Diffusion akantu 00ca1e91f39a

Merge branch 'master' into features/petsc
00ca1e91f39a
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Authored by richart on Jun 5 2019, 17:47.

Description

Merge branch 'master' into features/petsc

Details

Committed

richart

Jun 5 2019, 17:47

Pushed

gitlab-richart

Jul 29 2021, 09:01

Parents

rAKA6d5d7eb67dcf: Few modifications
rAKAe31046f5809d: Minor bug fixes

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Event Timeline

richart committed rAKA00ca1e91f39a: Merge branch 'master' into features/petsc (authored by richart).Jun 5 2019, 17:47

Merged Changes

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

Commit		Author	Details	Committed
e31046f5809d		richart	Minor bug fixes	Jun 5 2019
dd534854983b		richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Jun 4 2019
02f245d81e99		richart	Bug fix in the MSH reader version 4	Jun 2 2019
c9e67b83dadf		richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	May 31 2019
ce7807ee8dd8		anciaux/richart	correct the construction of the element filter with ek_regular	May 31 2019
45ceddff1be6		gallyamov/richart	Correction of the default element types within element_type_map:	May 31 2019
b747d8056676		richart	Update on mesh_io_msh read and write	May 29 2019
fba28721befa		richart	Update for latest findcgal.cmake	May 21 2019
7e48d8081c03		richart	Modified MSH reader for version 4.1 of the files	May 21 2019
7a4f63ed245b		richart	Reactivating anisotropic patch tests	May 14 2019
4929f9340ec6		richart	Bug fix in material anisotropic	May 14 2019
09132a7235f3		anciaux	change a path	May 9 2019
c88737402624		anciaux	adding an example extracting the stiffness amtrix	Mar 26 2019
14d9e2d154f1		anciaux	modifying the swig temporarily to have access to aij sparse matrices	Mar 26 2019
ef0e287ff1df		anciaux	adding an example extracting the stiffness amtrix	Mar 26 2019
de71b7128786		frerot	setting rpath for python extension	Mar 20 2019
b56f231301db		richart	exposing partitionate parameters in distribute	Feb 26 2019
df011ae4a4f0		richart	Adding traction test for Mazars	Feb 13 2019
5a3a1cdf8f53		richart	Correction in the ci handling	Feb 8 2019
6d7644e043fc		richart	Create matrices at the earliest moment	Feb 8 2019
b1a307ef66b1		richart	Bug fixing some tests + sanitizing them	Feb 8 2019
eda67ec08f6a		richart	Swig protection	Feb 8 2019
8ba22a520261	D197	fouad/richart	Correcting examples and tests	Feb 6 2019
5d33087ff395		richart	Adding a debug message to the ci	Feb 5 2019
3f1987165f52		richart	Adding iterator_traits to column_iterator	Feb 5 2019
902821c97efa		richart	Promoting the arange to a forward iterator	Feb 5 2019
01db2b140172		richart	some code cleaning	Jan 30 2019
05ddaf26a7c0		richart	zip cat iterator	Jan 30 2019
e6290e410ed8		richart	removing dead code	Jan 29 2019
dddb508f8340		richart	Bug fix in column iterator and some cleaning	Jan 29 2019
dfaa0e745adb		richart	Adding filtered iterator and zip iterator random_access possibility	Jan 29 2019
c46358f378c7		richart	pipefail illegal option...	Jan 29 2019
46d10f4b360e		richart	Proper way to set pipefail shell option	Jan 29 2019
25232ee996ec		richart	Factoring the tests	Jan 29 2019
402b15f3ac70		richart	Fighting to really make it fail urly	Jan 29 2019
0480e2e007db		richart	Do not try to continue if compilation error occurs	Jan 29 2019
b856484b2e49		richart	Missing arcanist dependencies	Jan 29 2019
b4c1554a7a84		richart	arcanist in the package of Dockerfile	Jan 29 2019
77b260d606a6		richart	Installing arcanist by hand in the dockerfile	Jan 29 2019
a0c78a6f504a		richart	Pushing file reports to harbormaster in case of failure	Jan 22 2019
3d5700f43abf		richart	Bug fix in heat transfer	Jan 22 2019
f959f4fd73d4		richart	Adding column iterator on Matrix	Jan 22 2019
6c6773b48d51		richart	Cleaning a bit the Jenkinsfile	Jan 21 2019
de1fca149331		richart	Adding linters in the dockerfile	Jan 18 2019
8497f13ab5d4		richart	Ok switch to stupid lint	Jan 17 2019
337d7cb4703a		richart	Escape character	Jan 17 2019
52b303457c87		richart	Typo in the Jenkinsfile	Jan 17 2019
216fea71cb16		richart	A bit more on the linter	Jan 17 2019
db395140fe3b		richart	Don't panic this will be linted next commit	Jan 16 2019
ac2cfab6b086		richart	Try harder	Jan 16 2019

Changes (132)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
M		.arcconfig
M		.arclint
M		CMakeLists.txt
V		{ → test/ci}/Dockerfile
M		Jenkinsfile
M		cmake/AkantuCleaning.cmake
M		cmake/akantu_environement.csh.in
M		cmake/akantu_environement.sh.in
M		cmake/akantu_test_driver.sh
M		examples/boundary_conditions/predefined_bc/predefined_bc.cc
M		examples/boundary_conditions/predefined_bc/square.geo
M		examples/boundary_conditions/user_defined_bc/fine_mesh.geo
M		examples/boundary_conditions/user_defined_bc/user_defined_bc.cc
M		examples/cohesive_element/cohesive_extrinsic/cohesive_extrinsic.cc
M		examples/cohesive_element/cohesive_extrinsic/material.dat
M		examples/cohesive_element/cohesive_extrinsic_ig_tg/material.dat
M		examples/embedded/embedded.cc
M		examples/implicit/implicit_dynamic.cc
M		examples/io/dumper/dumpable_interface.cc
M		examples/io/dumper/dumper_low_level.cc
M		examples/io/parser/example_parser.cc
M		examples/new_material/local_material_damage.cc
M		examples/new_material/new_local_material.cc
M		examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc
M		examples/python/CMakeLists.txt
A	(dir)	examples/python/stiffness_matrix/
A		examples/python/stiffness_matrix/CMakeLists.txt
A		examples/python/stiffness_matrix/material.dat
A		examples/python/stiffness_matrix/plate.geo
A		examples/python/stiffness_matrix/plate.msh
A		examples/python/stiffness_matrix/stiffness_matrix.py
M		extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.cc
M		extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.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/ntrf_contact.cc
M		packages/cgal.cmake
M		packages/solid_mechanics.cmake
M		python/setup.py.in
M		python/swig/aka_array.i
M		python/swig/mesh.i
M		python/swig/model.i
M		python/swig/sparse_matrix.i
M		src/common/aka_common.hh
M		src/common/aka_types.hh
M		src/fe_engine/fe_engine_template.hh
M		src/fe_engine/shape_cohesive_inline_impl.cc
M		src/fe_engine/shape_functions.hh
M		src/io/mesh_io.cc
M		src/io/mesh_io.hh
M		src/io/mesh_io/mesh_io_msh.cc
M		src/io/mesh_io/mesh_io_msh.hh
M		src/mesh/element_group.cc
M		src/mesh/element_group.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/group_manager_inline_impl.cc
M		src/mesh/mesh.cc
M		src/mesh/mesh.hh
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/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/model_solver.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
M		src/model/heat_transfer/heat_transfer_model.cc
M		src/model/solid_mechanics/material.cc
M		src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.cc
M		src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
M		src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
M		src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
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_embedded_interface/embedded_interface_intersector.cc
M		src/model/solid_mechanics/solid_mechanics_model_mass.cc
M		test/CMakeLists.txt
A	(dir)	test/ci/
V		{test/ci ← }/Dockerfile
A	(dir)	test/ci/scripts/
A		test/ci/scripts/CTestResults.xml
A	(dir)	test/ci/scripts/harbomaster/
A		test/ci/scripts/harbomaster/__init__.py
A		test/ci/scripts/harbomaster/arclint.py
A		test/ci/scripts/harbomaster/ctestresults.py
A		test/ci/scripts/harbomaster/hbm.py
A		test/ci/scripts/harbomaster/results.py
A		test/ci/scripts/hbm
V		test/{ ← test_fe_engine}/pybind11_akantu.cc
V		test/{ ← test_fe_engine}/pybind11_akantu.hh
M		test/test_common/test_iterators.cc
M		test/test_common/test_tensors.cc
M		test/test_fe_engine/CMakeLists.txt
V		test/{test_fe_engine → }/pybind11_akantu.cc
V		test/{test_fe_engine → }/pybind11_akantu.hh
M		test/test_fe_engine/test_gradient.cc
M		test/test_fe_engine/test_integrate.cc
M		test/test_fe_engine/test_inverse_map.cc
M		test/test_gtest_utils.hh
M		test/test_io/test_dumper/test_dumper.cc
M		test/test_mesh_utils/test_mesh_iterators.cc
M		test/test_model/patch_tests/CMakeLists.txt
V		test/test_model/patch_tests/data/{material_anisotropic.dat → material_anisotropic_3.dat}
A		test/test_model/patch_tests/data/material_anisotropic_1.dat
A		test/test_model/patch_tests/data/material_anisotropic_2.dat
V		test/test_model/patch_tests/data/{material_anisotropic_3.dat ← material_anisotropic.dat}
A		test/test_model/patch_tests/patch_test_linear_anisotropic.cc
D		test/test_model/patch_tests/patch_test_linear_anisotropic_explicit.cc
M		test/test_model/patch_tests/patch_test_linear_fixture.hh
M		test/test_model/test_common/test_dof_manager.cc
M		test/test_model/test_common/test_model_solver/test_dof_manager_default.cc
M		test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh
M		test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model.cc
M		test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc
M		test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_dynamics.cc
M		test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc
M		test/test_model/test_solid_mechanics_model/test_materials/CMakeLists.txt
A		test/test_model/test_solid_mechanics_model/test_materials/py_mazars.py
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_local_material.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/test_material_elasto_plastic_linear_isotropic_hardening.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_material_mazars.cc