Diffusion akantu b40b27462bba

akantu-private
b40b27462bba
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Authored by richart on Dec 12 2018, 15:41.

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Merge branch 'master' of c4science:/diffusion/AKAPRIV/akantu-private

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Committed

richart

Dec 12 2018, 15:41

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gitlab-richart

Jul 29 2021, 09:01

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rAKA5ab8d97f4c58: Merge branch 'master' of c4science:/diffusion/AKAPRIV/akantu-private
rAKAcdbf86d1c70d: Bug fix in material viscoelastic

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richart committed rAKAb40b27462bba: Merge branch 'master' of c4science:/diffusion/AKAPRIV/akantu-private (authored by richart).Dec 12 2018, 15:41

Merged Changes

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

Commit	Author	Details	Committed
cdbf86d1c70d	gallyamov	Bug fix in material viscoelastic	Nov 22 2018
ea7ead4751dd	gallyamov	Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private	Nov 20 2018
b4a66fd0988a	gallyamov	Merge branch 'features/viscoelasticity_maxwell'	Nov 20 2018
e1eeccd28964	gallyamov	Adding test and example on viscoelastic material	Nov 20 2018
e4e18007b260	gallyamov	Added energy computing functions to viscoelastic material	Nov 19 2018
59e098bb385c	richart	Minor changes in Jenkinsfile	Nov 9 2018
8694c737de99	richart	Bug fix in python interface	Nov 6 2018
9265c2128c1c	richart	Bug fix in the node data reader and synchronizer	Nov 6 2018
d949aa434059	richart	try more advances debug flags	Nov 6 2018
cff39378c9ad	richart	solved some swig issues	Nov 6 2018
519dde5353b5	richart	modernizing material macro	Nov 6 2018
81659b92f2fc	richart	Abaqus reader broken with Boost 1.67 (wont fix)	Nov 6 2018
6601b948c133	richart	Missing file	Nov 5 2018
0060d3f1a2a4	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Nov 2 2018
7afd32b484b1	richart	making firstType lastType deprecated + bug fix in internalfields	Nov 2 2018
d4a218d3966d	richart	bug fixes in 1d	Oct 31 2018
3c94f82ece2c	richart	modernizing some code	Oct 31 2018
0a98d22843aa	richart	Bug fix in array resize	Oct 31 2018
b6f3d2010716	Luke	Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private	Oct 30 2018
b9085cfb5cf2	richart	Protecting path	Oct 18 2018
efbcdc143d5e	richart	Jenkinsfile debugging	Oct 18 2018
c300675df99f	richart	Adding parameters to the build	Oct 17 2018
f37c3f49eee3	richart	Updated ntn contact to make it compile	Oct 17 2018
14a5c9406f1d	Luke	Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private	Oct 17 2018
f738ec593c37	richart	Cohesive element corretion due to pbc branch merge	Oct 17 2018
e27fd77ac2ad	Luke	revised PYTHON and LDPATH	Oct 17 2018
d7b94b74fcf8	richart	Adding computeBarycenters to the python interface	Oct 16 2018
19368095d709	richart	Correcting the bug of insertion finite_deformation and dump (again)	Oct 12 2018
057a7338660e	richart	Merge branch 'features/pbc'	Oct 10 2018
b2c7ec465ed6	richart	correcting mesh_io_msh nodedata	Oct 9 2018
33710fe43077	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Sep 25 2018
caa62dff9737	richart	Adding the mesh nodal data to the python interface	Sep 25 2018
5e18b3fb8fb4	frerot	default values for InternalField members	Sep 13 2018
9039ed82b00c	frerot	modernizing InternalField	Sep 13 2018
ee46ef34e455	richart	Adding transform adaptor and nodedata in mesh data	Sep 12 2018
b9556bb7142a	gallyamov	Bug fixed. Both relaxation and creep tests work now.	Sep 6 2018
dbae85499748	richart	make periodic debugging	Sep 5 2018
b2e3aaf7f89b	richart	Making compilation work with gcc >= 8	Sep 5 2018
1b4456d7ae8a	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Aug 29 2018
0652e679fb0b	richart	Adding some functions in the python interface	Aug 29 2018
4accfdcef9e3	gallyamov	Expanding single Maxwell element to Maxwell chain	Aug 29 2018
cc25cf27fe4e	brink	Expanded the "Compiling your simulation" part of the manual.	Aug 15 2018
f377553b72f1	richart	Sourcing the environment file	Aug 15 2018
40cfe4f7da48	richart	modified fe_engine python interface	Aug 14 2018
f5cd671b0d2d	richart	Modified Jenkinsfile to report states	Aug 14 2018
ad8d20ef3a99	richart	refactoring fieldTimesShapes in computeNtb	Aug 10 2018
d70d5d512379	richart	Few compilation fixes for gcc>=8	Aug 10 2018
df0bceaf33e6	richart	commit to push before vacations: this version is currently broken	Jul 19 2018
97c250077a6f	richart	Implementing missing function fir makePeriodic	Jun 19 2018
970b5eee332a	richart	Add google-benchmark for benchmarking	Jun 19 2018

Changes (227)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
M		CMakeLists.txt
M		Jenkinsfile
M		cmake/AkantuExtraCompilationProfiles.cmake
M		cmake/akantu_environement.csh.in
M		cmake/akantu_environement.sh.in
M		doc/manual/manual-gettingstarted.tex
M		examples/explicit/explicit_dynamic.cc
P		examples/new_material/CMakeLists.txt Copied to examples/new_material/viscoelastic_maxwell/CMakeLists.txt
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		extra_packages/igfem/src/integrator_gauss_igfem_inline_impl.cc
M		extra_packages/igfem/src/material_igfem/material_igfem_elastic.cc
M		extra_packages/igfem/src/mesh_igfem_spherical_growing_gel_tmpl.hh
M		extra_packages/igfem/test/test_fe_engine/igfem_mesh_generation.cc
M		extra_packages/traction-at-split-node-contact/src/boundary_conditions/force_based_dirichlet.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb_tmpl.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive_tmpl.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing_tmpl.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_tmpl.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.hh
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_base_contact.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.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/ntn_contact.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction_tmpl.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.cc
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh
M		extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction_tmpl.hh
M		packages/core.cmake
A		packages/google-benchmark.cmake
M		packages/pythonlibs.cmake
M		packages/solid_mechanics.cmake
M		python/swig/aka_array.i
M		python/swig/aka_common.i
M		python/swig/akantu.i
A		python/swig/fe_engine.i
M		python/swig/mesh.i
M		python/swig/model.i
M		python/swig/solid_mechanics_model.i
M		python/swig/solid_mechanics_model_cohesive.i
M		src/common/aka_array.cc
M		src/common/aka_array.hh
M		src/common/aka_array_tmpl.hh
A		src/common/aka_bbox.hh
M		src/common/aka_common.hh
M		src/common/aka_common_inline_impl.cc
M		src/common/aka_csr.hh
V		src/{common/aka_element_classes_info_inline_impl.cc ← io/mesh_io/mesh_io_abaqus.hh}
A		src/common/aka_enum_macros.hh
M		src/common/aka_error.cc
M		src/common/aka_iterators.hh
M		src/common/aka_math.cc
M		src/common/aka_math_tmpl.hh
M		src/common/aka_random_generator.hh
M		src/common/aka_static_memory.cc
M		src/common/aka_types.hh
M		src/fe_engine/fe_engine.hh
M		src/fe_engine/fe_engine_template.hh
M		src/fe_engine/fe_engine_template_tmpl.hh
M		src/fe_engine/fe_engine_template_tmpl_field.hh
M		src/fe_engine/shape_cohesive.hh
M		src/fe_engine/shape_functions.cc
M		src/fe_engine/shape_lagrange.hh
M		src/fe_engine/shape_lagrange_inline_impl.cc
M		src/fe_engine/shape_structural.hh
M		src/io/dumper/dumper_compute.hh
M		src/io/dumper/dumper_element_partition.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/dumper/dumper_iohelper.cc
M		src/io/dumper/dumper_text.cc
M		src/io/mesh_io.cc
M		src/io/mesh_io.hh
D		src/io/mesh_io/mesh_io_abaqus.cc
V		src/{io/mesh_io/mesh_io_abaqus.hh → common/aka_element_classes_info_inline_impl.cc}
M		src/io/mesh_io/mesh_io_diana.cc
M		src/io/mesh_io/mesh_io_msh.cc
M		src/io/parser/parameter_registry.hh
M		src/io/parser/parameter_registry_tmpl.hh
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_accessor.hh
M		src/mesh/mesh_data.cc
M		src/mesh/mesh_data.hh
M		src/mesh/mesh_data_tmpl.hh
M		src/mesh/mesh_inline_impl.cc
A		src/mesh/mesh_periodic.cc
M		src/mesh_utils/cohesive_element_inserter.cc
M		src/mesh_utils/cohesive_element_inserter.hh
M		src/mesh_utils/global_ids_updater.cc
M		src/mesh_utils/global_ids_updater.hh
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/mesh_utils/mesh_utils_distribution.cc
M		src/model/boundary_condition_functor.hh
M		src/model/boundary_condition_tmpl.hh
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/dof_manager_default_inline_impl.cc
M		src/model/model.cc
M		src/model/model.hh
M		src/model/non_linear_solver_lumped.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_plastic/material_linear_isotropic_hardening.cc
M		src/model/solid_mechanics/materials/material_python/material_python.cc
M		src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
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_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/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
M		src/model/solid_mechanics/solid_mechanics_model_mass.cc
M		src/model/time_step_solvers/time_step_solver_default.cc
M		src/solver/sparse_matrix_aij.cc
M		src/synchronizer/communication_buffer.hh
M		src/synchronizer/communication_buffer_inline_impl.cc
M		src/synchronizer/communication_tag.hh
M		src/synchronizer/communicator.cc
M		src/synchronizer/communicator.hh
M		src/synchronizer/communicator_mpi_inline_impl.cc
M		src/synchronizer/data_accessor.hh
M		src/synchronizer/dof_synchronizer.hh
M		src/synchronizer/dof_synchronizer_inline_impl.cc
M		src/synchronizer/element_info_per_processor.cc
M		src/synchronizer/element_info_per_processor.hh
M		src/synchronizer/element_info_per_processor_tmpl.hh
M		src/synchronizer/element_synchronizer.cc
M		src/synchronizer/element_synchronizer.hh
M		src/synchronizer/grid_synchronizer.cc
M		src/synchronizer/master_element_info_per_processor.cc
M		src/synchronizer/node_info_per_processor.cc
M		src/synchronizer/node_info_per_processor.hh
M		src/synchronizer/node_synchronizer.cc
M		src/synchronizer/node_synchronizer.hh
A		src/synchronizer/periodic_node_synchronizer.cc
A		src/synchronizer/periodic_node_synchronizer.hh
M		src/synchronizer/synchronizer_impl.hh
M		src/synchronizer/synchronizer_impl_tmpl.hh
M		test/CMakeLists.txt
P		test/test_common/CMakeLists.txt Copied to test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/CMakeLists.txt
D		test/test_common/test_arange_iterator.cc
M		test/test_common/test_array.cc
M		test/test_common/test_grid.cc
V		test/test_common/{test_iterators.cc ← test_zip_iterator.cc}
V		test/test_common/{test_zip_iterator.cc → test_iterators.cc}
M		test/test_fe_engine/test_facet_element_mapping.cc
M		test/test_fe_engine/test_fe_engine_precomputation_bernoulli_3.cc
M		test/test_fe_engine/test_fe_engine_precomputation_structural.cc
A	(dir)	test/test_mesh/
A		test/test_mesh/CMakeLists.txt
A		test/test_mesh/cube_periodic.geo
A		test/test_mesh/square_periodic.geo
A		test/test_mesh/test_mesh_periodic.cc
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_model_solver.cc
M		test/test_model/test_model_solver/test_model_solver_dynamic.cc
M		test/test_model/test_model_solver/test_model_solver_my_model.hh
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_embedded_interface/test_embedded_element_matrix.cc
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_materials/CMakeLists.txt
A	(dir)	test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/
P		test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/CMakeLists.txt Copied from test/test_common/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_3.cc
M		test/test_solver/test_sparse_solver_mumps.cc
M		test/test_synchronizer/test_data_distribution.cc
M		test/test_synchronizer/test_synchronizers_fixture.hh
A		third-party/cmake/gbenchmark.cmake
A		third-party/gbenchmark.cmake.in
M		third-party/iohelper/src/iohelper_common.hh
M		third-party/iohelper/src/paraview_helper.tcc