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

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 - 3.7 (Note: Python <= 3.5 is not supported!)
• Python packages: numpy, scipy, pandas, networkx, scikit-learn, matplotlib, hmmlearn, ASE, scour, tqdm, jinja2, coloredlogs, htmlmin, jsmin, cssmin
• Extra libraries: OpenBabel, RDKit
• Javascript and CSS frameworks (already packaged): jQuery, jQuery Easing Plugin, Magnific Popup, ScrollReveal, Bootstrap, Start Bootstrap - Creative, D3, JSNetworkX

Installation

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

3. Download ReacNetGenerator and install it from source:

git clone https://github.com/njzjz/reacnetgenerator
cd reacnetgenerator
pip install .

You can test whether ReacNetGenerator is running normally:

python setup.py pytest

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