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

Project description

MDDatasetBuilder

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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

Research Group

Requirements

Installation

git clone https://github.com/njzjz/mddatasetbuilder
cd mddatasetbuilder
pip install .

You can test whether ReacNetGenerator is running normally:

python3 setup.py pytest

Simple example

A LAMMPS bond file and a LAMMPS dump file should be prepared.

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

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Files for mddatasetbuilder, version 1.1.8
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