conflict with master resolved
47c3bed53838
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Authored by pundir on Jun 19 2019, 14:14.

Description

conflict with master resolved

Details

Committed

pundir

Jun 19 2019, 14:14

Pushed

gitlab-richart

Jul 29 2021, 09:01

Parents

rAKAf2a8abd6b849: Bug fixed again after merge
rAKA5eb7cda6aae0: changed fillNodestoElement in mesh/ use meshfacets for coupling

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pundir committed rAKA47c3bed53838: conflict with master resolved (authored by pundir).Jun 19 2019, 14:14

Merged Changes

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

Commit	Author	Details	Committed
f2a8abd6b849	richart	Bug fixed again after merge	Jun 16 2019
870eeccd5cd4	richart	Bug fix on static patch tests	Jun 16 2019
f255dcc453be	richart	Small leak fix	Jun 16 2019
1f6e9e513dbb	richart	Bug fix in non linear tests	Jun 16 2019
4bf5f548d40e	richart	Bug fix in the python patch tests	Jun 16 2019
473a2fed5387	richart	Modified gitignore	Jun 16 2019
d56d4c73db45	richart	Bug fix in Dumper shared_ptr changes	Jun 16 2019
7bf5844d231d	richart	Bug fixing in the python interface	Jun 16 2019
7211363d92dc	richart	Merge branch 'features/pybind11' of c4science:/diffusion/AKAPRIV/akantu-private…	Jun 16 2019
604abe561a78	richart	Merge branch 'master' into features/pybind11	Jun 15 2019
d8dd5f613d84	anciaux	remove a warning	Jun 14 2019
2249f672325a	anciaux	added the possibility to build dumper::Field in python	Jun 14 2019
5679bae8c1dc	anciaux	Remove the raw pointers on dumper::Fields	Jun 14 2019
1d9772fd8e9c	richart	Bug fix in the createElementGroups function	Jun 13 2019
39deb14038fd	richart	Version change	Jun 13 2019
0c6888ff380d	richart	Fixing bugs in parallel:	Jun 12 2019
c4f2158a9313	richart	Make it compatible with the new versions of google-test	Jun 12 2019
f433098ce4ca	richart	Compiling with clang with -fsanitize=memory	Jun 12 2019
ece172541773	richart	Bug fix in cohesive elements	Jun 5 2019
d615f3390f78	richart	Repairing some swig things	Jun 5 2019
00ca1e91f39a	richart	Merge branch 'master' into features/petsc	Jun 5 2019
6d5d7eb67dcf	richart	Few modifications	May 31 2019
1eeb3a40716a	anciaux	renaming a file	May 14 2019
0b242b8d30e9	anciaux	adding a full example with eigen mode treatments	May 14 2019
f80acecf97a9	anciaux	adding a few methods for solidmechanics model	May 14 2019
d3b1deda3441	anciaux	heat transfer patch test working	May 10 2019
c60d10efd8a2	anciaux	on my way to fix heattransfer tests	May 9 2019
61c6314e2e2c	anciaux	remove swig completely	May 9 2019
7fe63708dd78	anciaux	removing python files useless now thanks to pybind	May 9 2019
76529bcddfd3	anciaux	adding the heat transfert interface	May 9 2019
0781d52fe548	anciaux	revert the BC namespace	May 9 2019
42e787f146b2	anciaux	sparse matrix example working in pybind	May 9 2019
78bf3a3329f0	anciaux	towards sparsematrix	May 9 2019
e8ea53792fcf	anciaux	towards sparsematrix	May 9 2019
95bedb30177e	anciaux	change path and last example	May 9 2019
89806eb3fc70	anciaux	change a path	May 9 2019
c4e9e7754ea5	anciaux	removing swig	May 9 2019
e1e12ee01d80	anciaux	tests run with pytest-3: need cmake expert to make it clean	May 9 2019
c54a4f4fa6d8	anciaux	complement the python interface	May 9 2019
17c5a4b36d23	anciaux	adding a test for meshes	May 9 2019
a774861fccbe	anciaux	adapt the test for pytest and pybind	May 9 2019
fda9fcf18aa3	anciaux	update the patch tests for pybind and pytest	May 9 2019
b68cd632df17	anciaux	bc test in pytest	May 8 2019
b771333c08b9	anciaux	change getForce to getExternalForce in a test	May 8 2019
52084c9fb8e1	anciaux	bind node/element groups	May 8 2019
190abbca14dd	anciaux	correct the construction of the element filter with ek_regular	May 8 2019
2030e8779a0d	gallyamov/anciaux	Correction of the default element types within element_type_map:	May 8 2019
28cb4e0ace4b	anciaux	clang formating	May 8 2019
499684f3ef33	anciaux	remove Dirichlet namespace in test	May 8 2019
18fb3fce3807	anciaux	remove nonexisting call in the pybind interface	May 8 2019

Changes (552)
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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
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
M		examples/python/stiffness_matrix/stiffness_matrix.py
M		examples/static/static.cc
M		extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.cc
M		extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.hh
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/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		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		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
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/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_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
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_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_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/material_viscoelastic/material_viscoelastic_maxwell.hh
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_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
M		test/test_model/patch_tests/patch_test_linear_anisotropic.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_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/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_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_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