MD analysis using site occupation trajectories
Project description
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:
- Spherical cutoff: Atoms occupy a site if they lie within a spherical cutoff from a fixed position.
- Voronoi decomposition: Atoms are assigned to sites based on a Voronoi decomposition of the lattice into discrete volumes.
- 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 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.
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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for site_analysis-0.0.2-py3-none-any.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | e1939e45e2d89b20552c26b1c6ace977cbf7849cef60f1ef5337601d48c41038 |
|
| MD5 | 8e5c9ac441e1e7467114f4a63d6b6b5c |
|
| BLAKE2b-256 | c5eb17d4a11ffec8dcc0ada90943097c2a0bd82d46501c802b9c552849cac462 |
