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

1. Get session_id from file upload or catgo_dos_from_dir
2. Define atom groups: {"groups": [{"atoms": [0,1,2], "channels": "d", "label": "Surface Pt d"}]}
3. 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

1. catgo_dos_from_dir(remote_path="...") → 2. catgo_dos_total →
2. catgo_dos_dband(atoms=[surface]) → 4. catgo_dos_compute(groups=[...])

MD Water/Interface

1. catgo_md_rdf(pairs=[["O","H"],["O","O"]]) → 2. catgo_md_hbonds →
2. catgo_md_hbond_lifetime → 4. catgo_md_planar_density(plane="xy")