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
- Python packages: numpy, scikit-learn, ASE, GaussianRunner, tqdm, coloredlogs
- Software: Gaussian 16, DeePMD
Installation
git clone https://github.com/njzjz/mddatasetbuilder
cd mddatasetbuilder/
python3 setup.py install
You can test whether ReacNetGenerator is running normally:
python3 setup.py test
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
1 maintainer
Release files for mddatasetbuilder 1.1.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| mddatasetbuilder-1.1.3.tar.gz | 14.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| mddatasetbuilder-1.1.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 27.1 kB
Release files / mddatasetbuilder-1.1.3.tar.gz
| Download URL | mddatasetbuilder-1.1.3.tar.gz |
|---|---|
| Size | 14.1 kB |
| Tags | Source |
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Release files / mddatasetbuilder-1.1.3-py3-none-any.whl
| Download URL | mddatasetbuilder-1.1.3-py3-none-any.whl |
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| Size | 13.0 kB |
| Tags | Python 3 |
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