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
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
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
mddatasetbuilder-1.1.4.tar.gz
(14.9 kB
view details)
File details
Details for the file mddatasetbuilder-1.1.4.tar.gz.
File metadata
- Download URL: mddatasetbuilder-1.1.4.tar.gz
- Upload date:
- Size: 14.9 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/1.12.1 pkginfo/1.4.2 requests/2.20.0 setuptools/40.6.3 requests-toolbelt/0.8.0 tqdm/4.26.0 CPython/3.7.2
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
60f5f4a5c5aa30dfeaa9fa45be8a5dcd56da39f6e48864225895f8eb4eb4bc6b
|
|
| MD5 |
10b7d1a3a3fc53b228620d4a1f85b3fc
|
|
| BLAKE2b-256 |
fc03d753edd0a00ddb0e4cc0efa330657c75241d2f1624ce51df03117dc2480c
|
