site-analysis 0.0.2

MD analysis using site occupation trajectories

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 “sites” within the host structure.

The code is built on top of pymatgen 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 and install

git clone [e-mail]: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.

Example notebooks are also available of GitHub.

Tests

Automated testing of the latest build happens here.

Manual tests can be run using

python3 -m unittest discover

The code has been tested with Python versions 3.6 and above.