Source code for site_analysis.polyhedral_site

import itertools
import numpy as np 
from scipy.spatial import Delaunay, ConvexHull # type: ignore
from .site import Site
from .tools import x_pbc, species_string_from_site
from typing import List, Optional, Any, Dict
from pymatgen.core import Structure
from .atom import Atom

[docs]class PolyhedralSite(Site): """Describes a site defined by the polyhedral volume enclosed by a set of vertex atoms. Attributes: index (int): Numerical ID, intended to be unique to each site. label (`str`: optional): Optional string given as a label for this site. Default is `None`. contains_atoms (list): List of the atoms contained by this site in the structure last processed. trajectory (list): List of sites this atom has visited at each timestep? points (list): List of fractional coordinates for atoms assigned as occupying this site. transitions (collections.Counter): Stores observed transitions from this site to other sites. Format is {index: count} with ``index`` giving the index of each destination site, and ``count`` giving the number of observed transitions to this site. vertex_indices (list(int)): List of integer indices for the vertex atoms (counting from 0). label (:obj:`str`, optional): Optional label for the site. """ def __init__(self, vertex_indices: List[int], label: Optional[str]=None): """Create a PolyhedralSite instance. Args: vertex_indices (list(int)): List of integer indices for the vertex atoms (counting from 0). label (:obj:`str`, optional): Optional label for this site. Returns: None """ super(PolyhedralSite, self).__init__(label=label) self.vertex_indices = vertex_indices self.vertex_coords: Optional[np.ndarray] = None self._delaunay: Optional[Delaunay] = None def __repr__(self) -> str: string = ('site_analysis.PolyhedralSite(' f'index={self.index}, ' f'label={self.label}, ' f'vertex_indices={self.vertex_indices}, ' f'contains_atoms={self.contains_atoms})') return string
[docs] def reset(self) -> None: """Reset the trajectory for this site. Resets the contains_atoms and trajectory attributes to empty lists. Vertex coordinates and Delaunay tesselation are unset. Args: None Returns: None """ super(PolyhedralSite, self).reset() self.vertex_coords = None self._delaunay = None
@property def delaunay(self) -> Delaunay: """Delaunay tessellation of the vertex coordinates for this site. This is calculated the first time the attribute is requested, and then stored for reuse, unless the site is reset. Returns: scipy.spatial.Delaunay """ if not self._delaunay: self._delaunay = Delaunay(self.vertex_coords) return self._delaunay @property def coordination_number(self) -> int: """Coordination number for this site, defined as the number of vertices Returns: int """ return len(self.vertex_indices) @property def cn(self) -> int: """Coordination number for this site, defined as the number of vertices Convenience property for coordination_number() Returns: int """ return self.coordination_number
[docs] def assign_vertex_coords(self, structure: Structure) -> None: """Assign fractional coordinates to the polyhedra vertices from the corresponding atom positions in a pymatgen Structure. Args: structure (Structure): The pymatgen Structure used to assign the vertices fractional coordinates. Returns: None Notes: This method assumes the coordinates of the vertices may have changed, so unsets the Delaunay tesselation for this site. """ frac_coords = np.array([ s.frac_coords for s in [ structure[i] for i in self.vertex_indices ] ] ) # Handle periodic boundary conditions: # If the range of fractional coordinates along x, y, or z # exceeds 0.5, assume that this polyhedron wraps around the # periodic boundary in that dimension. # Fractional coordinates for that dimension that are less # than 0.5 will be incremented by 1.0 for i in range(3): spread = max(frac_coords[:,i]) - min(frac_coords[:,i]) if spread > 0.5: for j, fc in enumerate(frac_coords): if fc[i] < 0.5: frac_coords[j,i] += 1.0 self.vertex_coords = frac_coords self._delaunay = None
[docs] def get_vertex_species(self, structure: Structure) -> List[str]: """Returns a list of species strings for the vertex atoms of this polyhedral site. Args: structure (Structure): Pymatgen Structure used to assign species to each vertex atom. Returns: (list(str)): List of species strings of the vertex atoms. """ return [structure[i].species_string for i in self.vertex_indices]
[docs] def contains_point(self, x: np.ndarray, structure: Optional[Structure]=None, algo: str='simplex', *args, **kwargs) -> bool: """Test whether a specific point is enclosed by this polyhedral site. Args: x (np.array): Fractional coordinates of the point to test (length 3 numpy array). structure (:obj:`Structure`, optional): Optional pymatgen Structure. If provided, the vertex coordinates for this polyhedral site will be assigned using this structure. Default is None. algo (str): Select the algorithm for testing whether a point is contained by the site: simplex: Use scipy.spatial.Delaunay.find_simplex to test if any of the simplices that make up this polyhedron contain the point. sn: Compute the sign of the surface normal for each polyhedron face with respect to the point, to test if the point lies "inside" every face. Returns: bool """ contains_point_algos = {'simplex': self.contains_point_simplex, 'sn': self.contains_point_sn} if algo not in contains_point_algos.keys(): raise ValueError(f'{algo} is not a valid algorithm keyword for contains_point()') if structure: self.assign_vertex_coords(structure) if self.vertex_coords is None: raise RuntimeError('no vertex coordinates set for polyhedral_site {}'.format(self.index)) return contains_point_algos[algo](x_pbc(x))
[docs] def contains_point_simplex(self, x: np.ndarray) -> bool: """Test whether one or more points are inside this site, by checking whether these points are contained inside the simplices of the Delaunay tesselation defined by the vertex coordinates. Args: x (np.array): Fractional coordinates for one or more points, as a (3x1) or (3xN) numpy array. Returns: bool """ return bool(np.any(self.delaunay.find_simplex(x) >= 0))
[docs] def contains_point_sn(self, x_list: np.ndarray) -> bool: """Test whether one or more points are inside this site, by calculating the sign of the surface normal for each face with respect to each point. Args: x (np.array): Fractional coordinates for one or more points, as a (3x1) or (3xN) numpy array. Returns: bool Note: This method could be made more efficient by caching the surface_normal vectors and in-face vectors. This is also a possible target for optimisation with f2py etc. """ hull = ConvexHull(self.vertex_coords) faces = hull.points[hull.simplices] centre = self.centre() inside = [] for x in x_list: dotsum = 0 for f in faces: surface_normal = np.cross(f[0]-f[2], f[1]-f[2]) c_sign = np.sign( surface_normal, centre-f[0])) p_sign = np.sign( surface_normal, x-f[0])) dotsum += c_sign * p_sign inside.append(dotsum == len(faces)) return any(inside)
[docs] def contains_atom(self, atom: Atom, algo: Optional[str]='simplex', *args: Any, **kwargs: Any) -> bool: """Test whether an atom is inside this polyhedron. Args: atom (Atom): The atom to test. algo (:obj:`str`, optional): Select the algorithm to us. Options are 'simplex' and 'sn'. See the documentation for the contains_point() method for more details. Default is 'simplex'. Returns: bool """ contains_point_algos = ['simplex', 'sn'] if algo not in contains_point_algos: raise ValueError(f'{algo} is not a valid algorithm keyword for contains_atom()') return self.contains_point(atom.frac_coords, algo=algo)
[docs] def as_dict(self) -> Dict: d = super(PolyhedralSite, self).as_dict() d['vertex_indices'] = self.vertex_indices d['vertex_coords'] = self.vertex_coords return d
[docs] @classmethod def from_dict(cls, d): polyhedral_site = cls(vertex_indices=d['vertex_indices']) polyhedral_site.vertex_coords = d['vertex_coords'] polyhedral_site.contains_atoms = d['contains_atoms'] polyhedral_site.label = d.get('label') return polyhedral_site
[docs] def centre(self) -> np.ndarray: """Returns the fractional coordinates of the centre point of this polyhedral site. Args: None Returns: (np.array): (3,) numpy array. """ assert(isinstance(self.vertex_coords, np.ndarray)) return np.mean(self.vertex_coords, axis=0)
[docs] @classmethod def sites_from_vertex_indices(cls, vertex_indices, label=None): sites = [cls(vertex_indices=vi, label=label) for vi in vertex_indices] return sites