Skip to content

Xmolout Workflow

CLI namespace: reaxkit xmolout <task> [flags]

xmolout trajectory-analysis workflow for ReaxKit.

This workflow provides a comprehensive set of tools for extracting, analyzing, and visualizing atomic trajectory data from ReaxFF xmolout files, which store time-resolved atomic coordinates and simulation cell information.

It supports: - Extracting atom trajectories for selected atoms or atom types in long or wide tabular formats, with flexible frame selection and axis conversion. - Computing mean squared displacement (MSD) for one or multiple atoms, with support for combined plots or per-atom subplots. - Computing radial distribution functions (RDFs) using FREUD or OVITO backends, either as averaged curves or as RDF-derived properties over frames. - Extracting simulation box (cell) dimensions as functions of frame, iteration, or time, with optional plotting. - Writing trimmed xmolout files that retain only atom types and coordinates for lightweight storage or downstream processing.

The workflow is designed to bridge raw ReaxFF trajectory output with common structural and dynamical analyses in a reproducible, CLI-driven manner.

Available tasks

boxdims

Get box/cell dimensions from xmolout.

Examples

  • reaxkit xmolout boxdims --frames 0:500:5 --xaxis time --export box_dims.csv
  • reaxkit xmolout boxdims --frames 0:100:10 --xaxis iter --save box_dim_plots.png

Options

Flag Description
-h, --help show this help message and exit
--file FILE Path to xmolout file.
--plot Show plot interactively.
--save SAVE Path to save plot image.
--export EXPORT Path to export CSV data.
--frames FRAMES Frame selector: 'start:stop[:step]' or 'i,j,k'.
--xaxis {frame,iter,time} Quantity on x-axis (default: frame).

msd

Compute MSD from xmolout.

Examples

  • reaxkit xmolout msd --atoms 1 --xaxis frame --save atom1_msd.png --export atom1_msd.csv
  • reaxkit xmolout msd --atoms 1,2,3 --xaxis time --save msd.png --export msd.csv
  • reaxkit xmolout msd --atoms 1,2,3 --subplot --save msd_subplot.png --export msd_subplot.csv

Options

Flag Description
-h, --help show this help message and exit
--file FILE Path to xmolout file.
--plot Show plot interactively.
--save SAVE Path to save plot image.
--export EXPORT Path to export CSV data.
--atoms ATOMS Comma/space separated 1-based atom indices, e.g. '1,5,12'.
--xaxis {iter,frame,time} Quantity on x-axis (default: frame).
--subplot Plot each atom in its own subplot instead of a single combined plot.

rdf

Compute RDF using FREUD or OVITO backends.

Curve example:
reaxkit xmolout rdf --save rdf.png --export rdf.csv --frames 0 --bins 200 --r-max 5

Property example:
reaxkit xmolout rdf --prop area --bins 200 --r-max 5 --frames 0:10:1 --save rdf_area.png

Options

Flag Description
-h, --help show this help message and exit
--file FILE Path to xmolout file.
--plot Show plot interactively.
--save SAVE Path to save plot image.
--export EXPORT Path to export CSV data.
--backend {freud,ovito} RDF backend: freud or ovito (default: ovito).
--prop {first_peak,dominant_peak,area,excess_area} Compute this RDF-derived property per frame instead of a curve.
--types-a TYPES_A, --types_a TYPES_A Comma/space separated atom types for set A, e.g. 'Al,N'.
--types-b TYPES_B, --types_b TYPES_B Comma/space separated atom types for set B, e.g. 'N'.
--bins BINS Number of RDF bins.
--r-max R_MAX Max radius in Å; default depends on backend.
--frames FRAMES Frame selector: 'start:stop[:step]' or 'i,j,k'.
--every EVERY Use every Nth frame (default: 1).
--start START First frame index (0-based).
--stop STOP Last frame index (0-based).
--norm {extent,cell} FREUD normalization: extent or cell (default: extent).
--c-eff C_EFF FREUD only: effective c-length for --norm cell.

trajget

Get atom trajectories from xmolout.

Examples

  • reaxkit xmolout trajget --atoms 1 --dims z --xaxis time --save atom1_z.png --export atom1_z.csv
  • reaxkit xmolout trajget --atom-types Al --dims x y z --format wide --export Al_all_dims_traj.csv
  • reaxkit xmolout trajget --atom-types Al --frames 10:200:10 --dims z --export Al_z_dim_traj.csv

Options

Flag Description
-h, --help show this help message and exit
--file FILE Path to xmolout file.
--plot Show plot interactively.
--save SAVE Path to save plot image.
--export EXPORT Path to export CSV data.
--atoms ATOMS Comma/space separated 1-based atom indices, e.g. '1,5,12'.
--dims {x,y,z} [{x,y,z} ...] Coordinate dimensions to include (default: x y z).
--xaxis {iter,frame,time} Quantity on x-axis (default: frame).
--frames FRAMES Frame selector: 'start:stop[:step]' or 'i,j,k' (default: all).
--atom-types ATOM_TYPES, --types ATOM_TYPES Comma/space separated atom types, e.g. 'Al,N'.
--format {long,wide} Output table layout: long or wide (default: long).

trim

Trim xmolout to a lighter file with atom type and coordinates only.

Example:
reaxkit xmolout trim --file xmolout --output xmolout_trimmed

Options

Flag Description
-h, --help show this help message and exit
--file FILE Input xmolout file.
--output OUTPUT Output trimmed xmolout file.