hero

ReacNetGenerator

An automatic reaction network generator for reactive molecular dynamics simulation

Download

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

ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamic simulations, Phys. Chem. Chem. Phys., 2020, 22 (2): 683–691, doi: 10.1039/C9CP05091D

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

# Installation

You can install Anaconda or Miniconda to obtain conda, and install ReacNetGenerator easily with conda:

conda install reacnetgenerator -c conda-forge

See the build guide if you want to build ReacNetGenerator by yourself.

# 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

# Awards

  • The First Prize in 2019 (the 11th Session) Shanghai Computer Application Competition for College Students
  • The First Prize in 2019 (the 12th Session) Chinese Computer Design Competition for College Students

# 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)