Skip to main content

Reaction Network Generator

Project description

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)

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for reacnetgenerator, version 1.4.112
Filename, size File type Python version Upload date Hashes
Filename, size reacnetgenerator-1.4.112-cp36-cp36m-manylinux1_x86_64.whl (3.7 MB) File type Wheel Python version cp36 Upload date Hashes View
Filename, size reacnetgenerator-1.4.112-cp36-cp36m-manylinux2010_x86_64.whl (3.7 MB) File type Wheel Python version cp36 Upload date Hashes View
Filename, size reacnetgenerator-1.4.112-cp37-cp37m-manylinux1_x86_64.whl (3.7 MB) File type Wheel Python version cp37 Upload date Hashes View
Filename, size reacnetgenerator-1.4.112-cp37-cp37m-manylinux2010_x86_64.whl (3.7 MB) File type Wheel Python version cp37 Upload date Hashes View
Filename, size reacnetgenerator-1.4.112-cp38-cp38-manylinux1_x86_64.whl (4.6 MB) File type Wheel Python version cp38 Upload date Hashes View
Filename, size reacnetgenerator-1.4.112-cp38-cp38-manylinux2010_x86_64.whl (4.6 MB) File type Wheel Python version cp38 Upload date Hashes View
Filename, size reacnetgenerator-1.4.112.tar.gz (328.6 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page