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an automatic reaction network generator for reactive molecular dynamics simulation
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README.md

ReacNetGenerator

DOI:10.1039/C9CP05091D Research Group

An automatic reaction network generator for reactive molecular dynamics simulation.

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)

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

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)
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