polyhedral-analysis

polyhedral-analysis is a Python library for analysing coordination polyhedra in crystal structures and molecular dynamics trajectories. Built on top of pymatgen, it works with any structure that pymatgen can read.

Features include coordination polyhedron construction from distance cutoffs or nearest-neighbour rules, continuous symmetry measures (CSM) against reference geometries, bond lengths, angles, volumes, edge connectivity, neighbour-sharing analysis, and trajectory tracking.

Quick example

from pymatgen.io.vasp import Poscar
from polyhedral_analysis.configuration import Configuration
from polyhedral_analysis.polyhedra_recipe import PolyhedraRecipe

recipe = PolyhedraRecipe(
    method='distance cutoff',
    coordination_cutoff=3.0,
    central_atoms='Ti',
    vertex_atoms=['O', 'F'],
)

structure = Poscar.from_file('POSCAR').structure
config = Configuration(structure=structure, recipes=[recipe])

poly = config.polyhedra[0]
print(poly.coordination_number)   # 6
print(poly.best_fit_geometry)     # {'geometry': 'Octahedron', ...}