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fix(meshing): SPD-floor the mmpde metric to stop silent NaN-bail on deformed meshes - #259
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…eformed meshes _winslow_mmpde's energy/gradient use fractional powers (sqrt(detM), detM**((1-p)/2), and S**q with S = tr(J M^-1 J^T)) that are defined only for an SPD metric. The metric is a guide field FE-evaluated at a FIXED reference cloud; once the interior deforms, a reference point can fall outside the current mesh and the P1 density is then evaluated by FE extrapolation, going negative. A scalar density rho<0 gives M = rho*I with det = rho^2 > 0 (so a detM>0 check passes) but M negative-definite, so S<0 and S**q = NaN. The energy is then non-finite and the mover bails with zero displacement -> adaptation silently stops on roughly half the adapts of an adaptive convection loop (mesh under-resolves; the symptom was previously misread as adapt/solver coupling or "passive fault damping"). Project every evaluated metric tensor onto SPD with a small relative eigenvalue floor at the _eval_M chokepoint. A genuinely SPD metric is returned unchanged (short-circuit no-op); extrapolation garbage becomes a benign "coarsen here" instead of a NaN. No behaviour change on valid metrics (bit-identical), no API change. Tests: test_0762/0850/0750/0830 green (33 passed, 5 skipped MMG, 4 pre-existing xfail). Validated on the stagnant-lid adaptive convection driver: all forced adapts move, T stays in [0,1], vrms bounded over 52 steps (no-fault) and 32 steps (passive fault). Underworld development team with AI support from Claude Code
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Pull request overview
This PR hardens the Winslow/MMPDE mesh smoother against non-SPD metric tensors (typically produced by FE extrapolation after mesh deformation) by sanitizing the evaluated metric so fractional-power terms in the MMPDE functional do not generate NaNs and silently stall adaptation.
Changes:
- Wraps
_eval_Mwith an SPD projection step using eigenvalue flooring to ensure the metric is symmetric positive-definite. - Adds detailed in-code rationale describing how non-SPD metrics arise and how the sanitizer prevents NaN-driven no-op adapts.
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| def _spd_sanitise(M): | ||
| Ms = 0.5 * (M + np.swapaxes(M, -1, -2)) | ||
| w, Vc = np.linalg.eigh(Ms) | ||
| if w.size: | ||
| wmax = float(np.nanmax(w)) | ||
| else: | ||
| wmax = 1.0 | ||
| floor = max(wmax, 1.0) * 1.0e-8 | ||
| if np.all(np.isfinite(w)) and float(w.min()) >= floor: | ||
| return Ms # already SPD → no-op | ||
| w = np.clip(np.nan_to_num(w, nan=floor, posinf=wmax, neginf=floor), | ||
| floor, None) | ||
| return np.einsum('nij,nj,nkj->nik', Vc, w, Vc) |
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Addressed in 732557e: added an empty-batch early return (parallel rank with no owned cells no longer hits the zero-size reduction) and made the SPD test per-tensor — only the cells whose own eigenvalues fail are projected, every already-SPD tensor is returned bit-identical. Verified empty-safe + valid cells untouched + all outputs SPD.
Address Copilot review on _spd_sanitise: - Guard the empty batch (a parallel rank that owns no cells): return early before the eigenvalue reductions, which previously raised on a zero-size array. - Make the SPD test per-tensor: only the cells whose OWN eigenvalues are non-finite or below the floor are projected; every already-SPD tensor is returned bit-identical to the symmetrised input. One bad point can no longer perturb otherwise-valid cells (matches the "no-op for SPD" contract). Verified: empty input is safe, a single garbage cell leaves the rest bit-identical, all output tensors SPD. Underworld development team with AI support from Claude Code
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This was referenced Jun 21, 2026
lmoresi added a commit
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Jun 22, 2026
Restores the intended "RBF metric eval" robustness. The mmpde mover's RBF/Shepard metric path baked the metric via an FE evaluation at the FIXED reference cloud `ref`; on a deformed mesh that reference can mis-locate / drift outside the deformed interior and the FE evaluation returns garbage (the P1 density — strictly positive by construction — comes back NEGATIVE, even at a field's own DOFs). A negative density is a non-SPD metric, which the mover then either NaN-bails on (a hidden stall) or, with the #259 SPD-floor, acts on as "coarsen hard here" → giant cells / holes / divergence in the adapted mesh. Fix: bake the metric at the CURRENT mesh NODES (its own DOF locations) and Shepard-interpolate from there. A Shepard (positive-weight, convex) average of the positive nodal values is GUARANTEED >= 0 (monotone) — the metric can never go non-SPD from the eval — and nodes are always inside the mesh (no out-of-domain / drift) and need no per-step cell location (fast). `ref` is kept for the _edge_mats reference frame. Best paired with #264 (deformed-mesh point-location fix), which makes the nodal FE bake exact; together the adapted mesh stays clean under forced every-step adaptation at R=5 (folded=0, cell-area-ratio flat) where it previously tore holes. Validated in a sibling worktree (this is a one-line source change; CI runs the full mover suite). Underworld development team with AI support from Claude Code
lmoresi added a commit
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Jul 6, 2026
…og, value-first call-site sweep (WE-01..03,05,06,08,09,10) (#338) * docs(WE-01): adopt the one-governing-doc-per-topic authority map Repoint CLAUDE.md's Data Access 'Authoritative Reference' from the stale UW3_Style_and_Patterns_Guide.md to subsystems/data-access.md (the guide it crowned teaches patterns the code deprecates at runtime — DOC-04), and record the Style Charter §10 authority table in docs/developer/index.md as the master authority index. The Charter is added to the Getting Started toctree (removes a baseline 'not included in any toctree' warning). Finding: DOC-04 (docs/reviews/2026-07/DOCS-STANDARDS-COHERENCE.md). Underworld development team with AI support from Claude Code * docs(WE-02): de-drift the Style Guide's four stale normative sections Rewrites the sections DOC-01 verified as contradicting the settled standards: - Docstring format: the 'Markdown Docstrings for pdoc/pdoc3' section is replaced by the NumPy/Sphinx RST standard (worked example with :math: and Parameters/Returns/Examples/Notes; conversion tracked in docs/plans/docstring-conversion-plan.md), per Style Charter section 6. - Doc file format: Quarto .qmd prescription (zero .qmd files exist in the repo) replaced by MyST .md/Sphinx guidance matching CLAUDE.md; migration table row updated. - Data access examples: 'Preferred' coordinate examples now use the real, runnable API — mesh.X.coords (read), mesh.deform() (coordinate changes), and the swarm.coords getter/setter for particle positions. The previous 'Preferred' example swarm.data += displacement raises AttributeError (getter-only property — SWARM-13 evidence); mesh.data warns at runtime. The private-attribute migration advice (swarm._particle_coordinates, mesh._deform_mesh presented as the NEW pattern) is deleted. - Front matter: the 21-line Quarto YAML header is replaced by a minimal MyST title block, and the guide now states that the UW3 Style Charter is the normative contract and wins on conflict. All replacement examples verified against current source: Swarm.coords setter (swarm.py), Mesh.deform (discretisation_mesh.py:3133), uw.synchronised_array_update / NDArray_With_Callback.delay_callbacks_global. Findings: DOC-01, SWARM-13 (style-guide part). Underworld development team with AI support from Claude Code * docs(WE-03): regenerate the docstring review queue; add the sweep to the release checklist The queue (last generated 2026-01-13, cdf5bb2) misrepresented the codebase both ways: it flagged now-complete items (solve, SNES_Scalar) as missing and contained zero entries for the June 2026 API (DOC-02). Regenerated over src/underworld3/**/*.py + **/*.pyx at the current tip. Two bugs in scripts/docstring_sweep.py's regex-based Cython parser made the regenerated queue lie about .pyx docstrings and are fixed as part of making the regeneration meaningful: - the indent group '(\s*)' with re.MULTILINE consumed preceding blank lines, shifting the computed definition line so the docstring search started ON the def/class line and always missed; - the docstring search started at the definition line rather than after the (possibly multi-line) signature, so long signatures hid their docstrings; - raw-string docstrings (r""", the norm in the solver .pyx) were not recognised. DOC-02 cross-validation on the regenerated queue now passes: solve / SNES_Scalar in the solver pyx are no longer flagged 'none'; the queue contains the June API (add_nitsche_bc, add_rotated_freeslip_bc, boundary_flux, set_custom_fmg, consistent_jacobian: 13 mentions) and flags the DOC-05 targets (Swarm.advection x2, read_timestep, write_proxy) as undocumented. Also adds the sweep to the quarterly release checklist (guides/release-process.md) so the queue cannot go stale unnoticed again. Findings: DOC-02 (docs/reviews/2026-07/DOCS-STANDARDS-COHERENCE.md). Underworld development team with AI support from Claude Code * docs(WE-05): backfill the changelog for May - early July 2026; add the changelog sweep to the release checklist The changelog (the quarterly CIG/stakeholder record) ended in April 2026 while ~117 first-parent commits landed May through early July (DOC-03). Backfilled at the existing conceptual granularity — 14 grouped entries, grouped by subsystem rather than by PR, matching the established format (### Title (Month Year), bold lead sentence, hyphen bullets, inline PR references): - New '2026 Q3 (July - September)' section: the July 2026 quality campaign (#309-#313, #317, #322-#326, #329, #334 as grouped entries), rotated strong free-slip / boundary traction / dynamic topography (#293, #294, #298, #306), generalized geometric multigrid via custom prolongation (#290, #297), consistent Jacobian tangent (#258), swarm correctness (#216, #313, #323, #329), numpy 2 support (#301, #305). - Extended '2026 Q2' section with the May-June entries: mesh adaptation movers (#190, #209, #213, #228, #259, #264, #266), moving-mesh field transfer / deform() (#246, #249, #251), semi-Lagrangian accuracy controls (#164, #183, #185-#189, #208, #220), snapshot/checkpoint toolkit (#146, #195, #196, #198), Stokes_Constrained (#224, #229, #240, #265), local-h Nitsche + boundary-slip surfaces (#225, #241, #275), units interoperability (#277, #278, #283, #284), memory/evaluation/solver infrastructure (#161, #177-#179, #181, #182, #222, #237, #250, ...). Every entry is backed by a merged commit on development (verified against git log --first-parent aed517f..3184a40). Also adds a quarterly-changelog sweep step beside the docstring sweep in the release checklist (guides/release-process.md) per DOC-03's proposed fix. Findings: DOC-03 (docs/reviews/2026-07/DOCS-STANDARDS-COHERENCE.md). Underworld development team with AI support from Claude Code * docs(WE-06): status headers on the unmarked design docs (per-doc git verification) Adds one-to-three-line Status markers to the 13 design docs that lacked one, following the directory's existing conventions (**Status**: line under the title; status: key inside existing YAML frontmatter for the three frontmatter-only docs), and corrects the stale 'Design Phase' marker on MATHEMATICAL_MIXIN_DESIGN.md (the mixin ships in utilities/mathematical_mixin.py). Every stamp was verified against git history (git log --follow dates) and the current source tree before writing: - Implemented: jacobian-consistent-tangent (PR #258, c63cd70), fmg-checkpoint-hierarchy (3cd73cd), petsc-dmplex-checkpoint-reload-plan (PR #146, write_timestep(petsc_reload=True) in tree), fault-refinement-simplification (smooth_mesh_interior / metric_density_from_gradient / fault_comb_metric all in tree), MATHEMATICAL_MIXIN_DESIGN. - Current reference/contract: mesh-adaptation-formulation, ND_UNITS_BOUNDARY_CONTRACT (PR #278, e0ece9a). - Investigation records (preserved via PR #245, 34a9dd4; production geometric-MG is custom prolongation, PR #290): snesfas-feasibility, snesfas-vanka-feasibility-study. - Design notes / prototypes with honest gaps: in_memory_checkpoint_design (not implemented, per its own trailing Status section), submesh-solver-architecture (extract_region/extract_surface exist; coarsened_companion does not). - Historical: ARCHITECTURE_ANALYSIS (persistence.py layout superseded), COORDINATE_MIGRATION_GUIDE (transition shipped), WHY_UNITS_NOT_DIMENSIONALITY (decision record). The audit's ~16 estimate over-counted: re-derived at this tip, 13 docs were unmarked plus one marked-but-stale (DOC-07). Findings: DOC-07 (docs/reviews/2026-07/DOCS-STANDARDS-COHERENCE.md). Underworld development team with AI support from Claude Code * docs(WE-08): convert units.py public docstrings Google -> NumPy style Docstring-only conversion of the 18 public module-level functions that carried Google-style Args:/Returns:/Raises:/Examples: labels (check_units_consistency, get_dimensionality, get_units, non_dimensionalise, show_nondimensional_form, simplify_units, create_quantity, convert_units, to_base_units, to_reduced_units, to_compact, get_scaling_coefficients, set_scaling_coefficients, validate_expression_units, assert_dimensionality, validate_coordinates_dimensionality, enforce_units_consistency, require_units_if_active, convert_angle_to_degrees) to the NumPy/Sphinx standard (Style Charter section 6). dimensionalise was already NumPy style; one-line docstrings and private helpers are untouched. No code, signature, or behaviour changes (verified: every diff hunk is inside a docstring; ast.parse clean). Finding: API-12 (docs/reviews/2026-07/API-CONSISTENCY-REVIEW.md). Underworld development team with AI support from Claude Code * docs(WE-09): sweep call sites of the newer BC methods to value-first (conds, boundary, ...) order Wave C (#334) made the ORIGINAL value-first order canonical for add_nitsche_bc / add_rotated_freeslip_bc / add_constraint_bc (maintainer decisions D2/D3; Style Charter section 6) with deprecation shims for the legacy boundary-first and g= spellings. This sweep updates every call site of those THREE methods to the canonical order so nothing in the repository exercises the shims — 74 sites total: - tests/: 63 call sites across 12 files (test_1017, test_1018, test_1060, test_1061, test_1062, test_1064, test_1065 x2 serial; parallel test_1017, test_1062, test_1063, test_1064). tests/test_0641_wave_c_api_shims.py is deliberately untouched — its legacy-order calls ARE the deprecation contract. - docs/: 7 sites (curved-boundary-conditions.md x4, CONSTRAINED_FREESLIP_MULTIPLIER.md call + signature line, examples/submesh_investigation/test_region_ds_nitsche.py). - .claude/skills/: 3 sites (adapt-on-top-faults x2, free-surface-convection x1). - CLAUDE.md: 1 signature reference (free-slip BC preference section). The ~1,370 legacy-trio (add_dirichlet_bc/add_natural_bc/add_essential_bc) sites already conform and are untouched per the D2 decision. The audit review documents under docs/reviews/2026-07/ record the pre-decision state as evidence and are not swept. Discovered while verifying the swept tests run warning-free: the Wave C zero-datum guard in add_rotated_freeslip_bc rejects FLOAT zero (sympy.sympify(0.0) != 0 is structurally True), so the canonical add_rotated_freeslip_bc(0.0, boundary) raises NotImplementedError while conds=0 works. Filed as issue #336 with a TODO(BUG) marker at the guard (comment-only src touch); the swept call sites use the working integer form add_rotated_freeslip_bc(0, boundary). No fix applied here (Charter section 9 scope discipline). Findings: API-01/API-02 sweep (WE-09, REMEDIATION-WORKLIST.md). Underworld development team with AI support from Claude Code
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Problem
_winslow_mmpde's energy/gradient use fractional powers —sqrt(detM),detM**((1-p)/2), andS**qwithS = tr(J·M⁻¹·Jᵀ)— that are defined only for an SPD metric.The metric is a guide field FE-evaluated at a fixed reference cloud. Once the interior deforms, a reference point can fall outside the current mesh and the P1 density is then evaluated by FE extrapolation, going negative. A scalar density
ρ<0givesM = ρ·Iwithdet = ρ² > 0— so adetM>0check passes — butMis negative-definite, soS<0andS**q = NaN. The energy becomes non-finite and the mover bails with zero displacement.The effect is intermittent and silent: on an adaptive convection loop roughly half the adapts no-op, the mesh under-resolves, and the symptom is easily misread as an adapt/solver coupling problem or "passive-fault damping."
Fix
Project every evaluated metric tensor onto SPD with a small relative eigenvalue floor at the single
_eval_Mchokepoint:No API change. No behaviour change where the metric is already valid — verified bit-identical on the adapts that previously succeeded.
Validation
test_0762_fault_metric_tensor,test_0850_mesh_smoothing,test_0750_meshing_follow_metric,test_0830_mesh_adapt_variable_transfer: 33 passed, 5 skipped (MMG), 4 pre-existing xfail.[0,1], vrms bounded over 52 steps (no-fault) and 32 steps (passive fault). Without it, ~half the adapts NaN-bail and the mesh stops adapting.Underworld development team with AI support from Claude Code