Guide

ReacNetGenerator is an automatic reaction network generator for reactive molecular dynamics simulation. This page provides a easy way to start it.

Installation

You can easily use pip to install ReacNetGenerator:

pip install reacnetgenerator

You can also install Anaconda or Miniconda (opens new window) 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 --type lammpsdumpfile -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 --type lammpsbondfile -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

Python interface

You can use the Python interface:

from reacnetgenerator import ReacNetGenerator
ReacNetGenerator(inputfiletype="dump", inputfilename="dump.ch4", atomname=['C', 'H', 'O']).runanddraw()

See Python API for details.