def test_map_sites_ideal_structure(u):
from pylada.crystal.cppwrappers import map_sites
structure0, structure1, lattice = get_a_supercell(u)
assert map_sites(lattice, structure1)
for a, b in zip(structure0, structure1):
assert a.site == b.site
def test_b5(u):
""" Test b5 space-group and equivalents """
from random import randint, random
from numpy import array
from numpy.linalg import det
from pylada.crystal.cppwrappers import Structure, map_sites, supercell
x, y = u, 0.25 - u
lattice = Structure([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]]) \
.add_atom(5.000000e-01, 5.000000e-01, 5.000000e-01, "A") \
.add_atom(5.000000e-01, 2.500000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 5.000000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 2.500000e-01, 5.000000e-01, "A") \
.add_atom(8.750000e-01, 8.750000e-01, 8.750000e-01, "B") \
.add_atom(1.250000e-01, 1.250000e-01, 1.250000e-01, "B") \
.add_atom( x, x, x, "X") \
.add_atom( x, y, y, "X") \
.add_atom( y, x, y, "X") \
.add_atom( y, y, x, "X") \
.add_atom( -x, -x, -x, "X") \
.add_atom( -x, -y, -y, "X") \
.add_atom( -y, -x, -y, "X") \
.add_atom( -y, -y, -x, "X")
for i in xrange(5):
while True:
cell = [[randint(-2, 3) for j in xrange(3)] for k in xrange(3)]
if det(cell) != 0: break
structure0 = supercell(lattice, cell)
structure1 = structure0.copy()
for atom in structure1:
del atom.site
assert map_sites(lattice, structure1)
for a, b in zip(structure0, structure1):
assert a.site == b.site
for atom in structure1:
del atom.site
atom.pos += array(
[random() * 1e-3,
random() * 1e-3,
random() * 1e-3])
assert map_sites(lattice, structure1, tolerance=1e-2)
for a, b in zip(structure0, structure1):
assert a.site == b.site
def test_map_sites_perturbed_structure(u):
from numpy.random import random
from pylada.crystal.cppwrappers import map_sites
structure0, structure1, lattice = get_a_supercell(u)
for atom in structure1: atom.pos += random(3) * 1e-3
assert map_sites(lattice, structure1, tolerance=1e-2)
for a, b in zip(structure0, structure1):
assert a.site == b.site
def test_b5(u):
""" Test b5 space-group and equivalents """
from random import randint, random
from numpy import array
from numpy.linalg import det
from pylada.crystal.cppwrappers import Structure, map_sites, supercell
x, y = u, 0.25-u
lattice = Structure([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]]) \
.add_atom(5.000000e-01, 5.000000e-01, 5.000000e-01, "A") \
.add_atom(5.000000e-01, 2.500000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 5.000000e-01, 2.500000e-01, "A") \
.add_atom(2.500000e-01, 2.500000e-01, 5.000000e-01, "A") \
.add_atom(8.750000e-01, 8.750000e-01, 8.750000e-01, "B") \
.add_atom(1.250000e-01, 1.250000e-01, 1.250000e-01, "B") \
.add_atom( x, x, x, "X") \
.add_atom( x, y, y, "X") \
.add_atom( y, x, y, "X") \
.add_atom( y, y, x, "X") \
.add_atom( -x, -x, -x, "X") \
.add_atom( -x, -y, -y, "X") \
.add_atom( -y, -x, -y, "X") \
.add_atom( -y, -y, -x, "X")
for i in xrange(5):
while True:
cell = [ [randint(-2, 3) for j in xrange(3)] for k in xrange(3)]
if det(cell) != 0: break
structure0 = supercell(lattice, cell)
structure1 = structure0.copy()
for atom in structure1: del atom.site
assert map_sites(lattice, structure1)
for a, b in zip(structure0, structure1):
assert a.site == b.site
for atom in structure1:
del atom.site
atom.pos += array([random() * 1e-3, random() * 1e-3, random() * 1e-3])
assert map_sites(lattice, structure1, tolerance=1e-2)
for a, b in zip(structure0, structure1):
assert a.site == b.site
