Metadata-Version: 2.1
Name: xdatbus
Version: 0.0.113
Summary: A python package to analyze XDATCAR files generated from VASP
Author: Jiacheng Wang
Author-email: jiachengwang@umass.edu
Maintainer: Jiacheng Wang
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: ase~=3.22.1
Requires-Dist: pymatgen~=2023.10.11
Requires-Dist: pandas~=2.1.2
Requires-Dist: mdanalysis~=2.6.1
Requires-Dist: ovito~=3.9.4
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"


<p align="center"> 
<img src="https://github.com/jcwang587/xdatbus/blob/f7bc8411032e4aa1b3f47fc0ee7a0d56a053d857/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
