def test_representability():
import quantities
import numpy
dictionary = {Structure.__name__: Structure}
dictionary.update(numpy.__dict__)
dictionary.update(quantities.__dict__)
expected = Structure()
actual = eval(repr(expected), dictionary)
assert all(abs(expected.cell - actual.cell) < 1e-8)
assert abs(expected.scale - actual.scale) < 1e-8
assert len(expected) == len(actual)
expected = Structure([1, 2, 0], [3, 4, 5], [6, 7, 8], m=True)
actual = eval(repr(expected), dictionary)
assert all(abs(expected.cell - actual.cell) < 1e-8)
assert abs(expected.scale - actual.scale) < 1e-8
assert len(expected) == len(actual)
assert getattr(expected, 'm', False) == actual.m
expected = Structure([1, 2, 0], [3, 4, 5], [6, 7, 8], m=True) \
.add_atom(0, 1, 2, "Au", m=5) \
.add_atom(0, -1, -2, "Pd")
actual = eval(repr(expected), dictionary)
assert all(abs(expected.cell - actual.cell) < 1e-8)
assert abs(expected.scale - actual.scale) < 1e-8
assert len(expected) == len(actual)
assert all(abs(expected[0].pos - actual[0].pos) < 1e-8)
assert getattr(expected[0], 'm', 0) == actual[0].m
assert expected[0].type == actual[0].type
assert all(abs(expected[1].pos - actual[1].pos) < 1e-8)
assert expected[1].type == actual[1].type
assert getattr(expected, 'm', False) == actual.m
def test_transform():
a = Structure([0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0], scale=5.45, m=True)\
.add_atom(0, 0, 0, "Au")\
.add_atom(0.25, 0.5, 0.25, "Au", "Pd", m=True)
rotation = array([[1, -1, -1], [-1, 1, -1], [-1, -1, 1]])
a.transform(-rotation, [0, 1, 1])
assert all(abs(a.cell - identity(3)) < 1e-8)
assert all(abs(a[0].pos - [0, 1, 1]) < 1e-8)
assert all(abs(a[1].pos - [0.5, 1, 1.5]) < 1e-8)
def test_transform():
a = Structure([0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0], scale=5.45, m=True)\
.add_atom(0, 0, 0, "Au")\
.add_atom(0.25, 0.5, 0.25, "Au", "Pd", m=True)
rotation = array([[1, -1, -1], [-1, 1, -1], [-1, -1, 1]])
a.transform(-rotation, [0, 1, 1])
assert all(abs(a.cell - identity(3)) < 1e-8)
assert all(abs(a[0].pos - [0, 1, 1]) < 1e-8)
assert all(abs(a[1].pos - [0.5, 1, 1.5]) < 1e-8)
def test_initerror():
""" Checks initialization throws appropriately. """
with raises(ValueError):
Structure("A", 0, 0, 0, 2.5, 0, 0, 0, 2.5)
with raises(TypeError):
Structure(0, 0, 0, 2.5, 0, 0, 0, 2.5)
with raises(TypeError):
Structure(2.5, 0, 0, 0, 0, 2.5, 0, 0, 0, 2.5)
with raises(ValueError):
Structure([2.5, 0, 0, 0], [0, 2.5, 0], [0, 0, 2.5])
with raises(ValueError):
Structure([2.5, 0, 0], [0, 2.5], [0, 0, 2.5])
with raises(ValueError):
Structure([2.5, 0, 0], [0, 2.5, 0], [0, 0, 'A'])
with raises(TypeError):
Structure([2.5, 0, 0], [0, 2.5, 0], [0, 0, 0], cell='a')
with raises(ValueError):
Structure(cell='a')
def create_al():
types = 'ABCDEFGHIJKLMN'
result = Structure(identity(3) * 2.5, scale=5.45,
m=True), list(range(10))
for i in range(10):
result[0].add_atom(Atom(i, i, i, types[i]))
return result
def test_pickle():
""" Check pickling. """
from numpy import all, abs, array, identity
from pickle import loads, dumps
a = Structure(identity(3) * 2.5, scale=5.45, m=True)\
.add_atom(Atom(0, 0, 0, "Au"))\
.add_atom(Atom(0.25, 0.5, 0.25, "Au", "Pd", m=True))\
.add_atom(Atom(0.1, 0.1, 0.1, 6, m=True))
b = loads(dumps(a))
assert a is not b
assert b.__class__ is Structure
assert all(abs(a.cell - b.cell) < 1e-8)
assert abs(a.scale - b.scale) < 1e-8
assert getattr(b, 'm', False) == True
assert len(b) == 3
for i, j in zip(a, b):
assert i is not j
assert i.__class__ is j.__class__
assert all(abs(i.pos - j.pos) < 1e-8)
assert i.type == j.type
assert getattr(i, 'm', False) == getattr(j, 'm', False)
def test_initialization():
""" Test structure initialization. """
a = Structure()
assert all(abs(a.cell - identity(3)) < 1e-8)
assert abs(a.scale - 1e0 * angstrom) < 1e0
assert len(a.__dict__) == 3
a = Structure(identity(3) * 2.5, scale=5.45)
assert all(abs(a.cell - identity(3) * 2.5) < 1e-8)
assert abs(a.scale - 5.45 * angstrom) < 1e0
assert len(a.__dict__) == 3
a = Structure(identity(3) * 2.5, scale=0.545 * nanometer)
assert all(abs(a.cell - identity(3) * 2.5) < 1e-8)
assert abs(a.scale - 5.45 * angstrom) < 1e0
assert len(a.__dict__) == 3
a = Structure(2.5, 0, 0, 0, 2.5, 0, 0, 0, 2.5, scale=5.45)
assert all(abs(a.cell - identity(3) * 2.5) < 1e-8)
assert abs(a.scale - 5.45 * angstrom) < 1e0
assert len(a.__dict__) == 3
a = Structure([2.5, 0, 0], [0, 2.5, 0], [0, 0, 2.5], scale=5.45)
assert all(abs(a.cell - identity(3) * 2.5) < 1e-8)
assert abs(a.scale - 5.45 * angstrom) < 1e0
assert len(a.__dict__) == 3
a = Structure(cell=[[2.5, 0, 0], [0, 2.5, 0], [0, 0, 2.5]], scale=5.45)
assert all(abs(a.cell - identity(3) * 2.5) < 1e-8)
assert abs(a.scale - 5.45 * angstrom) < 1e0
assert len(a.__dict__) == 3
a = Structure(identity(3) * 2.5, scale=5.45, m=True)
assert all(abs(a.cell - identity(3) * 2.5) < 1e-8)
assert abs(a.scale - 5.45 * angstrom) < 1e0
assert len(a.__dict__) == 4 and getattr(a, 'm', False)
def test_sequence_of_atoms():
a = Structure(identity(3) * 2.5, scale=5.45, m=True)
a.add_atom(0, 0, 0, "Au")\
.add_atom(0.25, 0.5, 0.25, "Au", "Pd", m=True)
assert len(a) == 2
assert all(abs(a[0].pos) < 1e-8)
assert a[0].type == "Au"
assert all(abs(a[1].pos - (0.25, 0.5, 0.25)) < 1e-8)
assert a[1].type == ("Au", "Pd")
assert getattr(a[1], 'm', False) == True
a.insert(1, 0.1, 0.1, 0.1, 6)
assert len(a) == 3
assert all(abs(a[1].pos - 0.1) < 1e-8)
assert a[1].type == 6
b = a.pop(1)
assert all(abs(b.pos - 0.1) < 1e-8)
assert b.type == 6
assert len(a) == 2
a.append(b)
assert len(a) == 3
assert all(abs(a[2].pos - 0.1) < 1e-8)
assert a[2].type == 6
b = a[0], a[1], a[2]
a.clear()
assert len(a) == 0
a.extend(b)
assert len(a) == 3 and a[0] is b[0] and a[1] is b[1] and a[2] is b[2]
a.clear()
b = Structure(identity(3) * 2.5, scale=5.45, m=True)
b.add_atom(0, 0, 0, "Au")\
.add_atom(0.25, 0.5, 0.25, "Au", "Pd", m=True)\
.add_atom(0.1, 0.1, 0.1, 6, m=True)
assert len(a) == 0
a.extend(b)
assert len(b) == 3
assert a[0] is b[0]
assert a[1] is b[1]
assert a[2] is b[2]
assert a is not b
a[2] = Atom(-1, -1, -1, None)
assert abs(all(a[2].pos + 1) < 1e-8) and a[2].type is None
def test_sequence_of_atoms():
a = Structure(identity(3) * 2.5, scale=5.45, m=True)
a.add_atom(0, 0, 0, "Au")\
.add_atom(0.25, 0.5, 0.25, "Au", "Pd", m=True)
assert len(a) == 2
assert all(abs(a[0].pos) < 1e-8)
assert a[0].type == "Au"
assert all(abs(a[1].pos - (0.25, 0.5, 0.25)) < 1e-8)
assert a[1].type == ("Au", "Pd")
assert getattr(a[1], 'm', False) == True
a.insert(1, 0.1, 0.1, 0.1, 6)
assert len(a) == 3
assert all(abs(a[1].pos - 0.1) < 1e-8)
assert a[1].type == 6
b = a.pop(1)
assert all(abs(b.pos - 0.1) < 1e-8)
assert b.type == 6
assert len(a) == 2
a.append(b)
assert len(a) == 3
assert all(abs(a[2].pos - 0.1) < 1e-8)
assert a[2].type == 6
b = a[0], a[1], a[2]
a.clear()
assert len(a) == 0
a.extend(b)
assert len(a) == 3 and a[0] is b[0] and a[1] is b[1] and a[2] is b[2]
a.clear()
b = Structure(identity(3) * 2.5, scale=5.45, m=True)
b.add_atom(0, 0, 0, "Au")\
.add_atom(0.25, 0.5, 0.25, "Au", "Pd", m=True)\
.add_atom(0.1, 0.1, 0.1, 6, m=True)
assert len(a) == 0
a.extend(b)
assert len(b) == 3
assert a[0] is b[0]
assert a[1] is b[1]
assert a[2] is b[2]
assert a is not b
a[2] = Atom(-1, -1, -1, None)
assert abs(all(a[2].pos + 1) < 1e-8) and a[2].type is None