Add unstructured mesh infrastructure - #5687
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Introduce UnstructuredSubMesh, mesh generators, and Mesh interface coupling so arbitrary 2D/3D domains can be discretised later. Extracted from the unstructured finite-volume stack for isolated review. Co-authored-by: Cursor <cursoragent@cursor.com>
This was referenced Jul 31, 2026
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## main #5687 +/- ##
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+ Coverage 98.12% 98.21% +0.08%
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Files 339 340 +1
Lines 31996 32622 +626
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+ Hits 31396 32039 +643
+ Misses 600 583 -17 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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`_combine_unstructured_submeshes` put 110 lines of unstructured-specific node welding in the generic `meshes.py`, which then needed two function-level `from .unstructured_submesh import ...` calls to dodge the module-level cycle (`unstructured_submesh` already imports `SubMesh` and `MeshGenerator` from `meshes`). Move it to `UnstructuredSubMesh.combine`, where `_hex_to_tet` and the class itself are local, and reach `compute_interface_data` through the `pybamm` namespace like the rest of `meshes.py` does. `meshes.py` no longer references `unstructured_submesh` at all. Pure move: the welding and boundary-tag-recovery bodies are unchanged apart from `pybamm.UnstructuredSubMesh(...)` becoming `cls(...)`. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
…_ordering `interface_data` stores "left_cells" as this mesh's cells and "right_cells" as the neighbour's, but `optimize_ordering` permuted both with this mesh's `inv_perm`. That silently re-pointed the neighbour's indices, and where the neighbour has fewer cells it produced out-of-range indices (an 18-cell mesh next to a 12-cell one yielded `right_cells.max() == 17`). `compute_interface_data` also gives the neighbour a mirrored view of the same pairing, which aliases the very array being replaced, so the mirror went stale. Permute only this mesh's indices and write the result through to the neighbour's mirror. The existing test asserted only on "left_cells" — the one key that was already correct — so add a case that pins the neighbour's indices and the mirror, using meshes of different sizes so a mis-permutation is caught by bounds rather than by luck. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
`UnstructuredSubMesh.combine` welds coincident interface nodes so the seam becomes internal faces and TPFA carries flux across it. When the interface nodes don't coincide — mismatched transverse grids, wrong coordinate units, or a non-conforming input mesh — nothing welds, the seam stays boundary faces on both sides, and the domains form separate connected components. The solve then runs to completion with the regions silently decoupled and returns a physically wrong answer. Add a post-weld check that the combined mesh is a single connected component, using the integer face_owner/face_neighbor connectivity so it introduces no distance tolerance. Under the conforming-interface requirement welding is all-or-nothing, so total disconnection is the only failure mode and this check is sufficient. Document the conforming requirement on the two gmsh-reading generators. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Four review findings on #5687: - Reject non-manifold input: a face shared by more than two cells matched neither the internal (count 2) nor boundary (count 1) branch of _build_face_connectivity and silently vanished from the face list, losing flux paths. Now raises GeometryError. - Make the 3D generator honour element_type: _generate_3d always built hexes regardless of the argument (docstring claimed a tetrahedron default). Hexahedron stays the default, matching existing tests and the 3D DFN model; "tetrahedron" now works and records _hex_gen_params so combine() can rebuild tet domains with a cumulative parity offset, keeping interface triangulations conforming — previously that combine branch was unreachable. Unknown types raise. - Remove dead code: _cell_faces (unused since the vectorised connectivity path) and an n_fpc assignment overwritten two lines later. - Conventions: framework errors now raise pybamm.GeometryError instead of ValueError/KeyError/RuntimeError; meshio is imported via pybamm.import_optional_dependency; the CHANGELOG bullet carries the PR link. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Codecov flagged the meshio-backed generators as entirely untested. Add tests for UserSuppliedUnstructuredMesh (whole-file load with 2D trimming, subdomain filtering, missing-cell-data and unsupported-cell-type errors, lims-to-domain mapping) and TaggedSubMeshGenerator (region extraction with coordinate scaling, missing region, region with no tets), using synthetic meshio objects injected into the class cache so no .msh round-trip is needed. Also cover combine()'s custom boundary-tag recovery, compute_interface_data's no-matching-faces and transverse-mismatch raises, and Mesh leaving interface_data empty when grids don't pair. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Summary
UnstructuredSubMesh, generators (UnstructuredMeshGenerator,UserSuppliedUnstructuredMesh,TaggedSubMeshGenerator), andMeshinterface coupling.Stack
Full pre-split branch preserved on #5397 /
backup/unstructured-finite-volume-full.Test plan
tests/unit/test_meshes/test_unstructured_submesh.py(41 tests)Also in this stack: #5691 deprecates
pybamm.Magnitude.