Merge branch 'master' into features/phasefield
5acfa6ca970d
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Authored by pundir on Apr 2 2021, 01:37.

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Merge branch 'master' into features/phasefield

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Committed

pundir

Apr 2 2021, 01:37

Pushed

gitlab-richart

Apr 2 2021, 08:57

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rAKAbe0ea515f119: added eta parameter to avoid full degradation of elastic energy
rAKA5905a7ea8175: Merge branch 'features/python_fragment_manager'

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pundir committed rAKA5acfa6ca970d: Merge branch 'master' into features/phasefield (authored by pundir).Apr 2 2021, 01:37

Merged Changes

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

Commit	Author	Details	Committed
5905a7ea8175	richart	Merge branch 'features/python_fragment_manager'	Mar 30 2021
22eb3a214a25	anciaux	remove matplotlib things	Mar 30 2021
7f9fe3088b81	anciaux	add the possibility to return a vector of possible material allocators	Mar 30 2021
245660087964	anciaux	CMake generates the mesh	Mar 30 2021
f18bcf4c8e30	anciaux	CMake generates the mesh	Mar 30 2021
35cd9f678615	anciaux	correct code style	Mar 29 2021
2c2ac9d01138	anciaux	give better default to the fragmentation_manager tools	Mar 29 2021
3d563b45a618	anciaux	adding a fragmentation example	Mar 29 2021
c7e03d7ebae5	anciaux	adding the fragment manager to python interface	Mar 29 2021
ba9e2713a380	richart	Merge branch 'features/material_internals_memory' into 'master'	Mar 16 2021
ea2e7652da39	richart	Merge branch 'bugfixes/eigen_strain_failed_init' into 'master'	Mar 15 2021
5b3351523a74	richart	linting python structural mechanics examples	Mar 15 2021
3eea84761c29	richart	Merge branch 'master' into features/material_internals_memory	Mar 15 2021
cfebf6035747	anciaux	adding a reference to remove a bug visible with pre-strained materials	Mar 15 2021
01e9ee80de03	anciaux	Merge branch 'bugfixes/heat_virtual_dump' into 'master'	Mar 15 2021
bc514ea38833	richart	missing include in py_mesh	Mar 15 2021
e451f9f2d87d	richart	make the compute boundary loads compile and run in structural mechanics	Mar 15 2021
23ce2ae76c3b	richart	Fix the mesh to make the example run properly	Mar 15 2021
99b1b4059854	Lucas Frérot	Merge branch 'features/doc_material_parameters' into 'master'	Mar 15 2021
ae94c6a35b6a	richart	Remove warning with clang	Mar 15 2021
75d3faa8c041	richart	Reformating the license	Mar 15 2021
64df19a129e0	frerot	silenced override warnings on HeatTransferModel dump() overloads	Mar 15 2021
99815f41b5ad	frerot	[doc] added material parameters description and updated some figures	Mar 14 2021
797ec47f3478	richart	Bug fixes in examples	Mar 14 2021
a81c6b33ae37	richart	making matplotib optional for the ci	Mar 13 2021
d7eb0b0c18be	richart	Fixing dumper warnings	Mar 13 2021
95d0dced15d1	richart	Adapting due to changes in structural mechanics	Mar 13 2021
9528782b1b34	richart	Merge branch 'bugfixes/project_metadata' into 'master'	Mar 13 2021
e566eea29622	frerot	fixing copyright year and homepage url	Mar 13 2021
effcfe7920e4	frerot	[doc] fixed documentation metadata	Mar 13 2021
9cb01e0c3a12	richart	Merge branch 'master' into features/material_internals_memory	Mar 13 2021
cc50b397b4ba	richart	Merge branch 'bugfixes/dynamics_structural_mechnanics' into 'master'	Mar 13 2021
12c0a090caee	richart	Merge branch 'master' into features/material_internals_memory	Mar 13 2021
db203e90b229	richart	Merge branch 'master' into bugfixes/dynamics_structural_mechnanics	Mar 13 2021
1b9c3cd9e78d	richart	Merge branch 'features/doc' into 'master'	Mar 13 2021
cee77eb64fae	richart	Merge branch 'master' into 'features/doc'	Mar 13 2021
eb43f181a4cb	richart	Merge branch 'features/ci_code_quality' into 'master'	Mar 13 2021
e3075f54d103	richart	Cleaning the structural mechanics python examples	Mar 13 2021
bd91a3346147	richart	modified doc deploy branch to master	Mar 13 2021
3a985b5b05ed	richart	Deactivating clang-tidy, needs improvements	Mar 12 2021
87018e564d38	richart	Adding sphinxcontrib bibtex to the docker image	Mar 12 2021
44b77edd375b	richart	Reducing checks to make it faster	Mar 12 2021
ffccf8161507	richart	Improving a bit the code	Mar 12 2021
847f1fbd4e3b	richart	Cleaning the linting code	Mar 12 2021
fe44bbafd3ee	richart	More work on the code quality	Mar 12 2021
5a0113389fcb	richart	Debugging the runner for clang-tidy	Mar 12 2021
92d6c0d0324b	richart	Parse all files	Mar 12 2021
eebbf94c1a82	richart	Trying to activate dev engines	Mar 12 2021
94051cfb5abd	richart	Adding clang-tidy to code-quality	Mar 12 2021
bba044d80b99	richart	trying to improve code quality report	Mar 12 2021

Changes (330)
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M		.clang-tidy
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M		cmake/AkantuCleaning.cmake
M		cmake/AkantuConfig.cmake.in
M		cmake/AkantuExtraCompilationProfiles.cmake
M		cmake/AkantuUse.cmake
M		cmake/Modules/CMakePackagesSystem.cmake
M		cmake/Modules/CMakePackagesSystemPrivateFunctions.cmake
M		cmake/Modules/FindMumps.cmake
M		doc/CMakeLists.txt
M		doc/dev-doc/CMakeLists.txt
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A		doc/dev-doc/manual/appendix/material-parameters.rst
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A		doc/dev-doc/manual/figures/bc_and_ic_example.svg
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A		doc/dev-doc/manual/figures/cl/stress_strain_hook.tex
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A		doc/dev-doc/manual/solidmechanicsmodel.rst
A		doc/dev-doc/manual/structuralmechanicsmodel.rst
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M		doc/manual/manual-appendix-elements.tex
M		examples/cohesive_element/cohesive_extrinsic/CMakeLists.txt
A		examples/cohesive_element/cohesive_extrinsic/triangle.msh
M		examples/cohesive_element/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc
M		examples/cohesive_element/cohesive_intrinsic/CMakeLists.txt
A		examples/cohesive_element/cohesive_intrinsic/triangle.msh
M		examples/explicit/explicit_dynamic.cc
M		examples/python/CMakeLists.txt
M		examples/python/cohesive/plate.py
M		examples/python/custom-material/bi-material.py
M		examples/python/eigen_modes/eigen_modes.py
A	(dir)	examples/python/fragmentation/
A		examples/python/fragmentation/CMakeLists.txt
A		examples/python/fragmentation/fragmentation.py
A		examples/python/fragmentation/fragmentation_mesh.geo
A		examples/python/fragmentation/material.dat
A	(dir)	examples/python/structural_mechanics/
A		examples/python/structural_mechanics/CMakeLists.txt
A		examples/python/structural_mechanics/structural_mechanics.py
A		examples/python/structural_mechanics/structural_mechanics_dynamics.py
A		examples/python/structural_mechanics/structural_mechanics_softening.py
M		examples/structural_mechanics/CMakeLists.txt
V		examples/structural_mechanics/{bernoulli_beam_2_example.cc ← bernoulli_beam_2_exemple.cc}
V		examples/structural_mechanics/{bernoulli_beam_2_exemple.cc → bernoulli_beam_2_example.cc}
M		extra_packages/extra-materials/src/material_FE2/solid_mechanics_model_RVE.cc
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M		extra_packages/igfem/src/shape_igfem.cc
M		extra_packages/igfem/src/shape_igfem.hh
M		extra_packages/igfem/src/solid_mechanics_model_igfem.cc
M		extra_packages/igfem/src/solid_mechanics_model_igfem.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh
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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_base_friction.hh
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M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction_tmpl.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction_tmpl.hh
M		packages/core.cmake
M		packages/documentation_developer_manual.cmake
M		packages/documentation_user_manual.cmake
M		python/CMakeLists.txt
M		python/py_akantu.cc
A		python/py_fragment_manager.cc
A		python/py_fragment_manager.hh
M		python/py_heat_transfer_model.cc
M		python/py_material.cc
M		python/py_mesh.cc
M		python/py_model.cc
M		python/py_solid_mechanics_model.cc
M		python/py_solid_mechanics_model_cohesive.cc
M		python/py_solver.cc
M		python/py_solver.hh
A		python/py_structural_mechanics_model.cc
A		python/py_structural_mechanics_model.hh
M		src/CMakeLists.txt
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M		src/common/aka_common.hh
M		src/common/aka_common_inline_impl.hh
M		src/common/aka_error.hh
M		src/common/aka_event_handler_manager.hh
M		src/common/aka_factory.hh
M		src/common/aka_grid_dynamic.hh
M		src/common/aka_math.hh
D		src/common/aka_memory.cc
D		src/common/aka_memory.hh
D		src/common/aka_memory_inline_impl.hh
D		src/common/aka_static_memory.cc
D		src/common/aka_static_memory.hh
D		src/common/aka_static_memory_inline_impl.hh
D		src/common/aka_static_memory_tmpl.hh
M		src/fe_engine/element_class_structural.hh
M		src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh
M		src/fe_engine/element_classes/element_class_hermite_inline_impl.hh
M		src/fe_engine/fe_engine.cc
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M		src/fe_engine/fe_engine_template_tmpl_field.hh
M		src/fe_engine/integrator.hh
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M		src/fe_engine/shape_cohesive.hh
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M		src/fe_engine/shape_functions.cc
M		src/fe_engine/shape_functions.hh
M		src/fe_engine/shape_lagrange.hh
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M		src/fe_engine/shape_lagrange_base.hh
M		src/fe_engine/shape_lagrange_inline_impl.hh
M		src/fe_engine/shape_structural.cc
M		src/fe_engine/shape_structural.hh
M		src/fe_engine/shape_structural_inline_impl.hh
M		src/io/dumper/dumper_material_padders.hh
M		src/mesh/element_group.cc
M		src/mesh/element_group.hh
M		src/mesh/element_group_inline_impl.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/mesh.cc
M		src/mesh/mesh.hh
M		src/mesh/mesh_accessor.hh
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M		src/mesh/mesh_iterators.hh
M		src/mesh/mesh_periodic.cc
M		src/mesh/node_group.cc
M		src/mesh/node_group.hh
M		src/mesh_utils/mesh_partition.cc
M		src/mesh_utils/mesh_partition.hh
M		src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
M		src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
M		src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
M		src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
M		src/mesh_utils/mesh_utils.cc
M		src/model/common/dof_manager/dof_manager.cc
M		src/model/common/dof_manager/dof_manager.hh
M		src/model/common/dof_manager/dof_manager_default.cc
M		src/model/common/dof_manager/dof_manager_default.hh
M		src/model/common/dof_manager/dof_manager_petsc.cc
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M		src/model/common/model_solver.cc
M		src/model/common/model_solver.hh
M		src/model/common/non_linear_solver/non_linear_solver.cc
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M		src/model/common/non_linear_solver/non_linear_solver_linear.cc
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M		src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
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M		src/model/common/time_step_solvers/time_step_solver.cc
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M		src/model/model.cc
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M		src/model/solid_mechanics/solid_mechanics_model.cc
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M		src/model/solid_mechanics/solid_mechanics_model_io.cc
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M		src/model/structural_mechanics/structural_mechanics_model_mass.cc
M		src/solver/solver_petsc.cc
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A	(dir)	test/ci/codeclimate/codeclimate-clang-tidy/
A		test/ci/codeclimate/codeclimate-clang-tidy/Dockerfile
A	(dir)	test/ci/codeclimate/codeclimate-clang-tidy/bin/
A		test/ci/codeclimate/codeclimate-clang-tidy/bin/codeclimate-clang-tidy
A		test/ci/codeclimate/codeclimate-clang-tidy/bin/run-clang-tidy
A		test/ci/codeclimate/codeclimate-clang-tidy/engine.json
A	(dir)	test/ci/codeclimate/codeclimate-clang-tidy/lib/
A		test/ci/codeclimate/codeclimate-clang-tidy/lib/command.py
A		test/ci/codeclimate/codeclimate-clang-tidy/lib/issue_formatter.py
A		test/ci/codeclimate/codeclimate-clang-tidy/lib/runner.py
A		test/ci/codeclimate/codeclimate-clang-tidy/lib/workspace.py
M		test/ci/debian:testing/Dockerfile
A	(dir)	test/ci/includes_for_ci/
A		test/ci/includes_for_ci/aka_config.hh
A		test/ci/includes_for_ci/aka_element_classes_info.hh
A		test/ci/includes_for_ci/aka_fortran_mangling.hh
A		test/ci/includes_for_ci/material_list.hh
A		test/ci/scripts/clang-tidy2code-quality.py
M		test/test_model/test_common/test_dof_manager.cc
M		test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh
M		test/test_model/test_common/test_non_local_toolbox/my_model.hh
M		test/test_model/test_solid_mechanics_model/cube_two_materials.geo
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_reassign_material.cc
M		test/test_model/test_structural_mechanics_model/CMakeLists.txt
M		test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_2.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_bernoulli_beam_dynamics.cc
M		test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
M		test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh
D		test/test_static_memory
D		test/test_static_memory/CMakeLists.txt
D		test/test_static_memory/test_static_memory.cc
M		test/test_synchronizer/test_facet_synchronizer.cc
M		test/test_synchronizer/test_synchronizer_communication.cc
M		third-party/akantu_iterators/include/aka_iterators.hh
M		third-party/akantu_iterators/include/aka_tuple_tools.hh
A		third-party/akantu_iterators/include/iterators/aka_concatenate_iterator.hh
A		third-party/akantu_iterators/include/iterators/aka_iterator_tools.hh
M		third-party/akantu_iterators/include/iterators/aka_zip_iterator.hh
M		third-party/akantu_iterators/test/CMakeLists.txt
M		third-party/akantu_iterators/test/test_iterators.cc