python version PyPI Docker Build Status Build status Coverage Status codecov Codacy Badge DOI:10.26434/chemrxiv.7421534

An automatic generator of reaction network for reactive molecular dynamics simulation.

Please cite: J. Zeng, L. Cao, J.Z.H. Zhang, C.H. Chin, T. Zhu: ReacNetGen: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations, 2018, doi: 10.26434/chemrxiv.7421534

Author: Jinzhe Zeng, Liqun Cao, John ZH Zhang, Chih-Hao Chin, Tong Zhu


Research Group




Build from source with conda and pip

  1. Get conda and install Anaconda or Miniconda.
  2. Use conda to create environment:
conda create -q -n reacnetgenerator python=3.7 openbabel rdkit hmmlearn -c openbabel -c conda-forge
source activate reacnetgenerator # for Windows, just use: activate reacnetgenerator
  1. Download ReacNetGenerator and install it from source:
git clone
cd reacnetgenerator
pip install .

You can test whether ReacNetGenerator is running normally:

python pytest


If you have installed Docker, a Docker is provided:

docker pull njzjz/reacnetgenerator

You can start the ReacNetGenerator Docker where you can run ReacNetGenerator:

docker run -itv $(pwd):$(pwd) -w $(pwd) njzjz/reacnetgenerator


Simple example

Prepare a LAMMPS bond file named bonds.reaxc, then run the script:

reacnetgenerator -i bonds.reaxc -a C H O

where C, H, and O are atomic names in the input file. Analysis report will be generated automatically.

A LAMMPS dump file is also supported. You can prepare it by running "dump 1 all custom 100 dump.reaxc id type x y z" in LAMMPS.

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

You can running the following script for help:

reacnetgenerator -h

GUI version

You can open a GUI version for ReacNetGenerator by typing: