Xmolout Fort7 Workflow
CLI namespace: reaxkit xmolout_fort7 <task> [flags]
xmolout–fort.7 combined workflow for ReaxKit.
This workflow provides visualization and analysis tasks that require both
atomic coordinates from xmolout and per-atom properties from fort.7
(e.g. partial charges, bond-order–derived quantities).
It supports: - 3D scatter visualization of arbitrary fort.7 scalar properties mapped onto atomic positions across selected frames. - 2D projected heatmaps (xy/xz/yz) of atomic properties or atom counts, with flexible spatial binning and aggregation.
The workflow is designed for spatially resolved analysis of ReaxFF outputs, enabling intuitive inspection of per-atom quantities in real space and across time.
Available tasks
heatmap2d
Examples
reaxkit xmolfort7 heatmap2d --property partial_charge --plane xz --bins 10 --agg mean --frames 0:300:100
Options
| Flag | Description |
|---|---|
-h, --help |
show this help message and exit |
--xmolout XMOLOUT |
Path to xmolout file. |
--fort7 FORT7 |
Path to fort.7 file. |
--plot |
Show plot interactively. |
--export EXPORT |
Path to export CSV data. |
--frames FRAMES |
Frames: "0,10,20" or "0:100:5". |
--plane {xy,xz,yz} |
Projection plane. |
--bins BINS |
Grid bins: "N" or "Nx,Ny" (e.g., "10,25"). |
--agg AGG |
Aggregation: mean|max|min|sum|count. |
--property PROPERTY |
fort7 column or alias to aggregate (e.g., partial_charge|charge|q). |
--vmin VMIN |
Color scale min (auto if not set). |
--vmax VMAX |
Color scale max (auto if not set). |
--cmap CMAP |
Matplotlib colormap. |
--save SAVE |
Path to save plot image. |
plot3d
Examples
reaxkit xmolfort7 plot3d --property charge --frames 0:20:10
Options
| Flag | Description |
|---|---|
-h, --help |
show this help message and exit |
--xmolout XMOLOUT |
Path to xmolout file. |
--fort7 FORT7 |
Path to fort.7 file. |
--plot |
Show plot interactively. |
--export EXPORT |
Path to export CSV data. |
--property PROPERTY |
Column name or alias (e.g., partial_charge, charge, q). |
--frames FRAMES |
Frames: "0,10,20" or "0:100:5". |
--atoms ATOMS |
Atom indices: "0,1,2" (0-based). |
--vmin VMIN |
Color scale min (auto if not set). |
--vmax VMAX |
Color scale max (auto if not set). |
--size SIZE |
Marker size. |
--alpha ALPHA |
Marker transparency. |
--cmap CMAP |
Matplotlib colormap. |
--elev ELEV |
3D view elevation. |
--azim AZIM |
3D view azimuth. |
--save SAVE |
Path to save plot image. |