def test_primitive(cell):
""" Tests whether primitivization works. """
from numpy import abs, dot
from numpy.linalg import inv
from pylada.crystal import supercell, Structure, are_periodic_images as api, primitive, \
is_primitive
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)
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)
assert atom.type == lattice[atom.site].type
assert getattr(lattice[atom.site], 'm',
False) == getattr(atom, 'm', False)
assert (getattr(atom, 'm', False) or atom.site == 0)
def test_primitive(cell):
""" Tests whether primitivization works. """
from numpy import abs, dot
from numpy.linalg import inv
from pylada.crystal import supercell, Structure, are_periodic_images as api, primitive, \
is_primitive
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)
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)
assert atom.type == lattice[atom.site].type
assert getattr(lattice[atom.site], 'm', False) == getattr(atom, 'm', False)
assert (getattr(atom, 'm', False) or atom.site == 0)
def test_supercell():
""" Simple supercell test. """
from numpy import identity, abs, all, dot
from numpy.linalg import inv
from pylada.crystal 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)
assert result[0].type == "As"
assert getattr(result[0], 'site', -1) == 0
assert api(result[0].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[1].pos - [0.25, 0.25, 0.25]) < 1e-8)
assert result[1].type == ["In", "Ga"]
assert getattr(result[1], 'm', False)
assert getattr(result[1], 'site', -1) == 1
assert api(result[1].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[2].pos - [0.50, 0.00, 0.50]) < 1e-8)
assert result[2].type == "As"
assert getattr(result[2], 'site', -1) == 0
assert api(result[2].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[3].pos - [0.75, 0.25, 0.75]) < 1e-8)
assert result[3].type == ["In", "Ga"]
assert getattr(result[3], 'm', False)
assert getattr(result[3], 'site', -1) == 1
assert api(result[3].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[4].pos - [0.50, 0.50, 0.00]) < 1e-8)
assert result[4].type == "As"
assert getattr(result[4], 'site', -1) == 0
assert api(result[4].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[5].pos - [0.75, 0.75, 0.25]) < 1e-8)
assert result[5].type == ["In", "Ga"]
assert getattr(result[5], 'm', False)
assert getattr(result[5], 'site', -1) == 1
assert api(result[5].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[6].pos - [0.00, 0.50, 0.50]) < 1e-8)
assert result[6].type == "As"
assert getattr(result[6], 'site', -1) == 0
assert api(result[6].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[7].pos - [0.25, 0.75, 0.75]) < 1e-8)
assert result[7].type == ["In", "Ga"]
assert getattr(result[7], 'm', False)
assert getattr(result[7], 'site', -1) == 1
assert 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 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)
assert result[0].type == "As"
assert getattr(result[0], 'site', -1) == 0
assert api(result[0].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[1].pos - [0.25, 0.25, 0.25]) < 1e-8)
assert result[1].type == ["In", "Ga"]
assert getattr(result[1], 'm', False)
assert getattr(result[1], 'site', -1) == 1
assert api(result[1].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[2].pos - [0.50, 0.00, 0.50]) < 1e-8)
assert result[2].type == "As"
assert getattr(result[2], 'site', -1) == 0
assert api(result[2].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[3].pos - [0.75, 0.25, 0.75]) < 1e-8)
assert result[3].type == ["In", "Ga"]
assert getattr(result[3], 'm', False)
assert getattr(result[3], 'site', -1) == 1
assert api(result[3].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[4].pos - [0.50, 0.50, 0.00]) < 1e-8)
assert result[4].type == "As"
assert getattr(result[4], 'site', -1) == 0
assert api(result[4].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[5].pos - [0.75, 0.75, 0.25]) < 1e-8)
assert result[5].type == ["In", "Ga"]
assert getattr(result[5], 'm', False)
assert getattr(result[5], 'site', -1) == 1
assert api(result[5].pos, lattice[1].pos, inv(lattice.cell))
assert all(abs(result[6].pos - [0.00, 0.50, 0.50]) < 1e-8)
assert result[6].type == "As"
assert getattr(result[6], 'site', -1) == 0
assert api(result[6].pos, lattice[0].pos, inv(lattice.cell))
assert all(abs(result[7].pos - [0.25, 0.75, 0.75]) < 1e-8)
assert result[7].type == ["In", "Ga"]
assert getattr(result[7], 'm', False)
assert getattr(result[7], 'site', -1) == 1
assert api(result[7].pos, lattice[1].pos, inv(lattice.cell))
def test_manysupercell():
from numpy import dot
from numpy.linalg import inv, det
from pylada.crystal import supercell, binary, are_periodic_images as api
lattice = binary.zinc_blende()
invlat = inv(lattice.cell)
for i in range(10):
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, are_periodic_images as api
lattice = binary.zinc_blende()
invlat = inv(lattice.cell)
for i in range(10):
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)
