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Vels Workflow

CLI namespace: reaxkit vels <task> [flags]

Velocity and acceleration (vels) analysis workflow for ReaxKit.

This workflow provides tools for inspecting, visualizing, and exporting data from ReaxFF velocity-related output files, including vels, moldyn.vel, and molsav.

It supports: - Extracting per-atom coordinates, velocities, accelerations, or previous-step accelerations for all atoms or selected subsets. - Printing extracted data to the console or exporting it to CSV. - Visualizing scalar velocity or acceleration components (e.g. vx, vz, ax) mapped onto atomic positions using 3D scatter plots. - Generating 2D projected heatmaps (xy, xz, yz) of scalar quantities by spatial binning and aggregation.

The workflow is designed for spatially resolved analysis of atomic motion and dynamics in ReaxFF molecular dynamics simulations.

Available tasks

get

Examples

  • reaxkit vels get --key velocities --atoms 1,3,7 --print
  • reaxkit vels get --key coordinates --atoms 1-50 --export coords.csv
  • reaxkit vels get --key metadata --print

Options

Flag Description
-h, --help show this help message and exit
--file FILE Path to vels/moldyn.vel/molsav file.
--atoms ATOMS 1-based atom indices (optional). Examples: "1,3,7" or "1-10,25".
--export EXPORT Path to export CSV data.
--print Print output to console.
--key {metadata,coordinates,velocities,accelerations,prev_accelerations} Which dataset to return.

heatmap2d

Examples

  • reaxkit vels heatmap2d --value vz --plane xz --bins 60 --agg mean --save vz_xz.png
  • reaxkit vels heatmap2d --value vz --plane xy --bins 80,40 --agg max

Options

Flag Description
-h, --help show this help message and exit
--file FILE Path to vels/moldyn.vel/molsav file.
--atoms ATOMS 1-based atom indices. Examples: "1,3,7" or "1-10,25".
--value VALUE Scalar to plot: vx,vy,vz, ax,ay,az, pax,pay,paz.
--plane {xy,xz,yz} Projection plane.
--bins BINS Grid bins: "N" or "Nx,Ny" (e.g., "80,40").
--agg AGG Aggregation: mean|max|min|sum|count.
--save SAVE Path to save plot image (dir or full filename).
--vmin VMIN Color scale min (auto if not set).
--vmax VMAX Color scale max (auto if not set).
--cmap CMAP Matplotlib colormap.

plot3d

Examples

  • reaxkit vels plot3d --value vz --save vz_3d.png
  • reaxkit vels plot3d --value vz --atoms 1-500 --cmap coolwarm

Options

Flag Description
-h, --help show this help message and exit
--file FILE Path to vels/moldyn.vel/molsav file.
--atoms ATOMS 1-based atom indices. Examples: "1,3,7" or "1-10,25".
--value VALUE Scalar to plot: vx,vy,vz, ax,ay,az, pax,pay,paz.
--save SAVE Path to save plot image (dir or full filename).
--vmin VMIN Color scale min (auto if not set).
--vmax VMAX Color scale max (auto if not set).
--cmap CMAP Matplotlib colormap.
--size SIZE Marker size.
--alpha ALPHA Marker transparency.
--elev ELEV 3D view elevation.
--azim AZIM 3D view azimuth.