Plotter Workflow

CLI namespace: reaxkit plotter <task> [flags]

General-purpose plotting workflow for ReaxKit.

This workflow provides flexible plotting utilities for arbitrary tabular data (text, CSV, TSV, or whitespace-delimited files), without assuming any specific ReaxFF file format or column headers.

It supports multiple plot types, including: - single and multi-series line or scatter plots, - directed (arrowed) line plots, - dual y-axis plots, - tornado plots for sensitivity-style visualization, - 3D scatter plots with scalar coloring, - 2D aggregated heatmaps projected from 3D data.

Columns are selected using simple 1-based column tokens (e.g. c1, c2, c3), making the workflow suitable for rapid visualization of simulation outputs, summaries, and post-processed analysis tables.

Available tasks

directed

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to input txt/csv/tsv table.
--save SAVE	Path to save plot (file or directory). If omitted, show interactively.
--title TITLE	Optional custom plot title.
--plot	Generate and display/save the plot
--xaxis XAXIS	Single x column (e.g., 'c1').
--yaxis YAXIS	Single y column (e.g., 'c2').
--xlabel XLABEL	Optional x-axis label.
--ylabel YLABEL	Optional y-axis label.

dual

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to input txt/csv/tsv table.
--save SAVE	Path to save plot (file or directory). If omitted, show interactively.
--title TITLE	Optional custom plot title.
--plot	Generate and display/save the plot
--xaxis XAXIS	Single x column (e.g., 'c1').
--y1 Y1	Left y-axis column (e.g., 'c2').
--y2 Y2	Right y-axis column (e.g., 'c3').
--xlabel XLABEL	Optional x-axis label.
--ylabel1 YLABEL1	Optional left y-axis label.
--ylabel2 YLABEL2	Optional right y-axis label.

heatmap2d

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to input txt/csv/tsv table.
--save SAVE	Path to save plot (file or directory). If omitted, show interactively.
--title TITLE	Optional custom plot title.
--plot	Generate and display/save the plot
--x X	x coordinate column (e.g., 'c1').
--y Y	y coordinate column (e.g., 'c2').
--z Z	z coordinate column (e.g., 'c3').
--value VALUE	value column to aggregate (e.g., 'c4').
--plane {xy,xz,yz}	Projection plane for heatmap (default: xy).
--bins BINS	Grid resolution: int (e.g., 50) or 'nx,ny' (e.g., '50,100').

scatter3d

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to input txt/csv/tsv table.
--save SAVE	Path to save plot (file or directory). If omitted, show interactively.
--title TITLE	Optional custom plot title.
--plot	Generate and display/save the plot
--x X	x coordinate column (e.g., 'c1').
--y Y	y coordinate column (e.g., 'c2').
--z Z	z coordinate column (e.g., 'c3').
--value VALUE	Value column for coloring (e.g., 'c4').

single

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to input txt/csv/tsv table.
--save SAVE	Path to save plot (file or directory). If omitted, show interactively.
--title TITLE	Optional custom plot title.
--plot	Generate and display/save the plot
--xaxis XAXIS	Comma-separated list of x columns (e.g., 'c1' or 'c1,c3').
--yaxis YAXIS	Comma-separated list of y columns (e.g., 'c2' or 'c2,c4').
--xlabel XLABEL	Optional x-axis label.
--ylabel YLABEL	Optional y-axis label.
--scatter	Use scatter instead of line plot.

tornado

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to input txt/csv/tsv table.
--save SAVE	Path to save plot (file or directory). If omitted, show interactively.
--title TITLE	Optional custom plot title.
--plot	Generate and display/save the plot
--label LABEL	Column for labels (e.g., 'c1').
--min MIN	Column for minimum values (e.g., 'c2').
--max MAX	Column for maximum values (e.g., 'c3').
--median MEDIAN	Optional column for median values (e.g., 'c4').
--top TOP	Show only top-N widest bars (0 = all).
--vline VLINE	Optional vertical reference line (e.g., 0.0).
--xlabel XLABEL	Optional x-axis label.
--ylabel YLABEL	Optional y-axis label.