RxNetGen

The reaction network generator & event table exploration.

RxNetGen builds reaction networks and explores event tables for KMC simulation. The chemical core (systems, graphs, geometry, dataclasses and array-api helpers) is provided by the graphatoms package; RxNetGen depends on it and provides the application layer: configuration, reaction network storage/commands, runners, parallel executors, reaction/event classes and the CLI entry points.

Installation

pip install -e .

Or with uv / pixi:

uv sync
pixi install

CLI entry points

Module structure

src/rxnetgen/
├── config/     # Hydra/OmegaConf configuration (atoms, bonds, calculator)
├── network/    # Reaction network: scheduler, recorder, metadata, commands
├── parallel/   # Pluggable executors (serial, multiprocessing, joblib, ray, dask, executorlib)
├── reaction/   # Reaction classes and KMC events
├── runner/     # Runners (otfkmc, rxngen) and helpers
└── utils/      # Vendored copy of graphatoms.utils (app-level helpers)

Note: rxnetgen.utils is a vendored copy of graphatoms.utils kept so that the application layer can evolve independently. Changes made upstream in graphatoms.utils must be synchronized here when they affect the migrated modules.

Running tests

pytest src/tests -v

The tests use the datasets under src/tests-datasets/.