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 built for Python >=3.2 (the older version, v1.0.1, supports Python 2.7). We recommend the use of a virtual environment (virtualenv, conda, etc.). sitator has a number of optional dependencies that enable various features:

• Landmark Analysis
  • 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.)
• Site Type Analysis
  • For SOAP-based site types: either the quip binary from QUIP with GAP or the DScribe Python library.
  • The Python 2.7 bindings for QUIP (quippy) are not required. Generally, DScribe is much simpler to install than QUIP. Please note, however, that the SOAP descriptor vectors differ between QUIP and DScribe and one or the other may give better results depending on the system you are analyzing.
  • For coordination environment analysis (sitator.site_descriptors.SiteCoordinationEnvironment), we integrate the pymatgen.analysis.chemenv package; a somewhat recent installation of pymatgen is required.

After downloading, the package is installed with pip:

```bash

git clone ... OR unzip ... OR ...

cd sitator pip install . ```

To enable site type analysis, add the [SiteTypeAnalysis] option (this adds two dependencies -- Python packages pydpc and dscribe):

bash pip install ".[SiteTypeAnalysis]"

Examples and Documentation

Two example Jupyter notebooks for conducting full landmark analyses of LiAlSiO<sub>4</sub> and Li<sub>12</sub>La<sub>3</sub>Zr<sub>2</sub>O<sub>12</sub> as in our paper, including data files, can be found on Materials Cloud.

Full API documentation can be found at ReadTheDocs.

sitator generally assumes units of femtoseconds for time, Angstroms for space, and Cartesian (not crystal) coordinates.

Global Options

sitator uses the tqdm.autonotebook tool to automatically produce the correct fancy progress bars for terminals and iPython notebooks. To disable all progress bars, run with the environment variable SITATOR_PROGRESSBAR set to false.

The SITATOR_ZEO_PATH and SITATOR_QUIP_PATH environment variables can set the default paths to the Zeo++ network and QUIP quip executables, respectively.

License

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