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ReacNetGenerator

An automatic generator of reaction network for reactive molecular dynamics simulation

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Trajectory

Processing of MD trajectory containing atomic coordinates or bond orders

Filtering

Hidden Markov Model (HMM) based noise filtering

Isomers

Isomers identifying accoarding to SMILES

Network

Generation of reaction network for visualization using force-directed algorithm

HTML5

Showing an interactive web page

Fast

Parallel computing and performance optimization

Citation and contact

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

Installation

  1. Download the source code on our group website.
  2. Install Anaconda or Miniconda to obtain conda.
  3. Decompress reacnetgenerator.zip and build in the main directory:
conda config --add channels conda-forge
conda build conda/recipe
conda install reacnetgenerator --use-local

Usage

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:

reacnetgeneratorgui

Dependencies