ahzeeshan / sitator

Unsupervised landmark analysis for jump detection in molecular dynamics simulations.

sitator

A modular framework for conducting and visualizing site analysis of molecular dynamics trajectories.

Visualizations of complete landmark site analyses, created with sitator, of the superionic conductors (a) LGPS, (b) LLZO, and (c) LASO. Source: figures 11, 14, and 18 from our paper, linked below.

sitator contains an efficient implementation of our method, landmark analysis, as well as visualization tools, generic data structures for site analysis, pre- and post-processing tools, and more.

For details on landmark analysis and its application, please see our paper:

L. Kahle, A. Musaelian, N. Marzari, and B. Kozinsky
Unsupervised landmark analysis for jump detection in molecular dynamics simulations
Phys. Rev. Materials 3, 055404 – 21 May 2019

If you use sitator in your research, please consider citing this paper. The BibTeX citation can be found in CITATION.bib.

Installation

sitator is currently built for Python 2.7. (The Python 3 port can be found in the py3 branch which is under active development; once it has been further tested and improved it will become the stable version.) We recommend the use of a Python 2.7 virtual environment (virtualenv, conda, etc.). sitator has two external dependencies:

• The network executable from Zeo++ is required for computing the Voronoi decomposition. (It does not have to be installed in PATH; the path to it can be given with the zeopp_path option of VoronoiSiteGenerator.)
• If you want to use the site type analysis features, a working installation of Quippy with GAP and Python bindings is required for computing SOAP descriptors.

After downloading, the package is installed with pip:

# git clone ... OR unzip ... OR ...
cd sitator
pip install .

To enable site type analysis, add the [SiteTypeAnalysis] option:

pip install ".[SiteTypeAnalysis]"

Examples and Documentation

Two example Jupyter notebooks for conducting full landmark analyses of LiAlSiO4 and Li12La3Zr2O12, including data files, can be found on Materials Cloud.

All individual classes and parameters are documented with docstrings in the source code.

License

This software is made available under the MIT License. See LICENSE for more details.