hello-qm/catgo-lrg/electronic-analysis

Electronic Structure & MD Trajectory Analysis

Density of States (DOS)

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

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

Hydrogen Bond Analysis

Methods: baker_hubbard or wernet_nilsson. Default: D-A 3.5 A, D-H-A angle 150 deg.

Conformational 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")