ReacNetGenerator

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

Email: tzhu@lps.ecnu.edu.cn, jzzeng@stu.ecnu.edu.cn

Research Group

Features

• 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
• Parallel computing

Requirements

• Python 3.6 (Note: Python 2, 3.1-3.5, 3.7 is not supported!)
• Python packages: numpy, scipy, networkx, scikit-learn, matplotlib, hmmlearn, htmlmin, ASE, scour
• Extra packages: OpenBabel, RDKit

Installation

1. Get conda to install Python 3.

2. Use conda to install extra packages:

conda install -c openbabel openbabel 
conda install -c rdkit rdkit

3. Use pip to install required packages:

$ pip install numpy scipy networkx scikit-learn matplotlib hmmlearn htmlmin ase scour

4. Download ReacNetGenerator and build it from source:

$ cd ReacNetGenerator/
$ python3 setup.py install

You can test whether ReacNetGenerator is running normally:

% python3 setup.py test

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:

$ reacnetgeneratorgui