Diffusion akantu e1cf091ecc43

Merge branch 'master' into features/viscoel-damage
e1cf091ecc43
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Authored by gallyamov on Jan 7 2019, 13:47.

Description

Merge branch 'master' into features/viscoel-damage

Details

Committed

gallyamov

Jan 7 2019, 13:47

Pushed

gitlab-richart

Jan 18 2021, 21:10

Parents

rAKA7ca95b0c942c: Descriptions to damage viscoelastic material
rAKA0df47c2f3757: Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private

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gallyamov committed rAKAe1cf091ecc43: Merge branch 'master' into features/viscoel-damage (authored by gallyamov).Jan 7 2019, 13:47

Merged Changes

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

Commit	Author	Details	Committed
0df47c2f3757	gallyamov	Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private	Jan 7 2019
3e66e9dd3a1c	richart	Merge branch 'master' of c4science:/diffusion/AKAPRIV/akantu-private	Dec 24 2018
f3474ad9c8d7	richart	Merge branch 'master' of c4science.ch:/diffusion/AKAPRIV/akantu-private	Dec 24 2018
f80af9943df5	brink	Added tests for extrinsic cohesive elements with finite def elastic material.	Dec 20 2018
f5f630999cd5	gallyamov	Correction in the energies output	Dec 19 2018
e9aecedaa1d5	richart	Merge branch 'master' of c4science:/diffusion/AKAPRIV/akantu-private	Dec 12 2018
0927545f8e25	gallyamov	Update of the example	Nov 22 2018
089d572bcbb4	gallyamov	Bug fix in material viscoelastic	Nov 22 2018
e317d05f3111	gallyamov	Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private	Nov 20 2018
aa499870207c	gallyamov	Merge branch 'features/viscoelasticity_maxwell'	Nov 20 2018
7b2e468f963a	richart	Bug fix in parallel cohesive insertion:	Nov 9 2018
74848b91ed80	richart	increasing compatibility of iterators with stl iterators	Nov 9 2018
e29cbbbae46b	richart	Adding -ggdb3 as compilation flags	Nov 9 2018
71ddf3ad432b	richart	Adding scan and exclusiveScan in the communicator	Nov 9 2018
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

Changes (179)
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Very Large Commit

This commit is very large. Load each file individually.

				Path
	M			.arclint
	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			examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc
	M			examples/python/plate-hole/plate.py
	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
	M			packages/pythonlibs.cmake
	M			python/setup.py.in
	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
	M			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_iterators.hh
	M			src/common/aka_math.cc
	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_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.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
	M			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_inline_impl.cc
	M			src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
	M			src/mesh_utils/mesh_utils.cc
	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_inline_impl.cc
	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_viscoelastic_maxwell.cc
	M			src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.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/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.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_dummy_inline_impl.cc
	M			src/synchronizer/communicator_mpi_inline_impl.cc
	M			src/synchronizer/element_info_per_processor_tmpl.hh
	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
	M			src/synchronizer/periodic_node_synchronizer.cc
	M			src/synchronizer/slave_element_info_per_processor.cc
	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
	M			test/test_mesh/CMakeLists.txt
	M			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/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_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