Analysis

After a trajectory file is prepared, you can process the file using the command line:

reacnetgenerator --type dump -i dump.reaxc -a C H O --nohmm

where C, H, and O are atomic names in the input file. --type decides the format of the trajectory file dump.reaxc. --nohmm controls whether HMM filter is enabled.

For example, if you want to process a LAMMPS bond file instead:

reacnetgenerator --type bond -i bonds.reaxc -a C H O --nohmm

A serial of files will be generated. You can start with a web page for Analysis report, which ends with the .html suffix.

You can run the following script for help:

reacnetgenerator -h

See here for the usage of the command line.

Oversized connected components

ReacNetGenerator stops before molecule naming when a connected component is larger than both 256 atoms and 10% of the analyzed system. Large components can be physically meaningful, but they can also indicate that a coordinate-based bond detector has interpreted non-covalent contacts as bonds. Continuing with an unintended system-spanning graph can produce extremely large molecule names and reaction-path output.

For coordinate trajectories, ASE provides explicit control over element-pair cutoffs:

reacnetgenerator --type dump -i trajectory.dump -a Na Cl --use-ase \
    --ase-pair-cutoffs Na-Cl:0

Use --max-component-atoms and --max-component-fraction to adjust the limits. Set --max-component-atoms 0 to disable the guard when a large covalent component is intentional.