skills/robustness/simulation-failure-triage/SKILL.md
Triage cross-code simulation failures and propose safe retry ladders for nonconvergence, NaN/Inf, exploding energies, unstable timesteps, pressure blow-up, missing potentials, bad pseudopotentials, corrupted output, and incomplete runs. Use when an agent sees a failed or suspicious materials simulation and needs a defensible first response.
npx skillsauth add HeshamFS/materials-simulation-skills simulation-failure-triageInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Classify common simulation failure signatures and return immediate actions, retry ladders, and stop conditions.
| Input | Description | Example |
|-------|-------------|---------|
| Code | Simulation code | LAMMPS, VASP, MOOSE, QE |
| Stage | Setup, runtime, postprocess | runtime |
| Symptoms | Failure signs | nan,pressure-blowup |
| Log text or file | Error evidence | Lost atoms, ZBRENT |
| Recent change | Last modified setting | larger timestep |
scripts/failure_triage.py emits:
likely_causesimmediate_actionsretry_ladderstop_conditionsevidencepython3 skills/robustness/simulation-failure-triage/scripts/failure_triage.py \
--code LAMMPS \
--stage runtime \
--symptoms nan,pressure-blowup \
--recent-change "increased timestep" \
--json
Invalid stages or oversized log files stop with exit code 2. Unknown symptoms are retained as custom evidence.
This skill gives first-response triage. It does not guarantee that a failed simulation can be repaired.
Bash only to run its bundled script.references/failure_patterns.md for common failure signatures and retry ladders.development
Plan verification and validation campaigns for simulation codes using manufactured solutions, canonical benchmark problems, grid/time refinement, uncertainty propagation, and pass/fail acceptance criteria. Use when an agent needs to prove a solver, model, or result is trustworthy rather than only plausible.
testing
Map computational materials tasks onto workflow engines such as atomate2, jobflow, AiiDA, pyiron, or a simple one-off script. Use when deciding how to structure a reproducible campaign, DAG, restart strategy, provenance record, storage layout, or migration path from ad hoc scripts to managed workflows.
development
Plan molecular dynamics post-processing for materials simulations, including RDF, MSD and diffusion, VACF/VDOS, coordination numbers, bond-angle distributions, stress-strain curves, equilibration detection, PBC unwrapping, and trajectory format choices. Use before writing MD analysis scripts or trusting trajectory-derived results.
documentation
Diagnose HPC runtime and scheduler problems for materials simulations, including MPI/OpenMP/GPU layout, modules, CUDA/Kokkos hints, scratch paths, walltime, job arrays, restart strategy, scheduler portability, and resource mismatch. Use when jobs fail, run slowly, get killed, or behave differently on a cluster than on a workstation.