xdatbus

xdatbus 🚌

Xdatbus is a Python package designed specifically for Vienna Ab-initio Simulation Package (VASP) users conducting ab-initio molecular dynamics (AIMD) simulations, as well as biased MD simulations. The name of the package is derived from the MD trajectory file (XDATCAR) generated by VASP. The documentation for the package can be accessed here, and a collection of 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 git+https://github.com/jcwang587/xdatbus

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

conda install --channel xdatbus xdatbus

If you plan to use PLUMED to analyze enhanced sampling AIMD 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 a single file and unwrap the coordinates into an .xyz file.

As is often the case when you have submitted a continuous AIMD job, it is likely that you would have subfolders for each submission. XDATCAR files can be first gathered in a separate directory by:

$ mkdir xdc_files && for i in {01..10}; do cp RUN$i/XDATCAR xdc_files/XDATCAR_$i; done

Then, try aggregating and unwrapping the coordinate data from the XDATCAR files:

import os
from xdatbus import xdc_aggregate, xdc_unwrap

xdc_dir = "./xdc_files"
xdb_dir = os.path.dirname(xdc_dir)
xdb_path = os.path.join(xdb_dir, "XDATBUS")
xyz_path = os.path.join(xdb_dir, "XDATBUS_unwrap.xyz")

xdc_aggregate(xdc_dir=xdc_dir, output_dir=xdb_dir)
xdc_unwrap(xdc_path=xdb_path, output_path=xyz_path)

There are also entry points included with the installation for the Command Line Interface (CLI) to perform similar tasks:

$ xdc_aggregate --xdc_dir ./xdc_files --output_dir ./

$ xdc_unwrap --xdc_path ./XDATBUS --output_path ./XDATBUS_unwrap.xyz

Visualization

This is testing functionality for visualizing the molecular dynamics trajectory with Blender. There is a strict Python version required for compatibility with Blender. Please check the compatible version of Python for bpy to ensure there are no conflicts in your environment.

pip install molecularnodes bpy

Major Changelog

0.3.8 Added functions for locating minima and running NEB in a 2D FES.

0.2.5 Enabled a command-line interface that runs through the rich package.

0.2.0 Added a function to generate extxyz data for training machine learning interatomic potentials.