Coordination Workflow

CLI namespace: reaxkit coordination <task> [flags]

Coordination workflow for ReaxKit.

This workflow analyzes atomic coordination using ReaxFF bond-order data from fort.7 and structural information from xmolout.

It provides two main capabilities:

• Analyze coordination status per atom per frame (under-, correctly-, or over-coordinated) based on atom valence and total bond order.
• Relabel atom types according to coordination status and write a new xmolout file for visualization or downstream analysis.

The workflow supports flexible frame selection, user-defined or ffield-derived valences, and multiple labeling modes.

Available tasks

analyze

Analyzes coordination per atom per frame.
It determines if an atom is under-coordinated, over-coordinated, or coordinates, based on its valence and total bond order.

Examples

• reaxkit coord analyze --export coord_analysis.csv
• reaxkit coord analyze --valences 'Mg=2,O=2' --frames 0:200:2 --export coord_0_200_2.csv

Options

Flag	Description
-h, --help	show this help message and exit
--xmolout XMOLOUT	Path to xmolout.
--fort7 FORT7	Path to fort.7 file.
--valences VALENCES	Optional: override type valences, e.g. 'Mg=2,O=2,H=1'. If omitted, reads from ffield atom section ('valency').
--ffield FFIELD	Path to ffield (used if --valences not given).
--threshold THRESHOLD	Tolerance around valence.
--frames FRAMES	Frame selection, e.g. '0:100:5' or '0,5,10'.
--allow-missing-valences	Keep atoms with unknown valence (status=NaN).
--export EXPORT	Path to export coordination CSV.

relabel

Relabel atom types by coordination and write a new xmolout.

Examples

• reaxkit coord relabel --output xmolout_relabeled --mode global --labels=-1=U,0=C,1=O
• reaxkit coord relabel --output xmolout_type --mode by_type --keep-coord-original
• reaxkit coord relabel --valences 'Mg=2,O=2,Zn=2' --frames 0:400:5 --output xmolout_relabeled --mode global

Options

Flag	Description
-h, --help	show this help message and exit
--xmolout XMOLOUT	Path to xmolout.
--fort7 FORT7	Path to fort.7 file.
--valences VALENCES	Optional: override type valences, e.g. 'Mg=2,O=2,H=1'. If omitted, reads from ffield atom section ('valency').
--ffield FFIELD	Path to ffield (used if --valences not given).
--threshold THRESHOLD	Tolerance around valence.
--frames FRAMES	Frame selection, e.g. '0:100:5' or '0,5,10'.
--allow-missing-valences	Keep atoms with unknown valence (status=NaN).
--output OUTPUT	Output xmolout path.
--mode {global,by_type}	Relabeling mode.
--labels LABELS	Status→tag map, e.g. '-1=U,0=C,1=O'.
--keep-coord-original	In by_type mode, keep original label when status==0.
--simulation SIMULATION	Override header simulation name.
--precision PRECISION	Float precision.