| name | electronic-analysis |
| description | 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).
|
Electronic Structure & MD Trajectory Analysis
Density of States (DOS)
| 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 |
PDOS Workflow
- Get
session_id from file upload or catgo_dos_from_dir
- Define atom groups:
{"groups": [{"atoms": [0,1,2], "channels": "d", "label": "Surface Pt d"}]}
- Call
catgo_dos_compute with session_id and groups
Channel syntax: "d", "s,p", "dxy,dz2"
D-Band Analysis
catgo_dos_dband(session_id, atoms=[surface_indices]) — Returns d-band center, width, filling.
- Higher center = stronger adsorbate binding
occupied_only_center=True (default) for occupied d-band center
Band Structure
| 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.
COHP (Bonding Analysis)
catgo_cohp_data — Crystal Orbital Hamilton Population from LOBSTER output.
bond_indices: 1-based bond numbers- Negative -COHP below Fermi = bonding; positive = antibonding
- ICOHP = quantitative bond strength
MD Trajectory Analysis
All MD tools accept trajectory_b64 (base64-encoded file) and format (pdb, xyz, extxyz, lammpstrj).
Structural Analysis
| 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 |
Hydrogen Bond Analysis
| 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.
Conformational Analysis
| 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) |
Workflow Recipes
Surface Catalysis DOS
catgo_dos_from_dir(remote_path="...") → 2. catgo_dos_total →catgo_dos_dband(atoms=[surface]) → 4. catgo_dos_compute(groups=[...])
MD Water/Interface
catgo_md_rdf(pairs=[["O","H"],["O","O"]]) → 2. catgo_md_hbonds →catgo_md_hbond_lifetime → 4. catgo_md_planar_density(plane="xy")
