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Status](https://readthedocs.org/projects/site-analysis/badge/?version=latest)](https://site-analysis.readthedocs.io/en/latest/?badge=latest)\n[![PyPI version](https://badge.fury.io/py/site-analysis.svg)](https://badge.fury.io/py/site-analysis)\n[![status](https://joss.theoj.org/papers/0a447aeb167964e77c8d381f7d1db89a/status.svg)](https://joss.theoj.org/papers/0a447aeb167964e77c8d381f7d1db89a)\n\n`site-analysis` is a Python module for analysing molecular dynamics simulations of solid-state ion transport, by assigning positions of mobile ions to specific \u0026ldquo;sites\u0026rdquo; within the host structure.\n\nThe code is built on top of [`pymatgen`](https://pymatgen.org) 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.\n\nThe code can use the following definitions for assigning mobile ions to sites:\n1. **Spherical cutoff**: Atoms occupy a site if they lie within a spherical cutoff from a fixed position.\n2. **Voronoi decomposition**: Atoms are assigned to sites based on a Voronoi decomposition of the lattice into discrete volumes.\n3. **Polyhedral decomposition**: Atoms are assigned to sites based on occupation of polyhedra defined by the instantaneous positions of lattice atoms.\n4. **Dynamic Voronoi sites**: Sites using Voronoi decomposition but with centres calculated dynamically based on framework atom positions.\n\n## Quick Start\n\n```python\nfrom site_analysis.builders import TrajectoryBuilder\nfrom pymatgen.io.vasp import Xdatcar\n\n# Load MD trajectory as a list of pymatgen Structure objects.\n# Here we load from a VASP XDATCAR file, but any source of\n# pymatgen Structure objects can be used as input.\nxdatcar = Xdatcar(\"example_data/XDATCAR\")\nmd_structures = xdatcar.structures\n\n# Define sites and track Li+ ion movements between them\ntrajectory = (TrajectoryBuilder()\n              .with_structure(md_structures[0])  # Use first frame as reference\n              .with_mobile_species(\"Li\")\n              .with_spherical_sites(centres=[[0.25, 0.25, 0.25],\n                                             [0.75, 0.25, 0.25]],\n                                    radii=1.5)\n              .build())\n\ntrajectory.trajectory_from_structures(md_structures)\n\n# Get site occupancies over time\nprint(trajectory.atoms_trajectory)  # Which site each atom occupies\nprint(trajectory.sites_trajectory)  # Which atoms in each site\n```\n\nFor detailed examples and tutorials, see the [documentation](https://site-analysis.readthedocs.io/en/latest/).\n\n## Installation\n\n### Standard Installation\n\n```bash\npip install site-analysis\n```\n\nFor faster polyhedral site analysis, install with numba acceleration:\n\n```bash\npip install site-analysis[fast]\n```\n\n### Development Installation\n\nFor development or to access the latest features:\n\n```bash\n# Clone the repository\ngit clone https://github.com/bjmorgan/site-analysis.git\ncd site-analysis\n\n# Install in development mode with dev dependencies\npip install -e \".[dev]\"\n```\n\n## Documentation\n\nComplete documentation, including tutorials, examples, and API reference, is available at [Read the Docs](https://site-analysis.readthedocs.io/en/latest/).\n\n## Testing\n\nAutomated testing of the latest build happens on [GitHub Actions](https://github.com/bjmorgan/site-analysis/actions).\n\nTo run tests locally:\n\n```bash\n# Using pytest (recommended)\npytest\n\n# Using unittest\npython -m unittest discover\n```\n\nThe code requires Python 3.10 or above.\n\n## Contributing\n\nBug reports, feature requests, and pull requests are welcome. 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