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

{"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

{"tool": "catgo_fetch", "arguments": {"action": "crystal", "formula": "TiO2", "source": "mp"}}
{"tool": "catgo_fetch", "arguments": {"action": "molecule", "name": "water"}}

catgo_view — Inspect and push structures

{"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)

{"tool": "catgo_fetch", "arguments": {
  "action": "crystal", "formula": "Pt", "source": "mp"
}}

{"tool": "catgo_structure", "arguments": {
  "action": "slab", "miller_index": [1,1,1],
  "min_slab_size": 12.0, "min_vacuum_size": 15.0
}}

{"tool": "catgo_structure", "arguments": {
  "action": "supercell", "scaling": [2, 2, 1]
}}

{"tool": "catgo_structure", "arguments": {
  "action": "add_atom", "element": "O", "position": [2.77, 1.60, 14.5]
}}

{"tool": "catgo_structure", "arguments": {
  "action": "add_atom", "element": "H", "position": [2.77, 1.60, 15.47]
}}

{"tool": "catgo_view", "arguments": {"action": "get_state"}}

Python API

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.
2. Make the supercell BEFORE placing adsorbates. Supercell operation replicates all atoms, including adsorbates.
3. For Materials Project fetch, use reduced formula (e.g., "TiO2" not "Ti2O4").
4. After each structure modification, verify with catgo_view before proceeding to the next step.
5. The viewer shows the structure in the browser. MCP tools modify the viewer state directly -- there is no separate "save" step.