def test2():
from random import randint
from numpy import all, abs, dot, array
from pylada.crystal.cppwrappers import HFTransform, Structure, supercell
unitcell = array([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]])
lattice = Structure(unitcell).add_atom(0,0,0, "Si")
supercell = supercell(lattice, dot(lattice.cell, [[3,0,5],[0,0,-1],[-2,1,2]]))
a = HFTransform(unitcell, supercell)
assert all(abs(a.transform-[[0, 2, 0],[1, 5, -1],[-2, -4, 0]]) < 1e-8)
assert all(abs(a.quotient-[1,1,3]) < 1e-8)
all_indices = set()
for atom in supercell:
indices = a.indices(atom.pos)
index = a.index(atom.pos)
assert index not in all_indices, (index, all_indices )
assert all(indices >= 0)
assert all(indices <= a.quotient )
assert index == a.flatten_indices(*indices)
all_indices.add(index)
for i in xrange(20):
vec = dot(supercell.cell, array([randint(-20, 20), randint(-20, 20), randint(-20, 20)], dtype="float64"))
vec += atom.pos
assert all(abs(a.indices(vec)-indices) < 1e-8)
try: a.indices(vec + [0.1, 0.1, 0])
except ValueError: pass
else: raise RuntimeError("Should have failed.")
assert index == a.index(vec)
try: a.index(vec + [0.1, 0.1, 0])
except ValueError: pass
else: raise RuntimeError("Should have failed.")
assert len(all_indices) == len(supercell)
def test_coordination_shells():
from random import random
from numpy import array
from numpy.random import randint, random
from pylada.crystal.cppwrappers import supercell, Structure
lattice = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]]) \
.add_atom(0, 0, 0, "Si") \
.add_atom(0.25, 0.25, 0.25, "Ge")
for atom in lattice: check(lattice, atom)
structure = supercell(lattice, [1, 1, 0, -5, 2, 0, 0, 0, 1])
for index in randint(len(structure), size=4):
check(structure, structure[index])
for atom in lattice: atom.pos += random(3) * 1e-4 - 5e-5
for atom in lattice:
check(lattice, atom, 1e-2)
for atom in structure: atom.pos += random(3) * 1e-4 - 5e-5
for index in randint(len(structure), size=4):
check(structure, structure[index], 1e-2)
check_against_neighbors(structure, 1e-2)
lattice = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]]) \
.add_atom(0, 0, 0, "Si")
check_against_neighbors(structure, 1e-8)
lattice = Structure([[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5], [0.5, 0.5, -0.5]]) \
.add_atom(0, 0, 0, "Si")
check_against_neighbors(structure, 1e-8)
def test_primitive():
""" Tests whether primitivization works. """
from numpy import abs, dot
from numpy.linalg import inv
from pylada.crystal.cppwrappers import supercell, Structure, are_periodic_images as api, \
primitive, is_primitive
from pylada.math import is_integer
lattice = Structure( 0.0, 0.5, 0.5,
0.5, 0.0, 0.5,
0.5, 0.5, 0.0, scale=2.0, m=True ) \
.add_atom(0, 0, 0, "As") \
.add_atom(0.25, 0.25, 0.25, ['In', 'Ga'], m = True)
assert is_primitive(lattice)
for cell in itercells(10):
structure = supercell(lattice, dot(lattice.cell, cell))
assert not is_primitive(structure)
structure = primitive(structure, 1e-8)
assert is_primitive(structure)
assert abs(structure.volume - lattice.volume) < 1e-8
assert len(structure) == len(lattice)
assert is_integer(dot(structure.cell, inv(lattice.cell)))
assert is_integer(dot(lattice.cell, inv(structure.cell)))
invcell = inv(lattice.cell)
for atom in structure:
assert api(lattice[atom.site].pos, atom.pos, invcell) and \
atom.type == lattice[atom.site].type and \
getattr(lattice[atom.site], 'm', False) == getattr(atom, 'm', False) and \
(getattr(atom, 'm', False) or atom.site == 0)
def test_ediff():
from pickle import loads, dumps
from pylada.crystal.cppwrappers import Structure, supercell
from pylada.vasp.incar._params import Ediff, Ediffg
structure = (
Structure([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
.add_atom(0, 0, 0, "Si")
.add_atom(0.25, 0.25, 0.25, "Si")
)
assert Ediff(None).incar_string(structure=structure) is None
a = loads(dumps(Ediff(1e-4))).incar_string(structure=structure).split()
assert a[0] == "EDIFF" and a[1] == "=" and abs(float(a[2]) - 1e-4 * 2.0) < 1e-8
a = loads(dumps(Ediff(-1e-4))).incar_string(structure=structure).split()
assert a[0] == "EDIFF" and a[1] == "=" and abs(float(a[2]) - 1e-4) < 1e-8 and float(a[2]) > 0e0
assert Ediffg(None).incar_string(structure=structure) is None
a = loads(dumps(Ediffg(1e-4))).incar_string(structure=structure).split()
assert a[0] == "EDIFFG" and a[1] == "=" and abs(float(a[2]) - 1e-4 * 2.0) < 1e-8
a = loads(dumps(Ediffg(-1e-4))).incar_string(structure=structure).split()
assert a[0] == "EDIFFG" and a[1] == "=" and abs(float(a[2]) + 1e-4) < 1e-8
structure = supercell(structure, [[1, 0, 0], [0, 1, 0], [0, 0, 1]])
a = loads(dumps(Ediff(1e-4))).incar_string(structure=structure).split()
assert a[0] == "EDIFF" and a[1] == "=" and abs(float(a[2]) - 1e-4 * 8.0) < 1e-8
a = loads(dumps(Ediff(-1e-4))).incar_string(structure=structure).split()
assert a[0] == "EDIFF" and a[1] == "=" and abs(float(a[2]) - 1e-4) < 1e-8 and float(a[2]) > 0e0
a = loads(dumps(Ediffg(1e-4))).incar_string(structure=structure).split()
assert a[0] == "EDIFFG" and a[1] == "=" and abs(float(a[2]) - 1e-4 * 8.0) < 1e-8
a = loads(dumps(Ediffg(-1e-4))).incar_string(structure=structure).split()
assert a[0] == "EDIFFG" and a[1] == "=" and abs(float(a[2]) + 1e-4) < 1e-8
def test3(u):
from random import randint
from numpy import all, abs, dot, array, concatenate
from pylada.crystal.cppwrappers import HFTransform, supercell
lattice = b5(u)
supercell = supercell(lattice, dot(lattice.cell, [[2,2,0],[0,2,2],[4,0,4]]))
a = HFTransform(lattice.cell, supercell)
assert all(abs(a.transform-[[-1, 1, 1],[1, -1, 1],[5, -3, -1]]) < 1e-8)
assert all(abs(a.quotient-[2,2,8]) < 1e-8)
all_indices = set()
others = set()
for atom in supercell:
indices = a.indices(atom.pos - lattice[atom.site].pos)
index = a.index(atom.pos - lattice[atom.site].pos, atom.site)
assert index not in all_indices, (index, all_indices )
assert all(indices >= 0)
assert all(indices <= a.quotient )
all_indices.add(index)
assert str(concatenate((indices, [atom.site]))) not in others
others.add(str(concatenate((indices, [atom.site]))))
for i in xrange(20):
vec = dot(supercell.cell, array([randint(-20, 20), randint(-20, 20), randint(-20, 20)], dtype="float64"))
vec += atom.pos - lattice[atom.site].pos
assert all(abs(a.indices(vec)-indices) < 1e-8)
try: a.indices(vec + [0.1, 0.1, 0])
except ValueError: pass
else: raise RuntimeError("Should have failed.")
assert index == a.index(vec, atom.site)
try: a.index(vec + [0.1, 0.1, 0])
except ValueError: pass
else: raise RuntimeError("Should have failed.")
assert len(all_indices) == len(supercell)
def newstructure(i=10):
from numpy import zeros
from numpy.linalg import det
from random import randint
from pylada.crystal.cppwrappers import supercell
lattice = b5()
cell = zeros((3,3))
while det(cell) == 0:
cell[:] = [[randint(-i, i+1) for j in xrange(3)] for k in xrange(3)]
if det(cell) < 0: cell[:, 0], cell[:, 1] = cell[:, 1].copy(), cell[:, 0].copy()
return supercell(lattice, cell)
def test1():
from pylada.crystal.cppwrappers import Structure, supercell
zb = Structure( 0,0.5,0.5,
0.5,0,0.5,
0.5,0.5,0 )\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
sc = supercell(zb, [[3, 0, 0], [0, 0.5,-0.5], [0, 0.5, 0.5]])
sc[0].type = "Ge"
sc[1].type = "Ge"
sc[3].type = "Ge"
decoration(sc, sc, zb)
def get_a_supercell(u):
from random import randint
from numpy import array
from numpy.linalg import det
from pylada.crystal.cppwrappers import supercell
lattice = get_some_lattice(u)
while True:
cell = [ [randint(-2, 3) for j in xrange(3)] for k in xrange(3)]
if det(cell) != 0: break
structure = supercell(lattice, cell)
copy = structure.copy()
for atom in copy: del atom.site
return structure, copy, lattice
def test1():
from pylada.crystal.cppwrappers import Structure, supercell
zb = Structure( 0,0.5,0.5,
0.5,0,0.5,
0.5,0.5,0 )\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
sc = supercell(zb, [[3, 0, 0], [0, 0.5, -0.5], [0, 0.5, 0.5]])
sc[0].type = "Ge"
sc[1].type = "Ge"
sc[3].type = "Ge"
decoration(sc, sc, zb)
def test2():
from random import random
from pylada.crystal.cppwrappers import Structure, supercell
zb = Structure( 0,0.5,0.5,
0.5,0,0.5,
0.5,0.5,0 )\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
sc = supercell(zb, [[2, 0, 0], [0, 2,0], [0, 0, 2]])
del sc.lattice
for i in xrange(1):
x = random() * 0.5
for atom in sc:
atom.type = "Si" if x > random() else "Ge"
decoration(sc, sc, zb)
def test_primitive():
""" Tests whether primitivization works. """
from numpy import abs, dot
from numpy.linalg import inv
from pylada.crystal.cppwrappers import supercell, Structure, are_periodic_images as api, primitive, is_primitive
from pylada.math import is_integer
lattice = (
Structure(0.0, 0.5, 0.5, 0.5, 0.0, 0.5, 0.5, 0.5, 0.0, scale=2.0, m=True)
.add_atom(0, 0, 0, "As")
.add_atom(0.25, 0.25, 0.25, ["In", "Ga"], m=True)
)
assert is_primitive(lattice)
for cell in itercells(10):
structure = supercell(lattice, dot(lattice.cell, cell))
assert not is_primitive(structure)
def test2():
from random import random
from pylada.crystal.cppwrappers import Structure, supercell
zb = Structure( 0,0.5,0.5,
0.5,0,0.5,
0.5,0.5,0 )\
.add_atom(0,0,0, "Si")\
.add_atom(0.25,0.25,0.25, "Si")
sc = supercell(zb, [[2, 0, 0], [0, 2, 0], [0, 0, 2]])
del sc.lattice
for i in xrange(1):
x = random() * 0.5
for atom in sc:
atom.type = "Si" if x > random() else "Ge"
decoration(sc, sc, zb)
def test3(u):
from random import randint
from numpy import all, abs, dot, array, concatenate
from pylada.crystal.cppwrappers import HFTransform, supercell
lattice = b5(u)
supercell = supercell(lattice,
dot(lattice.cell, [[2, 2, 0], [0, 2, 2], [4, 0, 4]]))
a = HFTransform(lattice.cell, supercell)
assert all(abs(a.transform - [[-1, 1, 1], [1, -1, 1], [5, -3, -1]]) < 1e-8)
assert all(abs(a.quotient - [2, 2, 8]) < 1e-8)
all_indices = set()
others = set()
for atom in supercell:
indices = a.indices(atom.pos - lattice[atom.site].pos)
index = a.index(atom.pos - lattice[atom.site].pos, atom.site)
assert index not in all_indices, (index, all_indices)
assert all(indices >= 0)
assert all(indices <= a.quotient)
all_indices.add(index)
assert str(concatenate((indices, [atom.site]))) not in others
others.add(str(concatenate((indices, [atom.site]))))
for i in xrange(20):
vec = dot(
supercell.cell,
array([randint(-20, 20),
randint(-20, 20),
randint(-20, 20)],
dtype="float64"))
vec += atom.pos - lattice[atom.site].pos
assert all(abs(a.indices(vec) - indices) < 1e-8)
try:
a.indices(vec + [0.1, 0.1, 0])
except ValueError:
pass
else:
raise RuntimeError("Should have failed.")
assert index == a.index(vec, atom.site)
try:
a.index(vec + [0.1, 0.1, 0])
except ValueError:
pass
else:
raise RuntimeError("Should have failed.")
assert len(all_indices) == len(supercell)
def test2():
from random import randint
from numpy import all, abs, dot, array
from pylada.crystal.cppwrappers import HFTransform, Structure, supercell
unitcell = array([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
lattice = Structure(unitcell).add_atom(0, 0, 0, "Si")
supercell = supercell(
lattice, dot(lattice.cell, [[3, 0, 5], [0, 0, -1], [-2, 1, 2]]))
a = HFTransform(unitcell, supercell)
assert all(abs(a.transform - [[0, 2, 0], [1, 5, -1], [-2, -4, 0]]) < 1e-8)
assert all(abs(a.quotient - [1, 1, 3]) < 1e-8)
all_indices = set()
for atom in supercell:
indices = a.indices(atom.pos)
index = a.index(atom.pos)
assert index not in all_indices, (index, all_indices)
assert all(indices >= 0)
assert all(indices <= a.quotient)
assert index == a.flatten_indices(*indices)
all_indices.add(index)
for i in xrange(20):
vec = dot(
supercell.cell,
array([randint(-20, 20),
randint(-20, 20),
randint(-20, 20)],
dtype="float64"))
vec += atom.pos
assert all(abs(a.indices(vec) - indices) < 1e-8)
try:
a.indices(vec + [0.1, 0.1, 0])
except ValueError:
pass
else:
raise RuntimeError("Should have failed.")
assert index == a.index(vec)
try:
a.index(vec + [0.1, 0.1, 0])
except ValueError:
pass
else:
raise RuntimeError("Should have failed.")
assert len(all_indices) == len(supercell)
def test_primitive():
""" Tests whether primitivization works. """
from numpy import abs, dot
from numpy.linalg import inv
from pylada.crystal.cppwrappers import supercell, Structure, are_periodic_images as api, \
primitive, is_primitive
from pylada.math import is_integer
lattice = Structure( 0.0, 0.5, 0.5,
0.5, 0.0, 0.5,
0.5, 0.5, 0.0, scale=2.0, m=True ) \
.add_atom(0, 0, 0, "As") \
.add_atom(0.25, 0.25, 0.25, ['In', 'Ga'], m = True)
assert is_primitive(lattice)
for cell in itercells(10):
structure = supercell(lattice, dot(lattice.cell, cell))
assert not is_primitive(structure)
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_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_manysupercell():
from numpy import dot
from numpy.linalg import inv, det
from pylada.crystal import supercell, binary
from pylada.crystal.cppwrappers import are_periodic_images as api
lattice = binary.zinc_blende()
invlat = inv(lattice.cell)
for i in xrange(100):
cell = get_cell()
struc = supercell(lattice, dot(lattice.cell, cell))
assert len(struc) == len(lattice) * int(abs(det(cell))+0.01)
invcell = inv(struc.cell)
for i, atom in enumerate(struc):
# compare to lattice
tolat = [api(atom.pos, site.pos, invlat) for site in lattice]
assert tolat.count(True) == 1
assert tolat.index(True) == atom.site
assert lattice[tolat.index(True)].type == atom.type
# compare to self
tolat = [api(atom.pos, site.pos, invcell) for site in struc]
assert tolat.count(True) == 1
assert i == tolat.index(True)
def test_manysupercell():
from numpy import dot
from numpy.linalg import inv, det
from pylada.crystal import supercell, binary
from pylada.crystal.cppwrappers import are_periodic_images as api
lattice = binary.zinc_blende()
invlat = inv(lattice.cell)
for i in xrange(100):
cell = get_cell()
struc = supercell(lattice, dot(lattice.cell, cell))
assert len(struc) == len(lattice) * int(abs(det(cell)) + 0.01)
invcell = inv(struc.cell)
for i, atom in enumerate(struc):
# compare to lattice
tolat = [api(atom.pos, site.pos, invlat) for site in lattice]
assert tolat.count(True) == 1
assert tolat.index(True) == atom.site
assert lattice[tolat.index(True)].type == atom.type
# compare to self
tolat = [api(atom.pos, site.pos, invcell) for site in struc]
assert tolat.count(True) == 1
assert i == tolat.index(True)
def test_ediff():
from pickle import loads, dumps
from pylada.crystal.cppwrappers import Structure, supercell
from pylada.vasp.incar._params import Ediff, Ediffg
structure = Structure([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]])\
.add_atom(0, 0, 0, 'Si')\
.add_atom(0.25, 0.25, 0.25, 'Si')
assert Ediff(None).incar_string(structure=structure) is None
a = loads(dumps(Ediff(1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFF' and a[1] == '=' and abs(float(a[2]) -
1e-4 * 2.) < 1e-8
a = loads(dumps(Ediff(-1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFF' and a[1] == '=' and abs(float(a[2]) -
1e-4) < 1e-8 and float(
a[2]) > 0e0
assert Ediffg(None).incar_string(structure=structure) is None
a = loads(dumps(Ediffg(1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFFG' and a[1] == '=' and abs(float(a[2]) -
1e-4 * 2.) < 1e-8
a = loads(dumps(Ediffg(-1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFFG' and a[1] == '=' and abs(float(a[2]) + 1e-4) < 1e-8
structure = supercell(structure, [[1, 0, 0], [0, 1, 0], [0, 0, 1]])
a = loads(dumps(Ediff(1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFF' and a[1] == '=' and abs(float(a[2]) -
1e-4 * 8.) < 1e-8
a = loads(dumps(Ediff(-1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFF' and a[1] == '=' and abs(float(a[2]) -
1e-4) < 1e-8 and float(
a[2]) > 0e0
a = loads(dumps(Ediffg(1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFFG' and a[1] == '=' and abs(float(a[2]) -
1e-4 * 8.) < 1e-8
a = loads(dumps(Ediffg(-1e-4))).incar_string(structure=structure).split()
assert a[0] == 'EDIFFG' and a[1] == '=' and abs(float(a[2]) + 1e-4) < 1e-8
def test_supercell():
""" Simple supercell test. """
from numpy import identity, abs, all, dot
from numpy.linalg import inv
from pylada.crystal.cppwrappers import supercell, Structure, are_periodic_images as api
from quantities import angstrom
lattice = Structure( 0.0, 0.5, 0.5,
0.5, 0.0, 0.5,
0.5, 0.5, 0.0, scale=2.0, m=True ) \
.add_atom(0, 0, 0, "As") \
.add_atom(0.25, 0.25, 0.25, ['In', 'Ga'], m = True)
result = supercell(lattice, dot(lattice.cell, [ [-1, 1, 1],
[1, -1, 1],
[1, 1, -1] ] ) )
assert all(abs(result.cell - identity(3)) < 1e-8)
assert abs(result.scale - 2 * angstrom) < 1e-8
assert getattr(result, 'm', False)
assert all(abs(result[0].pos - [0.00, 0.00, 0.00]) < 1e-8) and result[0].type == "As" \
and getattr(result[0], 'site', -1) == 0 and api(result[0].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[1].pos - [0.25, 0.25, 0.25]) < 1e-8) and result[1].type == ["In", "Ga"] \
and getattr(result[1], 'm', False) and getattr(result[1], 'site', -1) == 1 \
and api(result[1].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[2].pos - [0.50, 0.00, 0.50]) < 1e-8) and result[2].type == "As" \
and getattr(result[2], 'site', -1) == 0 and api(result[2].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[3].pos - [0.75, 0.25, 0.75]) < 1e-8) and result[3].type == ["In", "Ga"] \
and getattr(result[3], 'm', False) and getattr(result[3], 'site', -1) == 1 \
and api(result[3].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[4].pos - [0.50, 0.50, 0.00]) < 1e-8) and result[4].type == "As" \
and getattr(result[4], 'site', -1) == 0 and api(result[4].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[5].pos - [0.75, 0.75, 0.25]) < 1e-8) and result[5].type == ["In", "Ga"] \
and getattr(result[5], 'm', False) and getattr(result[5], 'site', -1) == 1 \
and api(result[5].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[6].pos - [0.00, 0.50, 0.50]) < 1e-8) and result[6].type == "As" \
and getattr(result[6], 'site', -1) == 0 and api(result[6].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[7].pos - [0.25, 0.75, 0.75]) < 1e-8) and result[7].type == ["In", "Ga"] \
and getattr(result[7], 'm', False) and getattr(result[7], 'site', -1) == 1 \
and api(result[7].pos, lattice[1].pos, inv(lattice.cell))
def test_supercell():
""" Simple supercell test. """
from numpy import identity, abs, all, dot
from numpy.linalg import inv
from pylada.crystal.cppwrappers import supercell, Structure, are_periodic_images as api
from quantities import angstrom
lattice = Structure( 0.0, 0.5, 0.5,
0.5, 0.0, 0.5,
0.5, 0.5, 0.0, scale=2.0, m=True ) \
.add_atom(0, 0, 0, "As") \
.add_atom(0.25, 0.25, 0.25, ['In', 'Ga'], m = True)
result = supercell(lattice,
dot(lattice.cell, [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]))
assert all(abs(result.cell - identity(3)) < 1e-8)
assert abs(result.scale - 2 * angstrom) < 1e-8
assert getattr(result, 'm', False)
assert all(abs(result[0].pos - [0.00, 0.00, 0.00]) < 1e-8) and result[0].type == "As" \
and getattr(result[0], 'site', -1) == 0 and api(result[0].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[1].pos - [0.25, 0.25, 0.25]) < 1e-8) and result[1].type == ["In", "Ga"] \
and getattr(result[1], 'm', False) and getattr(result[1], 'site', -1) == 1 \
and api(result[1].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[2].pos - [0.50, 0.00, 0.50]) < 1e-8) and result[2].type == "As" \
and getattr(result[2], 'site', -1) == 0 and api(result[2].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[3].pos - [0.75, 0.25, 0.75]) < 1e-8) and result[3].type == ["In", "Ga"] \
and getattr(result[3], 'm', False) and getattr(result[3], 'site', -1) == 1 \
and api(result[3].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[4].pos - [0.50, 0.50, 0.00]) < 1e-8) and result[4].type == "As" \
and getattr(result[4], 'site', -1) == 0 and api(result[4].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[5].pos - [0.75, 0.75, 0.25]) < 1e-8) and result[5].type == ["In", "Ga"] \
and getattr(result[5], 'm', False) and getattr(result[5], 'site', -1) == 1 \
and api(result[5].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[6].pos - [0.00, 0.50, 0.50]) < 1e-8) and result[6].type == "As" \
and getattr(result[6], 'site', -1) == 0 and api(result[6].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[7].pos - [0.25, 0.75, 0.75]) < 1e-8) and result[7].type == ["In", "Ga"] \
and getattr(result[7], 'm', False) and getattr(result[7], 'site', -1) == 1 \
and api(result[7].pos, lattice[1].pos, inv(lattice.cell))
if i < N: continue
x.extend([(atom.pos[0] + trans[0]) for atom, trans, inbox in box if not inbox])
y.extend([(atom.pos[1] + trans[1]) for atom, trans, inbox in box if not inbox])
z.extend([(atom.pos[2] + trans[2]) for atom, trans, inbox in box if not inbox])
s.extend([float(i+2) + (0. if inbox else 0.4) for atom, trans, inbox in box if not inbox])
break
points3d(x,y,z,s, scale_factor=0.01, opacity=0.3)
if __name__ == "__main__":
from sys import argv, path
if len(argv) > 0: path.extend(argv[1:])
from random import randint
from numpy import zeros
from numpy.linalg import det
from pylada.crystal.cppwrappers import supercell
lattice = b5()
check(lattice)
for i in xrange(10):
cell = zeros((3,3))
while det(cell) == 0:
cell[:] = [[randint(-10, 11) for j in xrange(3)] for k in xrange(3)]
if det(cell) < 0: cell[:, 0], cell[:, 1] = cell[:, 1].copy(), cell[:, 0].copy()
structure = supercell(lattice, cell)
check(structure)
assert a is d
assert all(abs(b-e)) < tolerance
assert abs(c-f) < tolerance
# check neighbor completeness.
assert len(neighbors(structure, 2, center,tolerance)) == 4
assert len(neighbors(structure, 4, center,tolerance)) == 4
assert len(neighbors(structure, 6, center,tolerance)) == 16
if __name__ == "__main__":
from sys import argv, path
if len(argv) > 0: path.extend(argv[1:])
from random import random
from numpy import array
from pylada.crystal.cppwrappers import supercell, Structure
lattice = Structure([[0, 0.5, 0.5],[0.5, 0, 0.5], [0.5, 0.5, 0]]) \
.add_atom(0, 0, 0, "Si") \
.add_atom(0.25, 0.25, 0.25, "Ge")
for atom in lattice: check(lattice, atom)
structure = supercell(lattice, [1, 1, 0, -5, 2, 0, 0, 0, 1])
for atom in structure: check(structure, atom)
for atom in lattice: atom.pos += array([random(), random(), random()])*1e-4-5e-5
for atom in lattice: check(lattice, atom, 1e-2)
for atom in structure: atom.pos += array([random(), random(), random()])*1e-4-5e-5
for atom in structure: check(structure, atom, 1e-2)
