xdatbus 0.0.115

A python package to analyze XDATCAR files generated from VASP

xdatbus

xdatbus is a Python library designed specifically for VASP users engaged in research on ab-initio MD simulations, as well as biased MD simulations. The primary file addressed by the package is the XDATCAR, a trajectories file generated by the Vienna Ab-initio Simulation Package (VASP). The package documentation can be accessed here and the Jupyter Notebook tutorial is also available.

Installation

Make sure you have a Python interpreter, preferably version 3.10 or higher. Then, you can simply install xdatbus from pypi using pip:

pip install xdatbus

If you'd like to use the latest unreleased version on the main branch, you can install it directly from GitHub:

pip install -U git+https://https://github.com/jcwang587/xdatbus

The package is also availabe from conda-based installation. It is generally recommended you first create a separate environment, then you can install xdatbus via conda as well via the xdatbus channel on Anaconda cloud:

conda install --channel xdatbus xdatbus

If you plan to use PLUMED to analyze biased MD sampling results, you can also install the conda version of PLUMED together:

conda install -c xdatbus -c conda-forge xdatbus plumed

Get Started

This is a brief example demonstrating how to use the basic function of xdatbus to aggregate multiple xdatcar files into one and unwrap the coordinates into an .xyz file:

import os
from xdatbus import xdc_aggregate, xdc_unwrap

xdc_dir = "./data"
xdb_path = os.path.dirname(xdc_dir)

xdc_aggregate(xdc_dir=xdc_dir, output_path=xdb_path)
xdc_unwrap(xdc_path=xdb_path)

Update log

0.0.6 first upload for test