Diffusion akantu 5043ab55f161

Merge branch 'master' into features/11-computation-of-contact-energy-with…
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Authored by richart on Aug 10 2021, 10:40.

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Merge branch 'master' into features/11-computation-of-contact-energy-with-getenergy-contact

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richart

Aug 10 2021, 10:40

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gitlab-richart

Aug 10 2021, 10:41

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rAKA9643ca54fc81: adding clangd cache to gitignore
rAKA020d57e328cd: Merge branch 'bugfixes/boundary_changes_in_solver' into 'master'

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richart committed rAKA5043ab55f161: Merge branch 'master' into features/11-computation-of-contact-energy-with… (authored by richart).Aug 10 2021, 10:40

Merged Changes

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

Commit	Author	Details	Committed
020d57e328cd	richart	Merge branch 'bugfixes/boundary_changes_in_solver' into 'master'	Aug 3 2021
3ba310f2399e	anciaux	Merge branch 'features/contact' into 'master'	Jul 29 2021
93cfdbc5065a	richart	Merge branch 'features/contact' of gitlab.com:akantu/akantu into…	Jul 28 2021
67d8f5cfd95f	richart	Code quality corrections	Jul 28 2021
eb9967b52897	anciaux/richart	Apply 3 suggestion(s) to 1 file(s)	Jul 28 2021
054f2d50c5e7	anciaux/richart	Apply 1 suggestion(s) to 1 file(s)	Jul 28 2021
721e10971f05	richart	Adding exception when not converged	Jul 28 2021
c8d9385f5ff2	richart	Correction based on @ganciaux review	Jul 28 2021
8df6b0ee7569	richart	Merge branch 'master' into features/contact	Jul 28 2021
6262bb9b0011	richart	Resetting the J matrix if the boundary changed	Jul 28 2021
e895177e362a	richart	Warp too long equations	Jul 26 2021
f203057a27a5	Lucas Frérot	Merge branch 'bugfixes/16-examples-structrual_mechanics…	Jul 23 2021
9a8da1fd222f	richart	Update .readthedocs.yaml	Jul 23 2021
bbecb2ab64c4	richart	Merge branch 'master' into bugfixes/16-examples-structrual_mechanics…	Jul 23 2021
06d7980ded6a	richart	pinning the versions	Jul 23 2021
3859fc311ebc	richart	Making the example behave like the test	Jul 23 2021
703e28f5b4ab	richart	pinning the versions	Jul 22 2021
19864460b300	richart	Correcting macros	Jul 22 2021
f2a330c6ea76	richart	Left over from a merge	Jul 20 2021
251af691556a	richart	Merge branch 'master' into features/contact	Jul 20 2021
d8aff94f3dbd	richart	Update Dockerfile	Jul 20 2021
67a78b03ef1c	tdroch	Merge branch 'features/22-problem-in-the-documentation-for-the-viscoelastic…	Jul 7 2021
92bb4e260b29	anciaux	Merge branch 'features/material-selector-python' into 'master'	Jun 30 2021
a03d6f83ea72	richart	Adding a section for visco elsatic materials	Jun 29 2021
ce886d011389	richart	Adding information on Einf	Jun 29 2021
18da45a064ab	richart	Renamed mesh	Jun 28 2021
7d0cc3b36cbd	richart	Bug fix following factorization	Jun 26 2021
7841f146511f	richart	Bug fix refixed	Jun 25 2021
91648043ab07	gallyamov	Corrected the Maxwell chain pic + swapped two words	Jun 25 2021
88e4bdd1fc1d	richart	Missing symbols with clang	Jun 25 2021
40104a165ba1	richart	Corrected clang compilation error and linted some part of the contact code	Jun 24 2021
2985136e8a09	richart	Correction based on remarks on MR !9	Jun 24 2021
13da75edd185	richart	Bug fix from the previous refactoring	Jun 24 2021
80a7ec7d8c7d	richart	Merge branch 'master' into features/contact	Jun 24 2021
e1422234d910	richart	Merge branch 'features/contact' of gitlab.com:akantu/akantu into…	Jun 23 2021
b75e7eac6591	richart	refactoring the code of the coupler solid contact	Jun 23 2021
e6faf34e0cc7	richart	Bug fix in the dumper for enums	Jun 23 2021
2dd62fc28d21	Mohit Pundir	Added missing documentation on contact couplers	Jun 23 2021
0ac630be3038	richart	Trying to correct mesh for ubuntu	Jun 20 2021
f03394d43907	Mohit Pundir	added example for cohesive contact	Jun 19 2021
d4516410c368	Mohit Pundir	changes the dof manage for coupler solid cohesive contact	Jun 19 2021
c0747665d674	richart	Merge branch 'features/22-problem-in-the-documentation-for-the-viscoelastic…	Jun 17 2021
84f1afcae8b4	richart	Few fixes in the doc	Jun 17 2021
5934bdd68d94	gallyamov	Merge branch 'features/22-problem-in-the-documentation-for-the-visco-elastic…	Jun 17 2021
b0fda780253c	gallyamov	Adding references to maxwell material	Jun 17 2021
c7dff3d506b7	richart	protecting mathjax in rtd	Jun 17 2021
ea734ad5b8fc	richart	Adding mathjax3_config for rtd	Jun 17 2021
89a397692c83	richart	Adding missing packages in requirements	Jun 17 2021
4981ca04fefb	richart	another bug fix in conf.py for rtd version	Jun 17 2021
a928467efa85	richart	typo in conf.py	Jun 17 2021

Changes (254)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
M		.gitignore
M		.gitlab-ci.yml
A		.readthedocs.yaml
M		VERSION
M		cmake/AkantuExtraCompilationProfiles.cmake
M		doc/dev-doc/CMakeLists.txt
D		doc/dev-doc/akantu.dox.in
A		doc/dev-doc/akantu.dox.j2
V		doc/dev-doc/{conf.py ← conf.py.in}
V		doc/dev-doc/{conf.py.in → conf.py}
M		doc/dev-doc/index.rst
M		doc/dev-doc/manual/appendix.rst
D		doc/dev-doc/manual/appendix/material-parameters.rst
M		doc/dev-doc/manual/bibliography.rst
M		doc/dev-doc/manual/constitutive-laws.rst
A		doc/dev-doc/manual/contactmechanicsmodel.rst
A		doc/dev-doc/manual/figures/cl/maxwell_chain.png
M		doc/dev-doc/manual/figures/cl/visco_elastic_law.svg
A		doc/dev-doc/manual/figures/contact_mechanics_schematic.png
A		doc/dev-doc/manual/figures/contact_mechanics_schematic.svg
M		doc/dev-doc/manual/getting_started.rst
M		doc/dev-doc/manual/heattransfermodel.rst
M		doc/dev-doc/manual/io.rst
M		doc/dev-doc/manual/manual-bibliography.bib
M		doc/dev-doc/manual/phasefieldmodel.rst
M		doc/dev-doc/manual/structuralmechanicsmodel.rst
M		doc/dev-doc/reference.rst
A		doc/dev-doc/requirements.txt
A		doc/manual/manual-contactmechanicsmodel.tex
M		examples/CMakeLists.txt
M		examples/cohesive_element/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc
A	(dir)	examples/contact_mechanics/
P		examples/contact_mechanics/CMakeLists.txt Copied from packages/model_couplers.cmake
A		examples/contact_mechanics/cohesive-contact.geo
A		examples/contact_mechanics/cohesive_contact_explicit_dynamic.cc
A		examples/contact_mechanics/contact_explicit_dynamic.cc
A		examples/contact_mechanics/contact_explicit_static.cc
A		examples/contact_mechanics/hertz.geo
A		examples/contact_mechanics/material-cohesive.dat
A		examples/contact_mechanics/material.dat
M		examples/python/CMakeLists.txt
A	(dir)	examples/python/contact-mechanics/
A		examples/python/contact-mechanics/CMakeLists.txt
A		examples/python/contact-mechanics/compression.py
A		examples/python/contact-mechanics/detection-explicit.py
A	(dir)	examples/python/contact-mechanics/materials/
A		examples/python/contact-mechanics/materials/compression.dat
A		examples/python/contact-mechanics/materials/detection-explicit.dat
A	(dir)	examples/python/contact-mechanics/mesh/
A		examples/python/contact-mechanics/mesh/compression.geo
A		examples/python/contact-mechanics/mesh/detection-explicit.msh
M		examples/structural_mechanics/bernoulli_beam_2_example.cc
A		packages/contact_mechanics.cmake
M		packages/core.cmake
M		packages/damage_non_local.cmake
M		packages/documentation_developer_manual.cmake
P		packages/model_couplers.cmake Copied to examples/contact_mechanics/CMakeLists.txt
M		packages/phase_field.cmake
M		packages/solid_mechanics.cmake
M		python/CMakeLists.txt
M		python/py_aka_common.cc
M		python/py_akantu.cc
A		python/py_akantu_pybind11_compatibility.hh
M		python/py_boundary_conditions.cc
A		python/py_contact_mechanics_model.cc
A		python/py_contact_mechanics_model.hh
M		python/py_fe_engine.cc
M		python/py_group_manager.cc
M		python/py_material.cc
M		python/py_material.hh
A		python/py_material_selector.cc
A		python/py_material_selector.hh
M		python/py_mesh.cc
M		python/py_model.cc
A		python/py_model_couplers.cc
A		python/py_model_couplers.hh
M		python/py_solid_mechanics_model.cc
M		src/common/aka_array.hh
P		src/common/aka_array_filter.hh Copied from src/mesh/element_type_map_filter.hh
M		src/common/aka_bbox.hh
M		src/common/aka_common.hh
M		src/common/aka_config.hh.in
M		src/common/aka_factory.hh
M		src/common/aka_grid_dynamic.hh
M		src/common/aka_math.hh
M		src/common/aka_math_tmpl.hh
M		src/fe_engine/element_class.hh
A		src/fe_engine/element_class_helper.hh
M		src/fe_engine/element_class_tmpl.hh
M		src/fe_engine/element_classes/element_class_quadrangle_4_inline_impl.hh
M		src/fe_engine/element_classes/element_class_segment_2_inline_impl.hh
M		src/fe_engine/element_classes/element_class_triangle_3_inline_impl.hh
M		src/fe_engine/element_classes/element_class_triangle_6_inline_impl.hh
M		src/fe_engine/fe_engine_inline_impl.hh
M		src/fe_engine/integrator_gauss_inline_impl.hh
M		src/io/dumper/dumper_compute.hh
M		src/io/dumper/dumper_elemental_field.hh
M		src/io/dumper/dumper_generic_elemental_field.hh
M		src/io/dumper/dumper_homogenizing_field.hh
M		src/io/dumper/dumper_internal_material_field.hh
M		src/io/dumper/dumper_material_padders.hh
M		src/io/dumper/dumper_nodal_field.hh
M		src/io/dumper/dumper_text.cc
P		src/io/dumper/dumper_text.hh Copied to src/model/contact_mechanics/contact_element.hh
M		src/io/dumper/dumper_type_traits.hh
M		src/io/parser/parser.hh
M		src/mesh/element_type_map.hh
P		src/mesh/element_type_map_filter.hh Copied to src/common/aka_array_filter.hh
M		src/mesh/group_manager_inline_impl.hh
M		src/mesh/mesh.cc
M		src/mesh/mesh.hh
M		src/mesh/mesh_inline_impl.hh
M		src/mesh/node_group_inline_impl.hh
M		src/mesh_utils/cohesive_element_inserter_helper.cc
M		src/model/common/boundary_condition/boundary_condition.hh
M		src/model/common/boundary_condition/boundary_condition_functor_inline_impl.hh
M		src/model/common/boundary_condition/boundary_condition_tmpl.hh
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/integration_scheme/generalized_trapezoidal.cc
M		src/model/common/integration_scheme/newmark-beta.cc
M		src/model/common/integration_scheme/newmark-beta.hh
M		src/model/common/integration_scheme/pseudo_time.cc
M		src/model/common/model_solver.cc
M		src/model/common/model_solver.hh
M		src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
M		src/model/common/time_step_solvers/time_step_solver.cc
M		src/model/common/time_step_solvers/time_step_solver.hh
M		src/model/common/time_step_solvers/time_step_solver_default.cc
M		src/model/common/time_step_solvers/time_step_solver_default.hh
A	(dir)	src/model/contact_mechanics/
A		src/model/contact_mechanics/contact_detector.cc
A		src/model/contact_mechanics/contact_detector.hh
A		src/model/contact_mechanics/contact_detector_inline_impl.cc
P		src/model/contact_mechanics/contact_element.hh Copied from src/io/dumper/dumper_text.hh
A		src/model/contact_mechanics/contact_mechanics_model.cc
A		src/model/contact_mechanics/contact_mechanics_model.hh
A		src/model/contact_mechanics/geometry_utils.cc
A		src/model/contact_mechanics/geometry_utils.hh
A		src/model/contact_mechanics/geometry_utils_inline_impl.cc
A		src/model/contact_mechanics/resolution.cc
A		src/model/contact_mechanics/resolution.hh
A		src/model/contact_mechanics/resolution_utils.cc
A		src/model/contact_mechanics/resolution_utils.hh
A	(dir)	src/model/contact_mechanics/resolutions/
A		src/model/contact_mechanics/resolutions/resolution_penalty.cc
A		src/model/contact_mechanics/resolutions/resolution_penalty.hh
A		src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.cc
A		src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.hh
A		src/model/contact_mechanics/surface_selector.cc
A		src/model/contact_mechanics/surface_selector.hh
M		src/model/heat_transfer/heat_transfer_model.cc
M		src/model/heat_transfer/heat_transfer_model.hh
M		src/model/model.cc
M		src/model/model.hh
A		src/model/model_couplers/cohesive_contact_solvercallback.cc
A		src/model/model_couplers/cohesive_contact_solvercallback.hh
A		src/model/model_couplers/coupler_solid_cohesive_contact.cc
P		src/model/model_couplers/coupler_solid_cohesive_contact.hh Copied from src/model/solid_mechanics/materials/material_non_local_includes.hh
A		src/model/model_couplers/coupler_solid_contact.cc
P		src/model/model_couplers/coupler_solid_contact.hh Copied from src/model/model_couplers/coupler_solid_phasefield.hh
A		src/model/model_couplers/coupler_solid_contact_tmpl.hh
P		src/model/model_couplers/coupler_solid_phasefield.hh Copied to src/model/model_couplers/coupler_solid_contact.hh
M		src/model/model_inline_impl.hh
M		src/model/model_options.hh
M		src/model/phase_field/phase_field_model.cc
M		src/model/phase_field/phase_field_model.hh
M		src/model/phase_field/phasefield.hh
M		src/model/phase_field/phasefields/phasefield_exponential.cc
M		src/model/phase_field/phasefields/phasefield_exponential.hh
M		src/model/solid_mechanics/material.cc
M		src/model/solid_mechanics/material_inline_impl.hh
M		src/model/solid_mechanics/material_selector.hh
M		src/model/solid_mechanics/material_selector_tmpl.hh
M		src/model/solid_mechanics/materials/material_core_includes.hh
M		src/model/solid_mechanics/materials/material_damage/material_damage.hh
A		src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.cc
A		src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.hh
A		src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_inline_impl.hh
A		src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.cc
A		src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.hh
M		src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
M		src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
P		src/model/solid_mechanics/materials/material_non_local_includes.hh Copied to multiple locations: src/model/model_couplers/coupler_solid_cohesive_contact.hh test/test_model/test_contact_mechanics_model/test_detector/test_detection.cc test/test_model/test_contact_mechanics_model/test_resolution/test_explicit_resolution.cc test/test_model/test_contact_mechanics_model/test_selector/test_selection.cc
A		src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.cc
A		src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.hh
A		src/model/solid_mechanics/materials/material_plastic/material_drucker_prager_inline_impl.hh
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/materials/constitutive_laws/material_cohesive_linear_friction.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_inline_impl.hh
M		src/model/solid_mechanics/solid_mechanics_model_io.cc
M		src/model/structural_mechanics/structural_mechanics_model.hh
M		src/solver/sparse_matrix.hh
M		src/solver/sparse_matrix_aij.hh
M		src/solver/sparse_matrix_aij_inline_impl.hh
M		src/synchronizer/grid_synchronizer.cc
M		test/ci/debian:testing/Dockerfile
M		test/ci/manylinux/Dockerfile
P		test/test_model/CMakeLists.txt Copied to multiple locations: test/test_model/test_contact_mechanics_model/CMakeLists.txt test/test_model/test_contact_mechanics_model/test_coupler/CMakeLists.txt test/test_model/test_contact_mechanics_model/test_resolution/CMakeLists.txt
M		test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh
A	(dir)	test/test_model/test_contact_mechanics_model/
P		test/test_model/test_contact_mechanics_model/CMakeLists.txt Copied from test/test_model/CMakeLists.txt
A		test/test_model/test_contact_mechanics_model/flat_on_flat.geo
A		test/test_model/test_contact_mechanics_model/material-friction.dat
A		test/test_model/test_contact_mechanics_model/material.dat
A		test/test_model/test_contact_mechanics_model/sliding-block-2D.geo
A	(dir)	test/test_model/test_contact_mechanics_model/test_coupler/
P		test/test_model/test_contact_mechanics_model/test_coupler/CMakeLists.txt Copied from test/test_model/CMakeLists.txt
A		test/test_model/test_contact_mechanics_model/test_coupler/coupling.geo
A		test/test_model/test_contact_mechanics_model/test_coupler/flat_on_flat.geo
A		test/test_model/test_contact_mechanics_model/test_coupler/material.dat
A		test/test_model/test_contact_mechanics_model/test_coupler/material_stiffness.dat
A		test/test_model/test_contact_mechanics_model/test_coupler/test_contact_coupling.cc
A		test/test_model/test_contact_mechanics_model/test_coupler/test_coupled_stiffness.cc
A	(dir)	test/test_model/test_contact_mechanics_model/test_detector/
P		test/test_model/test_contact_mechanics_model/test_detector/CMakeLists.txt Copied from test/test_model/test_phase_field_model/CMakeLists.txt
A	(dir)	test/test_model/test_contact_mechanics_model/test_detector/data/
A		test/test_model/test_contact_mechanics_model/test_detector/data/cohesive_1D.geo
A		test/test_model/test_contact_mechanics_model/test_detector/data/cohesive_strait_2D.geo
A		test/test_model/test_contact_mechanics_model/test_detector/data/cohesive_strait_2D.msh
A		test/test_model/test_contact_mechanics_model/test_detector/data/cohesive_strait_2D_mixte.geo
A		test/test_model/test_contact_mechanics_model/test_detector/data/cohesive_strait_2D_structured.geo
A		test/test_model/test_contact_mechanics_model/test_detector/data/cohesive_strait_3D.geo
A		test/test_model/test_contact_mechanics_model/test_detector/data/cohesive_strait_3D_structured.geo
A		test/test_model/test_contact_mechanics_model/test_detector/data/test.msh
A		test/test_model/test_contact_mechanics_model/test_detector/node.geo
A		test/test_model/test_contact_mechanics_model/test_detector/options.dat
P		test/test_model/test_contact_mechanics_model/test_detector/test_detection.cc Copied from src/model/solid_mechanics/materials/material_non_local_includes.hh
A		test/test_model/test_contact_mechanics_model/test_detector/test_detection_fixture.hh
A		test/test_model/test_contact_mechanics_model/test_explicit_dynamic.cc
A		test/test_model/test_contact_mechanics_model/test_explicit_friction.cc
A	(dir)	test/test_model/test_contact_mechanics_model/test_resolution/
P		test/test_model/test_contact_mechanics_model/test_resolution/CMakeLists.txt Copied from test/test_model/CMakeLists.txt
A		test/test_model/test_contact_mechanics_model/test_resolution/explicit_2d.geo
A		test/test_model/test_contact_mechanics_model/test_resolution/options.dat
P		test/test_model/test_contact_mechanics_model/test_resolution/test_explicit_resolution.cc Copied from src/model/solid_mechanics/materials/material_non_local_includes.hh
A		test/test_model/test_contact_mechanics_model/test_resolution/test_resolution.cc
A	(dir)	test/test_model/test_contact_mechanics_model/test_selector/
P		test/test_model/test_contact_mechanics_model/test_selector/CMakeLists.txt Copied from test/test_model/test_phase_field_model/CMakeLists.txt
A	(dir)	test/test_model/test_contact_mechanics_model/test_selector/data/
A		test/test_model/test_contact_mechanics_model/test_selector/data/selection_1D.geo
A		test/test_model/test_contact_mechanics_model/test_selector/data/selection_2D.geo
A		test/test_model/test_contact_mechanics_model/test_selector/data/selection_3D.geo
A		test/test_model/test_contact_mechanics_model/test_selector/material.dat
P		test/test_model/test_contact_mechanics_model/test_selector/test_selection.cc Copied from src/model/solid_mechanics/materials/material_non_local_includes.hh
A		test/test_model/test_contact_mechanics_model/test_selector/test_selection_fixture.hh
P		test/test_model/test_phase_field_model/CMakeLists.txt Copied to multiple locations: test/test_model/test_contact_mechanics_model/test_detector/CMakeLists.txt test/test_model/test_contact_mechanics_model/test_selector/CMakeLists.txt
M		test/test_model/test_phase_field_model/test_phase_solid_explicit.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/material_damage_non_local.dat
M		test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_reassign_material.cc