Metadata-Version: 2.1
Name: site-analysis
Version: 0.0.2
Summary: MD analysis using site occupation trajectories
Home-page: https://github.com/bjmorgan/site-analysis
Author: Benjamin J. Morgan
Author-email: b.j.morgan@bath.ac.uk
License: MIT
Download-URL: https://github.com/bjmorgan/site-analysis/archive/0.0.2.tar.gz
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: codeclimate-test-reporter
Requires-Dist: coverage (==4.3.4)
Requires-Dist: monty
Requires-Dist: pymatgen
Requires-Dist: tqdm

# site-analysis

<img src='https://github.com/bjmorgan/site-analysis/blob/master/logo/site-analysis-logo.png' width='100'>

[![Build Status](https://travis-ci.org/bjmorgan/site-analysis.svg?branch=master)](https://travis-ci.org/bjmorgan/site-analysis)
[![Test Coverage](https://api.codeclimate.com/v1/badges/cb871e86f11b715efad6/test_coverage)](https://codeclimate.com/github/bjmorgan/site-analysis/test_coverage)
[![Documentation Status](https://readthedocs.org/projects/site-analysis/badge/?version=latest)](https://site-analysis.readthedocs.io/en/latest/?badge=latest)
[![PyPI version](https://badge.fury.io/py/site-analysis.svg)](https://badge.fury.io/py/site-analysis)

`site-analysis` is a Python module for analysing molecular dynamics simulations of solid-state ion transport, by assigning positions of mobile ions to specific &ldquo;sites&rdquo; within the host structure.

The code is built on top of [`pymatgen`](https://pymatgen.org) and takes VASP XDATCAR files as molecular dynamics trajectory inputs.

The code can use the following definitions for assigning mobile ions to sites:
1. Spherical cutoff: Atoms occupy a site if they lie within a spherical cutoff from a fixed position.
2. Voronoi decomposition: Atoms are assigned to sites based on a Voronoi decomposition of the lattice into discrete volumes.
3. Polyhedral decomposition: Atoms are assigned to sites based on occupation of polyhedra defined by the instantaneous positions of lattice atoms.

## Installation

From PyPI:
```
pip install site-analysis
```

Or clone the latest development version from [GitHub](https://github.com/bjmorgan/site-analysis) and install
```
git clone git@github.com:bjmorgan/site-analysis.git
cd site-analysis
python setup.py install
```

Alternatively you can install the latest version using `pip`, direct from GitHub, e.g.
```
pip3 install git+https://github.com/bjmorgan/site-analysis.git
```

## Documentation
Documentation and tutorials live at [Read the Docs](https://site-analysis.readthedocs.io/en/latest/).

Example notebooks are also available of [GitHub](https://github.com/bjmorgan/site-analysis/examples).

## Tests
Automated testing of the latest build happens [here](https://travis-ci.org/github/bjmorgan/site-analysis).

Manual tests can be run using 
```
python3 -m unittest discover
```
The code has been tested with Python versions 3.6 and above.


