Geometry Optimization

5-30 minutesPaperCodeProduction Ready

Find the lowest-energy 3D structure of a molecule

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass_xtb_gfn2_optimization
Storage: <5
Strategy: shared python312_slim.sif + staged xTB 6.4.1 binary from QupKake tool assets
Next: Production Ready for scoped GFN2-xTB water/default XYZ mode. Optional hardening: add molecule upload controls and method/basis controls only after broader QM validation.

No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged QM CPU SIF/artifacts/runner. Geometry optimization needs a small Psi4/xTB/RDKit/OpenBabel SIF or micromamba overlay before direct smoke. Kept Smoke Pending. 2026-07-05 18:24 +08:00 backend re-audit: no staged QM runtime/artifacts/runner found and no optimized-structure/energy Slurm artifacts found. Kept Smoke Pending. 2026-07-06 implementation pass: ran direct Slurm job 450 at /media/nik/seagate_nik/bio_server/runs/qm_xtb_batch/smoke_20260706_143000. Water GFN2-xTB optimization generated xtbopt.xyz plus finite energy summary.json/results.csv artifacts. 2026-07-08T12:13:39+08:00: Production Ready promotion: backend runner API job 1783ccfe9130 / Slurm job 546 completed cleanly using shared python312_slim.sif and staged xTB 6.4.1 at /media/nik/seagate_nik/bio_server/tools/qupkake/qupkake/xtb-641/bin/xtb. Slurm stdout/stderr were zero-byte; GFN2-xTB optimization on water produced finite energy and xtbopt.xyz.