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

Merged

baagaard-usgs merged 50 commits intogeodynamics:mainfrom

baagaard-usgs:feature-meshio-hdf5

May 6, 2025

Commits on Apr 23, 2025

Remove CPPUNIT_INCDIR from include path (no longer used).
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Create lower dimension mesh (BCs) using DMPlexFilter().
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Use label value (not 1) when getting pointIS.
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Switch creating lower dimension mesh from DMPlexFilter() to DMPlexCreateSubmesh().
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FIX: Adjust code to avoid restoring indices with nullptr (parallel bug).
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Add comment on why we need to use DMPlexLabelAddFaceCells() when setting Dirichlet BCs using projection from the submesh.
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Clean cells label and face labels when refining.
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Add ability to write PETSc HDF5 mesh files.
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Add testing of writing and reading PETSc HDF5 files.
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Add application to convert from one mesh format to another.
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Add support for reading face groups (sidesets) for BCs.
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Fix name of fake mesh file to match HDF5 format.
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Remove 2D in 3D test case (not used).
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Updates to MeshIOCubit SWIG and Python files (remove useNodeSetNames).
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Check for vertices and cell+side that are not in mesh when creating labels for BCs.
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Fixes to mesh readers. Update meshio test data.
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Small improvements to MeshIOPetsc (update write version to 3.1.0).
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Update fault topology tests for changes to ASCII mesh format and add face groups.
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Update ASCII meshes for libtests/feassemble.
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Update ASCII meshes for libtests/materials.
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Update ASCII meshes for libtests/problems.
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Improve MeshBuilder interface (get number of vertices on face using shape).
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Update ASCII mesh files and test data for libtests/topology.
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Add LaTeX mesh output to MMSTests diagnostic output. Update meshes in MMS tests to use faces for boundary conditions.
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Update MeshIOPetsc Python interface to allow setting Gmsh marking vertices flag.
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Update Python unit tests for changes to MeshIO factory methods (mesh_io -> mesh_input, mesh_output).
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FIX: Update pytest module function name (test_classes -> test_modules).
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Set boundary conditions using faces in full-scale tests.
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Update Gmsh files to use face groups for boundary conditions.
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FIX: Set name of subdomain mesh using label and label value.
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Use Pyre component identifier and name in Field and Mesh labels.
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Deprecate setting label for material (switched to using Pyre name and identifier).
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Clean up of meshio Gmsh scripts.
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Update Gmsh files to use face groups for boundary conditions.
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Update list of changes.
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Update to PETSc 3.23.0. Update fault kernels (dim is now spatial dimension).
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Commits on Apr 29, 2025

Commits on Apr 30, 2025

DOCS: Update components.
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