An automatic generator of reaction network for reactive molecular dynamics simulation



Processing of MD trajectory containing atomic coordinates or bond orders


Hidden Markov Model (HMM) based noise filtering


Isomers identifying accoarding to SMILES


Generation of reaction network for visualization using force-directed algorithm


Showing an interactive web page


Parallel computing and performance optimization

Citation and contact

ReacNetGenerator: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations, 2019, doi: 10.26434/chemrxiv.7421534

[email protected] (Jinzhe Zeng), [email protected] (Tong Zhu)


First, you need to download the source code from the Releases page. Then install ReacNetGenerator with one of the following guides:

Building a conda package

  1. Install Anaconda or Miniconda to obtain conda.
  2. Decompress reacnetgenerator.zip and build in the main directory of ReacNetGenerator:
conda config --add channels conda-forge
conda build conda/recipe
conda install reacnetgenerator --use-local
reacnetgenerator -h

Building a Docker Image

  1. Install Docker.
  2. Decompress reacnetgenerator.zip and build in the main directory of ReacNetGenerator:
docker build . -t njzjz/reacnetgenerator
docker run njzjz/reacnetgenerator reacnetgenerator -h


Command line

ReacNetGenerator can process any kind of trajectory files containing atomic coordinates, e.g. a LAMMPS dump file prepared 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

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

Also, ReacNetGenerator can process files containing bond information, e.g. LAMMPS bond file:

reacnetgenerator -i bonds.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:



  • The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students
  • The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students