Automated Fragmentation AIMD Calculation

A automated fragmentation method for Ab Initio Molecular Dynamics (AIMD).

Author: Jinzhe Zeng

Email: jzzeng@stu.ecnu.edu.cn

Requirements

• OpenBabel
• numpy
• ASE
• GaussianRunner

Installation

Using pip

$ pip install aimdfragmentation

Build from source

You should install Gaussian 16 and OpenBabel first. Then:

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

Example

Run a Python program

You can see examples/example.py as an example, and run with:

python example.py

Run MD with LAMMPS

See njzjz/Pyforce repository and install Pyforce module. Then rename examples/example.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