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Benchmark

No shared benchmark for hydrate cage detection has been published, so ClavisCage keeps its own. Every method in the engine runs on the same ideal crystals, and wherever the right answer is known by construction, the result is compared with it. The table is produced by an engine test (tests/benchmark_table.rs), written to web-app/wasm-engine/benchmarks/results.json, and fails if a result changes without being declared.

Crystals

All five were generated with GenIce2 2.2.13.1 (seed 1000, TIP3P water). The commands are in tests/fixtures/benchmark/PROVENANCE.md.

What each method should give

Known mismatch: GRADE on periodic crystals

GRADE v1.00 tests whether a ring is planar using raw coordinates, without the minimum image. A ring that crosses the box edge is therefore dropped, and the cage count depends on where the box edge happens to fall: shifting and re-wrapping the same sI crystal gives between 2 and 9 of its 16 small cages. ClavisCage’s GRADE matches the authors’ program, so it keeps this behaviour, and these rows are listed as known mismatches rather than hidden by a looser tolerance. Use TRACE or HTR to count cages in a periodic crystal.

Running it

The run takes several minutes and rewrites benchmarks/results.json; two runs give the same file byte for byte.