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import numpy as np
import pytest
from ase.cluster.decahedron import Decahedron
from ase.cluster.icosahedron import Icosahedron
from ase.cluster.octahedron import Octahedron
from ase.neighborlist import neighbor_list
sym = 'Au'
a0 = 4.05
ico_cubocta_sizes = [0, 1, 13, 55, 147, 309, 561, 923, 1415]
ico_corner_coordination = 6
ico_corners = 12
fcc_maxcoordination = 12
def coordination_numbers(atoms):
return np.bincount(neighbor_list('i', atoms, 0.80 * a0))
@pytest.mark.parametrize('shells', range(1, 7))
def test_icosa(shells):
atoms = Icosahedron(sym, shells)
assert len(atoms) == ico_cubocta_sizes[shells]
coordination = coordination_numbers(atoms)
if shells == 1:
return
assert min(coordination) == ico_corner_coordination
ncorners = sum(coordination == ico_corner_coordination)
assert ncorners == ico_corners
octa_sizes = [0, 1, 6, 19, 44, 85, 146, 231, 344]
@pytest.mark.parametrize('shells', range(1, 8))
def test_regular_octahedron(shells):
octa = Octahedron(sym, length=shells, cutoff=0)
coordination = coordination_numbers(octa)
assert len(octa) == octa_sizes[shells]
if shells == 1:
return
assert min(coordination) == 4 # corner atoms
assert sum(coordination == 4) == 6 # number of corners
# All internal atoms must have coordination as if in bulk crystal:
expected_internal_atoms = octa_sizes[shells - 2]
assert sum(coordination == fcc_maxcoordination) == expected_internal_atoms
@pytest.mark.parametrize('shells', range(1, 7))
def test_cuboctahedron(shells):
cutoff = shells - 1
length = 2 * cutoff + 1
cubocta = Octahedron(sym, length=length, cutoff=cutoff)
print(cubocta)
assert len(cubocta) == ico_cubocta_sizes[shells]
coordination = coordination_numbers(cubocta)
expected_internal_atoms = ico_cubocta_sizes[shells - 1]
assert sum(coordination == fcc_maxcoordination) == expected_internal_atoms
def test_decahedron():
p = 3 # Number of atoms along edges of icosahedron-like fivefold structure
q = 4 # number of "repetitive" layers between icosahedron-like endings
r = 2 # Number of atoms cut off corners of icosahedron-like structure
deca = Decahedron(sym, p, q, r)
# Does anyone know the formula for how many atoms there are supposed to be?
# It "looks good" so just assert things are as they apparently should be:
assert len(deca) == 520
coordination = coordination_numbers(deca)
internal_atoms = sum(coordination == fcc_maxcoordination)
next_smaller_deca = Decahedron(sym, p - 1, q - 1, r)
assert internal_atoms == len(next_smaller_deca)
def test_smallest_decahedron():
assert len(Decahedron(sym, 1, 1, 0)) == 1
def clusters():
yield Icosahedron(sym, 2)
yield Octahedron(sym, length=3, cutoff=1)
yield Decahedron(sym, 2, 3, 3)
@pytest.mark.parametrize('cluster', clusters())
def test_centering(cluster):
assert cluster.cell.rank == 0
assert cluster.positions.sum(0) == pytest.approx(np.zeros(3), abs=1e-10)
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