data: regenerate all 5 systems with MM3 angle gradient fix (2 newly significant)#10
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…nt fix Companion to q2mm fix branch fix/mm3-non-smooth-gradient (commit 78e72fa, PR #TBD). Re-runs the convergence pipeline with --n-evals 10 against q2mm patched for the angle-term gradient correctness bug documented in q2mm#284. Results — two previously "no improvement" verdicts now SIGNIFICANT: | System | Pre-fix Δ% | Post-fix Δ% | Verdict | |-----------------|------------------|------------------|---------------| | ch3f | 99.83 % (det.) | 99.83 % (det.) | unchanged ✅ | | rh-enamide | 44.66 % ± 0.29 % | 44.73 % ± 0.29 % | unchanged ✅ | | pd-allyl | -0.029 % ± 0.34% | -0.01 % ± 0.40 % | still NS ❌ | | rh-conjugate | -0.080 % ± 1.18% | 18.00 % ± 4.17 % | NEWLY ✅ | | heck-relay* | -0.59 % ± 3.26 % | 52.82 % ± 1.54 % | NEWLY ✅ | (*) heck-relay run with --ratio-tol none; with the fix the ratio actually drops from 1.378 → 1.085, so the gate would now pass at default tolerance. Bypass retained here for direct comparison against the pre-fix #9 baseline. What this PR contains Per-system, the convergence/ directory now has: - <system>_optimized.fld — optimized force field - validation_results.json — n=10 mean+CI numbers, full provenance - paper_metrics.json — paper-comparable Seminario vs. optimized stats Provenance (every JSON): - q2mm git_sha: 78e72fa (the fix branch's HEAD) - q2mm-data git_sha: a3cc8d7 (main, post-#8) - n_evals: 10 - ratio_tol: 0.15 (default) for 4 systems; null for heck-relay pd-allyl's pd-allyl_optimized.fld is bit-identical to the previous version — the surrogate-guided step still worsened the real OF slightly (within noise), so ScipyOptimizer reverted to initial params. Even the fix doesn't unlock pd-allyl: its FF really does sit at a JaxLoss local minimum, distinct from the rh-conjugate / heck-relay cases where the clip-arccos bug was preventing the optimizer from finding real descent directions. Wall time on RTX 5090: - ch3f: ~3 s (deterministic, n=5) - rh-enamide: ~26 min (opt + n=5 post-eval) - pd-allyl: ~50 min (opt + n=10 post-eval) - rh-conjugate: ~36 min (opt + n=10 post-eval) - heck-relay: ~98 min (opt + n=10 post-eval) - Total: ~3.5 hr GPU The audit-orphans CI workflow (q2mm-data#8) is expected to pass since every directory modified is already referenced in q2mm/docs/systems/*.md. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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Summary
Regenerated artifacts for all 5 published-FF systems with the q2mm MM3 angle gradient correctness fix (ericchansen/q2mm#288).
Companion code PR: ericchansen/q2mm#288
Results — two newly unlocked
heck-relay's ratio dropped from 1.378 → 1.085 with the fix, so it would now pass the default
ratio_tol=0.15gate. The--ratio-tol noneflag is retained in the regen command here only for direct comparison against the pre-fix #9 baseline.What this PR contains
Per-system, the convergence/ directory now has:
<system>_optimized.fld— optimized force fieldvalidation_results.json— n=10 mean+CI numbers, full provenancepaper_metrics.json— paper-comparable Seminario vs. optimized statsProvenance (every JSON):
855c086(the fix branch's HEAD)a3cc8d7(main, post-ci: run audit-orphans.sh on every PR + weekly cron #8)nullfor heck-relaypd-allyl's
pd-allyl_optimized.fldis bit-identical to the previous version — even after the gradient fix the optimizer correctly reverts to initial params because no real descent direction exists for that system.Wall time (RTX 5090)
Audit-orphans CI
This PR is exercising the workflow merged in #8 — every directory modified is already referenced in
q2mm/docs/systems/*.md, so it should pass.