MDDatasetBuilder
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
Requirements
- Python 3.6 - 3.7
- Python packages: numpy, scikit-learn, ASE, GaussianRunner, tqdm, coloredlogs, lz4, pybase64
- Software: Gaussian 16, DeePMD, OpenBabel
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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mddatasetbuilder-1.2.3.tar.gz
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