Diffusion akantu c3b8aecba3ce

conflict with master resolved
c3b8aecba3ce
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Authored by pundir on Feb 21 2020, 13:25.

Description

conflict with master resolved

Details

Committed

pundir

Feb 21 2020, 13:25

Pushed

gitlab-richart

Jul 29 2021, 09:01

Parents

rAKA1945e593c93f: working in parallel
rAKA488760c3e3f3: Correcting compilation problem

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Event Timeline

pundir committed rAKAc3b8aecba3ce: conflict with master resolved (authored by pundir).Feb 21 2020, 13:25

Merged Changes

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

Commit	Author	Details	Committed
488760c3e3f3	richart	Correcting compilation problem	Feb 18 2020
28993b463c33	richart	Example of using python as boundary condition	Feb 18 2020
c67b978cb04e	richart	Adding a possibility to insert cohesive element only in some	Feb 18 2020
9929d0a08e7f	richart	Bug fix in pythonpath	Jan 24 2020
b23200851fdc	richart	Correcting install directory for old cmake versions	Jan 23 2020
667ed59814ab	richart	Installing python binding and akantu-iterators properly	Jan 23 2020
be8e3f9d35f2	richart	improving the install process	Jan 22 2020
84127a482549	richart	Actually running the examples as tests	Jan 15 2020
547777110e55	richart	make the new_material a bit faster	Jan 15 2020
89c853c10096	richart	factorizing scatter/gather from dof_synchronizer to synchronizer_impl	Jan 15 2020
60b28fcdab22	richart	adding detection of the mpiseq library	Jan 10 2020
b6bcc70eec56	richart	tuple concat trick	Jan 10 2020
6d890200f749	richart	Seting policy for the <package>_ROOT variable in the environment	Dec 20 2019
f600d5b63508	richart	Wrongly protected compilation	Dec 20 2019
58bf31d34709	richart	Bug fix in the export of the target akantu	Dec 18 2019
551d547afddd	richart	mpi skip mpicxx	Dec 13 2019
ac4f37242023	richart	extanding SparseMatrix and DOFManager interface in python	Dec 13 2019
36ba3a35a3dc	richart	Make the test work with older version of gtest	Dec 13 2019
e64ab77154c7	richart	Merge commit '5e1ea8c938d8b63d462d21c8ea8292f3fdeaeebf'	Dec 13 2019
5e1ea8c938d8	richart	A bit to aggressive with the clang-tidy	Dec 13 2019
14731a9413a1	richart	Merge commit 'f8bcabd419ba24966eb8679e9610897dca660db1'	Dec 12 2019
f8bcabd419ba	richart	Added named_zip	Dec 12 2019
bd71d08c3d98	richart	tidied and formated version	Dec 12 2019
596b60c4bdf3	richart	some cleaning to many class in the same file	Dec 12 2019
1e38564b9582	richart	Merge branch 'master' of c4science:/diffusion/AKAPRIV/akantu-private	Dec 11 2019
8eadccc15c0a	richart	The fix for clang breaks gcc	Dec 11 2019
5461568ecf20	frerot	fixed warning [-Wempty-body] in Mesh::read	Dec 11 2019
f553aa3c8bf8	richart	bug fix to compile on clang	Dec 11 2019
c4f89da9ae78	richart	Merge branch 'master' of gitlab.com:akantu/akantu	Dec 11 2019
3a7f4d5d5151	richart	Merge commit '0b3ffcd1a0d6eb6b458c72f62f21cd1400f64066'	Dec 11 2019
0b3ffcd1a0d6	richart	adding support for non gnu compilers	Dec 10 2019
7ca19f1effd2	richart	Adding named_tuples and string_literal	Dec 10 2019
480f4c7eee34	richart	Correcting namespace + warnings	Dec 10 2019
24c0dfa18072	richart	trying to accelerate the ci	Dec 9 2019
14042a61b3ad	richart	improving ci	Dec 9 2019
a07873cdbd98	richart	Add .gitlab-ci.yml	Dec 9 2019
dcda0b809401	richart	small improvements in ci	Dec 9 2019
66e3133c8270	richart	inceasing timeouts	Dec 9 2019
8a2af02b08a5	richart	cleaning a bit the repo	Dec 9 2019
63499ac0083d	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Dec 9 2019
071c9fee244f	richart	Merge commit '05b77d3f6ef7d01e805b865ade26ac3acec3d668'	Dec 9 2019
05b77d3f6ef7	richart	bug fix in the filter iterator	Dec 9 2019
ce29a60dc324	richart	Solving the gtest download failing the second time	Dec 9 2019
e3494c51066d	richart	linting	Dec 9 2019
f9b8db2f4c06	richart	changing the way to do filter adaptor	Dec 9 2019
e4fb2fa229fe	richart	correcting the tests	Dec 9 2019
c70e24267884	richart	flags to specify when akantu runs in docker	Dec 9 2019
ecd4b6b18e86	richart	Simplifying the jobs since it fails between caches and makefiles...	Dec 6 2019
1f0ee966f6ce	richart	cleaning the readme	Dec 6 2019
a9fc7dd91ac1	richart	wrong variable	Dec 5 2019

Changes (228)
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This commit is very large. Load each file individually.

		Path
P		.gitignore Copied to third-party/akantu_iterators/.gitignore
A		.gitlab-ci.yml
M		CMakeLists.txt
P		Jenkinsfile Copied to third-party/akantu_iterators/Jenkinsfile
M		README
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/FindMumps.cmake
A		cmake/Modules/FindPythonLibsNew.cmake
M		doc/manual/CMakeLists.txt
M		doc/manual/manual-changelog.tex
M		doc/manual/manual-heattransfermodel.tex
M		doc/manual/manual-io.tex
M		examples/boundary_conditions/CMakeLists.txt
A	(dir)	examples/boundary_conditions/python_user_defined_bc/
A		examples/boundary_conditions/python_user_defined_bc/CMakeLists.txt
A		examples/boundary_conditions/python_user_defined_bc/boundary_condition.py
A		examples/boundary_conditions/python_user_defined_bc/fine_mesh.geo
P		examples/boundary_conditions/python_user_defined_bc/material.dat Copied from test/test_model/patch_tests/data/material_check_stress_plane_stress.dat
A		examples/boundary_conditions/python_user_defined_bc/python_user_defined_bc.cc
P		examples/cohesive_element/cohesive_extrinsic_ig_tg/CMakeLists.txt Copied to packages/akantu_iterators.cmake
M		examples/cohesive_element/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc
M		examples/cohesive_element/cohesive_extrinsic_ig_tg/material.dat
D		examples/cohesive_element/cohesive_extrinsic_ig_tg/square.msh
A		examples/cohesive_element/cohesive_extrinsic_ig_tg/triangle.geo
M		examples/new_material/barre_trou.geo
M		examples/new_material/material.dat
M		examples/new_material/new_local_material.cc
M		examples/python/eigen_modes/eigen_modes.py
P		packages/akantu_iterators.cmake Copied from examples/cohesive_element/cohesive_extrinsic_ig_tg/CMakeLists.txt
M		packages/core.cmake
M		packages/implicit.cmake
M		packages/mpi.cmake
M		packages/mumps.cmake
M		packages/pybind11.cmake
M		packages/python_interface.cmake
M		packages/pythonlibs.cmake
M		packages/structural_mechanics.cmake
M		python/CMakeLists.txt
M		python/py_aka_array.hh
M		python/py_dumpable.cc
M		python/py_fe_engine.cc
M		python/py_group_manager.cc
M		python/py_material.cc
M		python/py_mesh.cc
M		python/py_model.cc
M		python/py_solid_mechanics_model.cc
M		src/CMakeLists.txt
M		src/common/aka_array.hh
M		src/common/aka_common.hh
V		{src/common → third-party/akantu_iterators/include}/aka_compatibilty_with_cpp_standard.hh
M		src/common/aka_element_classes_info.hh.in
M		src/common/aka_factory.hh
M		src/common/aka_grid_dynamic.hh
D		src/common/aka_iterators.hh
M		src/common/aka_random_generator.hh
V		{src/common → third-party/akantu_iterators/include}/aka_static_if.hh
M		src/common/aka_types.hh
M		src/common/aka_voigthelper.hh
M		src/common/aka_voigthelper_tmpl.hh
M		src/fe_engine/fe_engine.hh
M		src/fe_engine/fe_engine_template.hh
M		src/fe_engine/fe_engine_template_tmpl_field.hh
M		src/io/dumper/dumper_material_padders.hh
M		src/io/parser/parameter_registry_tmpl.hh
M		src/io/parser/parser_tmpl.hh
M		src/mesh/mesh.cc
M		src/mesh_utils/cohesive_element_inserter.cc
M		src/mesh_utils/cohesive_element_inserter.hh
M		src/mesh_utils/mesh_partition.cc
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_default.cc
M		src/model/common/dof_manager/dof_manager_inline_impl.cc
M		src/model/common/integration_scheme/integration_scheme.cc
M		src/model/common/integration_scheme/integration_scheme.hh
M		src/model/common/integration_scheme/integration_scheme_1st_order.hh
P		src/model/common/non_linear_solver/non_linear_solver_default.hh Copied to third-party/akantu_iterators/include/aka_iterators.hh
P		src/model/common/non_linear_solver/non_linear_solver_linear.cc Copied to src/synchronizer/dof_synchronizer_inline_impl.cc
M		src/model/common/non_linear_solver/non_linear_solver_lumped.cc
M		src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
M		src/model/common/non_linear_solver/non_linear_solver_newton_raphson.hh
M		src/model/common/non_linear_solver/non_linear_solver_petsc.cc
M		src/model/common/non_linear_solver/non_linear_solver_petsc.hh
M		src/model/common/solver_callback.hh
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
M		src/model/heat_transfer/heat_transfer_model.cc
M		src/model/model.hh
M		src/model/model_inline_impl.cc
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_elastic.cc
M		src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.cc
M		src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
M		src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
M		src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.cc
M		src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
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/solid_mechanics_model.cc
M		src/model/solid_mechanics/solid_mechanics_model.hh
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_io.cc
M		src/model/solid_mechanics/solid_mechanics_model_mass.cc
M		src/model/structural_mechanics/structural_mechanics_model.cc
M		src/solver/sparse_matrix.hh
M		src/solver/sparse_matrix_aij.cc
M		src/synchronizer/communication_buffer.hh
M		src/synchronizer/dof_synchronizer.cc
M		src/synchronizer/dof_synchronizer.hh
P		src/synchronizer/dof_synchronizer_inline_impl.cc Copied from src/model/common/non_linear_solver/non_linear_solver_linear.cc
M		src/synchronizer/node_synchronizer.cc
M		src/synchronizer/node_synchronizer.hh
A		src/synchronizer/node_synchronizer_inline_impl.cc
M		src/synchronizer/periodic_node_synchronizer.hh
M		src/synchronizer/synchronizer_impl.hh
M		src/synchronizer/synchronizer_impl_tmpl.hh
P		test/ci/Dockerfile Deleted after being copied to multiple locations: test/ci/debian.testing/Dockerfile test/ci/ubuntu.lts/Dockerfile third-party/akantu_iterators/test/ci/Dockerfile
A		test/ci/ctest2junit.xsl
A	(dir)	test/ci/debian.testing/
P		test/ci/debian.testing/Dockerfile Copied from test/ci/Dockerfile
A	(dir)	test/ci/ubuntu.lts/
P		test/ci/ubuntu.lts/Dockerfile Copied from test/ci/Dockerfile
M		test/test_common/CMakeLists.txt
M		test/test_common/test_array.cc
P		test/test_common/test_iterators.cc Copied to third-party/akantu_iterators/test/test_iterators.cc
A		test/test_common/test_voigt_helper.cc
M		test/test_fe_engine/test_fe_engine_fixture.hh
M		test/test_gtest_utils.hh
M		test/test_model/patch_tests/CMakeLists.txt
P		test/test_model/patch_tests/data/material_check_stress_plane_strain.dat Copied to multiple locations: test/test_model/patch_tests/data/material_check_stress_plane_strain_finite_deformation.dat test/test_model/patch_tests/data/material_check_stress_plane_stress_finite_deformation.dat test/test_model/test_solid_mechanics_model/material_elastic.dat
P		test/test_model/patch_tests/data/material_check_stress_plane_strain_finite_deformation.dat Copied from test/test_model/patch_tests/data/material_check_stress_plane_strain.dat
P		test/test_model/patch_tests/data/material_check_stress_plane_stress.dat Copied to examples/boundary_conditions/python_user_defined_bc/material.dat
P		test/test_model/patch_tests/data/material_check_stress_plane_stress_finite_deformation.dat Copied from test/test_model/patch_tests/data/material_check_stress_plane_strain.dat
M		test/test_model/patch_tests/patch_test_linear_elastic_explicit.cc
M		test/test_model/patch_tests/patch_test_linear_elastic_implicit.cc
M		test/test_model/test_common/test_dof_manager.cc
M		test/test_model/test_common/test_non_local_toolbox/CMakeLists.txt
M		test/test_model/test_common/test_non_local_toolbox/my_model.hh
M		test/test_model/test_common/test_non_local_toolbox/test_non_local_neighborhood_base.verified
M		test/test_model/test_common/test_non_local_toolbox/test_remove_damage_weight_function.cc
M		test/test_model/test_solid_mechanics_model/CMakeLists.txt
P		test/test_model/test_solid_mechanics_model/material_elastic.dat Copied from test/test_model/patch_tests/data/material_check_stress_plane_strain.dat
M		test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh
M		test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc
A		test/test_model/test_solid_mechanics_model/test_materials/1_tetrahedron.msh
A		test/test_model/test_solid_mechanics_model/test_materials/1_tetrehedron.geo
M		test/test_model/test_solid_mechanics_model/test_materials/CMakeLists.txt
A		test/test_model/test_solid_mechanics_model/test_materials/cube.geo
A		test/test_model/test_solid_mechanics_model/test_materials/material_finite_deformation.dat
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
A		test/test_model/test_solid_mechanics_model/test_materials/test_finite_deformation.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_material_fixtures.hh
M		test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/CMakeLists.txt
M		test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh
A		test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_large_rotation.cc
M		test/test_synchronizer/test_dof_synchronizer.cc
M		test/test_synchronizer/test_node_synchronizer.cc
A	(dir)	third-party/akantu_iterators/
A		third-party/akantu_iterators/.arcconfig
A		third-party/akantu_iterators/.arclint
A		third-party/akantu_iterators/.clang-format
A		third-party/akantu_iterators/.clang-tidy
P		third-party/akantu_iterators/.gitignore Copied from .gitignore
A		third-party/akantu_iterators/.gitlab-ci.yml
A	(dir)	third-party/akantu_iterators/.linters/
A	(dir)	third-party/akantu_iterators/.linters/clang-format-linter/
A		third-party/akantu_iterators/.linters/clang-format-linter/.arclint
A		third-party/akantu_iterators/.linters/clang-format-linter/.gitignore
A		third-party/akantu_iterators/.linters/clang-format-linter/LICENSE
A		third-party/akantu_iterators/.linters/clang-format-linter/README.md
A		third-party/akantu_iterators/.linters/clang-format-linter/__phutil_library_init__.php
A		third-party/akantu_iterators/.linters/clang-format-linter/__phutil_library_map__.php
A	(dir)	third-party/akantu_iterators/.linters/clang-format-linter/lint/
A	(dir)	third-party/akantu_iterators/.linters/clang-format-linter/lint/linter/
A		third-party/akantu_iterators/.linters/clang-format-linter/lint/linter/ClangFormatLinter.php
A		third-party/akantu_iterators/CMakeLists.txt
A		third-party/akantu_iterators/COPYING
A		third-party/akantu_iterators/COPYING.lesser
P		third-party/akantu_iterators/Jenkinsfile Copied from Jenkinsfile
A	(dir)	third-party/akantu_iterators/cmake/
A		third-party/akantu_iterators/cmake/AkantuIteratorsTools.cmake
A		third-party/akantu_iterators/cmake/GTest.cmake
A	(dir)	third-party/akantu_iterators/include/
V		{third-party/akantu_iterators/include ← src/common}/aka_compatibilty_with_cpp_standard.hh
P		third-party/akantu_iterators/include/aka_iterators.hh Copied from src/model/common/non_linear_solver/non_linear_solver_default.hh
V		{third-party/akantu_iterators/include ← src/common}/aka_static_if.hh
A		third-party/akantu_iterators/include/aka_str_hash.hh
A		third-party/akantu_iterators/include/aka_tuple_tools.hh
A	(dir)	third-party/akantu_iterators/include/iterators/
A		third-party/akantu_iterators/include/iterators/aka_arange_iterator.hh
A		third-party/akantu_iterators/include/iterators/aka_enumerate_iterator.hh
A		third-party/akantu_iterators/include/iterators/aka_filter_iterator.hh
A		third-party/akantu_iterators/include/iterators/aka_transform_iterator.hh
A		third-party/akantu_iterators/include/iterators/aka_zip_iterator.hh
A	(dir)	third-party/akantu_iterators/test/
A		third-party/akantu_iterators/test/CMakeLists.txt
A	(dir)	third-party/akantu_iterators/test/ci/
A		third-party/akantu_iterators/test/ci/.arcconfig
A		third-party/akantu_iterators/test/ci/.arclint
V		{third-party/akantu_iterators ← }/test/ci/Dockerfile
A		third-party/akantu_iterators/test/ci/ctest2junit.xsl
A	(dir)	third-party/akantu_iterators/test/ci/scripts/
A		third-party/akantu_iterators/test/ci/scripts/COPYING
A		third-party/akantu_iterators/test/ci/scripts/COPYING.lesser
A	(dir)	third-party/akantu_iterators/test/ci/scripts/harbomaster/
A		third-party/akantu_iterators/test/ci/scripts/harbomaster/__init__.py
A		third-party/akantu_iterators/test/ci/scripts/harbomaster/arclint.py
A		third-party/akantu_iterators/test/ci/scripts/harbomaster/hbm.py
A		third-party/akantu_iterators/test/ci/scripts/harbomaster/results.py
A		third-party/akantu_iterators/test/ci/scripts/harbomaster/testresults.py
A		third-party/akantu_iterators/test/ci/scripts/hbm
A		third-party/akantu_iterators/test/test_gtest_main.cc
P		third-party/akantu_iterators/test/test_iterators.cc Copied from test/test_common/test_iterators.cc
A		third-party/akantu_iterators/test/test_str.cc
A		third-party/akantu_iterators/test/test_tuples.cc
A		third-party/cmake/akantu_iterators.cmake
M		third-party/cmake/gtest.cmake