Metadata-Version: 2.1
Name: xdatbus
Version: 0.0.129
Summary: A python package to analyze XDATCAR files generated from VASP
Author-email: Jiacheng Wang <jiachengwang@umass.edu>
Maintainer: Jiacheng Wang
License: MIT License
        
        Copyright (c) 2023 Jiacheng Wang
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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Project-URL: homepage, https://xdatbus.readthedocs.io/en/latest/
Project-URL: documentation, https://xdatbus.readthedocs.io/en/latest/
Project-URL: repository, https://github.com/jcwang587/xdatbus
Keywords: python,vasp,xdatcar,aimd
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: numpy ~=1.26.1
Requires-Dist: pandas ~=2.1.2
Requires-Dist: ase ~=3.22.1
Requires-Dist: pymatgen ~=2023.10.11
Requires-Dist: mdanalysis ~=2.6.0
Provides-Extra: vis
Requires-Dist: rdkit-pypi ~=2022.9.5 ; extra == 'vis'
Requires-Dist: biotite ==0.37.0 ; extra == 'vis'
Requires-Dist: bpy ~=3.6.0 ; extra == 'vis'
Requires-Dist: molecularnodes ~=2.11.0 ; extra == 'vis'
Requires-Dist: pyyaml ~=6.0.1 ; extra == 'vis'
Requires-Dist: ovito ~=3.9.4 ; extra == 'vis'

<p align="center"> 
<img src="https://raw.githubusercontent.com/jcwang587/xdatbus/main/docs/logo.png"/>
</p>

# xdatbus

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**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](https://xdatbus.readthedocs.io/en/latest/) and the Jupyter Notebook [tutorial](https://github.com/jcwang587/xdatbus/tree/main/examples) 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`:

```bash
pip install xdatbus
```

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

```bash
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:
```bash
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:
```bash
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:

```python
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
