Pymatgen crystal structure parsing starter

Pymatgen Crystal Structure Parsing Starter

Use this skill to parse one crystal structure file with pymatgen and return a deterministic structural summary with lattice, composition, density, and symmetry metadata.

What it does

• Loads a structure file such as CIF with pymatgen.core.Structure.
• Summarizes formula, reduced formula, lattice parameters, volume, density, and species counts.
• Uses SpacegroupAnalyzer to report a space-group symbol, number, and crystal system when symmetry analysis succeeds.

When to use it

• You need a runnable starter for the crystal structure parsing leaf.
• You want a lightweight structure summary before feature engineering or property modeling.

Example

slurm/envs/materials/bin/python skills/materials-science-and-engineering/pymatgen-crystal-structure-parsing-starter/scripts/run_pymatgen_structure_summary.py \
  --input skills/materials-science-and-engineering/pymatgen-crystal-structure-parsing-starter/examples/cscl.cif \
  --out scratch/materials/cscl_structure_summary.json

Verification

• Skill-local tests: python3 -m unittest discover -s skills/materials-science-and-engineering/pymatgen-crystal-structure-parsing-starter/tests -p 'test_*.py'
• Repository smoke: python3 -m unittest tests.smoke.test_phase28_network_materials_cheminformatics_skills -v