Metadata-Version: 2.1
Name: site-analysis
Version: 0.0.1
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/0.0.1.tar.gz
Description: # site-analysis
        
        <img src='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)
        
        `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.
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
