Electrostatics Workflow

CLI namespace: reaxkit electrostatics <task> [flags]

Electrostatics workflow for ReaxKit.

This workflow provides tools for computing and analyzing electrostatic properties from ReaxFF simulations, including dipole moments, polarizations, and polarization–electric-field hysteresis behavior.

It supports: - Dipole moment and polarization calculations for single frames, at both total-system and local (core-atom cluster) levels. - Polarization–field hysteresis analysis using time-dependent electric fields (via fort.78 and control files), including extraction of coercive fields and remnant polarizations. - Visualization of local electrostatics through 3D scatter plots and 2D projected heatmaps based on atomic coordinates.

The workflow integrates xmolout, fort.7, fort.78, and control files, and is designed to bridge atomistic ReaxFF simulations with experiment-facing electrostatic observables.

Available tasks

dipole

Examples

• reaxkit elect dipole --frame 10 --scope total --export dipole_pol_total_frame10.csv --polarization
• reaxkit elect dipole --frame 10 --scope local --core Al --export dipole_pol_local_frame10.csv --polarization

Options

Flag	Description
-h, --help	show this help message and exit
--xmolout XMOLOUT	Path to xmolout file
--fort7 FORT7	Path to fort.7 file
--frame FRAME	0-based frame index in xmolout
--scope {total,local}	Electrostatics scope: total or local
--core CORE	Comma-separated core atom types for local scope (e.g. Al,Mg)
--export EXPORT	CSV file to export the dipole/polarization data
--polarization	If present, compute polarization instead of dipole

heatmap2d

Examples

• reaxkit elect heatmap2d --core Al --component mu_z --plane xz --bins 10 --frames 0:2:1 --save reaxkit_outputs/elect/local_mu_2d

Options

Flag	Description
-h, --help	show this help message and exit
--xmolout XMOLOUT	Path to xmolout file
--fort7 FORT7	Path to fort.7 file
--core CORE	Comma-separated core atom types (e.g. Al,Mg)
--component COMPONENT	Which component to aggregate (e.g. pol_z, P_z (uC/cm^2), mu_z)
--frames FRAMES	Frames: "0,10,20" or "0:100:5"
--polarization	Use polarization components (P_x/y/z) instead of dipole
--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
--vmin VMIN	Color scale min (auto if not set)
--vmax VMAX	Color scale max (auto if not set)
--cmap CMAP	Matplotlib colormap
--save SAVE	Directory to save PNGs (one per frame)

hyst

Examples

• reaxkit elect hyst --plot --yaxis pol_z --xaxis field_z --aggregate mean --roots

Options

Flag	Description
-h, --help	show this help message and exit
--xmolout XMOLOUT	Path to xmolout file
--fort7 FORT7	Path to fort.7 file
--fort78 FORT78	Path to fort.78 file
--control CONTROL	Path to control file
--plot	Show the hysteresis or time-series plot
--save SAVE	If set, save plot to file (e.g. hyst.png)
--export EXPORT	CSV file to export aggregated hysteresis data
--summary SUMMARY	Text file to write coercive fields and remnant polarizations
--yaxis YAXIS	Quantity for y-axis (e.g. pol_z, mu_z, time, P_z)
--xaxis XAXIS	Quantity for x-axis (e.g. field_z, time, iter)
--aggregate {mean,max,min,last}	Aggregation method
--roots	Also print coercive and remnant values to terminal

plot3d

Examples

• reaxkit elect plot3d --core Al --component mu_z --frames 0:3:1 --save reaxkit_outputs/elect/local_mu_3d/

Options

Flag	Description
-h, --help	show this help message and exit
--xmolout XMOLOUT	Path to xmolout file
--fort7 FORT7	Path to fort.7 file
--core CORE	Comma-separated core atom types (e.g. Al,Mg)
--component COMPONENT	Which component to color by (e.g. pol_z, P_z (uC/cm^2), mu_z)
--frames FRAMES	Frames: "0,10,20" or "0:100:5"
--polarization	Use polarization components (P_x/y/z) instead of dipole
--save SAVE	Directory to save PNGs (one per frame)
--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