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Meta Plotting with gen-plot

This tutorial updates the older plotter ... style to the current presentation workflow command:

reaxkit gen-plot --type <plot_type> ...

gen-plot is file-agnostic: it reads tabular files and plots by column selectors (c1, c2, ...), without requiring ReaxFF-specific semantics. As a result, it can be used for any tabular data.

Supported plot types

  • single which is a flexible line/scatter plot with multiple series and shared x-axis
  • directed which is a directed curve plot with arrows indicating directionality along the curve
  • dual which is a dual y-axis plot
  • tornado which is a tornado plot
  • scatter3d which is a 3D scatter plot with optional value-based coloring
  • heatmap2d which is a 2D heatmap generated from 3D coordinates by projecting onto a plane and binning

All are selected through --type.

Input model

gen-plot accepts text/CSV/TSV tables: - CSV/TSV or whitespace-delimited text - optional comment lines with # - columns referenced with 1-based tokens (c1, c2, ...)

Core examples

1) Single line/scatter plot

To get a simple line plot of column 2 vs column 1:

reaxkit gen-plot --type single --file summary.txt --xaxis c1 --yaxis c2 --plot

Multi-series with shared x:

reaxkit gen-plot --type single --file summary.txt --xaxis c1 --yaxis c2,c3,c4 --plot

Pairwise x-y mode, meaning c1 vs c2 and c3 vs c4:

reaxkit gen-plot --type single --file data.txt --xaxis c1,c3 --yaxis c2,c4 --plot

Use markers instead of lines:

reaxkit gen-plot --type single --file data.txt --xaxis c1 --yaxis c2 --scatter --plot

2) Directed curve

This type of plot is useful for visualizing gradients or trajectories where the direction of change along the curve is important. Arrows are automatically placed along the curve to indicate directionality.

reaxkit gen-plot --type directed --file summary.txt --xaxis c1 --yaxis c2 --save directed.png

3) Dual y-axis

reaxkit gen-plot --type dual --file summary.txt --xaxis c1 --y1 c2 --y2 c3 --save dual_plot.png

4) Tornado

reaxkit gen-plot --type tornado --file results.txt --label c1 --min c2 --max c3 --median c4 --top 10 --save tornado.png

5) 3D scatter

reaxkit gen-plot --type scatter3d --file points.txt --x c1 --y c2 --z c3 --value c4 --save scatter3d.png

6) 2D heatmap from 3D coordinates

reaxkit gen-plot --type heatmap2d --file points.txt --x c1 --y c2 --z c3 --value c4 --plane xz --bins 100,80 --save heatmap_xz.png

Output behavior

  • --plot displays interactively
  • --save writes figure to file
  • you can use both
  • if neither is given, no plot artifact is produced

Data cleaning behavior

Before plotting, selected columns are coerced to numeric (where applicable) and invalid rows are dropped. If no valid rows remain, the command exits with a clear error.

Handoff to video generation

When you save frame sequences, use:

reaxkit gen-video --folder <frames_dir> --output output.mp4 --fps 10

This keeps plotting (gen-plot) and video composition (gen-video) as two clean, composable steps.

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