Tong Zhu Research Group

The first and greatest victory is to conquer yourself; to be conquered by yourself is of all things most shameful and vile!

ReacNetGenerator

An automatic generator of reaction network for reactive molecular dynamics simulation

Citation and contact

ReacNetGenerator: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations, Phys. Chem. Chem. Phys., 2019, doi: 10.1039/C9CP05091D

jinzhe.zeng@rutgers.edu (Jinzhe Zeng), tzhu@lps.ecnu.edu.cn (Tong Zhu)

Installation

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:

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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:

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docker build . -t njzjz/reacnetgenerator
docker run njzjz/reacnetgenerator reacnetgenerator -h

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:

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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:

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reacnetgenerator -i bonds.reaxc -a C H O

You can run the following script for help:

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reacnetgenerator -h

GUI version

You can open a GUI version for ReacNetGenerator by typing:

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reacnetgeneratorgui

Awards

  • The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students (2019年（第十一届）上海市大学生计算机应用能力大赛一等奖)
  • The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students (2019年（第12届）中国大学生计算机设计大赛一等奖)

Acknowledge

  • National Natural Science Foundation of China (Grants No. 91641116)
  • National Innovation and Entrepreneurship Training Program for Undergraduate (201910269080)
  • ECNU Multifunctional Platform for Innovation (No. 001)
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