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Fix examples broken on current LAMMPS; add example smoke test - #442
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Adds `npm run test:examples` (src/examples.smoke.ts + vitest.examples.config.mts),
which runs every example in public/examples/examples.json against the real
atomify wasm build the way the app does: the same LammpsAdapter, the same -k on/-sf kk
startup args, the same KOKKOS serial-style and group-inspection
preprocessing, #/bond directives, per-step snapshot calls, and the final
post-run snapshot. Any LAMMPS error, ERROR output line, or snapshot exception
fails the test. Not part of `npm test` (it takes minutes and needs the real
module).
Fixed examples:
- deposit_atom, deposit_molecule, pour_2d, pour_2d_molecule, pour_3d:
`compute_modify ... dynamic yes extra 0` -> `dynamic/dof yes extra/dof 0`.
The old keywords were removed from LAMMPS, which made the deposit examples
error out.
- benzene: a lone apostrophe in a `print "..."` line ("I'm") is an unmatched
quote error once LAMMPS re-parses the print text; reworded.
- pour/granular examples also need lammps.js's fix pour KOKKOS patch (next
lammps.js release).
Group-inspection marker: match __ATOMIFY_GROUPS_READY__ as a line suffix
(splitGroupReady). Output that lacks a trailing newline — the new LAMMPS's
ReaxFF "Changed valency_val" warning — otherwise glues onto the marker, the
include file is never written, and the run fails.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019ZnTFmiih3xq95b7ioCPY7
…uential) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019ZnTFmiih3xq95b7ioCPY7
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Before: several bundled examples fail on current LAMMPS (removed
compute_modifykeywords, an unmatched quote inbenzene), unterminated ReaxFF output can swallow the group-inspection marker, and nothing checks that the example library actually runs.After: those example scripts are fixed, the worker matches the group marker as a line suffix (
splitGroupReady), andnpm run test:examplesruns all 53 examples against the real lammps.js wasm build exactly as the app drives them.This PR does not bump lammps.js; main stays on 1.5.1. The
fix pourexamples (pour_2d,pour_2d_molecule,pour_3d,granular_patterns) still fail with "Cannot yet use fix pour with the KOKKOS package" until lammps.js 1.6.x is published and bumped in a follow-up.How
deposit_atom,deposit_moleculeand the 3 pour scripts:dynamic yes extra 0→dynamic/dof/extra/dof.benzene: reworded aprintwith an apostrophe.src/utils/lammpsGroups.ts:splitGroupReadyplus a unit test; used bysrc/wasm/lammps.worker.ts.src/examples.smoke.ts+vitest.examples.config.mts: the smoke test (not part of the regularvitest run).Testing
npm run test:exampleson lammps.js 1.5.1: only the 4fix pourexamples fail.🤖 Generated with Claude Code
https://claude.ai/code/session_019ZnTFmiih3xq95b7ioCPY7