reacnet-md-tools 0.1.0

Helpers around reactive MD post-processing workflows (ReacNetGenerator).

reacnet-md-tools

Small, dependency-light helpers around reactive MD post-processing workflows, built to make ReacNetGenerator runs more repeatable.

Design goals:

• minimal dependencies
• safe subprocess execution (no shell=True)
• clear, agent-friendly CLIs

Install / run

Run without installing (recommended)

uvx --from reacnet-md-tools rng-pipeline --help

Install into an environment

python -m pip install -U reacnet-md-tools

Commands

rng-xs2x

Convert a LAMMPS dump with scaled coordinates xs/ys/zs into absolute coordinates x/y/z.

rng-xs2x -i in.lammpstrj -o out.lammpstrj

Limitations: orthorhombic boxes only (triclinic tilt factors are rejected with an error).

rng-infer-atomnames

Infer reacnetgenerator -a atomname order from a LAMMPS data file by parsing the Masses section and matching masses to common elements.

rng-infer-atomnames path/to/system.data
# -> e.g. "C H O Cl"

rng-pipeline

End-to-end helper:

1. If the input is a LAMMPS dump and uses xs/ys/zs, convert it to x/y/z into out/<basename>/dump_with_xyz.lammpstrj.
2. If --atomnames is not provided, try to infer them from a nearby LAMMPS data file (or ask you to pick one with --pick-data).
3. Run ReacNetGenerator, writing everything into out/<basename>/.

Example:

rng-pipeline \
  --input /path/to/traj.lammpstrj \
  --type dump \
  --outroot out \
  --pick-data \
  --stepinterval 10 \
  --maxspecies 50

ReacNetGenerator runner selection

• default --runner auto:
  • use local reacnetgenerator if found on PATH
  • otherwise run via: uvx --from reacnetgenerator reacnetgenerator ...

Development

Build (wheel + sdist):

python -m pip install -U build
python -m build

License

MIT (see LICENSE).