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 operates on molecular dynamics trajectories represented as lists of pymatgen Structure objects. Any trajectory source that can produce pymatgen structures can be used as input.

Site Types

The package offers several approaches for defining sites:

1. Spherical sites: Simple spherical volumes defined by a center position and radius

2. Polyhedral sites: Sites defined by polyhedra with vertices at specified atomic positions

3. Voronoi sites: Sites defined by Voronoi decomposition of the lattice

4. Dynamic Voronoi sites: Sites using Voronoi decomposition but with centers calculated dynamically based on framework atom positions

Documentation Structure

Getting Started

• Introduction to site-analysis
• Installation
• Quickstart Guide

Concepts

• What is “Site Analysis”?
• Sites
• Site Collections
• Atoms
• Trajectories
• Handling Periodic Boundary Conditions

Guides

• Using the Builder Pattern
• The Reference-Based Sites Workflow
• Working with Spherical Sites
• Working with Voronoi Sites
• Working with Dynamic Voronoi Sites
• Working with Polyhedral Sites
• Working with Trajectories
• Residence Time Analysis
• Transition Tables

Tutorials

• Tutorials

Resources

• Publications using site-analysis
• Changelog

API Reference

• API documentation
  • Submodules

Code Requirements

• Python 3.10 or later

• Dependencies: pymatgen, numpy, scipy, tqdm

Development

For development or to access the latest features:

# Clone the repository
git clone https://github.com/bjmorgan/site-analysis.git
cd site-analysis

# Install in development mode with dev dependencies
pip install -e ".[dev]"

Reference

• Index

• Module Index