| name | surface-catalysis |
| description | Use when the user asks about surface slabs, Miller indices, adsorbate placement, adsorption sites, water layers, passivation, heterostructures, lattice matching, moire bilayers, or catalysis workflows.
|
Surface & Catalysis Workflow
Surface Slab Generation
- Start with a bulk crystal (fetch or use current)
catgo_generate_slab with miller_index as [h, k, l]
- Defaults:
min_slab_size=10.0 A, min_vacuum_size=15.0 A
- Returns all symmetrically distinct terminations
- Inspect result with
catgo_structure_info
Miller index selection:
| Surface | Miller Index | Common Use |
|---|
| FCC (111) | [1,1,1] | Close-packed, catalysis |
| FCC (100) | [1,0,0] | Open surface |
| BCC (110) | [1,1,0] | Close-packed |
| Rutile (110) | [1,1,0] | TiO2 catalysis |
| Perovskite (001) | [0,0,1] | ABO3 surfaces |
Adsorbate Placement
catgo_adsorption_sites — Find top, bridge, hollow sites. height default 2.0 A.catgo_adsorption_place — Place adsorbate at chosen site coordinates.
Get adsorbate molecules via catgo_fetch_molecule:
- CO, CO2, H2O, NH3, O2, CH4, etc.
Surface Passivation
catgo_passivate — Cap dangling bonds with pseudo-hydrogen on slab bottom surface.
Requires both slab and bulk reference structure dicts.
Water Layer
catgo_water_layer — Add TIP4P water layer for solid/liquid interface models.
Parameters: z_start, z_end, min_distance (overlap removal), equilibrate (optional LAMMPS).
Heterostructure & Interface
ZSL Lattice Matching (Two-Step)
catgo_hetero_search — Find lattice-matched substrate/film pairscatgo_hetero_build — Build interface from selected match
One-Step Interface
catgo_hetero_build_intermat — Simpler pipeline, less control but faster prototyping.
Moire Bilayer
catgo_moire_search — Find commensurate twist angles with supercell sizescatgo_moire_build — Build bilayer at selected angle
Complete Catalysis Recipe
catgo_fetch_crystal (bulk, e.g. Pt)catgo_generate_slab (miller_index=[1,1,1], min_slab_size=12, min_vacuum_size=15)catgo_passivate (bottom surface)catgo_adsorption_sites (find sites)catgo_fetch_molecule (get adsorbate)catgo_adsorption_place (place at chosen site)catgo_structure_info (verify)- Generate DFT input (see computational-input skill)
