Use when the user asks to load, fetch, build, modify, or transform crystal/molecular structures. Covers database import, supercell, defects, doping, intercalation, nanotubes, and atom-level editing.
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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:
mp (largest database)twodmatpediacatgo_fetch_molecule, not OPTIMADECall catgo_structure_info to inspect the loaded structure. All structure-modifying tools
auto-fetch the current viewer structure — no need to pass structure dicts.
| 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 |
| 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 |
| 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) |
| Tool | Use When |
|---|---|
catgo_nanotube_build | Carbon or BN nanotubes from chiral indices (n, m) |
catgo_nanotube_info | Compute nanotube geometry before building |
catgo_fetch_crystal → 2. catgo_supercell → 3. catgo_doping → 4. catgo_structure_infocatgo_supercell (large enough to avoid defect-defect interaction) →catgo_build_defect → 4. catgo_structure_infocatgo_fetch_crystal (e.g. MoS2) → 2. catgo_intercalation (species="Li") → 3. VerifyNo reviews yet. Tell others what you thought.
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Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
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Use when the user asks to place an adsorbate molecule on a surface, find adsorption sites, or set up a surface+adsorbate model for DFT.
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Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.
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Use when the user asks to analyze computational results: Gibbs free energy, OER/HER/CO2RR overpotentials, adsorption energy, convergence tests, DOS/d-band analysis, or Bader charge analysis.
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Use AmberTools antechamber for molecular force field parameterization. Generates GAFF/GAFF2 parameters and AM1-BCC or RESP charges for use in AMBER or LAMMPS classical MD simulations.
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One-shot recipes for adding, deleting, moving, and replacing individual atoms in the active CatGo viewer structure. Use whenever the user asks to "add an atom", "delete atoms", "remove this atom", "move atom N", "replace H with Li", or any single-atom edit — including "add a hydrogen on top of atom 12" / "delete atoms 5–9" / "swap the oxygen at site 3 for fluorine". Skips the discovery loop (no need to list structure tools or check adsorption sites first); goes straight to the matching `catgo_structure` action. Triggers in Chinese on 加原子, 删原子, 减原子, 移动原子, 替换原子, 增加氢, 删除氧, 把 ... 换成 ....
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