M		test/CMakeLists.txt
D		test/pybind11_akantu.cc
D		test/pybind11_akantu.hh
M		test/test_common/test_array.cc
M		test/test_fe_engine/CMakeLists.txt
M		test/test_fe_engine/py_engine/py_engine.py
M		test/test_fe_engine/test_fe_engine_fixture.hh
M		test/test_fe_engine/test_fe_engine_gauss_integration.cc
M		test/test_fe_engine/test_fe_engine_precomputation.cc
M		test/test_fe_engine/test_fe_engine_precomputation_structural.cc
M		test/test_fe_engine/test_fe_engine_structural_fixture.hh
M		test/test_fe_engine/test_gradient.cc
M		test/test_fe_engine/test_integrate.cc
M		test/test_fe_engine/test_inverse_map.cc
M		test/test_gtest_utils.hh
M		test/test_io/test_dumper/test_dumper.cc
M		test/test_mesh/test_mesh_periodic.cc
M		test/test_mesh_utils/test_mesh_iterators.cc
M		test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_scotch.cc
M		test/test_model/CMakeLists.txt
M		test/test_model/patch_tests/CMakeLists.txt
V		test/test_model/patch_tests/data/{material_anisotropic.dat → material_anisotropic_3.dat}
A		test/test_model/patch_tests/data/material_anisotropic_1.dat
A		test/test_model/patch_tests/data/material_anisotropic_2.dat
V		test/test_model/patch_tests/data/{material_anisotropic_3.dat ← material_anisotropic.dat}
A		test/test_model/patch_tests/patch_test_linear_anisotropic.cc
D		test/test_model/patch_tests/patch_test_linear_anisotropic_explicit.cc
V		test/test_model/patch_tests/{patch_test_linear_anisotropic_explicit.py → test_patch_linear_anisotropic_explicit.py}
V		test/test_model/patch_tests/{patch_test_linear_elastic_explicit.py → test_patch_linear_elastic_explicit.py}
M		test/test_model/patch_tests/patch_test_linear_elastic_implicit.cc
V		test/test_model/patch_tests/{patch_test_linear_elastic_static.py → test_patch_linear_elastic_static.py}
M		test/test_model/patch_tests/patch_test_linear_fixture.hh
M		test/test_model/patch_tests/patch_test_linear_fixture.py
V		test/test_model/patch_tests/{patch_test_linear_heat_transfer_explicit.py → test_patch_linear_heat_transfer_explicit.py}
M		test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.hh
M		test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.py
V		test/test_model/patch_tests/{patch_test_linear_heat_transfer_implicit.py → test_patch_linear_heat_transfer_implicit.py}
M		test/test_model/patch_tests/patch_test_linear_heat_transfer_static.cc
V		test/test_model/patch_tests/{patch_test_linear_heat_transfer_static.py → test_patch_linear_heat_transfer_static.py}
M		test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.hh
M		test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.py
M		test/test_model/patch_tests/test_lumped_mass.cc
V		test/test_model/patch_tests/{test_patch_linear_anisotropic_explicit.py ← patch_test_linear_anisotropic_explicit.py}
V		test/test_model/patch_tests/{test_patch_linear_elastic_explicit.py ← patch_test_linear_elastic_explicit.py}
V		test/test_model/patch_tests/{test_patch_linear_elastic_static.py ← patch_test_linear_elastic_static.py}
V		test/test_model/patch_tests/{test_patch_linear_heat_transfer_explicit.py ← patch_test_linear_heat_transfer_explicit.py}
V		test/test_model/patch_tests/{test_patch_linear_heat_transfer_implicit.py ← patch_test_linear_heat_transfer_implicit.py}
V		test/test_model/patch_tests/{test_patch_linear_heat_transfer_static.py ← patch_test_linear_heat_transfer_static.py}
A	(dir)	test/test_model/test_common/
A		test/test_model/test_common/CMakeLists.txt
A		test/test_model/test_common/mesh.geo
A		test/test_model/test_common/test_dof_manager.cc
A	(dir)	test/test_model/test_common/test_model_solver/
V		test/test_model/{test_common ← }/test_model_solver/CMakeLists.txt
V		test/test_model/{test_common ← }/test_model_solver/test_dof_manager_default.cc
V		test/test_model/{test_common ← }/test_model_solver/test_dof_manager_default.verified
V		test/test_model/{test_common ← }/test_model_solver/test_model_solver.cc
V		test/test_model/{test_common ← }/test_model_solver/test_model_solver.py
V		test/test_model/{test_common ← }/test_model_solver/test_model_solver_dynamic.cc
V		test/test_model/{test_common ← }/test_model_solver/test_model_solver_dynamic.py
V		test/test_model/{test_common ← }/test_model_solver/test_model_solver_dynamic_explicit.verified
V		test/test_model/{test_common ← }/test_model_solver/test_model_solver_dynamic_implicit.verified
A		test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.cc
A		test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.verified
P		test/test_model/test_common/test_model_solver/test_model_solver_mumps.verified Copied from test/test_model/test_model_solver/test_model_solver.verified
V		test/test_model/{test_common ← }/test_model_solver/test_model_solver_my_model.hh
V		test/test_model/{test_common/test_model_solver/test_model_solver_petsc.verified ← test_model_solver/test_model_solver.verified}
A	(dir)	test/test_model/test_common/test_non_local_toolbox/
V		test/test_model/{test_common ← }/test_non_local_toolbox/CMakeLists.txt
V		test/test_model/{test_common ← }/test_non_local_toolbox/fine_mesh.msh
V		test/test_model/{test_common ← }/test_non_local_toolbox/material.dat
V		test/test_model/{test_common ← }/test_non_local_toolbox/material_avg.dat
V		test/test_model/{test_common ← }/test_non_local_toolbox/material_parallel_test.dat
V		test/test_model/{test_common ← }/test_non_local_toolbox/material_remove_damage.dat
V		test/test_model/{test_common ← }/test_non_local_toolbox/material_weight_computation.dat
V		test/test_model/{test_common ← }/test_non_local_toolbox/my_model.hh
V		test/test_model/{test_common ← }/test_non_local_toolbox/pair_test.msh
V		test/test_model/{test_common ← }/test_non_local_toolbox/parallel_test.msh
V		test/test_model/{test_common ← }/test_non_local_toolbox/plate.geo
V		test/test_model/{test_common ← }/test_non_local_toolbox/plate.msh
V		test/test_model/{test_common ← }/test_non_local_toolbox/plot_neighborhoods.py
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_build_neighborhood_parallel.cc
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_material.cc
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_material.hh
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_material_damage.cc
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_material_damage.hh
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_non_local_averaging.cc
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_non_local_neighborhood_base.cc
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_non_local_neighborhood_base.verified
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_pair_computation.cc
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_remove_damage_weight_function.cc
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_remove_damage_weight_function.verified
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_weight_computation.cc
V		test/test_model/{test_common ← }/test_non_local_toolbox/test_weight_computation.verified
D		test/test_model/test_model_solver
V		test/test_model/{ → test_common}/test_model_solver/CMakeLists.txt
V		test/test_model/{ → test_common}/test_model_solver/test_dof_manager_default.cc
V		test/test_model/{ → test_common}/test_model_solver/test_dof_manager_default.verified
V		test/test_model/{ → test_common}/test_model_solver/test_model_solver.cc
V		test/test_model/{ → test_common}/test_model_solver/test_model_solver.py
P		test/test_model/test_model_solver/test_model_solver.verified Deleted after being copied to multiple locations: test/test_model/test_common/test_model_solver/test_model_solver_mumps.verified test/test_model/test_common/test_model_solver/test_model_solver_petsc.verified
V		test/test_model/{ → test_common}/test_model_solver/test_model_solver_dynamic.cc
V		test/test_model/{ → test_common}/test_model_solver/test_model_solver_dynamic.py
V		test/test_model/{ → test_common}/test_model_solver/test_model_solver_dynamic_explicit.verified
V		test/test_model/{ → test_common}/test_model_solver/test_model_solver_dynamic_implicit.verified
V		test/test_model/{ → test_common}/test_model_solver/test_model_solver_my_model.hh
D		test/test_model/test_non_local_toolbox
V		test/test_model/{ → test_common}/test_non_local_toolbox/CMakeLists.txt
V		test/test_model/{ → test_common}/test_non_local_toolbox/fine_mesh.msh
V		test/test_model/{ → test_common}/test_non_local_toolbox/material.dat
V		test/test_model/{ → test_common}/test_non_local_toolbox/material_avg.dat
V		test/test_model/{ → test_common}/test_non_local_toolbox/material_parallel_test.dat
V		test/test_model/{ → test_common}/test_non_local_toolbox/material_remove_damage.dat
V		test/test_model/{ → test_common}/test_non_local_toolbox/material_weight_computation.dat
V		test/test_model/{ → test_common}/test_non_local_toolbox/my_model.hh
V		test/test_model/{ → test_common}/test_non_local_toolbox/pair_test.msh
V		test/test_model/{ → test_common}/test_non_local_toolbox/parallel_test.msh
V		test/test_model/{ → test_common}/test_non_local_toolbox/plate.geo
V		test/test_model/{ → test_common}/test_non_local_toolbox/plate.msh
V		test/test_model/{ → test_common}/test_non_local_toolbox/plot_neighborhoods.py
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_build_neighborhood_parallel.cc
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_material.cc
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_material.hh
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_material_damage.cc
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_material_damage.hh
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_non_local_averaging.cc
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_non_local_neighborhood_base.cc
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_non_local_neighborhood_base.verified
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_pair_computation.cc
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_remove_damage_weight_function.cc
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_remove_damage_weight_function.verified
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_weight_computation.cc
V		test/test_model/{ → test_common}/test_non_local_toolbox/test_weight_computation.verified
M		test/test_model/test_solid_mechanics_model/CMakeLists.txt
M		test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh
M		test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic_impl/test_cohesive_intrinsic_impl.cc
M		test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_linear_friction/test_cohesive_friction.cc
M		test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_linear.cc
M		test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_element_matrix.cc
M		test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model.cc
M		test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc
M		test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_dynamics.cc
M		test/test_model/test_solid_mechanics_model/test_materials/CMakeLists.txt
M		test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.cc
M		test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.hh
M		test/test_model/test_solid_mechanics_model/test_materials/py_mazars.py
M		test/test_model/test_solid_mechanics_model/test_materials/test_damage_materials.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_elastic_materials.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_finite_def_materials.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_local_material.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/test_material_elasto_plastic_linear_isotropic_hardening.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_material_mazars.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_material_thermal.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/test_material_viscoelastic_maxwell_relaxation.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_plastic_materials.cc
M		test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_dynamics.cc
M		test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh
M		test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_eigenstrain.cc
M		test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_3.cc
M		test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh
M		test/test_python_interface/CMakeLists.txt
A		test/test_python_interface/elastic.dat
D		test/test_python_interface/input_test.dat
M		test/test_python_interface/mesh_dcb_2d.geo
D		test/test_python_interface/test_boundary_condition_functors.py
A		test/test_python_interface/test_common.cc
D		test/test_python_interface/test_mesh_interface.py
D		test/test_python_interface/test_multiple_init.py
A		test/test_python_interface/test_pybind.py
M		test/test_solver/CMakeLists.txt
M		test/test_solver/test_petsc_matrix_profile.cc
M		test/test_solver/test_petsc_matrix_profile_parallel.cc
M		test/test_solver/test_solver_petsc.cc
M		test/test_solver/test_sparse_matrix_product.cc
M		test/test_solver/test_sparse_solver_mumps.cc
M		test/test_synchronizer/CMakeLists.txt
A		test/test_synchronizer/test_communicator.cc
M		test/test_synchronizer/test_data_distribution.cc
M		test/test_synchronizer/test_dof_synchronizer.cc
M		test/test_synchronizer/test_dof_synchronizer_communication.cc
M		test/test_synchronizer/test_facet_synchronizer.cc
M		test/test_synchronizer/test_grid_synchronizer.cc
M		test/test_synchronizer/test_node_synchronizer.cc
M		test/test_synchronizer/test_synchronizer_communication.cc
M		third-party/cmake/gtest.cmake