def test_toarray():
""" Tests label exchange """
from random import choice
from numpy import all, zeros
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations 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 range(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)
def test_labelexchange():
""" Tests label exchange """
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations 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 = [21112222221111123331111231122131, # <- this is x
21112222221111122221111321133121,
21112222221111123332222132211232,
21112222221111121112222312233212,
21112222221111122223333123311323,
21112222221111121113333213322313,
12221111112222213331111231122131,
12221111112222212221111321133121,
12221111112222213332222132211232,
12221111112222211112222312233212,
12221111112222212223333123311323,
12221111112222211113333213322313]
permutations = transforms.label_exchange(hft)
for a, b in zip(permutations(x), results[1:]):
assert int(str(a)[1:-1].replace(' ', '')) == b
def test_translations(cell):
from numpy import abs, all
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
# create random structure
structure = supercell(lattice, cell)
hft = HFTransform(lattice, structure)
# these are all the translations
translations = Transforms(lattice).translations(hft)
assert translations.shape == (len(structure) // len(lattice) - 1,
len(structure))
# compute each translation and gets decorations
for atom in structure:
if atom.site != 0:
continue
# create translation
trans = atom.pos - lattice[0].pos
if all(abs(trans) < 1e-8):
continue
# figure out its index
index = hft.index(trans) - 1
for site in structure:
pos = site.pos - lattice[site.site].pos
i = hft.index(pos, site.site)
j = hft.index(pos + trans, site.site)
assert translations[index, i] == j
def test_inverse_spinel():
from numpy import all
from pylada.crystal import A2BX4
from pylada.decorations import Transforms
lattice = A2BX4.b5()
for atom in lattice:
if atom.type in ['A', 'B']:
atom.type = 'A', 'B'
lattice[0], lattice[-1] = lattice[-1], lattice[0]
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 3
assert all([transforms.lattice[i].asymmetric for i in [0, 1, 4]])
assert all([
not transforms.lattice[i].asymmetric
for i in list(range(2, 4)) + list(range(5, 14))
])
assert all(
[transforms.lattice[i].equivto == 0 for i in [0] + list(range(6, 13))])
assert all(
[transforms.lattice[i].equivto == 1 for i in list(range(1, 4)) + [13]])
assert all([transforms.lattice[i].equivto == 4 for i in [4, 5]])
assert all([
transforms.lattice[i].nbflavors == 1 for i in [0] + list(range(6, 13))
])
assert all([
transforms.lattice[i].nbflavors == 2 for i in list(range(1, 4)) + [13]
])
assert all([transforms.lattice[i].nbflavors == 2 for i in [4, 5]])
index = 0
for i, atom in enumerate(transforms.lattice):
if atom.nbflavors == 1:
assert not hasattr(atom, 'index')
else:
assert atom.index == index
index += 1
def test_labelexchange():
""" Tests label exchange """
from pylada.crystal import binary, supercell, HFTransform
from pylada.decorations 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 = [
21112222221111123331111231122131, # <- this is x
21112222221111122221111321133121,
21112222221111123332222132211232,
21112222221111121112222312233212,
21112222221111122223333123311323,
21112222221111121113333213322313,
12221111112222213331111231122131,
12221111112222212221111321133121,
12221111112222213332222132211232,
12221111112222211112222312233212,
12221111112222212223333123311323,
12221111112222211113333213322313
]
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(cell):
from numpy import all, dot, zeros
from numpy.linalg import inv
from pylada.crystal import binary, supercell, HFTransform, space_group, \
which_site
from pylada.decorations 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)
# 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_rotations(cell):
from numpy import all, dot, zeros
from numpy.linalg import inv
from pylada.crystal import binary, supercell, HFTransform, space_group, \
which_site
from pylada.decorations 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)
# 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.decorations 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 range(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)
def test_zinc_blende_lattice_diff_occupations():
from numpy import all
from pylada.crystal import binary
from pylada.decorations import Transforms
lattice = binary.zinc_blende()
lattice[0].type = ['Si', 'Ge']
lattice[1].type = ['Si', 'Ge', 'C']
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 2
assert transforms.lattice[0].asymmetric
assert transforms.lattice[0].equivto == 0
assert transforms.lattice[0].nbflavors == 2
assert transforms.lattice[0].index == 0
assert transforms.lattice[0].asymmetric
assert transforms.lattice[1].equivto == 1
assert transforms.lattice[1].nbflavors == 3
assert transforms.lattice[1].index == 1
assert all(
all(a == b)
for a, b in zip(transforms.flavors, (list(range(1)), list(range(2)))))
def test_spinel():
from numpy import all
from pylada.crystal import A2BX4
from pylada.decorations import Transforms
lattice = A2BX4.b5()
for atom in lattice:
if atom.type in ['A', 'B']:
atom.type = 'A', 'B'
transforms = Transforms(lattice)
assert len([u for u in transforms.lattice if u.asymmetric]) == 3
assert all([transforms.lattice[i].asymmetric for i in [0, 4, 6]])
assert all([
not transforms.lattice[i].asymmetric
for i in list(range(1, 4)) + [5] + list(range(7, 14))
])
assert all([transforms.lattice[i].equivto == 0 for i in range(4)])
assert all([transforms.lattice[i].equivto == 4 for i in range(4, 6)])
assert all([transforms.lattice[i].equivto == 6 for i in range(6, 14)])
assert all([transforms.lattice[i].nbflavors == 2 for i in range(4)])
assert all([transforms.lattice[i].nbflavors == 2 for i in range(4, 6)])
assert all([transforms.lattice[i].nbflavors == 1 for i in range(6, 14)])
assert all([transforms.lattice[i].index == i for i in range(6)])
assert all(
[not hasattr(transforms.lattice[i], 'index') for i in range(6, 14)])
