Merge branch 'master' into features/phasefield
00d14211d024
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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

Jul 29 2021, 09:01

Parents

rAKA34d21a7b59df: added eta parameter to avoid full degradation of elastic energy
rAKAa05e053f088c: Merge branch 'features/python_fragment_manager'

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pundir committed rAKA00d14211d024: 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
a05e053f088c	richart	Merge branch 'features/python_fragment_manager'	Mar 30 2021
dd0187ec5861	anciaux	remove matplotlib things	Mar 30 2021
8552d3ad87d8	anciaux	add the possibility to return a vector of possible material allocators	Mar 30 2021
a156575e6ada	anciaux	CMake generates the mesh	Mar 30 2021
ab587884ce44	anciaux	CMake generates the mesh	Mar 30 2021
22752a5861d6	anciaux	correct code style	Mar 29 2021
8a42a425df9d	anciaux	give better default to the fragmentation_manager tools	Mar 29 2021
865647670389	anciaux	adding a fragmentation example	Mar 29 2021
4aff21aa2c2a	anciaux	adding the fragment manager to python interface	Mar 29 2021
e1a94b307393	richart	Merge branch 'features/material_internals_memory' into 'master'	Mar 16 2021
96d721e75caf	richart	Merge branch 'bugfixes/eigen_strain_failed_init' into 'master'	Mar 15 2021
c287bfa68439	richart	linting python structural mechanics examples	Mar 15 2021
566986b729dd	richart	Merge branch 'master' into features/material_internals_memory	Mar 15 2021
e7a551f32e9a	anciaux	adding a reference to remove a bug visible with pre-strained materials	Mar 15 2021
4e9800eeb138	anciaux	Merge branch 'bugfixes/heat_virtual_dump' into 'master'	Mar 15 2021
2d55c02870b7	richart	missing include in py_mesh	Mar 15 2021
48cd41bb1b6d	richart	make the compute boundary loads compile and run in structural mechanics	Mar 15 2021
a58c0aa0bed8	richart	Fix the mesh to make the example run properly	Mar 15 2021
41860c0d43d8	Lucas Frérot	Merge branch 'features/doc_material_parameters' into 'master'	Mar 15 2021
265eef7cc4c6	richart	Remove warning with clang	Mar 15 2021
ff59a8a88933	richart	Reformating the license	Mar 15 2021
d1204ff2107e	frerot	silenced override warnings on HeatTransferModel dump() overloads	Mar 15 2021
aa1a96d7acf7	frerot	[doc] added material parameters description and updated some figures	Mar 14 2021
31f6fd181ec8	richart	Bug fixes in examples	Mar 14 2021
bce187dcb622	richart	making matplotib optional for the ci	Mar 13 2021
9d302f1bae82	richart	Fixing dumper warnings	Mar 13 2021
64cf152a54e1	richart	Adapting due to changes in structural mechanics	Mar 13 2021
e50a815abc63	richart	Merge branch 'bugfixes/project_metadata' into 'master'	Mar 13 2021
1bb2b72b7131	frerot	fixing copyright year and homepage url	Mar 13 2021
99533bb2a0d1	frerot	[doc] fixed documentation metadata	Mar 13 2021
bc650421eb69	richart	Merge branch 'master' into features/material_internals_memory	Mar 13 2021
e99fbce86d23	richart	Merge branch 'bugfixes/dynamics_structural_mechnanics' into 'master'	Mar 13 2021
526b254b52f6	richart	Merge branch 'master' into features/material_internals_memory	Mar 13 2021
e7a653b7101a	richart	Merge branch 'master' into bugfixes/dynamics_structural_mechnanics	Mar 13 2021
8858a4b6e52e	richart	Merge branch 'features/doc' into 'master'	Mar 13 2021
21552a692368	richart	Merge branch 'master' into 'features/doc'	Mar 13 2021
c8c85566dabb	richart	Merge branch 'features/ci_code_quality' into 'master'	Mar 13 2021
a2b23bf363b1	richart	Cleaning the structural mechanics python examples	Mar 13 2021
3ceda41725e1	richart	modified doc deploy branch to master	Mar 13 2021
822dff9cfbd3	richart	Deactivating clang-tidy, needs improvements	Mar 12 2021
426dbe2c5125	richart	Adding sphinxcontrib bibtex to the docker image	Mar 12 2021
3db7fb0070ee	richart	Reducing checks to make it faster	Mar 12 2021
20f2142d0955	richart	Improving a bit the code	Mar 12 2021
b55a41d487a7	richart	Cleaning the linting code	Mar 12 2021
ec1059276144	richart	More work on the code quality	Mar 12 2021
060caca10a13	richart	Debugging the runner for clang-tidy	Mar 12 2021
078aab353255	richart	Parse all files	Mar 12 2021
34d6a7763d56	richart	Trying to activate dev engines	Mar 12 2021
73fb168cae5a	richart	Adding clang-tidy to code-quality	Mar 12 2021
b1051faa5603	richart	trying to improve code quality report	Mar 12 2021

Changes (330)
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M		.clang-tidy
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M		.gitlab-ci.yml
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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/constitutive-laws.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_el.svg
A		doc/dev-doc/manual/figures/cl/stress_strain_hook.tex
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A		doc/dev-doc/manual/new-constitutive-laws.rst
A		doc/dev-doc/manual/solidmechanicsmodel.rst
A		doc/dev-doc/manual/structuralmechanicsmodel.rst
M		doc/dev-doc/reference.rst
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/integrator_gauss_igfem_inline_impl.hh
M		extra_packages/igfem/src/non_local_manager_igfem.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/friction_laws/ntn_friclaw_linear_cohesive.hh
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M		extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.cc
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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
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/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_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.hh
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M		src/fe_engine/fe_engine_template_tmpl_field.hh
M		src/fe_engine/integrator.hh
M		src/fe_engine/integrator_gauss.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
M		src/fe_engine/shape_lagrange_base.cc
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
M		src/mesh/mesh_data.cc
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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
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M		src/model/common/model_solver.cc
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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/common/time_step_solvers/time_step_solver_default.cc
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M		src/model/heat_transfer/heat_transfer_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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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