Structure Enumeration

Structure Enumeration Skill

Generate candidate crystal structures by substituting elements in a prototype structure. Supports three prototype sources: Materials Project lookup, local CIF files, or building from spacegroup + Wyckoff positions.

Scripts

enumerate_structures.py — Substitute elements in a prototype

From Materials Project (for ambient-pressure phases):

python3 {baseDir}/scripts/enumerate_structures.py \
  --prototypes LaH3,CaH2 \
  --metals Y,Ca,Sc,Ce \
  --format json

From Wyckoff positions (for high-pressure or hypothetical phases not in MP):

python3 {baseDir}/scripts/enumerate_structures.py \
  --wyckoff '[{"name":"LaH10","spacegroup":225,"lattice":{"a":5.1},"species":["La","H","H"],"coords":[[0,0,0],[0.25,0.25,0.25],[0.118,0.118,0.118]]}]' \
  --metals Y,Ca,Sc,Ce \
  --format json

Multiple prototypes via Wyckoff:

python3 {baseDir}/scripts/enumerate_structures.py \
  --wyckoff '[{"name":"LaH10","spacegroup":225,"lattice":{"a":5.1},"species":["La","H","H"],"coords":[[0,0,0],[0.25,0.25,0.25],[0.118,0.118,0.118]]},{"name":"CaH6","spacegroup":229,"lattice":{"a":3.54},"species":["Ca","H"],"coords":[[0,0,0],[0.25,0,0.5]]}]' \
  --metals Y,Sc,Ce,Ba \
  --format json

Parameters

Wyckoff Spec Format

Each prototype is a JSON object with:

{
  "name": "LaH10",
  "spacegroup": 225,
  "lattice": {"a": 5.1},
  "species": ["La", "H", "H"],
  "coords": [[0,0,0], [0.25,0.25,0.25], [0.118,0.118,0.118]]
}

• name: label for the prototype
• spacegroup: international space group number
• lattice: {"a": ...} for cubic, {"a": ..., "c": ...} for hexagonal
• species: element at each Wyckoff site (first non-H element is the metal site for substitution)
• coords: fractional coordinates for each Wyckoff site

Common superhydride prototypes

How It Works

1. Loads each prototype structure (from MP, local file, or Wyckoff construction)
2. Identifies the metal site (heaviest non-hydrogen element)
3. For each target metal, substitutes the metal site and writes a new CIF file
4. The original prototype is also saved (with _prototype suffix)
5. All CIF files are written to --output-dir

Output (JSON)

{
  "status": "success",
  "output_dir": "/home/user/.scienceclaw/enumerated_structures",
  "prototypes_used": ["LaH10", "CaH6"],
  "metals": ["Y", "Ca", "Sc"],
  "total_generated": 6,
  "structures": [
    {
      "label": "YH10_from_LaH10",
      "formula": "YH10",
      "prototype": "LaH10",
      "metal": "Y",
      "n_atoms": 44,
      "cif_path": "/home/user/.scienceclaw/enumerated_structures/YH10_from_LaH10.cif"
    }
  ]
}