FAIR Simulation Packager

Goal

Build a minimal reproducibility manifest for materials simulation results so another person or agent can understand what was run, with which inputs, and how outputs should be interpreted.

Requirements

• Python 3.10+
• No external dependencies
• Works on Linux, macOS, and Windows

Inputs to Gather

Decision Guidance

• Always include input files, output files, code version, and units.
• Include hashes for every file that exists locally.
• Include structure identifiers when using Materials Project, NOMAD, OPTIMADE, CIF, POSCAR, or internal database records.
• Record missing files as warnings instead of silently dropping them.

Script Outputs

scripts/fair_packager.py emits:

• manifest
• file_inventory
• missing_files
• fair_checks
• recommended_next_steps

Workflow

python3 skills/data-management/fair-simulation-packager/scripts/fair_packager.py \
  --project-name al-cu-diffusion \
  --engine LAMMPS \
  --inputs in.lammps,data.lmp \
  --outputs log.lammps,traj.dump \
  --units energy=eV,length=angstrom,time=ps \
  --structure-id local:alcu-cell-001 \
  --json

Use --out manifest.json only when the user wants a manifest file written.

Error Handling

Missing files are reported in missing_files; invalid unit fields or unsafe paths stop with exit code 2.

Limitations

This skill creates a metadata manifest. It does not upload to NOMAD, Materials Project, or an OPTIMADE provider.

Security

• File paths are read only for metadata and SHA-256 hashing.
• The script rejects control characters and oversized files above 500 MB.
• Optional manifest writing is restricted to the requested output path.
• The skill uses Bash only to run the bundled script.

References

• See references/fair_manifest.md for recommended manifest fields.

Version History

• 1.0.0: Initial FAIR simulation packaging skill.