Tutorials

Executable Jupyter notebook tutorials are available in the tutorials/ directory of the GitHub repository. The tutorials include example data and are designed to be run locally.

To get the tutorials, clone the repository:

git clone https://github.com/bjmorgan/site-analysis.git
cd site-analysis/tutorials
jupyter notebook

The tutorials are designed to be worked through in order:

Comparing Site Definitions — comparing_site_definitions.ipynb

An introductory tutorial that demonstrates the three site definition methods — spherical, Voronoi, and polyhedral — using a synthetic lithium-ion migration trajectory in an FCC lattice. This tutorial uses generated data, so no external files are needed.

You will learn how to:

  • Set up a TrajectoryBuilder and define sites

  • Compare how different site types assign ions during migration events

  • Understand the tradeoffs between site definitions

Argyrodite Site Analysis — argyrodite_site_analysis.ipynb

A realistic example analysing lithium-ion site occupations in Li6PS5Cl argyrodite solid electrolytes with varying degrees of anion disorder. Uses MD trajectory data included in the repository at tutorials/data/.

You will learn how to:

  • Define multiple crystallographically distinct site types using a reference structure with dummy atoms

  • Use structure alignment and species mapping for structures with different compositions

  • Analyse how site occupations change with anion disorder

Residence Times and Transition Probabilities — residence_times_and_transitions.ipynb

Builds on the argyrodite tutorial to compute residence times and transition probabilities. Uses the same MD trajectory data.

You will learn how to:

  • Compute and filter residence times for different site types

  • Visualise residence time distributions

  • Calculate and visualise transition probability matrices