Fort7 Workflow

CLI namespace: reaxkit fort7 <task> [flags]

fort.7 analysis workflow for ReaxKit.

This workflow provides tools for inspecting and analyzing ReaxFF fort.7 files, which contain per-frame bond-order information and derived atomic connectivity.

It supports: - Extracting atom-level or system-level features (e.g. charges, coordination, bond-order–derived quantities) as functions of frame, iteration, or time. - Building explicit connectivity representations (edge lists) from bond orders, with configurable thresholds and directionality. - Computing connection statistics over time, such as mean or maximum coordination. - Generating bond-order time series for specific atom pairs. - Detecting bond formation and breakage events using threshold and hysteresis criteria, with optional diagnostic visualizations.

The workflow is designed to bridge raw ReaxFF bond-order output with higher-level connectivity, dynamics, and event-based analyses in a reproducible, CLI-driven way.

Available tasks

bond-events

Examples

• reaxkit fort7 bond-events --export events.csv
• reaxkit fort7 bond-events --src 1 --dst 19 --threshold 0.38 --hysteresis 0.10 --smooth ema --window 7 --min-run 4 --export events_1_19.csv --save overlay.png

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to fort.7 file.
--frames FRAMES	Frame selection.
--src SRC	Source atom.
--dst DST	Destination atom.
--threshold THRESHOLD	Schmitt trigger base threshold.
--hysteresis HYSTERESIS	Hysteresis width around threshold.
--smooth {ma,ema,none}	Smoothing method.
--window WINDOW	Window size for MA/EMA.
--ema-alpha EMA_ALPHA	Optional EMA alpha.
--min-run MIN_RUN	Minimum consecutive points.
--xaxis {iter,frame}	Internal event x-axis.
--directed	Do not merge A–B/B–A.
--save SAVE	Save debug overlay (requires --src --dst).
--export EXPORT	Export detected events CSV.

bond-ts

Examples

• reaxkit fort7 bond-ts --frames 0:500 --export bo.csv
• reaxkit fort7 bond-ts --src 1 --dst 19 --plot
• reaxkit fort7 bond-ts --wide --bo-threshold 0.1 --export wide.csv

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to fort.7 file.
--frames FRAMES	Frame selection.
--directed	Do not merge A–B with B–A.
--bo-threshold BO_THRESHOLD	Zero out BO below this.
--wide	Return wide matrix (frames × bonds).
--xaxis {iter,frame,time}	X-axis for quick plot.
--control CONTROL	Control file for --xaxis time.
--src SRC	Source atom for quick plot.
--dst DST	Destination atom for quick plot.
--plot	Show plot interactively.
--save SAVE	Save bond time-series plot.
--export EXPORT	Export bond-order time series CSV.

constats

Examples

• reaxkit fort7 constats --frames 0:1000 --how mean --export stats.csv
• reaxkit fort7 constats --how count --min-bo 0.4 --export counts.csv

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to fort.7 file.
--frames FRAMES	Frame selection.
--min-bo MIN_BO	BO threshold before stats.
--directed	Do not merge A–B with B–A.
--how {mean,max,count}	Statistic to compute.
--save SAVE	(Unused) No plot.
--export EXPORT	Export connection stats as CSV.

edges

Examples

• reaxkit fort7 edges --frames 0:1000:10 --min-bo 0.4 --export edges.csv
• reaxkit fort7 edges --plot --min-bo 0.3

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to fort.7 file.
--frames FRAMES	Frame selection.
--min-bo MIN_BO	Minimum BO.
--directed	Treat edges as directed.
--aggregate {max,mean}	Aggregation for undirected edges.
--include-self	Keep self-edges.
--xaxis {iter,frame,time}	X-axis for quick plot.
--control CONTROL	Control file for --xaxis time.
--plot	Show plot interactively.
--save SAVE	Save edge-count plot.
--export EXPORT	Export edge list CSV.

get

Examples

• reaxkit fort7 get --yaxis charge --atom 'all' --plot
• reaxkit fort7 get --yaxis charge --atom 1 --plot
• reaxkit fort7 get --yaxis q_.* --regex --export charges.csv to get all columns starting with 'q_'

Options

Flag	Description
-h, --help	show this help message and exit
--file FILE	Path to fort.7 file.
--yaxis YAXIS	Feature name or regex (with --regex).
--atom ATOM	Atom selection: a number (e.g., 5), a list (e.g., 1,2,7), or 'all'.
--frames FRAMES	Frame selection: 'a:b[:c]' or 'i,j,k'.
--xaxis {iter,frame,time}	X-axis mode.
--control CONTROL	Control file (for --xaxis time).
--regex	Interpret --feature as regex, which calls ally-columns with the given --yaxis
--plot	Show plot interactively.
--save SAVE	Save feature plot image.
--export EXPORT	Export extracted feature(s) as CSV.