Use surfacemesh.import instead of the hand-rolled mesh readers
surfacefun's surfacemesh.import (gmsh) now reads the uploaded mesh, so the
custom load_gmsh_quads.m / surfacemesh_from_quads.m are gone. Its gmsh
reader parses MSH 4.1 node-entity blocks, so the meshio bridge and sample
generator now emit 4.1. Requires numbl >= 0.4.11 (enumeration classes +
1x1-tensor broadcast fix, which surfacefun's patchtype needs).
13 changed files+1586−1160
CLAUDE.mdmodified+20−20View file
@@ -8,9 +8,7 @@ Tips for future agents working in this repo.
88 matlab/ the MATLAB project each solve runs standalone
99 main.m `mip load --install surfacefun` -> jsondecode params.json
1010 -> solve_pde('mesh.msh', params) -> write result.json
11- solve_pde.m mesh -> surfacemesh -> resample -> surfaceop -> per-patch data
12- load_gmsh_quads.m minimal MSH 2.2 ASCII reader (canonical form only)
13- surfacemesh_from_quads.m replaces surfacemesh.fromGmsh (see below)
11+ solve_pde.m surfacemesh.import -> resample -> surfaceop -> per-patch data
1412 src/mesh/ Pyodide + meshio upload pipeline (bridge.py runs in Pyodide)
1513 src/engine/ run-per-solve wrapper over numbl/browser's
1614 createNumblSession: solve() boots a fresh session with
@@ -26,19 +24,20 @@ scripts/engine-test.mjs headless Node check of the whole MATLAB pipeline
2624
2725 ## Key gotchas
2826
29-- **numbl >= 0.4.10 from npm** (`NumblSession.readFile`, which the engine
30- uses to fetch result.json, landed in 0.4.10; the `numbl/browser` entry and
31- executeCode searchPaths scanning landed in 0.4.9). To develop against a
32- local numbl checkout, point package.json at `file:../../numbl` and run
33- `npm run build:lib && npm run build:browser` there after source changes.
34-- **surfacemesh.fromGmsh is not used.** It locates the QUADS field via
35- `startsWith(fieldnames(...), 'QUADS')` (cellstr startsWith — unsupported in
36- numbl) and handles high-order gmsh quads. Our converter only emits 4-node
37- quads, so `surfacemesh_from_quads.m` builds the 2x2 patches directly.
38-- **Canonical .msh only.** `load_gmsh_quads.m` assumes what
39- `src/mesh/bridge.py` writes: MSH 2.2 ASCII, sequential 1-based node ids,
40- type-3 elements, two tags. Uploaded .msh files in other layouts are fine —
41- they pass through meshio and get rewritten canonically.
27+- **numbl >= 0.4.11 from npm.** Needs `NumblSession.readFile` (0.4.10) plus
28+ enumeration-class support and the 1×1-tensor broadcast-assignment fix
29+ (0.4.11 — surfacefun's `surfacemesh.patchtype` / `dealm` idiom depend on
30+ both). To develop against a local numbl checkout, point package.json at
31+ `file:../../numbl` and run `npm run build:lib && npm run build:browser`
32+ there after source changes; when switching back to a `^` range,
33+ `rm -rf node_modules package-lock.json && npm install` (else `npm ci` fails
34+ on the stale `file:` link).
35+- **surfacemesh.import needs MSH 4.1.** surfacefun's gmsh reader
36+ (`+surfacemesh/+import/gmsh.m`) parses MSH 4.1 node-entity blocks, not
37+ 2.2. `src/mesh/bridge.py` and `scripts/make_samples.py` both write the
38+ canonical 4.1 form (one surface entity block, sequential 1-based ids,
39+ type-3 quads). Uploaded .msh files in other layouts pass through meshio
40+ and get rewritten to 4.1.
4241 - **Solve errors reject the solve() promise** with the MATLAB error message
4342 (a failed script run is a numbl bootError). Each solve is a fresh session,
4443 so nothing needs to stay alive across failures.
@@ -46,10 +45,11 @@ scripts/engine-test.mjs headless Node check of the whole MATLAB pipeline
4645 (p+1)^2 >= 9 long so it never bites here, but remember it when adding
4746 payload fields.
4847 - Package caching: numbl/browser persists /system (mip + installed
49- packages) in IndexedDB, wiped after 24 h of inactivity — the prewarm
50- session at page load re-downloads ~28 MB on a fresh day; solves after
51- that only pay a per-run `mip load` (~1 s). Delete the
52- `numbl-embed-system` IndexedDB database to test cold boots.
48+ packages) in IndexedDB, wiped after 30 min of inactivity (numbl's default;
49+ lowered from 24 h so a rebuilt surfacefun package refreshes without a manual
50+ clear) — the prewarm session at page load re-downloads ~28 MB after a wipe;
51+ solves after that only pay a per-run `mip load` (~1 s). Delete the
52+ `numbl-embed-system` IndexedDB database to force a cold boot.
5353
5454 ## Testing
5555
README.mdmodified+6−6View file
@@ -31,7 +31,7 @@ Whether the surface is closed or open is detected from the edge connectivity.
3131 ## How it works
3232
3333 1. `src/mesh/` — meshio in Pyodide parses the upload, keeps the quad cells,
34- and writes a canonical Gmsh MSH 2.2 ASCII file plus preview arrays.
34+ and writes a canonical Gmsh MSH 4.1 ASCII file plus preview arrays.
3535 2. `src/engine/` — each solve boots a fresh managed numbl session
3636 (`createNumblSession` from `numbl/browser`): numbl owns the worker and
3737 VFS and bootstraps the [mip](https://github.com/mip-org) package manager.
@@ -39,9 +39,8 @@ Whether the surface is closed or open is detected from the edge connectivity.
3939 [`matlab/main.m`](matlab/main.m) standalone — it begins with
4040 `mip load --install surfacefun`, solves, and writes `result.json`, which
4141 the host reads back before disposing the worker.
42-3. `matlab/solve_pde.m` — parses the mesh (`load_gmsh_quads.m`), builds a
43- `surfacemesh` from the quads, `resample`s it to the requested order, and
44- solves with `surfaceop`.
42+3. `matlab/solve_pde.m` — loads the mesh with `surfacemesh.import`,
43+ `resample`s it to the requested order, and solves with `surfaceop`.
4544 4. `src/render/SurfaceView.tsx` — three.js view of the quad mesh or the
4645 per-patch solution grids with a parula colormap.
4746
@@ -65,5 +64,6 @@ numbl's synchronous-XHR `websave`/`webread` with curl (responses cached in
6564 `.cache/`), and checks a Poisson solve against an exact spherical-harmonic
6665 solution.
6766
68-Requires numbl >= 0.4.10 (the `numbl/browser` managed-session entry with
69-`readFile`).
67+Requires numbl >= 0.4.11 — `NumblSession.readFile` (0.4.10) plus
68+enumeration-class support and the 1×1-tensor broadcast-assignment fix (0.4.11),
69+which surfacefun's `surfacemesh.import` / `patchtype` depend on.
matlab/load_gmsh_quads.mdeleted+0−56View file
@@ -1,56 +0,0 @@
1-function msh = load_gmsh_quads(filename)
2-%LOAD_GMSH_QUADS Minimal Gmsh MSH 2.2 ASCII reader for all-quad meshes.
3-% Returns a struct with POS (n-by-3 node coordinates) and QUADS
4-% (m-by-5: four 1-based node indices plus a tag), the layout that
5-% surfacemesh.fromGmsh expects.
6-%
7-% Only the canonical form written by this app's converter is supported:
8-% sequential node ids starting at 1, and 4-node quadrangle elements
9-% (type 3) with exactly two tags.
10-
11-txt = fileread(filename);
12-
13-block = extract_block(txt, '$Nodes', '$EndNodes');
14-vals = sscanf(block, '%f');
15-nn = vals(1);
16-if numel(vals) ~= 1 + 4*nn
17- error('load_gmsh_quads:badNodes', 'Unexpected $Nodes layout.');
18-end
19-data = reshape(vals(2:end), 4, nn);
20-if any(data(1, :) ~= 1:nn)
21- error('load_gmsh_quads:badNodes', 'Node ids must be sequential from 1.');
22-end
23-pos = data(2:4, :)';
24-
25-block = extract_block(txt, '$Elements', '$EndElements');
26-vals = sscanf(block, '%f');
27-ne = vals(1);
28-% Each element line: id type(=3) ntags(=2) tag tag n1 n2 n3 n4
29-if numel(vals) ~= 1 + 9*ne
30- error('load_gmsh_quads:badElements', ...
31- 'Expected only 4-node quadrangles with two tags.');
32-end
33-data = reshape(vals(2:end), 9, ne);
34-if any(data(2, :) ~= 3)
35- error('load_gmsh_quads:badElements', ...
36- 'Expected only 4-node quadrangle elements (type 3).');
37-end
38-idx = data(6:9, :)';
39-if any(idx(:) < 1) || any(idx(:) > nn)
40- error('load_gmsh_quads:badElements', 'Element node index out of range.');
41-end
42-quads = [idx, ones(ne, 1)];
43-
44-msh = struct();
45-msh.POS = pos;
46-msh.QUADS = quads;
47-end
48-
49-function block = extract_block(txt, startMarker, endMarker)
50-i1 = strfind(txt, startMarker);
51-i2 = strfind(txt, endMarker);
52-if isempty(i1) || isempty(i2)
53- error('load_gmsh_quads:badFile', 'Missing %s section.', startMarker);
54-end
55-block = txt(i1(1) + length(startMarker) : i2(1) - 1);
56-end
matlab/solve_pde.mmodified+1−2View file
@@ -8,8 +8,7 @@ function result = solve_pde(mshfile, params)
88 % closed - true if every mesh edge is shared by exactly two quads
99 % (determined host-side from the connectivity)
1010
11-msh = load_gmsh_quads(mshfile);
12-dom = surfacemesh_from_quads(msh);
11+dom = surfacemesh.import(mshfile, 'gmsh');
1312 dom = resample(dom, params.p + 1);
1413
1514 fh = eval(['@(x, y, z) ', params.f]);
matlab/surfacemesh_from_quads.mdeleted+0−29View file
@@ -1,29 +0,0 @@
1-function dom = surfacemesh_from_quads(msh)
2-%SURFACEMESH_FROM_QUADS Build a surfacemesh from a 4-node quad msh struct.
3-% Adapted from surfacemesh.fromGmsh (surfacefun): that version locates a
4-% QUADS* field via startsWith over fieldnames — which numbl's startsWith
5-% does not support for cell arrays — and handles high-order gmsh quads.
6-% Our converter only ever emits plain 4-node quads (Gmsh corner order
7-% 1-2-3-4 counterclockwise), where the equispaced and Chebyshev 2-point
8-% grids coincide, so each patch is just its corner values arranged as a
9-% 2-by-2 tensor grid.
10-
11-quads = msh.QUADS;
12-nelem = size(quads, 1);
13-x = cell(nelem, 1);
14-y = cell(nelem, 1);
15-z = cell(nelem, 1);
16-
17-for k = 1:nelem
18- idx = quads(k, 1:4);
19- px = msh.POS(idx, 1);
20- py = msh.POS(idx, 2);
21- pz = msh.POS(idx, 3);
22- % Gmsh corners 1,2,3,4 -> tensor grid (1,1),(2,1),(2,2),(1,2)
23- x{k} = [px(1) px(4); px(2) px(3)];
24- y{k} = [py(1) py(4); py(2) py(3)];
25- z{k} = [pz(1) pz(4); pz(2) pz(3)];
26-end
27-
28-dom = surfacemesh(x, y, z);
29-end
package-lock.jsonmodified+4−4View file
@@ -9,7 +9,7 @@
99 "version": "0.0.0",
1010 "dependencies": {
1111 "fflate": "^0.8.2",
12- "numbl": "^0.4.10",
12+ "numbl": "^0.4.11",
1313 "react": "^19.2.7",
1414 "react-dom": "^19.2.7",
1515 "three": "^0.185.1"
@@ -2483,9 +2483,9 @@
24832483 }
24842484 },
24852485 "node_modules/numbl": {
2486- "version": "0.4.10",
2487- "resolved": "https://registry.npmjs.org/numbl/-/numbl-0.4.10.tgz",
2488- "integrity": "sha512-rckOPXCjh6u6LnLoXVy4MupKG/f5wPK77NRq7vWtKjO5vq+9BN6cHgkh92xQkAKnmUFEkFebH2jqmN5OqSZJfQ==",
2486+ "version": "0.4.11",
2487+ "resolved": "https://registry.npmjs.org/numbl/-/numbl-0.4.11.tgz",
2488+ "integrity": "sha512-3ire6HYNNQNODaUbDItIL2Hx8HJC521d/alzELIDvGn3MClwGmSCqPVBeliTP+qNK3h4tcnzZnC2hUm4BhidAA==",
24892489 "hasInstallScript": true,
24902490 "license": "Apache-2.0",
24912491 "dependencies": {
package.jsonmodified+1−1View file
@@ -12,7 +12,7 @@
1212 },
1313 "dependencies": {
1414 "fflate": "^0.8.2",
15- "numbl": "^0.4.10",
15+ "numbl": "^0.4.11",
1616 "react": "^19.2.7",
1717 "react-dom": "^19.2.7",
1818 "three": "^0.185.1"
public/samples/sphere.mshmodified+656−436View file
@@ -1,443 +1,663 @@
11 $MeshFormat
2-2.2 0 8
2+4.1 0 8
33 $EndMeshFormat
44 $Nodes
5+1 218 1 218
6+2 1 0 218
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5224 218
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585875 $EndElements
scripts/engine-test.mjsmodified+1−6View file
@@ -75,12 +75,7 @@ async function main() {
7575 }
7676 console.log(`mip core: ${nMip} files into VFS`)
7777
78- const projectFiles = [
79- 'main.m',
80- 'solve_pde.m',
81- 'surfacemesh_from_quads.m',
82- 'load_gmsh_quads.m',
83- ]
78+ const projectFiles = ['main.m', 'solve_pde.m']
8479 for (const name of projectFiles) {
8580 vfs.writeFile(`/project/${name}`, enc.encode(readProjectFile(name)))
8681 }
scripts/make_samples.pymodified+13−9View file
@@ -1,8 +1,9 @@
11 """Generate the bundled sample quad meshes (public/samples/*.msh).
22
3-Writes Gmsh MSH 2.2 ASCII files in the same canonical form the in-app
4-converter produces: sequential 1-based node ids and 4-node quadrangle
5-elements (type 3) with two tags.
3+Writes Gmsh MSH 4.1 ASCII files in the same canonical form the in-app
4+converter produces: one surface entity block, sequential 1-based node ids,
5+and 4-node quadrangle elements (type 3) — the layout surfacemesh.import
6+reads.
67
78 Run from the repo root: python3 scripts/make_samples.py
89 """
@@ -14,17 +15,20 @@ OUT_DIR = os.path.join(os.path.dirname(__file__), "..", "public", "samples")
1415
1516
1617 def write_msh(path, points, quads):
17- lines = ["$MeshFormat", "2.2 0 8", "$EndMeshFormat"]
18+ n, m = len(points), len(quads)
19+ lines = ["$MeshFormat", "4.1 0 8", "$EndMeshFormat"]
1820 lines.append("$Nodes")
19- lines.append(str(len(points)))
20- for i, (x, y, z) in enumerate(points, start=1):
21- lines.append(f"{i} {x:.16g} {y:.16g} {z:.16g}")
21+ lines.append(f"1 {n} 1 {n}") # numEntityBlocks numNodes minTag maxTag
22+ lines.append(f"2 1 0 {n}") # entityDim entityTag parametric numNodes
23+ lines.extend(str(i) for i in range(1, n + 1))
24+ lines.extend(f"{x:.16g} {y:.16g} {z:.16g}" for x, y, z in points)
2225 lines.append("$EndNodes")
2326 lines.append("$Elements")
24- lines.append(str(len(quads)))
27+ lines.append(f"1 {m} 1 {m}") # numEntityBlocks numElements minTag maxTag
28+ lines.append(f"2 1 3 {m}") # entityDim entityTag elementType(3=quad) numElements
2529 for i, q in enumerate(quads, start=1):
2630 a, b, c, d = (v + 1 for v in q) # 0-based -> 1-based
27- lines.append(f"{i} 3 2 1 1 {a} {b} {c} {d}")
31+ lines.append(f"{i} {a} {b} {c} {d}")
2832 lines.append("$EndElements")
2933 with open(path, "w") as f:
3034 f.write("\n".join(lines) + "\n")
src/engine/engine.tsmodified+0−4View file
@@ -7,8 +7,6 @@
77 import { createNumblSession, type NumblSession } from 'numbl/browser'
88 import main from '../../matlab/main.m?raw'
99 import solvePde from '../../matlab/solve_pde.m?raw'
10-import surfacemeshFromQuads from '../../matlab/surfacemesh_from_quads.m?raw'
11-import loadGmshQuads from '../../matlab/load_gmsh_quads.m?raw'
1210
1311 const SOLVE_TIMEOUT_MS = 300_000
1412
@@ -78,8 +76,6 @@ export async function solve(
7876 files: [
7977 { path: 'main.m', content: main },
8078 { path: 'solve_pde.m', content: solvePde },
81- { path: 'surfacemesh_from_quads.m', content: surfacemeshFromQuads },
82- { path: 'load_gmsh_quads.m', content: loadGmshQuads },
8379 { path: 'params.json', content: JSON.stringify(params) },
8480 { path: 'mesh.msh', content: meshBytes },
8581 ],
src/mesh/bridge.pymodified+16−9View file
@@ -2,9 +2,10 @@
22 #
33 # parse_quad_mesh reads an uploaded mesh file with meshio, keeps only its
44 # quadrilateral cells, and produces three outputs in Pyodide's in-memory
5-# filesystem: the canonical Gmsh MSH 2.2 ASCII file the numbl solver reads
6-# (full float64 precision), plus float32 positions and uint32 quad indices
7-# for the JS-side preview and connectivity checks. See meshio.ts.
5+# filesystem: the canonical Gmsh MSH 4.1 ASCII file the numbl solver reads
6+# with surfacemesh.import (full float64 precision), plus float32 positions
7+# and uint32 quad indices for the JS-side preview and connectivity checks.
8+# See meshio.ts.
89
910 import json
1011 import os
@@ -51,15 +52,21 @@ def _collect_quads(mesh, warnings):
5152
5253
5354 def _write_msh(path, points, quads):
54- """Canonical Gmsh MSH 2.2 ASCII: sequential ids, type-3 quads, two tags."""
55- lines = ["$MeshFormat", "2.2 0 8", "$EndMeshFormat", "$Nodes", str(len(points))]
56- for i, p in enumerate(points, start=1):
57- lines.append("%d %.16g %.16g %.16g" % (i, p[0], p[1], p[2]))
55+ """Canonical Gmsh MSH 4.1 ASCII: one surface entity block, sequential
56+ 1-based node ids, 4-node quads (type 3) — what surfacemesh.import reads."""
57+ n, m = len(points), len(quads)
58+ lines = ["$MeshFormat", "4.1 0 8", "$EndMeshFormat"]
59+ lines.append("$Nodes")
60+ lines.append("1 %d 1 %d" % (n, n)) # numEntityBlocks numNodes minTag maxTag
61+ lines.append("2 1 0 %d" % n) # entityDim entityTag parametric numNodes
62+ lines.extend(str(i) for i in range(1, n + 1))
63+ lines.extend("%.16g %.16g %.16g" % (p[0], p[1], p[2]) for p in points)
5864 lines.append("$EndNodes")
5965 lines.append("$Elements")
60- lines.append(str(len(quads)))
66+ lines.append("1 %d 1 %d" % (m, m)) # numEntityBlocks numElements minTag maxTag
67+ lines.append("2 1 3 %d" % m) # entityDim entityTag elementType(3=quad) numElements
6168 for i, q in enumerate(quads, start=1):
62- lines.append("%d 3 2 1 1 %d %d %d %d" % (i, q[0] + 1, q[1] + 1, q[2] + 1, q[3] + 1))
69+ lines.append("%d %d %d %d %d" % (i, q[0] + 1, q[1] + 1, q[2] + 1, q[3] + 1))
6370 lines.append("$EndElements")
6471 with open(path, "w") as f:
6572 f.write("\n".join(lines) + "\n")