Diffusion akantu 9c7d441921d8

Merge branch 'master' into features/solver-rewrite
9c7d441921d8
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Authored by anciaux on Feb 27 2024, 09:54.

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Merge branch 'master' into features/solver-rewrite

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Committed

anciaux

Feb 27 2024, 09:54

Pushed

gitlab-richart

Feb 27 2024, 10:00

Parents

rAKAe0d3caf99a5b: Merge branch 'master' into features/solver-rewrite
rAKAda80a4903812: Merge branch 'kyleniemeyer-master-patch-5c58' into 'master'

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anciaux committed rAKA9c7d441921d8: Merge branch 'master' into features/solver-rewrite (authored by anciaux).Feb 27 2024, 09:54

Merged Changes

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

Commit	Author	Details	Committed
da80a4903812	richart	Merge branch 'kyleniemeyer-master-patch-5c58' into 'master'	Feb 22
57d1db139355	Kyle Niemeyer	updates for JOSS publication	Feb 20
f3aad3a38f88	richart	Sorting bibtex to check for other duplicates	Feb 17
7a6ae0202a1e	richart	Removing duplicated reference	Feb 17
626f30e04c50	richart	Update paper.bib	Feb 16
01d5a6530006	richart	Update paper.md	Feb 14
380ba6aaae94	richart	Merge branch 'features/joss-2023' into 'master'	Feb 13
30e696f0862b	richart	JOSS paper	Feb 13
c5dcd9d8b6cc	richart	Merge branch 'features/perf-test-example' into 'master'	Feb 12
6ba918a53503	richart	Adding the perf test used for the joss paper as an example	Feb 12
160eaf086982	richart	Update semver.py	Feb 1
80c7a86eaf33	richart	Using VERSION file once generated to avoid different version definied at…	Feb 1
5902b9cfe7c4	richart	Still problem in the versions not matching between cmake and setup.py	Feb 1
8744657db7c4	richart	Adapting Changelog	Feb 1
50574cea5610	richart	Version do not match between mac and linux	Jan 31
8a72f6a17868	richart	Cannot Pull on a Tag	Jan 31
4865470699b5	richart	Make configuration safer when files already exists	Jan 31
1db5ba830ccb	anciaux	Merge branch 'bugfixes/ci_deploy_fixes' into 'master'	Jan 31
ef592d6afcab	richart	MR are not accessible with CI_JOB_TOKEN	Jan 30
f2b43d30518d	richart	missing login	Jan 24
da1317273f98	richart	Adding auth for gitlab cli	Jan 24
abb6de375307	richart	Adding merge request id in glab mr not	Jan 23
c9612692b012	richart	missing colon	Jan 23
bf34c3c255db	richart	Adding jq to debian:testing	Jan 23
c1140aaba4de	richart	Adding more mention en the tarball for the examples	Jan 23
83e354748f26	richart	Combine rules	Jan 23
b9eedadb3661	richart	Typo in th CI	Jan 23
a11f4d011169	richart	Triggering documentation build from the pipeline to avoid pipeline dulication	Jan 23
01369ceac77c	richart	missing underline to a link	Jan 23
844207c7e3db	richart	Correcting link to examples	Jan 20
58c3fe16f3f1	richart	Cleaning the tests of release	Jan 19
7e9876f1530a	richart	Update .gitlab-ci.yml file	Jan 19
a13543246ead	richart	Update .gitlab-ci.yml file	Jan 19
b442146018c7	richart	more typos in release	Jan 19
94980bba2d3f	richart	more typos	Jan 19
1477b046e013	richart	Weird effects with release-cli	Jan 19
06ceeb2290ef	richart	more typos	Jan 19
6cdddd6de443	richart	Force tag for tests	Jan 19
30f7aff3b4c2	richart	Still typos introduced by trial and error tests...	Jan 19
330beaa1675a	richart	More typos in the ci	Jan 19
dc0e14338442	richart	Wrong image for the release	Jan 19
7b93987c85d3	richart	tarball problem, might be a multiline command issue	Jan 19
53f6e14c2f79	richart	test cache	Jan 19
04bec461c737	richart	Caches not correctly passed	Jan 19
a834f245f43d	richart	switching to ninja	Jan 19
f5ffe386d46a	richart	output files where erasing each others	Jan 19
29a69978d644	richart	missing cache with the build folder for the release	Jan 19
a6e6df0a8ab9	richart	typo in reference	Jan 19
a8a649daae83	richart	Forcing it differently	Jan 19
51fd2edbe5e7	richart	Forcing release in the branch to test	Jan 19

Changes (177)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
M		.gitignore
M		.gitlab-ci.yml
M		.gitlab/ci.d/code-quality.yaml
M		.gitlab/ci.d/images.yaml
M		.gitlab/ci.d/templates.yaml
M		.gitpod.yml
M		CMakeLists.txt
M		README.md
M		cmake/AkantuConfig.cmake.in
M		cmake/AkantuExampleMacros.cmake
M		cmake/AkantuInstall.cmake
M		cmake/AkantuTestsMacros.cmake
M		cmake/Modules/CMakePackagesSystem.cmake
M		cmake/Modules/CMakePackagesSystemPrivateFunctions.cmake
M		cmake/Modules/CMakeVersionGenerator.cmake
M		cmake/Modules/FindMumps.cmake
M		cmake/Modules/FindParMETIS.cmake
M		cmake/Modules/FindScotch.cmake
M		cmake/semver.py
M		dev-requirements.txt
M		doc/dev-doc/CMakeLists.txt
M		doc/dev-doc/akantu.dox.j2
M		doc/dev-doc/changelog.md
M		doc/dev-doc/conf.py
M		doc/dev-doc/manual/contactmechanicsmodel.rst
M		doc/dev-doc/manual/diffusion.rst
M		doc/dev-doc/manual/getting_started.rst
M		doc/dev-doc/manual/solidmechanicsmodel.rst
M		doc/dev-doc/requirements.txt
M		doc/dev-doc/tutorials.rst
M		examples/README.rst
M		examples/c++/CMakeLists.txt
M		examples/c++/README.rst
M		examples/c++/contact_mechanics_model/README.rst
M		examples/c++/contact_mechanics_model/cohesive_contact_explicit_dynamic.cc
M		examples/c++/contact_mechanics_model/contact_explicit_dynamic.cc
M		examples/c++/contact_mechanics_model/contact_explicit_static.cc
M		examples/c++/diffusion_model/README.rst
M		examples/c++/diffusion_model/heat_diffusion_dynamics_2d.cc
M		examples/c++/diffusion_model/heat_diffusion_dynamics_3d.cc
M		examples/c++/diffusion_model/heat_diffusion_static_2d.cc
M		examples/c++/phase_field_model/README.rst
M		examples/c++/phase_field_model/phase_field_notch.cc
M		examples/c++/phase_field_model/phase_field_parallel.cc
A	(dir)	examples/c++/scalability_test/
A		examples/c++/scalability_test/CMakeLists.txt
A		examples/c++/scalability_test/README.rst
A		examples/c++/scalability_test/cohesive_extrinsic.cc
A		examples/c++/scalability_test/cube.geo
A		examples/c++/scalability_test/cube.msh
A	(dir)	examples/c++/scalability_test/images/
A		examples/c++/scalability_test/images/TTS.svg
A		examples/c++/scalability_test/images/cube.svg
A		examples/c++/scalability_test/material-cohesive.dat
A		examples/c++/scalability_test/material-elastic.dat
A		examples/c++/scalability_test/plot.py
A		examples/c++/scalability_test/run.sh
A		examples/c++/scalability_test/scalability.sh
M		examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic/README.rst
M		examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic/cohesive_extrinsic.cc
M		examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic_ig_tg/README.rst
M		examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc
M		examples/c++/solid_mechanics_cohesive_model/cohesive_intrinsic/README.rst
M		examples/c++/solid_mechanics_cohesive_model/cohesive_intrinsic/cohesive_intrinsic.cc
M		examples/c++/solid_mechanics_model/README.rst
M		examples/c++/solid_mechanics_model/boundary_conditions/CMakeLists.txt
M		examples/c++/solid_mechanics_model/boundary_conditions/README.rst
M		examples/c++/solid_mechanics_model/boundary_conditions/predefined_bc/predefined_bc.cc
M		examples/c++/solid_mechanics_model/boundary_conditions/python_user_defined_bc/boundary_condition.py
M		examples/c++/solid_mechanics_model/boundary_conditions/python_user_defined_bc/python_user_defined_bc.cc
M		examples/c++/solid_mechanics_model/boundary_conditions/user_defined_bc/user_defined_bc.cc
M		examples/c++/solid_mechanics_model/explicit/README.rst
M		examples/c++/solid_mechanics_model/explicit/explicit_dynamic.cc
M		examples/c++/solid_mechanics_model/implicit/README.rst
M		examples/c++/solid_mechanics_model/implicit/implicit_dynamic.cc
M		examples/c++/solid_mechanics_model/io/README.rst
M		examples/c++/solid_mechanics_model/io/dumper/dumpable_interface.cc
M		examples/c++/solid_mechanics_model/io/dumper/dumper_low_level.cc
M		examples/c++/solid_mechanics_model/io/parser/example_parser.cc
M		examples/c++/solid_mechanics_model/new_material/README.rst
M		examples/c++/solid_mechanics_model/new_material/new_local_material.cc
M		examples/c++/solid_mechanics_model/parallel/README.rst
M		examples/c++/solid_mechanics_model/parallel/parallel_2d.cc
M		examples/c++/solid_mechanics_model/static/README.rst
M		examples/c++/solid_mechanics_model/static/images/static_displ_mag.png
M		examples/c++/solid_mechanics_model/static/static.cc
M		examples/python/README.rst
M		examples/python/contact_mechanics_model/README.rst
M		examples/python/phase_field_model/README.rst
M		examples/python/solid_mechanics_cohesive_model/cohesive/README.rst
M		examples/python/solid_mechanics_cohesive_model/fragmentation/README.rst
M		examples/python/solid_mechanics_model/README.rst
M		examples/python/solid_mechanics_model/custom-material/README.rst
M		examples/python/solid_mechanics_model/dynamics/README.rst
M		examples/python/solid_mechanics_model/eigen_modes/README.rst
M		examples/python/solid_mechanics_model/plate-hole/README.rst
M		examples/python/solid_mechanics_model/solver_callback/README.rst
M		examples/python/solid_mechanics_model/stiffness_matrix/README.rst
A	(dir)	joss/
A		joss/.gitignore
A		joss/compile.sh
A		joss/paper.bib
A		joss/paper.md
A	(dir)	joss/results/
A		joss/results/TTS.svg
A		joss/results/cohesive_insertion.png
A		joss/results/cube.svg
A		joss/results/plot.py
A		joss/results/timmings_cohesive_gcc_jed_v4.0.1.csv
A		joss/results/timmings_cohesive_gcc_jed_v5.0.4.csv
A		joss/results/timmings_elastic_gcc_jed_v4.0.1.csv
A		joss/results/timmings_elastic_gcc_jed_v5.0.4.csv
M		packages/boost.cmake
M		packages/contact_mechanics.cmake
M		packages/core.cmake
M		packages/implicit.cmake
M		python/CMakeLists.txt
M		python/py_akantu.cc
M		python/py_heat_transfer_model.cc
M		python/py_phase_field_model.cc
M		setup.cfg
M		setup.py
M		src/common/aka_config.cc.in
M		src/common/aka_config.hh.in
M		src/common/aka_element_classes_info.hh
D		src/common/aka_element_classes_info.hh.in
M		src/common/aka_random_generator.hh
M		src/fe_engine/integration_point.hh
M		src/io/parser/algebraic_parser.hh
M		src/io/parser/input_file_parser.hh
D		src/io/parser/parser_random.cc
M		src/io/parser/parser_real.cc
D		src/io/parser/parser_types.cc
M		src/mesh/mesh.hh
M		src/model/common/constitutive_laws/constitutive_laws_handler_tmpl.hh
M		src/model/common/dof_manager/dof_manager_default.cc
M		src/model/common/non_linear_solver/non_linear_solver_default.hh
M		src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
M		src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
M		src/model/contact_mechanics/contact_detector.hh
V		src/model/contact_mechanics/{contact_detector_inline_impl.cc → contact_detector_inline_impl.hh}
V		src/model/contact_mechanics/{contact_detector_inline_impl.hh ← contact_detector_inline_impl.cc}
M		src/model/contact_mechanics/geometry_utils.hh
V		src/model/contact_mechanics/{geometry_utils_inline_impl.cc → geometry_utils_inline_impl.hh}
V		src/model/contact_mechanics/{geometry_utils_inline_impl.hh ← geometry_utils_inline_impl.cc}
M		src/model/diffusion_model/diffusion_law.cc
M		src/model/model.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.cc
M		src/model/phase_field/phasefield.hh
A		src/solver/sparse_solver_eigen.cc
A		src/solver/sparse_solver_eigen.hh
A	(dir)	test/ci/debian:testing/
A		test/ci/debian:testing/Dockerfile
A	(dir)	test/ci/macosx/
A		test/ci/macosx/build_env.sh
A		test/ci/macosx/configure_env.sh
A		test/ci/macosx/make-wheels.sh
A		test/ci/macosx/spack.yaml
V		test/ci/{ → manylinux:2014_x86_64}/make-wheels.sh
M		test/ci/manylinux:2014_x86_64/Dockerfile
A		test/ci/manylinux:2014_x86_64/build_env.sh
A		test/ci/manylinux:2014_x86_64/configure_env.sh
V		test/ci/{manylinux:2014_x86_64 ← }/make-wheels.sh
M		test/ci/manylinux:2014_x86_64/spack.yaml
M		test/test_model/test_phase_field_model/test_phase_field_anisotropic.cc
M		third-party/akantu_iterators/CMakeLists.txt
M		third-party/akantu_iterators/include/aka_str_hash.hh
M		third-party/akantu_iterators/include/iterators/aka_filter_iterator.hh
M		third-party/akantu_iterators/test/test_tuples.cc
M		third-party/iohelper/CMakeLists.txt
M		third-party/iohelper/src/CMakeLists.txt
M		third-party/iohelper/src/base64.hh
M		third-party/iohelper/src/file_manager.hh
M		third-party/iohelper/src/iohelper_common.hh