Diffusion akantu 7e653f041bc2

Merge branch 'master' into features/pybind11
7e653f041bc2
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Authored by anciaux on May 8 2019, 13:11.

Description

Merge branch 'master' into features/pybind11

Details

Committed

anciaux

May 8 2019, 13:11

Pushed

richart	Dec 6 2019, 13:35
richart	Dec 6 2019, 13:16
richart	Dec 6 2019, 12:16
richart	Dec 6 2019, 11:45
richart	Dec 5 2019, 22:54
richart	Dec 5 2019, 18:45

Parents

rAKA0a930296a24d: adding an example extracting the stiffness amtrix
rAKAec0ce126d3a6: adding element group and prepare pytest

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Event Timeline

anciaux committed rAKA7e653f041bc2: Merge branch 'master' into features/pybind11 (authored by anciaux).May 8 2019, 13:11

Merged Changes

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

Commit		Author	Details	Committed
0a930296a24d		anciaux	adding an example extracting the stiffness amtrix	Mar 26 2019
b879bd479ec6		anciaux	modifying the swig temporarily to have access to aij sparse matrices	Mar 26 2019
9eaed4318be9		anciaux	adding an example extracting the stiffness amtrix	Mar 26 2019
ad8da63e2e3d		frerot	setting rpath for python extension	Mar 20 2019
76e9be0a5b66		richart	exposing partitionate parameters in distribute	Feb 26 2019
431ad889f5c5		richart	Adding traction test for Mazars	Feb 13 2019
5424eed87428		richart	Correction in the ci handling	Feb 8 2019
cbdb1e7d0583		richart	Create matrices at the earliest moment	Feb 8 2019
f8a03d4d85b9		richart	Bug fixing some tests + sanitizing them	Feb 8 2019
87e540f9faa7		richart	Swig protection	Feb 8 2019
c263b07d61fc	D197	fouad/richart	Correcting examples and tests	Feb 6 2019
bd7e5993bf83		richart	Adding a debug message to the ci	Feb 5 2019
8e18d660550e		richart	Adding iterator_traits to column_iterator	Feb 5 2019
3f02cd677bf3		richart	Promoting the arange to a forward iterator	Feb 5 2019
832d879319a6		richart	some code cleaning	Jan 30 2019
5adae7dba462		richart	zip cat iterator	Jan 30 2019
1c60fe620524		richart	removing dead code	Jan 29 2019
4ffeb75ecfda		richart	Bug fix in column iterator and some cleaning	Jan 29 2019
3ceff0e60343		richart	Adding filtered iterator and zip iterator random_access possibility	Jan 29 2019
40783bf8df0e		richart	pipefail illegal option...	Jan 29 2019
8fa1db0f5b25		richart	Proper way to set pipefail shell option	Jan 29 2019
957db5e53127		richart	Factoring the tests	Jan 29 2019
93c5feeceadd		richart	Fighting to really make it fail urly	Jan 29 2019
204794a30ebd		richart	Do not try to continue if compilation error occurs	Jan 29 2019
602986794a95		richart	Missing arcanist dependencies	Jan 29 2019
7e77c430d622		richart	arcanist in the package of Dockerfile	Jan 29 2019
d0b37677147c		richart	Installing arcanist by hand in the dockerfile	Jan 29 2019
f429b1448a8a		richart	Pushing file reports to harbormaster in case of failure	Jan 22 2019
ca4fcfd6ba44		richart	Bug fix in heat transfer	Jan 22 2019
079fccbb5a42		richart	Adding column iterator on Matrix	Jan 22 2019
89dc921702b7		richart	Cleaning a bit the Jenkinsfile	Jan 21 2019
b3edd5d0b34d		richart	Adding linters in the dockerfile	Jan 18 2019
3478848b0145		richart	Ok switch to stupid lint	Jan 17 2019
4619ca8a2117		richart	Escape character	Jan 17 2019
2e32ebcb2e97		richart	Typo in the Jenkinsfile	Jan 17 2019
7dc72e378d3b		richart	A bit more on the linter	Jan 17 2019
1c327375818a		richart	Don't panic this will be linted next commit	Jan 16 2019
a40bfbf82923		richart	Try harder	Jan 16 2019
6f9525737c2e		richart	try not to fail all when only linter failed	Jan 16 2019
51dd90a78f08		richart	Adding linter informations	Jan 16 2019
c9e08c9d3bdb		richart	Copy past error	Jan 16 2019
a57e329353e0		richart	Missing test case	Jan 15 2019
dbfc4e205dda		richart	Trying more fancy tests states	Jan 15 2019
550a9c411591		richart	Cleaning the debug messages	Jan 15 2019
6082dc7d3f05		richart	Still missing some info	Jan 15 2019
0eabd86736a9		richart	This one should be the one	Jan 15 2019
b14a84cff3ab		richart	Adding the hosts informations	Jan 15 2019
f88f74a5f832		richart	PYTHONPATH not set properly still	Jan 15 2019
4db3886fd28e		richart	Typo	Jan 15 2019
ab2aec00e5f4		richart	Could not set the PATH in ci	Jan 15 2019

Changes (181)
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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/AkantuExtraCompilationProfiles.cmake
M		cmake/akantu_environement.csh.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
P		examples/new_material/CMakeLists.txt Copied to examples/new_material/viscoelastic_maxwell/CMakeLists.txt
M		examples/new_material/local_material_damage.cc
M		examples/new_material/new_local_material.cc
A	(dir)	examples/new_material/viscoelastic_maxwell/
P		examples/new_material/viscoelastic_maxwell/CMakeLists.txt Copied from examples/new_material/CMakeLists.txt
A		examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell.dat
A		examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc
A		examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_mesh.geo
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/ntn_contact/ntn_base_contact.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc
M		packages/core.cmake
M		packages/solid_mechanics.cmake
M		python/setup.py.in
M		python/swig/mesh.i
M		python/swig/model.i
M		python/swig/solid_mechanics_model_cohesive.i
M		python/swig/sparse_matrix.i
M		src/CMakeLists.txt
M		src/common/aka_array_tmpl.hh
M		src/common/aka_bbox.hh
M		src/common/aka_common.hh
M		src/common/aka_element_classes_info_inline_impl.cc
A		src/common/aka_enum_macros.hh
M		src/common/aka_iterators.hh
M		src/common/aka_math.cc
M		src/common/aka_types.hh
M		src/common/aka_voigthelper_tmpl.hh
M		src/fe_engine/fe_engine_template.hh
M		src/fe_engine/fe_engine_template_tmpl.hh
M		src/fe_engine/shape_cohesive_inline_impl.cc
M		src/fe_engine/shape_functions.cc
M		src/fe_engine/shape_functions.hh
M		src/io/dumper/dumper_compute.hh
M		src/io/dumper/dumper_generic_elemental_field.hh
M		src/io/dumper/dumper_generic_elemental_field_tmpl.hh
M		src/io/dumper/dumper_homogenizing_field.hh
M		src/io/mesh_io.cc
M		src/io/mesh_io/mesh_io_diana.cc
M		src/io/mesh_io/mesh_io_msh.cc
M		src/io/parser/parser.hh
M		src/mesh/element_group.cc
M		src/mesh/element_group.hh
M		src/mesh/element_group_inline_impl.cc
M		src/mesh/element_type_map.hh
M		src/mesh/element_type_map_filter.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_inline_impl.cc
M		src/mesh_utils/global_ids_updater.cc
M		src/mesh_utils/global_ids_updater_inline_impl.cc
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/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
M		src/model/dof_manager.cc
M		src/model/dof_manager.hh
M		src/model/dof_manager_default.cc
M		src/model/dof_manager_default.hh
M		src/model/heat_transfer/heat_transfer_model.cc
M		src/model/model_solver.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/internal_field.hh
M		src/model/solid_mechanics/materials/internal_field_tmpl.hh
M		src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
M		src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.cc
M		src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
M		src/model/solid_mechanics/materials/material_python/material_python.cc
A		src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc
A		src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh
M		src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.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/fragment_manager.cc
M		src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.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/time_step_solver.hh
M		src/model/time_step_solvers/time_step_solver.cc
M		src/model/time_step_solvers/time_step_solver_default.cc
M		src/model/time_step_solvers/time_step_solver_default.hh
M		src/synchronizer/communicator.cc
M		src/synchronizer/communicator.hh
M		src/synchronizer/communicator_dummy_inline_impl.cc
M		src/synchronizer/communicator_mpi_inline_impl.cc
M		src/synchronizer/master_element_info_per_processor.cc
M		src/synchronizer/node_info_per_processor.cc
M		src/synchronizer/node_synchronizer.cc
M		src/synchronizer/slave_element_info_per_processor.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_grid.cc
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_facet_element_mapping.cc
M		test/test_io/test_parser/test_parser.verified
M		test/test_mesh/CMakeLists.txt
M		test/test_mesh_utils/test_mesh_io/test_mesh_io_msh_physical_names.cc
M		test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_mesh_data.cc
M		test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_scotch.cc
M		test/test_model/test_model_solver/test_dof_manager_default.cc
M		test/test_model/test_model_solver/test_model_solver_dynamic.cc
M		test/test_model/test_model_solver/test_model_solver_dynamic_explicit.verified
M		test/test_model/test_model_solver/test_model_solver_dynamic_implicit.verified
M		test/test_model/test_model_solver/test_model_solver_my_model.hh
M		test/test_model/test_non_local_toolbox/test_build_neighborhood_parallel.cc
M		test/test_model/test_non_local_toolbox/test_pair_computation.cc
M		test/test_model/test_solid_mechanics_model/test_cohesive/CMakeLists.txt
A		test/test_model/test_solid_mechanics_model/test_cohesive/material_0_finite_def.dat
M		test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive.cc
M		test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh
M		test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_insertion/test_cohesive_insertion_along_physical_surfaces.cc
M		test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_fixture.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_material_mazars.cc
A	(dir)	test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/
A		test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/CMakeLists.txt
A		test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/material_viscoelastic_maxwell.dat
A		test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/test_material_viscoelastic_maxwell.geo
A		test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/test_material_viscoelastic_maxwell_relaxation.cc
M		test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc
M		test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_reassign_material.cc
M		test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_dynamics.cc
M		test/test_solver/test_sparse_matrix_product.verified