Skip to content

Atom-Property Plots and Video Workflows

Note

This tutorial replaces the old `xmolout_fort7` tutorial with the current
ReaxKit command structure.

You will use: - plot_atom_property for frame-wise 3D scatter or 2D heatmap plots of per-atom properties, and - gen-video to convert saved frame images into an animation.

Why this replaced the old tutorial

Earlier versions used an xmolout_fort7 workflow namespace.
Current ReaxKit exposes this behavior as direct commands:

  • analysis/presentation: plot_atom_property
  • video assembly: gen-video

The core concept is unchanged: combine geometry (usually from xmolout) and per-atom properties (usually from fort.7) and visualize them over frames.

Example 1: 3D scatter of partial charge

reaxkit plot_atom_property --type scatter3d --property charge --frames 0:20:5 --save charge_scatter_frames

This command: - loads trajectory coordinates, - loads per-atom charge values, - aligns frame/atom data, - saves one 3D image per selected frame.

Example 2: 2D heatmap of bond-order sum

reaxkit plot_atom_property --type heatmap2d --property sum_BOs --plane xz --bins 60 --frames 0:20:5 --save bo_heatmaps

This command: - projects atom coordinates to a 2D plane, - aggregates property values on a 2D grid, - saves one heatmap per frame.

Key flags

--property - Typical values: charge, q, partial_charge, sum_BOs - Aliases are normalized internally.

--frames and --every - --frames selects explicit frames/ranges. - --every subsamples selected frames.

--atom-ids / --atom-types - Restrict plotting to a subset of atoms.

--save - Directory for per-frame images.

--export - Exports assembled per-atom table (x,y,z,value) as CSV.

Build a video from saved frames

After generating images:

reaxkit gen-video --folder reaxkit_outputs/plot_atom_property/charge_scatter_frames --output charge_scatter.mp4 --fps 10

This creates an MP4 from ordered frame images.

  1. Start with sparse sampling (for example --frames 0:200:20).
  2. Validate scale/projection (--vmin, --vmax, --plane).
  3. Export one CSV (--export) for QA and reproducibility.
  4. Increase frame density for final rendering.
  5. Use gen-video for publication-ready animations.
  • See the next tutorial 03_eregime_generator to learn how to make eregime.in files with custom profile.

Back to Tutorials