Structure Builder
Loading Structures
From Online Databases
catgo_fetch_crystal — Load crystal by formula or structure_id from OPTIMADE providers
(mp=Materials Project, mc3d, alexandria, twodmatpedia, omdb)catgo_search_crystals — Search and list multiple matches. Use this first when browsing,
then catgo_fetch_crystal with a specific structure_id.catgo_fetch_molecule — Fetch molecules from PubChem by name, formula, or SMILES.
Provider heuristics:
- General inorganic crystals:
mp (largest database)
- 2D materials:
twodmatpedia
- Organic molecules: use
catgo_fetch_molecule, not OPTIMADE
From Current Viewer
Call catgo_structure_info to inspect the loaded structure. All structure-modifying tools
auto-fetch the current viewer structure — no need to pass structure dicts.
Atom-Level Operations
| Tool |
Use When |
catgo_add_atom / catgo_add_atoms |
Adding atoms at Cartesian positions (Angstroms) |
catgo_delete_atoms |
Removing atoms by 0-based index |
catgo_replace_atom |
Changing element at a site |
catgo_move_atom / catgo_move_atoms |
Repositioning atoms |
Lattice and Cell Operations
| Tool |
Use When |
catgo_supercell |
Expanding unit cell by [na, nb, nc] or 3x3 matrix |
catgo_set_lattice |
Adding/changing periodic cell (wraps molecules in a box) |
catgo_merge |
Combining two structures at a given position |
Defect Engineering
| Tool |
Use When |
catgo_build_defect |
Point defects: vacancy, substitution, interstitial |
catgo_doping |
Substitutional doping (replace host with dopant) |
catgo_substitution |
Combinatorial multi-site substitution |
catgo_intercalation |
Insert species (Li, Na) into layered structures |
catgo_build_strain |
Apply strain/deformation (Voigt notation or 3x3 matrix) |
Nanostructures
| Tool |
Use When |
catgo_nanotube_build |
Carbon or BN nanotubes from chiral indices (n, m) |
catgo_nanotube_info |
Compute nanotube geometry before building |
Common Recipes
Doped supercell
catgo_fetch_crystal → 2. catgo_supercell → 3. catgo_doping → 4. catgo_structure_info
Defective structure for DFT
- Fetch bulk → 2.
catgo_supercell (large enough to avoid defect-defect interaction) →
catgo_build_defect → 4. catgo_structure_info
Intercalated battery material
catgo_fetch_crystal (e.g. MoS2) → 2. catgo_intercalation (species="Li") → 3. Verify