Source code for matador.crystal.crystal_site

# coding: utf-8
# Distributed under the terms of the MIT License.

""" This submodule implements the Site class for handling
atomic sites.


import numpy as np
from matador.utils.cell_utils import cart2frac, frac2cart, wrap_frac_coords
from matador.orm.orm import DataContainer

[docs]class Site(DataContainer): """ The Site class contains a description of an individual site within a 3D periodic Crystal. """ # This dictionary defines the map between fields in :obj:`Crystal` # that correspond to arrays of site properties and between the # relevant keys the :obj:`Site` object _crystal_key_map = { "site_occupancy": "site_occupancy", "chemical_shielding_isos": "chemical_shielding_iso", "chemical_shift_isos": "chemical_shift_iso", "magnetic_shielding_tensors": "magnetic_shielding_tensor", "chemical_shift_anisos": "chemical_shift_aniso", "chemical_shift_asymmetries": "chemical_shift_asymmetry", "quadrupolar_couplings": "quadrupolar_coupling", "quadrupolar_asymmetries": "quadrupolar_asymmetry", "voronoi_substructure": "voronoi_substructure" } def __init__(self, species: str, position: list, lattice, position_unit='fractional', mutable: bool = False, **site_data): """ Initialise a Site object from its species, position and a reference to the lattice it exists in. Any other keys will be made available as site-level values. """ if site_data.get('voronoi_substructure') is not None: assert self.species == site_data['voronoi_substructure'][0] site_data['voronoi_substructure'] = site_data['voronoi_substructure'][1] # DataContainer will take a copy of all data passed to it, but lets keep # lattice as a reference so that it can change externally self._lattice = lattice super().__init__( species=species, position=position, site_data=site_data, mutable=mutable ) self._data["lattice_cart"] = self._lattice self.set_position(position, position_unit) self._occupancy = None self.site_data = {} self.site_data.update(site_data)
[docs] def get(self, key, default=None): try: return self[key] except (KeyError, AttributeError): return default
def __getitem__(self, key): """ Add extra look-up in `self.site_data` to :class:`DataContainer`'s `__getitem__`. Parameters: key (str): name of key or attribute to get. Raises: AttributeError: if key or attribute can't be found. """ if isinstance(key, int): raise ValueError("Object does not support indexing") try: super().__getitem__(key) except (AttributeError, KeyError): pass try: return self.site_data[key] except KeyError: raise KeyError('Site has no data/site_data or implementation for requested key: "{}"' .format(key)) def __setitem__(self, key: str, item): if key not in self.site_data or self.site_data[key] is None: self.site_data[key] = item return elif self.site_data[key] != item: try: import math if (math.isnan(item) and math.isnan(self.site_data[key])): return except TypeError: pass raise AttributeError('Cannot assign value {} to existing key {} with value {}' .format(item, key, self.site_data[key])) def __str__(self): site_str = '{species} {pos[0]:4.4f} {pos[1]:4.4f} {pos[2]:4.4f}'.format(species=self.species, pos=self.coords) for key in self.site_data: try: site_str += '\n{} = {:4.4f}'.format(key, np.asarray(self.site_data[key])) except (ValueError, TypeError): with np.printoptions(precision=2, threshold=6, edgeitems=2): site_str += ( '\n{} = \n{}' .format( key, "\n".join(f" {row}" for row in np.asarray(self.site_data[key]).__str__().split("\n")) ) ) site_str += "\n---" return site_str def __deepcopy__(self, memo): from copy import deepcopy species, position, lattice = (deepcopy(x) for x in (self.species, self.coords, self.lattice)) site_data = deepcopy(self.site_data) return Site(species, position, lattice, position_unit='fractional', **site_data)
[docs] def set_position(self, position, units): if len(position) != 3 or not all(isinstance(p, (float, int)) for p in position): raise RuntimeError('CrystalSite position has wrong shape: {}'.format(position)) if not hasattr(self, '_coords'): self._coords = dict() if units == 'fractional': self._coords['fractional'] = wrap_frac_coords( [float(pos) for pos in position], remove=False ) elif units == 'cartesian': self._coords['fractional'] = wrap_frac_coords( cart2frac(self.lattice, self.coords), remove=False ) else: raise RuntimeError('Unit system {} not understood, expecting `fractional`/`cartesian`'.format(units))
@property def coords(self): return np.asarray(self._coords['fractional']) @property def coords_cartesian(self): return np.asarray(frac2cart(self.lattice, self.coords)) @property def species(self): return self._data['species'] @species.setter def species(self, value): self._data['species'] = value @property def lattice(self): try: return self._lattice.lattice_cart except AttributeError: return self._lattice @property def occupancy(self): if "site_occupancy" not in self._data: self._data["site_occupancy"] = 1.0 return self._data["site_occupancy"] @property def coordination(self): if '_coordination' in self.__dict__: return self._coordination if self.voronoi_substructure is None: raise RuntimeError('Voronoi substructure not found.') coordination = {} eps = 0.05 for atom, weight in self.voronoi_substructure: if weight >= 1 - eps: if atom not in coordination: coordination[atom] = 1 else: coordination[atom] += 1 self._coordination = coordination return coordination
[docs] def displacement_between_sites(self, other_site): return self.coords_cartesian - other_site.coords_cartesian
[docs] def distance_between_sites(self, other_site): return np.linalg.norm( self.displacement_between_sites(other_site) )