ReacNetGenerator

An automatic generator of reaction network for reactive molecular dynamics simulation

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

AuthorJinzhe ZengLiqun CaoJohn ZH ZhangChih-Hao ChinTong Zhu

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

Installation

1. Download the source code:

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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 run the following script for help:

reacnetgenerator -h

GUI version

You can open a GUI version for ReacNetGenerator by typing:

reacnetgeneratorgui

Dependencies