Skip to content
A automated fragmentation method for Ab Initio Molecular Dynamics (AIMD).
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.github chore: update GitHub Actions (#28) May 23, 2019
aimdfragmentation fix: use c-based depth-first search (#21) Apr 7, 2019
docs fix: add test and common fixes Feb 4, 2019
examples
.gitignore fix: add test and common fixes Feb 4, 2019
.stickler.yml
setup.py fix: use c-based depth-first search (#21) Apr 7, 2019
tox.ini

README.md

Automated Fragmentation AIMD Calculation

python version PyPI Build Status Coverage Status codecov

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

Author: Jinzhe Zeng

Email: jzzeng@stu.ecnu.edu.cn

Requirements

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
You can’t perform that action at this time.