Vels Analyzer Analysis

vels / moldyn.vel / molsav analysis utilities.

This module provides a unified interface for accessing atomic coordinates, velocities, and accelerations stored in ReaxFF velocity output files via VelsHandler.

Typical use cases include:

• retrieving atomic coordinates or velocities for selected atoms
• extracting acceleration histories for diagnostics or plotting
• accessing file metadata (timestep, atom count, sections present)

get_vels_data(handler, key, *, atoms=None)

Retrieve metadata or a selected atomic table from a velocity output file.

Works on

VelsHandler — vels / moldyn.vel / molsav

Parameters:

Name	Type	Description	Default
handler	VelsHandler	Parsed velocity file handler.	required
key	('metadata', 'coordinates', 'velocities', 'accelerations', 'prev_accelerations')	Section to retrieve: - metadata: file-level information (returned as a dict) - coordinates: atomic positions - velocities: atomic velocities - accelerations: atomic accelerations - prev_accelerations: accelerations from the previous step	"metadata"
atoms	sequence of int	1-based atom indices to include. If None, all atoms are returned. Ignored when key="metadata".	None

Returns:

Type	Description
DataFrame or dict	If key="metadata", returns a metadata dictionary. Otherwise, returns a DataFrame with one row per atom containing the requested quantities and an atom_index column.

Examples:

>>> from reaxkit.io.handlers.vels_handler import VelsHandler
>>> from reaxkit.analysis.per_file.vels_analyzer import get_vels_data
>>> h = VelsHandler("moldyn.vel")
>>> v = get_vels_data(h, "velocities", atoms=[1, 2, 3])
>>> meta = get_vels_data(h, "metadata")