import math
import numpy as np
from ase import Atoms
from ase.cluster.base import ClusterBase
[docs]class Cluster(Atoms, ClusterBase):
symmetry = None
surfaces = None
lattice_basis = None
resiproc_basis = None
atomic_basis = None
[docs] def copy(self):
cluster = Atoms.copy(self)
cluster.symmetry = self.symmetry
cluster.surfaces = self.surfaces.copy()
cluster.lattice_basis = self.lattice_basis.copy()
cluster.atomic_basis = self.atomic_basis.copy()
cluster.resiproc_basis = self.resiproc_basis.copy()
return cluster
[docs] def get_surfaces(self):
"""Returns the miller indexs of the stored surfaces of the cluster."""
if self.surfaces is not None:
return self.surfaces.copy()
else:
return None
[docs] def get_layers(self):
"""Return number of atomic layers in stored surfaces directions."""
layers = []
for s in self.surfaces:
n = self.miller_to_direction(s)
c = self.get_positions().mean(axis=0)
r = np.dot(self.get_positions() - c, n).max()
d = self.get_layer_distance(s, 2)
l_ = 2 * np.round(r / d).astype(int)
ls = np.arange(l_ - 1, l_ + 2)
ds = np.array([self.get_layer_distance(s, i) for i in ls])
mask = (np.abs(ds - r) < 1e-10)
layers.append(ls[mask][0])
return np.array(layers, int)
[docs] def get_diameter(self, method='volume'):
"""Returns an estimate of the cluster diameter based on two different
methods.
Parameters
----------
method : {'volume', 'shape'}
'volume' (default) returns the diameter of a sphere with the same
volume as the atoms. 'shape' returns the averaged diameter
calculated from the directions given by the defined surfaces.
"""
if method == 'shape':
cen = self.get_positions().mean(axis=0)
pos = self.get_positions() - cen
d = 0.0
for s in self.surfaces:
n = self.miller_to_direction(s)
r = np.dot(pos, n)
d += r.max() - r.min()
return d / len(self.surfaces)
elif method == 'volume':
V_cell = np.abs(np.linalg.det(self.lattice_basis))
N_cell = len(self.atomic_basis)
N = len(self)
return 2.0 * (3.0 * N * V_cell /
(4.0 * math.pi * N_cell)) ** (1.0 / 3.0)
else:
return 0.0