Diffusion akantu 99d9c8ff4417

Merge branch 'features/changes-to-address-joss-review' into 'master'
99d9c8ff4417
Actions

Authored by richart on Oct 3 2023, 09:19.

Description

Merge branch 'features/changes-to-address-joss-review' into 'master'

Modifications to address JOSS review

See merge request akantu/akantu!97

Details

Committed

richart

Oct 3 2023, 09:19

Pushed

gitlab-richart

Oct 3 2023, 09:19

Parents

rAKAc93b3987d659: Merge branch 'features/changes-to-address-joss-review' of gitlab.com…
rAKA7ad57cd90f65: Merge branch 'features/make_multiple_materials_independant_solid_mechanics'…

Branches

Unknown

Tags

Unknown

Event Timeline

richart committed rAKA99d9c8ff4417: Merge branch 'features/changes-to-address-joss-review' into 'master' (authored by richart).Oct 3 2023, 09:19

Merged Changes

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

Commit	Author	Details	Committed
c93b3987d659	richart	Merge branch 'features/changes-to-address-joss-review' of gitlab.com…	Sep 29 2023
982b6210794e	richart	Adding a tutorial page	Sep 29 2023
1a8877f066dd	rferry	wrong figure in diffusion example	Sep 29 2023
6f699ae9f3be	rferry	diffusion examples	Sep 29 2023
f45a61a0abfe	richart	More dumper aliases	Sep 28 2023
848d37fab79a	richart	Merge branch 'features/changes-to-address-joss-review' of gitlab.com…	Sep 28 2023
45efee82a479	richart	Bug fixes everywhere	Sep 28 2023
96c4bcb7ed57	richart	Merge branch 'features/changes-to-address-joss-review' of gitlab.com…	Sep 28 2023
97c3bc3dfc05	richart	Addapting documentation to new namings	Sep 28 2023
8524c2299432	richart	Adding aliasses names for dumpers	Sep 28 2023
7f1ce2cdb794	richart	Addapting examples to the new material synthax	Sep 28 2023
34e4ba79a439	saduruss	fix conflict	Sep 28 2023
58cff193772f	saduruss	phase-field c++ example	Sep 28 2023
3be830a7a67e	rferry	Merge branch 'features/changes-to-address-joss-review' of gitlab.com…	Sep 28 2023
92294d60b0f3	rferry	parallel example	Sep 28 2023
bef9a046a233	richart	Correcting nammings and compilation error	Sep 28 2023
d6dc8dd6c426	richart	Merge remote-tracking branch 'origin/master' into features/changes-to-address…	Sep 27 2023
32090c8a7659	saduruss	clean phasefield dynamic example	Sep 27 2023
50f12b059cf5	saduruss	Merge branch 'features/changes-to-address-joss-review' of gitlab.com…	Sep 27 2023
14568f3c5e4f	saduruss	finished python examples for phasefield	Sep 27 2023
e8b6dcdb8f43	rferry	adjust figure size	Sep 27 2023
c97d2639dee6	rferry	resolve merge conflict with python examples readme: add everything	Sep 27 2023
0bd9759faea2	rferry	python contact examples	Sep 27 2023
4b03b5a2943a	saduruss	python example for phasefield	Sep 26 2023
8f5d1545d5db	rferry	adjust figure sizes	Sep 26 2023
478560935931	rferry	python solid mechanics + cohesive examples	Sep 26 2023
bbaff2e65896	richart	Moving more examples	Sep 26 2023
1e205a219ba3	rferry	wrong path for figures again	Sep 25 2023
09a515b7e6da	rferry	wrong path for figures	Sep 25 2023
d7e73ab21a43	rferry	python examples for solid mechanics	Sep 25 2023
3cc5334c6950	rferry	add solid mechanics cohesive model examples	Sep 25 2023
ab0691515e7c	rferry	Resolve merge conflict + resize figures	Sep 25 2023
1a3887af4088	rferry	add examples from solid mechanics cohesive model	Sep 25 2023
dd278f980d1e	richart	Trying to get the theme back	Sep 23 2023
b88a389507a6	richart	Theme is not the proper one on rtd	Sep 23 2023
fb64d83ba9f9	richart	Missing images or missplaced images	Sep 23 2023
fb90ccb3d292	richart	Missing includes	Sep 23 2023
78d0eab4847b	richart	Typo correction	Sep 23 2023
15a4365f4d86	richart	Moving the file copy from cmake to python	Sep 23 2023
5773fb19d836	richart	Merge branch 'features/changes-to-address-joss-review' of gitlab.com…	Sep 22 2023
06be0a86ecff	richart	Setting the architecture of the examples documentation	Sep 22 2023
24194d38e679	rferry	add two missing figures	Sep 22 2023
a45d79b59e60	rferry	continue to add fig and description to solid mechanics model examples	Sep 22 2023
e12c562d5a63	rferry	forgot to change folder for one figure	Sep 21 2023
18b6920a7d3e	rferry	correct wrong folder for examples figures	Sep 21 2023
e34671aa39b4	rferry	figures and description of static and BC examples	Sep 21 2023
0d4fa26ab263	rferry	Typos corrections mostly	Sep 20 2023
d776dc4b1879	richart	sorting lines	Sep 19 2023
a09fd962921b	richart	Correcting CI for the tests that where moved	Sep 19 2023
65c28d09fd68	Nicolas Richart	Switching back to requirements.txt and removing apt_packages	Sep 19 2023

Changes (531)
Show All Changes

Very Large Commit

This commit is very large. Load each file individually.

		Path
M		.gitignore
D		.gitlab-ci.d
V		{.gitlab-ci.d → .gitlab/ci.d}/code-quality.yaml
V		{.gitlab-ci.d → .gitlab/ci.d}/images.yaml
V		{.gitlab-ci.d → .gitlab/ci.d}/templates.yaml
M		.gitlab-ci.yml
A	(dir)	.gitlab/ci.d/
V		{.gitlab/ci.d ← .gitlab-ci.d}/code-quality.yaml
V		{.gitlab/ci.d ← .gitlab-ci.d}/images.yaml
V		{.gitlab/ci.d ← .gitlab-ci.d}/templates.yaml
M		.readthedocs.yaml
P		CHANGELOG.md Copied to doc/dev-doc/changelog.md
M		CMakeLists.txt
M		cmake/Modules/FindMumps.cmake
M		doc/dev-doc/CMakeLists.txt
M		doc/dev-doc/akantu.dox.j2
P		doc/dev-doc/changelog.md Copied from CHANGELOG.md
D		doc/dev-doc/changelog.rst
M		doc/dev-doc/conf.py
A		doc/dev-doc/examples.rst
M		doc/dev-doc/index.rst
P		doc/dev-doc/manual/basic_types.rst Copied from doc/dev-doc/manual/getting_started.rst
D		doc/dev-doc/manual/conf.py
M		doc/dev-doc/manual/constitutive-laws.rst
M		doc/dev-doc/manual/contactmechanicsmodel.rst
V		doc/dev-doc/manual/{diffusion.rst ← heattransfermodel.rst}
A		doc/dev-doc/manual/extra.rst
D		doc/dev-doc/manual/fe_engine.rst
A	(dir)	doc/dev-doc/manual/figures/examples/
A		doc/dev-doc/manual/figures/examples/cohesive_extrinsic.gif
A		doc/dev-doc/manual/figures/examples/cohesive_extrinsic_ig_tg.gif
A		doc/dev-doc/manual/figures/examples/cohesive_intrinsic.png
P		doc/dev-doc/manual/getting_started.rst Copied to doc/dev-doc/manual/basic_types.rst
V		doc/dev-doc/manual/{heattransfermodel.rst → diffusion.rst}
A		doc/dev-doc/manual/models.rst
A		doc/dev-doc/manual/models_commons.rst
M		doc/dev-doc/manual/new-constitutive-laws.rst
M		doc/dev-doc/manual/phasefieldmodel.rst
M		doc/dev-doc/manual/solidmechanicsmodel.rst
M		doc/dev-doc/manual/structuralmechanicsmodel.rst
M		doc/dev-doc/requirements.txt
A		doc/dev-doc/tutorials.rst
P		examples/CMakeLists.txt Copied from examples/io/parser/CMakeLists.txt
M		examples/README.rst
D		examples/boundary_conditions
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/CMakeLists.txt
V	(dir)	examples/{boundary_conditions/predefined_bc/ → c++/solid_mechanics_model/boundary_conditions/predefined_bc}
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/predefined_bc/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/predefined_bc/material.dat
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/predefined_bc/predefined_bc.cc
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/predefined_bc/square.geo
V	(dir)	examples/{boundary_conditions/python_user_defined_bc/ → c++/solid_mechanics_model/boundary_conditions/python_user_defined_bc}
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/python_user_defined_bc/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/python_user_defined_bc/boundary_condition.py
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/python_user_defined_bc/fine_mesh.geo
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/python_user_defined_bc/material.dat
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/python_user_defined_bc/python_user_defined_bc.cc
V	(dir)	examples/{boundary_conditions/user_defined_bc/ → c++/solid_mechanics_model/boundary_conditions/user_defined_bc}
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/user_defined_bc/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/user_defined_bc/fine_mesh.geo
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/user_defined_bc/material.dat
V		examples/{ → c++/solid_mechanics_model}/boundary_conditions/user_defined_bc/user_defined_bc.cc
A	(dir)	examples/c++/
A		examples/c++/CMakeLists.txt
A		examples/c++/README.rst
A	(dir)	examples/c++/contact_mechanics_model/
V		examples/{c++/contact_mechanics_model ← contact_mechanics}/CMakeLists.txt
A		examples/c++/contact_mechanics_model/README.rst
V		examples/{c++/contact_mechanics_model ← contact_mechanics}/cohesive-contact.geo
V		examples/{c++/contact_mechanics_model ← contact_mechanics}/cohesive_contact_explicit_dynamic.cc
V		examples/{c++/contact_mechanics_model ← contact_mechanics}/contact_explicit_dynamic.cc
V		examples/{c++/contact_mechanics_model ← contact_mechanics}/contact_explicit_static.cc
V		examples/{c++/contact_mechanics_model ← contact_mechanics}/hertz.geo
A	(dir)	examples/c++/contact_mechanics_model/images/
A		examples/c++/contact_mechanics_model/images/hertz.png
A		examples/c++/contact_mechanics_model/images/hertz.svg
V		examples/{c++/contact_mechanics_model ← contact_mechanics}/material-cohesive.dat
V		examples/{c++/contact_mechanics_model ← contact_mechanics}/material.dat
A	(dir)	examples/c++/diffusion_model/
V		examples/{c++/diffusion_model ← heat_transfer}/CMakeLists.txt
A		examples/c++/diffusion_model/README.rst
V		examples/{c++/diffusion_model ← heat_transfer}/cube.geo
V		examples/{c++/diffusion_model ← heat_transfer}/cube_tet.geo
V		examples/{c++/diffusion_model/heat_diffusion_dynamics_2d.cc ← heat_transfer/heat_transfer_dynamics_2d.cc}
V		examples/{c++/diffusion_model/heat_diffusion_dynamics_3d.cc ← heat_transfer/heat_transfer_dynamics_3d.cc}
V		examples/{c++/diffusion_model/heat_diffusion_static_2d.cc ← heat_transfer/heat_transfer_static_2d.cc}
A	(dir)	examples/c++/diffusion_model/images/
A		examples/c++/diffusion_model/images/diffusion_3d.gif
A		examples/c++/diffusion_model/images/diffusion_static.png
A		examples/c++/diffusion_model/images/hot-point-1.png
A		examples/c++/diffusion_model/images/hot-point-2.png
A		examples/c++/diffusion_model/material.dat
V		examples/{c++/diffusion_model ← heat_transfer}/square.geo
V	(dir)	examples/{c++/embedded_model/ ← embedded}
V		examples/{c++/embedded_model ← embedded}/CMakeLists.txt
V		examples/{c++/embedded_model ← embedded}/concrete.geo
V		examples/{c++/embedded_model ← embedded}/embedded.cc
V		examples/{c++/embedded_model ← embedded}/material.dat
V		examples/{c++/embedded_model ← embedded}/reinforcement.geo
A	(dir)	examples/c++/phase_field_model/
V		examples/{c++/phase_field_model ← phase_field}/CMakeLists.txt
A		examples/c++/phase_field_model/README.rst
A	(dir)	examples/c++/phase_field_model/images/
A		examples/c++/phase_field_model/images/phase_field_clusters.png
V		examples/{c++/phase_field_model ← phase_field}/material_notch.dat
V		examples/{c++/phase_field_model ← phase_field}/phase_field_notch.cc
V		examples/{c++/phase_field_model ← phase_field}/phase_field_parallel.cc
V		examples/{c++/phase_field_model ← phase_field}/square_notch.geo
A	(dir)	examples/c++/solid_mechanics_cohesive_model/
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/CMakeLists.txt
A		examples/c++/solid_mechanics_cohesive_model/README.rst
A	(dir)	examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic/
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_extrinsic/CMakeLists.txt
A		examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic/README.rst
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_extrinsic/cohesive_extrinsic.cc
A	(dir)	examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic/images/
A		examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic/images/cohesive_extrinsic.gif
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_extrinsic/material.dat
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_extrinsic/triangle.geo
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_extrinsic/triangle.msh
A	(dir)	examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic_ig_tg/
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_extrinsic_ig_tg/CMakeLists.txt
A		examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic_ig_tg/README.rst
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc
A	(dir)	examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic_ig_tg/images/
A		examples/c++/solid_mechanics_cohesive_model/cohesive_extrinsic_ig_tg/images/cohesive_extrinsic_ig_tg.gif
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_extrinsic_ig_tg/material.dat
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_extrinsic_ig_tg/triangle.geo
A	(dir)	examples/c++/solid_mechanics_cohesive_model/cohesive_intrinsic/
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_intrinsic/CMakeLists.txt
A		examples/c++/solid_mechanics_cohesive_model/cohesive_intrinsic/README.rst
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_intrinsic/cohesive_intrinsic.cc
A	(dir)	examples/c++/solid_mechanics_cohesive_model/cohesive_intrinsic/images/
A		examples/c++/solid_mechanics_cohesive_model/cohesive_intrinsic/images/cohesive_intrinsic.png
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_intrinsic/material.dat
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_intrinsic/triangle.geo
V		examples/{c++/solid_mechanics_cohesive_model ← cohesive_element}/cohesive_intrinsic/triangle.msh
A	(dir)	examples/c++/solid_mechanics_model/
A		examples/c++/solid_mechanics_model/CMakeLists.txt
A		examples/c++/solid_mechanics_model/README.rst
A	(dir)	examples/c++/solid_mechanics_model/boundary_conditions/
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/CMakeLists.txt
A		examples/c++/solid_mechanics_model/boundary_conditions/README.rst
A	(dir)	examples/c++/solid_mechanics_model/boundary_conditions/images/
A		examples/c++/solid_mechanics_model/boundary_conditions/images/predefined_bc.svg
A		examples/c++/solid_mechanics_model/boundary_conditions/images/user_defined_bc_displ_mag.png
V	(dir)	examples/{c++/solid_mechanics_model/boundary_conditions/predefined_bc/ ← boundary_conditions/predefined_bc}
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/predefined_bc/CMakeLists.txt
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/predefined_bc/material.dat
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/predefined_bc/predefined_bc.cc
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/predefined_bc/square.geo
V	(dir)	examples/{c++/solid_mechanics_model/boundary_conditions/python_user_defined_bc/ ← boundary_conditions/python_user_defined_bc}
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/python_user_defined_bc/CMakeLists.txt
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/python_user_defined_bc/boundary_condition.py
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/python_user_defined_bc/fine_mesh.geo
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/python_user_defined_bc/material.dat
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/python_user_defined_bc/python_user_defined_bc.cc
V	(dir)	examples/{c++/solid_mechanics_model/boundary_conditions/user_defined_bc/ ← boundary_conditions/user_defined_bc}
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/user_defined_bc/CMakeLists.txt
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/user_defined_bc/fine_mesh.geo
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/user_defined_bc/material.dat
V		examples/{c++/solid_mechanics_model ← }/boundary_conditions/user_defined_bc/user_defined_bc.cc
A	(dir)	examples/c++/solid_mechanics_model/explicit/
V		examples/{c++/solid_mechanics_model ← }/explicit/CMakeLists.txt
A		examples/c++/solid_mechanics_model/explicit/README.rst
V		examples/{c++/solid_mechanics_model ← }/explicit/bar.geo
V		examples/{c++/solid_mechanics_model ← }/explicit/explicit_dynamic.cc
A	(dir)	examples/c++/solid_mechanics_model/explicit/images/
A		examples/c++/solid_mechanics_model/explicit/images/bar_pulse.gif
A		examples/c++/solid_mechanics_model/explicit/images/explicit.svg
A		examples/c++/solid_mechanics_model/explicit/images/sphx_glr_explicit.png
V		examples/{c++/solid_mechanics_model ← }/explicit/material.dat
A	(dir)	examples/c++/solid_mechanics_model/implicit/
V		examples/{c++/solid_mechanics_model ← }/implicit/CMakeLists.txt
A		examples/c++/solid_mechanics_model/implicit/README.rst
V		examples/{c++/solid_mechanics_model ← }/implicit/beam.geo
A	(dir)	examples/c++/solid_mechanics_model/implicit/images/
A		examples/c++/solid_mechanics_model/implicit/images/dynamic_analysis.png
A		examples/c++/solid_mechanics_model/implicit/images/implicit_dynamic.svg
V		examples/{c++/solid_mechanics_model ← }/implicit/implicit_dynamic.cc
V		examples/{c++/solid_mechanics_model ← }/implicit/material_dynamic.dat
A	(dir)	examples/c++/solid_mechanics_model/io/
V		examples/{c++/solid_mechanics_model ← }/io/CMakeLists.txt
A		examples/c++/solid_mechanics_model/io/README.rst
A	(dir)	examples/c++/solid_mechanics_model/io/dumper/
V		examples/{c++/solid_mechanics_model ← }/io/dumper/CMakeLists.txt
V		examples/{c++/solid_mechanics_model ← }/io/dumper/dumpable_interface.cc
V		examples/{c++/solid_mechanics_model ← }/io/dumper/dumper_low_level.cc
V		examples/{c++/solid_mechanics_model ← }/io/dumper/locomotive_tools.cc
V		examples/{c++/solid_mechanics_model ← }/io/dumper/locomotive_tools.hh
V		examples/{c++/solid_mechanics_model ← }/io/dumper/swiss_train.geo
A	(dir)	examples/c++/solid_mechanics_model/io/images/
A		examples/c++/solid_mechanics_model/io/images/train.gif
V	(dir)	examples/{c++/solid_mechanics_model/io/parser/ ← io/parser}
V		examples/{c++/solid_mechanics_model ← }/io/parser/CMakeLists.txt
V		examples/{c++/solid_mechanics_model ← }/io/parser/example_parser.cc
V		examples/{c++/solid_mechanics_model ← }/io/parser/input_file.dat
V		examples/{c++/solid_mechanics_model ← }/io/parser/swiss_cheese.geo
A	(dir)	examples/c++/solid_mechanics_model/new_material/
V		examples/{c++/solid_mechanics_model ← }/new_material/CMakeLists.txt
A		examples/c++/solid_mechanics_model/new_material/README.rst
V		examples/{c++/solid_mechanics_model ← }/new_material/barre_trou.geo
A	(dir)	examples/c++/solid_mechanics_model/new_material/images/
A		examples/c++/solid_mechanics_model/new_material/images/barre_trou.svg
V		examples/{c++/solid_mechanics_model ← }/new_material/local_material_damage.cc
V		examples/{c++/solid_mechanics_model ← }/new_material/local_material_damage.hh
V		examples/{c++/solid_mechanics_model ← }/new_material/local_material_damage_inline_impl.hh
V		examples/{c++/solid_mechanics_model ← }/new_material/material.dat
V		examples/{c++/solid_mechanics_model ← }/new_material/new_local_material.cc
V	(dir)	examples/{c++/solid_mechanics_model/new_material/viscoelastic_maxwell/ ← new_material/viscoelastic_maxwell}
V		examples/{c++/solid_mechanics_model ← }/new_material/viscoelastic_maxwell/CMakeLists.txt
V		examples/{c++/solid_mechanics_model ← }/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell.dat
V		examples/{c++/solid_mechanics_model ← }/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc
V		examples/{c++/solid_mechanics_model ← }/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_mesh.geo
A	(dir)	examples/c++/solid_mechanics_model/parallel/
V		examples/{c++/solid_mechanics_model ← }/parallel/CMakeLists.txt
A		examples/c++/solid_mechanics_model/parallel/README.rst
A	(dir)	examples/c++/solid_mechanics_model/parallel/images/
A		examples/c++/solid_mechanics_model/parallel/images/parallel.png
V		examples/{c++/solid_mechanics_model ← }/parallel/material.dat
V		examples/{c++/solid_mechanics_model ← }/parallel/parallel_2d.cc
V		examples/{c++/solid_mechanics_model ← }/parallel/square_2d.geo
A	(dir)	examples/c++/solid_mechanics_model/static/
V		examples/{c++/solid_mechanics_model ← }/static/CMakeLists.txt
A		examples/c++/solid_mechanics_model/static/README.rst
A	(dir)	examples/c++/solid_mechanics_model/static/images/
A		examples/c++/solid_mechanics_model/static/images/static_BC.svg
A		examples/c++/solid_mechanics_model/static/images/static_displ_mag.png
V		examples/{c++/solid_mechanics_model ← }/static/material.dat
V		examples/{c++/solid_mechanics_model ← }/static/square.geo
V		examples/{c++/solid_mechanics_model ← }/static/static.cc
V	(dir)	examples/{c++/structural_mechanics_model/ ← structural_mechanics}
V		examples/{c++/structural_mechanics_model ← structural_mechanics}/CMakeLists.txt
V		examples/{c++/structural_mechanics_model ← structural_mechanics}/bernoulli_beam_2_example.cc
D		examples/cohesive_element
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/CMakeLists.txt
D		examples/cohesive_element/cohesive_extrinsic
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_extrinsic/CMakeLists.txt
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_extrinsic/cohesive_extrinsic.cc
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_extrinsic/material.dat
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_extrinsic/triangle.geo
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_extrinsic/triangle.msh
D		examples/cohesive_element/cohesive_extrinsic_ig_tg
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_extrinsic_ig_tg/CMakeLists.txt
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_extrinsic_ig_tg/material.dat
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_extrinsic_ig_tg/triangle.geo
D		examples/cohesive_element/cohesive_intrinsic
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_intrinsic/CMakeLists.txt
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_intrinsic/cohesive_intrinsic.cc
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_intrinsic/material.dat
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_intrinsic/triangle.geo
V		examples/{cohesive_element → c++/solid_mechanics_cohesive_model}/cohesive_intrinsic/triangle.msh
D		examples/contact_mechanics
V		examples/{contact_mechanics → c++/contact_mechanics_model}/CMakeLists.txt
V		examples/{contact_mechanics → c++/contact_mechanics_model}/cohesive-contact.geo
V		examples/{contact_mechanics → c++/contact_mechanics_model}/cohesive_contact_explicit_dynamic.cc
V		examples/{contact_mechanics → c++/contact_mechanics_model}/contact_explicit_dynamic.cc
V		examples/{contact_mechanics → c++/contact_mechanics_model}/contact_explicit_static.cc
V		examples/{contact_mechanics → c++/contact_mechanics_model}/hertz.geo
V		examples/{contact_mechanics → c++/contact_mechanics_model}/material-cohesive.dat
V		examples/{contact_mechanics → c++/contact_mechanics_model}/material.dat
V	(dir)	examples/{embedded/ → c++/embedded_model}
V		examples/{embedded → c++/embedded_model}/CMakeLists.txt
V		examples/{embedded → c++/embedded_model}/concrete.geo
V		examples/{embedded → c++/embedded_model}/embedded.cc
V		examples/{embedded → c++/embedded_model}/material.dat
V		examples/{embedded → c++/embedded_model}/reinforcement.geo
D		examples/explicit
V		examples/{ → c++/solid_mechanics_model}/explicit/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/explicit/bar.geo
V		examples/{ → c++/solid_mechanics_model}/explicit/explicit_dynamic.cc
V		examples/{ → c++/solid_mechanics_model}/explicit/material.dat
D		examples/heat_transfer
V		examples/{heat_transfer → c++/diffusion_model}/CMakeLists.txt
V		examples/{heat_transfer → c++/diffusion_model}/cube.geo
V		examples/{heat_transfer → c++/diffusion_model}/cube_tet.geo
V		examples/{heat_transfer/heat_transfer_dynamics_2d.cc → c++/diffusion_model/heat_diffusion_dynamics_2d.cc}
V		examples/{heat_transfer/heat_transfer_dynamics_3d.cc → c++/diffusion_model/heat_diffusion_dynamics_3d.cc}
V		examples/{heat_transfer/heat_transfer_static_2d.cc → c++/diffusion_model/heat_diffusion_static_2d.cc}
D		examples/heat_transfer/material.dat
V		examples/{heat_transfer → c++/diffusion_model}/square.geo
D		examples/implicit
V		examples/{ → c++/solid_mechanics_model}/implicit/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/implicit/beam.geo
V		examples/{ → c++/solid_mechanics_model}/implicit/implicit_dynamic.cc
V		examples/{ → c++/solid_mechanics_model}/implicit/material_dynamic.dat
D		examples/io
V		examples/{ → c++/solid_mechanics_model}/io/CMakeLists.txt
D		examples/io/dumper
V		examples/{ → c++/solid_mechanics_model}/io/dumper/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/io/dumper/dumpable_interface.cc
V		examples/{ → c++/solid_mechanics_model}/io/dumper/dumper_low_level.cc
V		examples/{ → c++/solid_mechanics_model}/io/dumper/locomotive_tools.cc
V		examples/{ → c++/solid_mechanics_model}/io/dumper/locomotive_tools.hh
V		examples/{ → c++/solid_mechanics_model}/io/dumper/swiss_train.geo
V	(dir)	examples/{io/parser/ → c++/solid_mechanics_model/io/parser}
P		examples/io/parser/CMakeLists.txt Deleted after being copied to multiple locations: examples/CMakeLists.txt examples/c++/solid_mechanics_model/io/parser/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/io/parser/example_parser.cc
V		examples/{ → c++/solid_mechanics_model}/io/parser/input_file.dat
V		examples/{ → c++/solid_mechanics_model}/io/parser/swiss_cheese.geo
D		examples/new_material
V		examples/{ → c++/solid_mechanics_model}/new_material/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/new_material/barre_trou.geo
V		examples/{ → c++/solid_mechanics_model}/new_material/local_material_damage.cc
V		examples/{ → c++/solid_mechanics_model}/new_material/local_material_damage.hh
V		examples/{ → c++/solid_mechanics_model}/new_material/local_material_damage_inline_impl.hh
V		examples/{ → c++/solid_mechanics_model}/new_material/material.dat
V		examples/{ → c++/solid_mechanics_model}/new_material/new_local_material.cc
V	(dir)	examples/{new_material/viscoelastic_maxwell/ → c++/solid_mechanics_model/new_material/viscoelastic_maxwell}
V		examples/{ → c++/solid_mechanics_model}/new_material/viscoelastic_maxwell/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell.dat
V		examples/{ → c++/solid_mechanics_model}/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc
V		examples/{ → c++/solid_mechanics_model}/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_mesh.geo
D		examples/parallel
V		examples/{ → c++/solid_mechanics_model}/parallel/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/parallel/material.dat
V		examples/{ → c++/solid_mechanics_model}/parallel/parallel_2d.cc
V		examples/{ → c++/solid_mechanics_model}/parallel/square_2d.geo
D		examples/phase_field
V		examples/{phase_field → c++/phase_field_model}/CMakeLists.txt
V		examples/{phase_field → c++/phase_field_model}/material_notch.dat
V		examples/{phase_field → c++/phase_field_model}/phase_field_notch.cc
V		examples/{phase_field → c++/phase_field_model}/phase_field_parallel.cc
V		examples/{phase_field → c++/phase_field_model}/square_notch.geo
M		examples/python/CMakeLists.txt
M		examples/python/README.rst
D		examples/python/cohesive
V		examples/python/{ → solid_mechanics_cohesive_model}/cohesive/CMakeLists.txt
V		examples/python/{ → solid_mechanics_cohesive_model}/cohesive/custom_material.py
V		examples/python/{ → solid_mechanics_cohesive_model}/cohesive/local_material.dat
V		examples/python/{ → solid_mechanics_cohesive_model}/cohesive/material.dat
V		examples/python/{ → solid_mechanics_cohesive_model}/cohesive/plate.geo
V		examples/python/{ → solid_mechanics_cohesive_model}/cohesive/plate.py
D		examples/python/contact-mechanics
V		examples/python/{contact-mechanics → contact_mechanics_model}/CMakeLists.txt
V		examples/python/{contact-mechanics → contact_mechanics_model}/compression.dat
V		examples/python/{contact-mechanics → contact_mechanics_model}/compression.geo
V		examples/python/{contact-mechanics → contact_mechanics_model}/compression.py
V		examples/python/{contact-mechanics → contact_mechanics_model}/detection-explicit.dat
V		examples/python/{contact-mechanics → contact_mechanics_model}/detection-explicit.msh
V		examples/python/{contact-mechanics → contact_mechanics_model}/detection-explicit.py
A	(dir)	examples/python/contact_mechanics_model/
V		examples/python/{contact_mechanics_model ← contact-mechanics}/CMakeLists.txt
A		examples/python/contact_mechanics_model/README.rst
V		examples/python/{contact_mechanics_model ← contact-mechanics}/compression.dat
V		examples/python/{contact_mechanics_model ← contact-mechanics}/compression.geo
V		examples/python/{contact_mechanics_model ← contact-mechanics}/compression.py
V		examples/python/{contact_mechanics_model ← contact-mechanics}/detection-explicit.dat
V		examples/python/{contact_mechanics_model ← contact-mechanics}/detection-explicit.msh
V		examples/python/{contact_mechanics_model ← contact-mechanics}/detection-explicit.py
A	(dir)	examples/python/contact_mechanics_model/images/
A		examples/python/contact_mechanics_model/images/compression.svg
A		examples/python/contact_mechanics_model/images/contact.gif
D		examples/python/custom-material
V		examples/python/{ → solid_mechanics_model}/custom-material/CMakeLists.txt
V		examples/python/{ → solid_mechanics_model}/custom-material/bar.geo
V		examples/python/{ → solid_mechanics_model}/custom-material/bi-material.py
V		examples/python/{ → solid_mechanics_model}/custom-material/custom-material.py
V		examples/python/{ → solid_mechanics_model}/custom-material/material.dat
V		examples/python/{ → solid_mechanics_model}/custom-material/square.geo
D		examples/python/dynamics
V		examples/python/{ → solid_mechanics_model}/dynamics/CMakeLists.txt
V		examples/python/{ → solid_mechanics_model}/dynamics/bar.geo
V		examples/python/{ → solid_mechanics_model}/dynamics/dynamics.py
V		examples/python/{ → solid_mechanics_model}/dynamics/material.dat
D		examples/python/eigen_modes
V		examples/python/{ → solid_mechanics_model}/eigen_modes/CMakeLists.txt
V		examples/python/{ → solid_mechanics_model}/eigen_modes/eigen_modes.py
V		examples/python/{ → solid_mechanics_model}/eigen_modes/image_saver.py
V		examples/python/{ → solid_mechanics_model}/eigen_modes/material.dat
D		examples/python/fragmentation
V		examples/python/{ → solid_mechanics_cohesive_model}/fragmentation/CMakeLists.txt
V		examples/python/{ → solid_mechanics_cohesive_model}/fragmentation/fragmentation.py
V		examples/python/{ → solid_mechanics_cohesive_model}/fragmentation/fragmentation_mesh.geo
V		examples/python/{ → solid_mechanics_cohesive_model}/fragmentation/material.dat
D		examples/python/phase-field
V		examples/python/{phase-field → phase_field_model}/CMakeLists.txt
V		examples/python/{phase-field → phase_field_model}/material.dat
V		examples/python/{phase-field → phase_field_model}/material_static.dat
V		examples/python/{phase-field → phase_field_model}/phasefield-dynamic.py
V		examples/python/{phase-field → phase_field_model}/phasefield-static.py
V		examples/python/{phase-field → phase_field_model}/plate.geo
V		examples/python/{phase-field → phase_field_model}/plate_static.geo
A	(dir)	examples/python/phase_field_model/
V		examples/python/{phase_field_model ← phase-field}/CMakeLists.txt
A		examples/python/phase_field_model/README.rst
A	(dir)	examples/python/phase_field_model/images/
A		examples/python/phase_field_model/images/phasefield-dynamic-geo.svg
A		examples/python/phase_field_model/images/phasefield-dynamic.png
A		examples/python/phase_field_model/images/phasefield-static-geo.svg
A		examples/python/phase_field_model/images/phasefield-static.png
V		examples/python/{phase_field_model ← phase-field}/material.dat
V		examples/python/{phase_field_model ← phase-field}/material_static.dat
V		examples/python/{phase_field_model ← phase-field}/phasefield-dynamic.py
V		examples/python/{phase_field_model ← phase-field}/phasefield-static.py
V		examples/python/{phase_field_model ← phase-field}/plate.geo
V		examples/python/{phase_field_model ← phase-field}/plate_static.geo
D		examples/python/plate-hole
V		examples/python/{ → solid_mechanics_model}/plate-hole/CMakeLists.txt
V		examples/python/{ → solid_mechanics_model}/plate-hole/material.dat
V		examples/python/{ → solid_mechanics_model}/plate-hole/plate.geo
V		examples/python/{ → solid_mechanics_model}/plate-hole/plate.py
A	(dir)	examples/python/solid_mechanics_cohesive_model/
A		examples/python/solid_mechanics_cohesive_model/CMakeLists.txt
A		examples/python/solid_mechanics_cohesive_model/README.rst
A	(dir)	examples/python/solid_mechanics_cohesive_model/cohesive/
V		examples/python/{solid_mechanics_cohesive_model ← }/cohesive/CMakeLists.txt
A		examples/python/solid_mechanics_cohesive_model/cohesive/README.rst
V		examples/python/{solid_mechanics_cohesive_model ← }/cohesive/custom_material.py
A	(dir)	examples/python/solid_mechanics_cohesive_model/cohesive/images/
A		examples/python/solid_mechanics_cohesive_model/cohesive/images/plate.gif
A		examples/python/solid_mechanics_cohesive_model/cohesive/images/plate.svg
V		examples/python/{solid_mechanics_cohesive_model ← }/cohesive/local_material.dat
V		examples/python/{solid_mechanics_cohesive_model ← }/cohesive/material.dat
V		examples/python/{solid_mechanics_cohesive_model ← }/cohesive/plate.geo
V		examples/python/{solid_mechanics_cohesive_model ← }/cohesive/plate.py
A	(dir)	examples/python/solid_mechanics_cohesive_model/fragmentation/
V		examples/python/{solid_mechanics_cohesive_model ← }/fragmentation/CMakeLists.txt
A		examples/python/solid_mechanics_cohesive_model/fragmentation/README.rst
V		examples/python/{solid_mechanics_cohesive_model ← }/fragmentation/fragmentation.py
V		examples/python/{solid_mechanics_cohesive_model ← }/fragmentation/fragmentation_mesh.geo
A	(dir)	examples/python/solid_mechanics_cohesive_model/fragmentation/images/
A		examples/python/solid_mechanics_cohesive_model/fragmentation/images/fragmentation.gif
V		examples/python/{solid_mechanics_cohesive_model ← }/fragmentation/material.dat
A	(dir)	examples/python/solid_mechanics_model/
A		examples/python/solid_mechanics_model/CMakeLists.txt
A		examples/python/solid_mechanics_model/README.rst
A	(dir)	examples/python/solid_mechanics_model/custom-material/
V		examples/python/{solid_mechanics_model ← }/custom-material/CMakeLists.txt
A		examples/python/solid_mechanics_model/custom-material/README.rst
V		examples/python/{solid_mechanics_model ← }/custom-material/bar.geo
V		examples/python/{solid_mechanics_model ← }/custom-material/bi-material.py
V		examples/python/{solid_mechanics_model ← }/custom-material/custom-material.py
A	(dir)	examples/python/solid_mechanics_model/custom-material/images/
A		examples/python/solid_mechanics_model/custom-material/images/pulse_bar_custom.gif
A		examples/python/solid_mechanics_model/custom-material/images/square_displ.png
V		examples/python/{solid_mechanics_model ← }/custom-material/material.dat
V		examples/python/{solid_mechanics_model ← }/custom-material/square.geo
A	(dir)	examples/python/solid_mechanics_model/dynamics/
V		examples/python/{solid_mechanics_model ← }/dynamics/CMakeLists.txt
A		examples/python/solid_mechanics_model/dynamics/README.rst
V		examples/python/{solid_mechanics_model ← }/dynamics/bar.geo
V		examples/python/{solid_mechanics_model ← }/dynamics/dynamics.py
A	(dir)	examples/python/solid_mechanics_model/dynamics/images/
A		examples/python/solid_mechanics_model/dynamics/images/bar.gif
A		examples/python/solid_mechanics_model/dynamics/images/bar_geom.svg
V		examples/python/{solid_mechanics_model ← }/dynamics/material.dat
A	(dir)	examples/python/solid_mechanics_model/eigen_modes/
V		examples/python/{solid_mechanics_model ← }/eigen_modes/CMakeLists.txt
A		examples/python/solid_mechanics_model/eigen_modes/README.rst
V		examples/python/{solid_mechanics_model ← }/eigen_modes/eigen_modes.py
V		examples/python/{solid_mechanics_model ← }/eigen_modes/image_saver.py
A	(dir)	examples/python/solid_mechanics_model/eigen_modes/images/
A		examples/python/solid_mechanics_model/eigen_modes/images/eigen_modes.png
V		examples/python/{solid_mechanics_model ← }/eigen_modes/material.dat
A	(dir)	examples/python/solid_mechanics_model/plate-hole/
V		examples/python/{solid_mechanics_model ← }/plate-hole/CMakeLists.txt
A		examples/python/solid_mechanics_model/plate-hole/README.rst
A	(dir)	examples/python/solid_mechanics_model/plate-hole/images/
A		examples/python/solid_mechanics_model/plate-hole/images/plate_hole.svg
A		examples/python/solid_mechanics_model/plate-hole/images/plate_hole_displ_mag.png
V		examples/python/{solid_mechanics_model ← }/plate-hole/material.dat
V		examples/python/{solid_mechanics_model ← }/plate-hole/plate.geo
V		examples/python/{solid_mechanics_model ← }/plate-hole/plate.py
A	(dir)	examples/python/solid_mechanics_model/solver_callback/
V		examples/python/{solid_mechanics_model ← }/solver_callback/CMakeLists.txt
A		examples/python/solid_mechanics_model/solver_callback/README.rst
V		examples/python/{solid_mechanics_model ← }/solver_callback/bar.geo
V		examples/python/{solid_mechanics_model ← }/solver_callback/material.dat
V		examples/python/{solid_mechanics_model ← }/solver_callback/solver_callback.py
A	(dir)	examples/python/solid_mechanics_model/stiffness_matrix/
V		examples/python/{solid_mechanics_model ← }/stiffness_matrix/CMakeLists.txt
A		examples/python/solid_mechanics_model/stiffness_matrix/README.rst
V		examples/python/{solid_mechanics_model ← }/stiffness_matrix/material.dat
V		examples/python/{solid_mechanics_model ← }/stiffness_matrix/plate.geo
V		examples/python/{solid_mechanics_model ← }/stiffness_matrix/plate.msh
V		examples/python/{solid_mechanics_model ← }/stiffness_matrix/stiffness_matrix.py
D		examples/python/solver_callback
V		examples/python/{ → solid_mechanics_model}/solver_callback/CMakeLists.txt
V		examples/python/{ → solid_mechanics_model}/solver_callback/bar.geo
V		examples/python/{ → solid_mechanics_model}/solver_callback/material.dat
V		examples/python/{ → solid_mechanics_model}/solver_callback/solver_callback.py
D		examples/python/stiffness_matrix
V		examples/python/{ → solid_mechanics_model}/stiffness_matrix/CMakeLists.txt
V		examples/python/{ → solid_mechanics_model}/stiffness_matrix/material.dat
V		examples/python/{ → solid_mechanics_model}/stiffness_matrix/plate.geo
V		examples/python/{ → solid_mechanics_model}/stiffness_matrix/plate.msh
V		examples/python/{ → solid_mechanics_model}/stiffness_matrix/stiffness_matrix.py
D		examples/python/structural_mechanics
V		examples/python/{structural_mechanics → structural_mechanics_model}/CMakeLists.txt
V		examples/python/{structural_mechanics → structural_mechanics_model}/structural_mechanics.py
V		examples/python/{structural_mechanics → structural_mechanics_model}/structural_mechanics_dynamics.py
V		examples/python/{structural_mechanics → structural_mechanics_model}/structural_mechanics_softening.py
A	(dir)	examples/python/structural_mechanics_model/
V		examples/python/{structural_mechanics_model ← structural_mechanics}/CMakeLists.txt
A	(dir)	examples/python/structural_mechanics_model/images/
A		examples/python/structural_mechanics_model/images/displacements.png
A		examples/python/structural_mechanics_model/images/displacements_softening.png
V		examples/python/{structural_mechanics_model ← structural_mechanics}/structural_mechanics.py
V		examples/python/{structural_mechanics_model ← structural_mechanics}/structural_mechanics_dynamics.py
V		examples/python/{structural_mechanics_model ← structural_mechanics}/structural_mechanics_softening.py
D		examples/static
V		examples/{ → c++/solid_mechanics_model}/static/CMakeLists.txt
V		examples/{ → c++/solid_mechanics_model}/static/material.dat
V		examples/{ → c++/solid_mechanics_model}/static/square.geo
V		examples/{ → c++/solid_mechanics_model}/static/static.cc
V	(dir)	examples/{structural_mechanics/ → c++/structural_mechanics_model}
V		examples/{structural_mechanics → c++/structural_mechanics_model}/CMakeLists.txt
V		examples/{structural_mechanics → c++/structural_mechanics_model}/bernoulli_beam_2_example.cc
M		packages/diffusion.cmake
M		src/mesh/element_type_map.hh
A	(dir)	src/model/diffusion_model/
V		src/model/{diffusion_model ← heat_transfer}/diffusion_law.cc
V		src/model/{diffusion_model ← heat_transfer}/diffusion_law.hh
V		src/model/{diffusion_model ← heat_transfer}/diffusion_model.cc
V		src/model/{diffusion_model ← heat_transfer}/diffusion_model.hh
V		src/model/{diffusion_model ← heat_transfer}/heat_diffusion.cc
V		src/model/{diffusion_model ← heat_transfer}/heat_diffusion.hh
V		src/model/{diffusion_model ← heat_transfer}/heat_transfer_model.hh
D		src/model/heat_transfer
V		src/model/{heat_transfer → diffusion_model}/diffusion_law.cc
V		src/model/{heat_transfer → diffusion_model}/diffusion_law.hh
V		src/model/{heat_transfer → diffusion_model}/diffusion_model.cc
V		src/model/{heat_transfer → diffusion_model}/diffusion_model.hh
V		src/model/{heat_transfer → diffusion_model}/heat_diffusion.cc
V		src/model/{heat_transfer → diffusion_model}/heat_diffusion.hh
D		src/model/heat_transfer/heat_transfer_model.cc
V		src/model/{heat_transfer → diffusion_model}/heat_transfer_model.hh
M		src/model/phase_field/phase_field_element_filter.hh
M		src/model/structural_mechanics/structural_mechanics_model.hh