def test_indices():
from random import randint
from numpy import all, abs, dot, array
from pytest import raises
from pylada.crystal import HFTransform
unitcell = array([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
a = HFTransform(unitcell, supercell)
assert all(abs(a.transform - [[1, 1, -1], [0, 2, 0], [0, 0, 2]]) < 1e-8)
assert all(abs(a.quotient - [1, 2, 2]) < 1e-8)
for i in range(20):
vec = dot(supercell, array(
[randint(-20, 20), randint(-20, 20), randint(-20, 20)], dtype="float64"))
vec += [0, -0.5, 0.5]
assert all(abs(a.indices(vec) - [0, 1, 1]) < 1e-8)
with raises(ValueError):
a.indices(vec + [0.1, 0.1, 0])
def test_supercell_indices():
from pytest import raises
from random import randint
from numpy import all, abs, dot, array
from pylada.crystal 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 range(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)
with raises(ValueError):
a.indices(vec + [0.1, 0.1, 0])
assert index == a.index(vec)
with raises(ValueError):
a.index(vec + [0.1, 0.1, 0])
assert len(all_indices) == len(supercell)
def test_deformed_b5(u):
from pytest import raises
from random import randint
from numpy import all, abs, dot, array, concatenate
from pylada.crystal 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 range(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)
with raises(ValueError):
a.indices(vec + [0.1, 0.1, 0])
assert index == a.index(vec, atom.site)
with raises(ValueError):
a.index(vec + [0.1, 0.1, 0])
assert len(all_indices) == len(supercell)
def test_indices():
from random import randint
from numpy import all, abs, dot, array
from pytest import raises
from pylada.crystal import HFTransform
unitcell = array([[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
a = HFTransform(unitcell, supercell)
assert all(abs(a.transform - [[1, 1, -1], [0, 2, 0], [0, 0, 2]]) < 1e-8)
assert all(abs(a.quotient - [1, 2, 2]) < 1e-8)
for i in range(20):
vec = dot(
supercell,
array([randint(-20, 20),
randint(-20, 20),
randint(-20, 20)],
dtype="float64"))
vec += [0, -0.5, 0.5]
assert all(abs(a.indices(vec) - [0, 1, 1]) < 1e-8)
with raises(ValueError):
a.indices(vec + [0.1, 0.1, 0])
def test_supercell_indices():
from pytest import raises
from random import randint
from numpy import all, abs, dot, array
from pylada.crystal 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 range(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)
with raises(ValueError):
a.indices(vec + [0.1, 0.1, 0])
assert index == a.index(vec)
with raises(ValueError):
a.index(vec + [0.1, 0.1, 0])
assert len(all_indices) == len(supercell)
def test_deformed_b5(u):
from pytest import raises
from random import randint
from numpy import all, abs, dot, array, concatenate
from pylada.crystal 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 range(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)
with raises(ValueError):
a.indices(vec + [0.1, 0.1, 0])
assert index == a.index(vec, atom.site)
with raises(ValueError):
a.index(vec + [0.1, 0.1, 0])
assert len(all_indices) == len(supercell)
