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Add support for specifying surfaces (BCs, faults) using faces and reading meshes in PETSc HDF5 format #821

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Merged
merged 50 commits into from
May 6, 2025
Merged

Add support for specifying surfaces (BCs, faults) using faces and reading meshes in PETSc HDF5 format #821

merged 50 commits into from
May 6, 2025

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@baagaard-usgs
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@baagaard-usgs baagaard-usgs commented May 6, 2025

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@baagaard-usgs
Remove CPPUNIT_INCDIR from include path (no longer used).
842cca2
@baagaard-usgs
Create lower dimension mesh (BCs) using DMPlexFilter().
ac86713
@baagaard-usgs
Use label value (not 1) when getting pointIS.
741bcfd
@baagaard-usgs
Switch creating lower dimension mesh from DMPlexFilter() to DMPlexCre…
7bb8687 
…ateSubmesh().
@baagaard-usgs
FIX: Adjust code to avoid restoring indices with nullptr (parallel bug).
b9e5ae9
@baagaard-usgs
Add comment on why we need to use DMPlexLabelAddFaceCells() when sett…
3b26247 
…ing Dirichlet BCs using projection from the submesh.
@baagaard-usgs
Clean cells label and face labels when refining.
da66ab6
@baagaard-usgs
Add ability to write PETSc HDF5 mesh files.
eab1b26
@baagaard-usgs
Add testing of writing and reading PETSc HDF5 files.
dae0175
@baagaard-usgs
Add application to convert from one mesh format to another.
d0ef2f1
@baagaard-usgs
Add support for reading face groups (sidesets) for BCs.
bcef394
@baagaard-usgs
Fix name of fake mesh file to match HDF5 format.
b0c40ba
@baagaard-usgs
Remove 2D in 3D test case (not used).
41a2ac0
@baagaard-usgs
Updates to MeshIOCubit SWIG and Python files (remove useNodeSetNames).
8086a72
@baagaard-usgs
Check for vertices and cell+side that are not in mesh when creating l…
bd0287b 
…abels for BCs.
@baagaard-usgs
Fixes to mesh readers. Update meshio test data.
80cc2b7
@baagaard-usgs
Small improvements to MeshIOPetsc (update write version to 3.1.0).
6bc26dd
@baagaard-usgs
Update fault topology tests for changes to ASCII mesh format and add …
1f27d78 
…face groups.
@baagaard-usgs
Update ASCII meshes for libtests/feassemble.
05f4cd2
@baagaard-usgs
Update ASCII meshes for libtests/materials.
c4a6bcd
@baagaard-usgs
Update ASCII meshes for libtests/problems.
a7bc534
@baagaard-usgs
Improve MeshBuilder interface (get number of vertices on face using s…
1b83cf6 
…hape).
@baagaard-usgs
Update ASCII mesh files and test data for libtests/topology.
f2310d5
@baagaard-usgs
Add LaTeX mesh output to MMSTests diagnostic output. Update meshes in…
66da08f 
… MMS tests to use faces for boundary conditions.
@baagaard-usgs
Update MeshIOPetsc Python interface to allow setting Gmsh marking ver…
627e7f3 
…tices flag.
@baagaard-usgs
Update Python unit tests for changes to MeshIO factory methods (mesh_…
29dfd60 
…io -> mesh_input, mesh_output).
@baagaard-usgs
FIX: Update pytest module function name (test_classes -> test_modules).
2b1bb5a
@baagaard-usgs
Set boundary conditions using faces in full-scale tests.
2f15e4c
@baagaard-usgs
Update Gmsh files to use face groups for boundary conditions.
9ebff80
@baagaard-usgs
FIX: Set name of subdomain mesh using label and label value.
5bae326
@baagaard-usgs
Use Pyre component identifier and name in Field and Mesh labels.
c79d41d
@baagaard-usgs
Deprecate setting label for material (switched to using Pyre name and…
ecaeda8 
… identifier).
@baagaard-usgs
Clean up of meshio Gmsh scripts.
06b43a7
@baagaard-usgs
Update Gmsh files to use face groups for boundary conditions.
326141b
@baagaard-usgs
Update list of changes.
4ef1693
@baagaard-usgs
Update to PETSc 3.23.0. Update fault kernels (dim is now spatial dime…
efa8d7e 
…nsion).
@baagaard-usgs
Fix integer types in MeshBuilder and MeshIOAscii.
f9f00df
@baagaard-usgs
Updates for making PETSc integration functions public.
f4624d3
@baagaard-usgs
DOCS: Update components.
390b703
@baagaard-usgs
DOCS: Update documentation for changes to mesh I/O (HDF5 and faces).
e6c1d24
@baagaard-usgs
Remove description from docstring for materials (deprecated).
0836fe0
@baagaard-usgs
Update libtests/meshio file to use face groups for boundary conditions.
d52c6e7
@baagaard-usgs
Update PETSC to 3.23.1.
bc7419e
@baagaard-usgs
Rename 'gmsh_mark_vertices' MeshIOPetsc option to 'gmsh_mark_recursiv…
245406c 
…e' to match behavior.
@baagaard-usgs
DOCS: Update formatting of 'New in vX.X.X.'
0c14a23
@baagaard-usgs
Update examples (source and examples) to use BC specified by faces.
9c7600b
@baagaard-usgs
FIX: Fix data dimension in fault_east_slip.spatialdb in examples/crus…
3e063a0 
…tal-strikeslip-3d.
@baagaard-usgs
Update pytests/Makefile.
51f6bce
@baagaard-usgs
Increment version to 5.0.0dev.
4019b2a
@baagaard-usgs
Update version restrictions in cfg files to allow compatibility with …
c512d26 
…v5.0.
@baagaard-usgs baagaard-usgs merged commit 9769ce9 into geodynamics:main May 6, 2025
11 checks passed
@baagaard-usgs baagaard-usgs deleted the feature-meshio-hdf5 branch May 6, 2025 18:49
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@baagaard-usgs