Diffusion akantu e317d05f3111

akantu-private
e317d05f3111
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Authored by gallyamov on Nov 20 2018, 10:33.

Description

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

Details

Committed

gallyamov

Nov 20 2018, 10:33

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

rAKA78e9ecbabded: Minor changes in Jenkinsfile
rAKAaa499870207c: Merge branch 'features/viscoelasticity_maxwell'

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gallyamov committed rAKAe317d05f3111: Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private (authored by gallyamov).Nov 20 2018, 10:33

Merged Changes

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

Commit	Author	Details	Committed
78e9ecbabded	richart	Minor changes in Jenkinsfile	Nov 9 2018
385484478fa9	richart	Bug fix in python interface	Nov 6 2018
0988ff27c1d9	richart	Bug fix in the node data reader and synchronizer	Nov 6 2018
195c4be2fa7a	richart	try more advances debug flags	Nov 6 2018
7e2cd66c9507	richart	solved some swig issues	Nov 6 2018
d02061c6e2d6	richart	modernizing material macro	Nov 6 2018
6b6d5ac0192c	richart	Abaqus reader broken with Boost 1.67 (wont fix)	Nov 6 2018
1422395dd95b	richart	Missing file	Nov 5 2018
36fec1bff140	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Nov 2 2018
052424c24651	richart	making firstType lastType deprecated + bug fix in internalfields	Nov 2 2018
41a834663730	richart	bug fixes in 1d	Oct 31 2018
ed8a2ee04528	richart	modernizing some code	Oct 31 2018
04f6203383ea	richart	Bug fix in array resize	Oct 31 2018
1867ffea9c11	Luke	Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private	Oct 30 2018
adda5cb009fb	richart	Protecting path	Oct 18 2018
d356df49d348	richart	Jenkinsfile debugging	Oct 18 2018
d93d78692b7e	richart	Adding parameters to the build	Oct 17 2018
86cbcad5ff57	richart	Updated ntn contact to make it compile	Oct 17 2018
a99d58033c6b	Luke	Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private	Oct 17 2018
c49e61deed71	richart	Cohesive element corretion due to pbc branch merge	Oct 17 2018
3275705df6f6	Luke	revised PYTHON and LDPATH	Oct 17 2018
33eaf7cb000e	richart	Adding computeBarycenters to the python interface	Oct 16 2018
091d83ec5d79	richart	Correcting the bug of insertion finite_deformation and dump (again)	Oct 12 2018
0dc284119849	richart	Merge branch 'features/pbc'	Oct 10 2018
e129d486a1a0	richart	correcting mesh_io_msh nodedata	Oct 9 2018
17fde1346772	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Sep 25 2018
7b78eda9f30a	richart	Adding the mesh nodal data to the python interface	Sep 25 2018
46063ac227c6	frerot	default values for InternalField members	Sep 13 2018
6068be0bf5d8	frerot	modernizing InternalField	Sep 13 2018
023a4b630b0e	richart	Adding transform adaptor and nodedata in mesh data	Sep 12 2018
8ec3c922e7ee	richart	make periodic debugging	Sep 5 2018
a835a3214c48	richart	Making compilation work with gcc >= 8	Sep 5 2018
7dc81cfc7ec7	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Aug 29 2018
71beddeb9549	richart	Adding some functions in the python interface	Aug 29 2018
a7b87ab7f810	brink	Expanded the "Compiling your simulation" part of the manual.	Aug 15 2018
cc267756e92b	richart	Sourcing the environment file	Aug 15 2018
00b736ea3a6f	richart	modified fe_engine python interface	Aug 14 2018
ce27c97d465b	richart	Modified Jenkinsfile to report states	Aug 14 2018
f4dd6b579644	richart	refactoring fieldTimesShapes in computeNtb	Aug 10 2018
ed8607e8f267	richart	Few compilation fixes for gcc>=8	Aug 10 2018
327aad04af0a	richart	commit to push before vacations: this version is currently broken	Jul 19 2018
d35974ef9782	richart	Implementing missing function fir makePeriodic	Jun 19 2018
ccded5305f53	richart	Add google-benchmark for benchmarking	Jun 19 2018
d06c0a0487e5	richart/gallyamov	Rewrote the equation numbers to work properly with pbc	Jun 19 2018
8b3453beaf64	• arichart	minor improvements	Jun 17 2018
f2c01b8dc4fc	• arichart	make it compile in sequential too	Jun 17 2018
9d1800564f97	• arichart	Fix for nodeflag change	Jun 17 2018
2ec7f7581cc7	• arichart	Bug fix if periodic mesh have more than one dof per node	Jun 17 2018
40c729a672b7	richart	Initialize the is_periodic variable	Jun 15 2018
d4f0b6028779	richart	Pre-working stage for PBC:	Jun 15 2018

Changes (212)
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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
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		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
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
M		test/test_common/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/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