RDF Analyzer Analysis

Radial Distribution Function (RDF) analysis utilities.

This module provides single-frame and multi-frame RDF calculations for ReaxFF trajectories using either the FREUD or OVITO backends, as well as helper utilities for extracting RDF-derived structural descriptors.

Typical use cases include:

computing total or partial RDFs for selected frames
averaging RDFs across multiple frames
extracting RDF-based properties such as peak positions or integrated areas

`rdf_property_over_frames(handler, *, backend='ovito', frames=None, property='first_peak', r_max=None, bins=200, types_a=None, types_b=None)`

Compute a single RDF-derived property for each simulation frame.

Works on

XmoloutHandler — xmolout

Parameters:

Name	Type	Description	Default
`backend`	`('ovito', 'freud')`	RDF backend to use.	`"ovito"`
`property`	`('first_peak', 'dominant_peak', 'area', 'excess_area')`	RDF-based property to compute.	`"first_peak"`
`frames`	`iterable of int`	Frame indices to include.	`None`
`types_a`	`iterable of str`	Atom types defining partial RDF.	`None`
`types_b`	`iterable of str`	Atom types defining partial RDF.	`None`

Returns:

Type	Description
`DataFrame`	One row per frame with frame index, iteration, and property values.

Examples:

>>> df = rdf_property_over_frames(xh, property="first_peak")

`rdf_using_freud(handler, *, frames=None, types_a=None, types_b=None, r_max=None, bins=200, average=True, return_stack=False)`

Compute RDFs across multiple frames using the FREUD backend.

Works on

XmoloutHandler — xmolout

Parameters:

Name	Type	Description	Default
`frames`	`iterable of int`	Frame indices to include.	`None`
`types_a`	`iterable of str`	Atom types defining A–B RDF.	`None`
`types_b`	`iterable of str`	Atom types defining A–B RDF.	`None`
`average`	`bool`	If True, return the average RDF across frames.	`True`
`return_stack`	`bool`	If True and `average=False`, return all per-frame RDFs.	`False`

Returns:

Name	Type	Description
`r`	`ndarray`	Radial distances.
`g`	`ndarray or list[ndarray]`	Averaged RDF, last RDF, or stack of RDFs.

Examples:

>>> r, g = rdf_using_freud(xh, frames=range(100), average=True)

`rdf_using_ovito(handler, *, frames=None, r_max=4.0, bins=200, types_a=None, types_b=None, average=True, return_stack=False)`

Compute RDFs across multiple frames using the OVITO backend.

Works on

XmoloutHandler — xmolout

Parameters:

Name	Type	Description	Default
`frames`	`iterable of int`	Frame indices to include.	`None`
`types_a`	`iterable of str`	If provided, compute partial RDF.	`None`
`types_b`	`iterable of str`	If provided, compute partial RDF.	`None`
`average`	`bool`	Return the average RDF across frames.	`True`

Returns:

Name	Type	Description
`r`	`ndarray`	Radial distances.
`g`	`ndarray or list[ndarray]`	RDF data.

Examples:

>>> r, g = rdf_using_ovito(xh, types_a=["Al"], types_b=["N"])