def test_labelexchange():
""" Tests label exchange """
from pylada.crystal import binary, supercell, HFTransform
from pylada.enum import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
transforms = Transforms(lattice)
lattice = transforms.lattice
structure = supercell(lattice, [[8, 0, 0], [0, 0.5, 0.5], [0, -0.5, 0.5]])
species = [ 'Ge', 'C', 'Si', 'C', 'Si', 'C', 'Si', 'Si', 'Ge', 'Si', 'Ge',
'Si', 'Ge', 'Si', 'Ge', 'Ge', 'Ge', 'C', 'Ge', 'Si', 'Si', 'Si',
'Si', 'Ge', 'Si', 'Ge', 'Si', 'Si', 'Si', 'C', 'Ge', 'Si']
for atom, s in zip(structure, species): atom.type = s
hft = HFTransform(lattice, structure)
x = transforms.toarray(hft, structure)
results = [ 21112222221111123331111231122131L, # <- this is x
21112222221111122221111321133121L,
21112222221111123332222132211232L,
21112222221111121112222312233212L,
21112222221111122223333123311323L,
21112222221111121113333213322313L,
12221111112222213331111231122131L,
12221111112222212221111321133121L,
12221111112222213332222132211232L,
12221111112222211112222312233212L,
12221111112222212223333123311323L,
12221111112222211113333213322313L ]
permutations = transforms.label_exchange(hft)
for a, b in zip(permutations(x), results[1:]):
assert int(str(a)[1:-1].replace(' ', '')) == b
def test_rotations():
from numpy import all, dot, zeros
from numpy.linalg import inv
from pylada.crystal import binary, supercell, HFTransform, space_group, \
which_site
from pylada.enum import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
sg = space_group(lattice)
invcell = inv(lattice.cell)
def get_cells(n):
for i in xrange(1, n):
yield [[i, 0, 0], [0, 0.5, 0.5], [0, -0.5, 0.5]]
for i in xrange(1, n):
yield [[i, 0, 0], [0, i, 0], [0, 0, 1]]
for i in xrange(1, n):
yield [[i, 0, 0], [0, i, 0], [0, 0, i]]
yield dot(lattice.cell, [[1, 0, 0], [0, 1, 0], [0, 0, 2]])
for cell in get_cells(8):
# create random structure
structure = supercell(lattice, cell)
hft = HFTransform(lattice, structure)
# these are all the translations
transforms = Transforms(lattice)
permutations = transforms.transformations(hft)
assert permutations.shape == (len(sg) - 1, len(structure))
operations = transforms.invariant_ops(structure)
assert any(operations)
# compute each translation and gets decorations
for index, (op, isgood) in enumerate(zip(sg[1:], operations)):
if not isgood: continue
# Create rotation and figure out its index
permutation = zeros(len(structure), dtype='int') - 1
for atom in structure:
pos = dot(op[:3], atom.pos) + op[3]
newsite = which_site(pos, lattice, invcell)
i = hft.index(atom.pos - lattice[atom.site].pos, atom.site)
j = hft.index(pos - lattice[newsite].pos, newsite)
permutation[i] = j
assert all(permutation == permutations[index])
def test_toarray():
""" Tests label exchange """
from random import choice
from numpy import all, zeros
from pylada.crystal import binary, supercell, HFTransform
from pylada.enum import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
transforms = Transforms(lattice)
lattice = transforms.lattice
for u in xrange(11):
structure = supercell(lattice, get_cell())
for atom in structure: atom.type = choice(atom.type)
hft = HFTransform(lattice, structure)
a = transforms.toarray(hft, structure)
b = zeros(len(structure), dtype='int')
for atom in structure:
site = lattice[atom.site]
b[hft.index(atom.pos-site.pos, atom.site)] \
= site.type.index(atom.type) + 1
assert all(a == b)