kconMD (k-Bags Convolutional Neural Network Molecular Dynamics)

Molecular Dynamics (MD) simulations supported by k-Bags Convolutional Neural Network (kCON).

Author: Jinzhe Zeng

Email: jzzeng@stu.ecnu.edu.cn

Acknowledgement

Many thanks to Xin Chen for his help and development of kCON.

Requirements

• numpy
• scipy
• matplotlib
• scikit-learn
• ASE
• TensorFlow

Installation

With pip

pip install kconmd

Build from source

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

Examples

Simple example

See examples/example.py.

Client–server model

See examples/server.py and examples/client.py.

Run MD with LAMMPS

See njzjz/Pyforce repository and install Pyforce module. Then rename examples/client.py as force.py and put it where you run LAMMPS. Add a line in the LAMMPS input file:

fix 1 all pyforce C H O