hello-qm/catgo-lrg/structure

Claude Code and agent skill by hello-qm/catgo-lrg

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Use when the user asks to build, modify, or prepare atomic structures: slabs, adsorbates, supercells, doping, defects, or fetching from databases.

Install

npx vskill@latest install hello-qm/catgo-lrg/structure

SKILL.md

Structure Building Router

This skill routes structure building requests to the correct sub-skill.

Routing Table

User IntentSub-SkillKey Indicators
Surface slab from bulkslab/"slab", "surface", "Miller index", "(111)", "(110)"
Place adsorbate on surfaceadsorbate/"adsorb", "place OH", "add CO", "binding site"
Substitutional dopingdoping/"dope", "substitute", "replace Fe with Co"
Fetch crystal from database(direct)"get from MP", "fetch TiO2", "Materials Project"
Fetch molecule(direct)"get CO molecule", "fetch water"
Make supercell(direct)"supercell", "2x2x1", "expand"

MCP Tools

catgo_structure — Build and modify structures
json
{"tool": "catgo_structure", "arguments": {"action": "slab", ...}}
{"tool": "catgo_structure", "arguments": {"action": "supercell", ...}}
{"tool": "catgo_structure", "arguments": {"action": "add_atom", ...}}
{"tool": "catgo_structure", "arguments": {"action": "delete_atoms", ...}}
{"tool": "catgo_structure", "arguments": {"action": "replace_atom", ...}}
catgo_fetch — Retrieve structures from databases
json
{"tool": "catgo_fetch", "arguments": {"action": "crystal", "formula": "TiO2", "source": "mp"}}
{"tool": "catgo_fetch", "arguments": {"action": "molecule", "name": "water"}}
catgo_view — Inspect and push structures
json
{"tool": "catgo_view", "arguments": {"action": "get_state"}}
{"tool": "catgo_view", "arguments": {"action": "push", "structure": {...}}}

Standard Build Sequence

Most catalysis workflows follow this structure preparation pipeline:

1. Fetch bulk crystal      catgo_fetch(action: crystal)
2. Generate slab           catgo_structure(action: slab)
3. Make supercell          catgo_structure(action: supercell)
4. (Optional) Dope         catgo_structure(action: replace_atom)
5. Place adsorbate         catgo_structure(action: add_atom)
6. Verify structure        catgo_view(action: get_state)
Example: OH on Pt(111)
json
{"tool": "catgo_fetch", "arguments": {
  "action": "crystal", "formula": "Pt", "source": "mp"
}}
json
{"tool": "catgo_structure", "arguments": {
  "action": "slab", "miller_index": [1,1,1],
  "min_slab_size": 12.0, "min_vacuum_size": 15.0
}}
json
{"tool": "catgo_structure", "arguments": {
  "action": "supercell", "scaling": [2, 2, 1]
}}
json
{"tool": "catgo_structure", "arguments": {
  "action": "add_atom", "element": "O", "position": [2.77, 1.60, 14.5]
}}
json
{"tool": "catgo_structure", "arguments": {
  "action": "add_atom", "element": "H", "position": [2.77, 1.60, 15.47]
}}
json
{"tool": "catgo_view", "arguments": {"action": "get_state"}}

Python API

python
from catgo.workflow import Workflow
wf = Workflow("Structure prep")
# Fetch and input
inp = wf.add_task("structure_input", structure=bulk_json)
# Build slab
slab = wf.add_task("slab_gen",
    structure=inp.output.structure,
    miller_index=[1, 1, 1],
    min_slab_size=12.0,
    min_vacuum_size=15.0)
# Place adsorbate
ads = wf.add_task("adsorbate_place",
    structure=slab.output.structure,
    adsorbate="OH",
    site_type="top",
    site_index=0)

Verification Checklist

After building any structure, verify:

  1. Atom count: expected number of atoms for the supercell size
  2. Vacuum: sufficient vacuum for surface calculations (>12 A)
  3. No overlaps: minimum interatomic distance > 0.5 A
  4. Correct composition: stoichiometry matches expectation
  5. Adsorbate position: reasonable height above surface (1.5-2.5 A)

Use catgo_view(action: get_state) to inspect the current structure.

Common Pitfalls

  1. Always fetch the bulk crystal BEFORE cutting a slab. Do not try to

cut a slab from an already-cut slab.

  1. Make the supercell BEFORE placing adsorbates. Supercell operation

replicates all atoms, including adsorbates.

  1. For Materials Project fetch, use reduced formula (e.g., "TiO2" not "Ti2O4").
  2. After each structure modification, verify with catgo_view before

proceeding to the next step.

  1. The viewer shows the structure in the browser. MCP tools modify the

viewer state directly -- there is no separate "save" step.

Security

  • Security scanPassed, 100 of 100Pattern checks on the skill's files.
  • Model reviewNot runA model review is scheduled for the next rescan.

See the full security report

Quality evaluation

  • Task evaluationNot runNo evaluation yet. Run one in Skill Studio.

See evaluation results

Source

Popularity

Repository stars
198
Repository forks
23
7-day trend score
26

Stars and forks are for the whole GitHub repository, not this skill alone. Not refreshed yet.

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