site_analysis is a Python module for analysing molecular dynamics simulations of solid-state ionic transport, by assigning mobile ions to discrete “sites” within host structures.
The code is built on top of pymatgen and takes VASP XDATCAR files as molecular dynamics trajectory inputs.
The code currently can use on of three schemes for assigning mobile ions to discrete sites:
- Spherical cutoff: Atoms occupy a site if they lie within a cutoff radis from a fixed position.
- Voronoi decomposition: Atoms are assigned to sites based on a Voronoi decomposition of the lattice into discrete volumes.
- Polyhedral decomposition: Atoms are assigned to sites based on occupation of polyhedra defined by the instantaneous positions of lattice atoms.