conflict with master resolved
bca70b4e93bf
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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

Jan 18 2021, 21:10

Parents

rAKAa0e19c5e89c6: changed fillNodestoElement in mesh/ use meshfacets for coupling
rAKA05c872f48feb: Bug fixed again after merge

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pundir committed rAKAbca70b4e93bf: 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
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
8a8cbaa53817	richart	Few modifications	May 31 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
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
3ba30aa1a99e	anciaux	change path and last example	May 9 2019
0d0f950ac257	anciaux	change a path	May 9 2019
84d2362e4f31	anciaux	removing swig	May 9 2019
ca3d0ab179d5	anciaux	tests run with pytest-3: need cmake expert to make it clean	May 9 2019
4a76700356f7	anciaux	complement the python interface	May 9 2019
6f0e746f4e18	anciaux	adding a test for meshes	May 9 2019
233c48a8f69f	anciaux	adapt the test for pytest and pybind	May 9 2019
964e2d0ba785	anciaux	update the patch tests for pybind and pytest	May 9 2019
9a2d8cd8e68b	anciaux	bc test in pytest	May 8 2019
9d83a1df7a5e	anciaux	change getForce to getExternalForce in a test	May 8 2019
a7017467bb54	anciaux	bind node/element groups	May 8 2019
16fe68ba4a6f	anciaux	correct the construction of the element filter with ek_regular	May 8 2019
2aa1e344ee31	gallyamov/anciaux	Correction of the default element types within element_type_map:	May 8 2019
3565525f24c3	anciaux	clang formating	May 8 2019
2ae4208c4135	anciaux	remove Dirichlet namespace in test	May 8 2019
d8014c9dd01d	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