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version: "1.0.0" name: structure-router description: > Use when the user asks to build, modify, or prepare atomic structures: slabs, adsorbates, supercells, doping, defects, or fetching from databases.

Structure Building Router

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

Routing Table

User Intent	Sub-Skill	Key Indicators
Surface slab from bulk	`slab/`	"slab", "surface", "Miller index", "(111)", "(110)"
Place adsorbate on surface	`adsorbate/`	"adsorb", "place OH", "add CO", "binding site"
Substitutional doping	`doping/`	"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:

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

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

Common Pitfalls

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

cut a slab from an already-cut slab.

Make the supercell BEFORE placing adsorbates. Supercell operation

replicates all atoms, including adsorbates.

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

proceeding to the next step.

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

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

All versions