A script to make molecular dynamics (MD) datasets for neural networks from given LAMMPS trajectories automatically.


Keywords
molecular dynamics dataset, chemistry, dataset, md, molecular-dynamics, neural-network, python
Install
pip install mddatasetbuilder==1.2.23

Documentation

MDDatasetBuilder

python version PyPI Build Status Coverage Status codecov Research Group

MDDatasetBuilder is a script to build molecular dynamics (MD) datasets for neural networks from given LAMMPS trajectories automatically.

Author: Jinzhe Zeng

Email: jzzeng@stu.ecnu.edu.cn

Installation

pip install git+https://github.com/njzjz/mddatasetbuilder

Simple example

A LAMMPS dump file should be prepared. A LAMMPS bond file can be added for the addition information.

datasetbuilder -d dump.ch4 -b bonds.reaxc.ch4_new -a C H O -n ch4 -i 25

Then you can calculate generated Gaussian files:

qmcalc -d dataset_ch4_GJf/000
qmcalc -d dataset_ch4_GJf/001

Next, prepare DeePMD datas and use DeePMD-kit to train a model.

preparedeepmd -p dataset_ch4_GJf -a C H O
cd train && dp train train.json