Use when the user asks to analyze DOS, band structure, COHP bonding, d-band center, or MD trajectory properties (RDF, RMSD, RMSF, hydrogen bonds, clustering, dimensionality reduction, dihedral angles, planar density).
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| Tool | Purpose |
|---|---|
catgo_dos_total | Total DOS |
catgo_dos_compute | Projected DOS (PDOS) for atom groups |
catgo_dos_dband | D-band center, width, filling (catalysis) |
catgo_dos_from_dir | Load DOS from remote HPC directory |
session_id from file upload or catgo_dos_from_dir{"groups": [{"atoms": [0,1,2], "channels": "d", "label": "Surface Pt d"}]}catgo_dos_compute with session_id and groupsChannel syntax: "d", "s,p", "dxy,dz2"
catgo_dos_dband(session_id, atoms=[surface_indices]) — Returns d-band center, width, filling.
occupied_only_center=True (default) for occupied d-band center| Tool | Purpose |
|---|---|
catgo_bands_data | Band energies, k-path, band gap |
catgo_bands_projections | Projected (fat) bands with orbital weights |
Report: direct/indirect gap, gap value, high-symmetry labels.
catgo_cohp_data — Crystal Orbital Hamilton Population from LOBSTER output.
bond_indices: 1-based bond numbersAll MD tools accept trajectory_b64 (base64-encoded file) and format (pdb, xyz, extxyz, lammpstrj).
| Tool | Purpose | Key Parameters |
|---|---|---|
catgo_md_rdf | Radial distribution g(r) | pairs, r_range, n_bins |
catgo_md_rmsd | RMSD over time (stability) | ref_frame, atom_indices |
catgo_md_rmsf | Per-atom fluctuation | atom_indices |
catgo_md_dihedrals | Dihedral angle evolution | atom_quartets |
| Tool | Purpose |
|---|---|
catgo_md_hbonds | Detect H-bonds per frame |
catgo_md_hbond_lifetime | H-bond lifetime autocorrelation |
Methods: baker_hubbard or wernet_nilsson. Default: D-A 3.5 A, D-H-A angle 150 deg.
| Tool | Purpose |
|---|---|
catgo_md_clustering | Cluster frames by structural similarity (kmeans/dbscan) |
catgo_md_dimreduce | PCA/t-SNE/UMAP embedding |
catgo_md_planar_density | 2D density map (diffusion analysis) |
catgo_dos_from_dir(remote_path="...") → 2. catgo_dos_total →catgo_dos_dband(atoms=[surface]) → 4. catgo_dos_compute(groups=[...])catgo_md_rdf(pairs=[["O","H"],["O","O"]]) → 2. catgo_md_hbonds →catgo_md_hbond_lifetime → 4. catgo_md_planar_density(plane="xy")No 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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