Unstructured finite volume by aabills · Pull Request #5397 · pybamm-team/PyBaMM

aabills · 2026-02-26T18:25:46Z

Description

Adds an unstructured finite volume method for 2 and 3D, allowing for simulations on arbitrary domains with user-provided meshes.

Fixes # (issue)

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #)

Important checks:

Please confirm the following before marking the PR as ready for review:

No style issues: nox -s pre-commit
All tests pass: nox -s tests
The documentation builds: nox -s doctests
Code is commented for hard-to-understand areas
Tests added that prove fix is effective or that feature works

codecov · 2026-02-27T02:20:15Z

Codecov Report

❌ Patch coverage is 80.72855% with 492 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.85%. Comparing base (1e9fbce) to head (8c15609).

Files with missing lines	Patch %	Lines
packages/pybamm/src/pybamm/plotting/quick_plot.py	23.65%	142 Missing ⚠️
...es/pybamm/src/pybamm/solvers/processed_variable.py	30.45%	137 Missing ⚠️
...s/pybamm/src/pybamm/meshes/unstructured_submesh.py	80.41%	105 Missing ⚠️
...ybamm/src/pybamm/discretisations/discretisation.py	44.28%	39 Missing ⚠️
packages/pybamm/src/pybamm/meshes/meshes.py	66.25%	27 Missing ⚠️
packages/pybamm/src/pybamm/plotting/plot_vtk.py	98.04%	11 Missing ⚠️
...ry_models/lithium_ion/basic_dfn_3d_unstructured.py	93.04%	8 Missing ⚠️
...ackages/pybamm/src/pybamm/plotting/dynamic_plot.py	41.66%	7 Missing ⚠️
...ry_models/lithium_ion/basic_dfn_2d_unstructured.py	94.49%	6 Missing ⚠️
packages/pybamm/src/pybamm/solvers/solution.py	44.44%	5 Missing ⚠️
... and 2 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #5397      +/-   ##
==========================================
- Coverage   98.12%   96.85%   -1.28%     
==========================================
  Files         339      344       +5     
  Lines       31996    34489    +2493     
==========================================
+ Hits        31396    33403    +2007     
- Misses        600     1086     +486

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Resolve conflicts: - __init__.py: keep both VTKQuickPlot and nyquist_plot imports - functions.py: take main's Max/Min _casadi_evaluate and _evaluate_for_shape - convert_to_casadi.py: accept deletion from main's OOP refactor; port VectorField casadi conversion to _to_casadi method on the class

- vector_field.py: 85% -> 100% - tensor_field.py: 90% -> 100% - unstructured_submesh.py: 64% -> 87% Added tests for quad/hex element types, boundary loops, contains_points_3d on hex, optimize_ordering on single cell, generator error paths, and _parse_lims string-variable handling. Added tensor/vector field getitem edge cases, all-on-edges path, and VectorField._to_casadi coverage.

* lock before big change * update * Add TaggedSubMeshGenerator for per-region Gmsh extraction One-instance-per-region MeshGenerator that pulls a single Gmsh physical group out of a .msh file and wraps it as an UnstructuredSubMesh. Simpler than UserSuppliedUnstructuredMesh when the model already supplies one generator per pybamm domain (e.g. multi-domain 3D thermal w/ body + tab regions). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

…inite-volume-check-858f6a # Conflicts: # packages/pybamm/src/pybamm/meshes/unstructured_submesh.py # packages/pybamm/src/pybamm/models/full_battery_models/base_battery_model.py # packages/pybamm/src/pybamm/models/full_battery_models/lithium_ion/basic_dfn_2d_unstructured.py # packages/pybamm/src/pybamm/models/full_battery_models/lithium_ion/basic_dfn_3d_unstructured.py # packages/pybamm/src/pybamm/parameters/parameter_substitutor.py # packages/pybamm/src/pybamm/plotting/plot_vtk.py # packages/pybamm/src/pybamm/spatial_methods/finite_volume_unstructured.py # packages/pybamm/tests/unit/test_meshes/test_unstructured_submesh.py # packages/pybamm/tests/unit/test_spatial_methods/test_finite_volume_unstructured.py # pyproject.toml

Resolve lint on the merged tree: replace .keys() iteration and dict() literals, merge isinstance calls, and drop the blanket except around interface auto-discovery in favour of an explicit dimension check in _interface_face_match, which already reports non-adjacency via its matched flag. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

- sigma() gained an sto parameter on main; pass sto=None in the unstructured DFN models, matching base_thermal and li_metal. - Restore main's strict 3D cell-geometry validation, which the branch had commented out; test_spm covers the arbitrary-geometry rejection. - Reduction._from_json clears domains again after restore, since SpecificFunction._from_json bypasses __init__ and Max/Min would otherwise come back carrying the child's domain. - Component serialises its index via to_json/_from_json, mirroring Magnitude, and gains a hypothesis strategy alongside Norm. - UnstructuredSubMesh joins _SUBMESH_EXEMPT (no _from_json), and Reduction joins _NOT_ROUND_TRIPPABLE as an abstract base. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Add API pages for UnstructuredSubMesh and its generators, the FiniteVolumeUnstructured spatial method, VTKQuickPlot, and the two unstructured DFN models, and record the feature in the changelog. Drop the root-level TODO.md: its main item (arbitrary domain names via an explicit tag) is implemented as TaggedSubMeshGenerator, and the workaround script it points at no longer exists. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Co-authored-by: Cursor <cursoragent@cursor.com>

Use OSMesa only on Linux and install the software GL backends in CI so save_gif no longer segfaults on headless runners. Co-authored-by: Cursor <cursoragent@cursor.com>

Headless Windows runners lack a software OpenGL backend, so save_gif segfaults; install mesa-dist-win OSMesa via the PyVista setup action. Co-authored-by: Cursor <cursoragent@cursor.com>

aabills · 2026-07-31T21:40:06Z

Split into stacked prior PRs (plan B) so this can be reviewed in smaller pieces. Original branch unstructured-finite-volume is unchanged, and tip 8c1560943 is also preserved on backup/unstructured-finite-volume-full.

Generalise VectorField to N components #5686 — VectorField N-comp
Add unstructured mesh infrastructure #5687 — Meshing
Add unstructured finite volume spatial method #5688 — Spatial method + ProcessedVariable
Add VTK plotting for unstructured meshes #5689 — VTK plotting
Add unstructured 2D/3D DFN battery models #5690 — Unstructured DFN models

Once that stack lands, this PR can be closed as superseded.

aabills · 2026-07-31T23:02:12Z

Added a 6th stacked PR: #TBD deprecates pybamm.Magnitude in favour of Component.

Updating once the PR number is known…

aabills · 2026-07-31T23:02:13Z

Also opened #5691: deprecate pybamm.Magnitude → pybamm.Component (6th in the stack).

Full stack:

Generalise VectorField to N components #5686 VectorField
Add unstructured mesh infrastructure #5687 Meshing
Add unstructured finite volume spatial method #5688 Spatial + ProcessedVariable
Add VTK plotting for unstructured meshes #5689 VTK plotting
Add unstructured 2D/3D DFN battery models #5690 Unstructured DFN models
Deprecate pybamm.Magnitude in favour of Component #5691 Deprecate Magnitude

aabills and others added 9 commits February 24, 2026 16:17

unstrucutred finite volume method

3e377c0

unstructured finite volume method

d3f0857

processed variables

9a0a7b6

update vector field

0516e58

add basicdfn2dunstructured

86875cc

unstructured DFN 3D

02cd880

improve plotting

4534639

Merge branch 'main' into unstructured-finite-volume

9d2dd6e

fix plotting and speed up discretisation

35a24b9

aabills and others added 20 commits February 27, 2026 10:36

Merge branch 'main' into unstructured-finite-volume

4d1907a

vtk

f17aa89

add vtk

e60cd95

fix weird expression tree thing

d1a8c9d

Merge branch 'main' into unstructured-finite-volume

a0e40a9

get pouch working

ec57d76

Merge branch 'main' into unstructured-finite-volume

a01f39b

style: pre-commit fixes

abc3991

fix: preserve symbols during broadcast

78f6f68

Co-authored-by: Cursor <cursoragent@cursor.com>

test: cover unstructured finite volume behavior

790123a

Co-authored-by: Cursor <cursoragent@cursor.com>

test: cover VTK plotting behavior

175c697

Co-authored-by: Cursor <cursoragent@cursor.com>

style: pre-commit fixes

feee7f3

fix: stabilize domain sizes and VTK headless render

f87a15e

Co-authored-by: Cursor <cursoragent@cursor.com>

aabills and others added 2 commits July 31, 2026 14:14

fix: make VTK offscreen GIF export headless-safe

459dddc

Use OSMesa only on Linux and install the software GL backends in CI so save_gif no longer segfaults on headless runners. Co-authored-by: Cursor <cursoragent@cursor.com>

ci: install OSMesa for VTK GIF tests on Windows

8c15609

Headless Windows runners lack a software OpenGL backend, so save_gif segfaults; install mesa-dist-win OSMesa via the PyVista setup action. Co-authored-by: Cursor <cursoragent@cursor.com>

This was referenced Jul 31, 2026

Generalise VectorField to N components #5686

Merged

Add unstructured mesh infrastructure #5687

Merged

Add VTK plotting for unstructured meshes #5689

Open

Add unstructured 2D/3D DFN battery models #5690

Open

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Unstructured finite volume - #5397

Unstructured finite volume#5397
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