def test_init():
""" Test atom initialization. """
from numpy import all, abs, array
# Try correct initialization. Check for garbage collection.
a = Atom()
assert a.type is None and all(abs(a.pos) < 1e-8) and len(a.__dict__) == 2
assert a.type is None and all(abs(a.pos) < 1e-8) and len(a.__dict__) == 2
a = Atom(0.1, 0.1, 0.1, "Au")
assert a.type == "Au"
assert all(abs(a.pos - 0.1) < 1e-8)
assert len(a.__dict__) == 2
a = Atom(0.1, 0.1, 0.1, type=["Au", "Pd"])
assert a.type == ["Au", "Pd"]
assert all(abs(a.pos - 0.1) < 1e-8)
assert len(a.__dict__) == 2
a = Atom(type="Au", pos=[0.1, 0.1, 0.1])
assert a.type == "Au" and all(abs(a.pos - 0.1) < 1e-8) and len(a.__dict__) == 2
a = Atom(type="Au", pos=[0.1, 0.1, 0.1], m=5)
assert a.type == "Au" and all(abs(a.pos - 0.1) < 1e-8) and len(a.__dict__) == 3 and getattr(a, "m", 3) == 5
a = Atom(0.1, 0.1, 0.1, 0.1, 0.1)
assert all(abs(array(a.type) - 0.1) < 1e-8) and all(abs(a.pos - 0.1) < 1e-8) and len(a.__dict__) == 2
l = [None]
a = Atom(0.1, 0.1, 0.1, l)
assert a.type is l
assert all(abs(a.pos - 0.1) < 1e-8) and len(a.__dict__) == 2
a.pos[0] = 0.2
a.pos[1] = 0.3
a.pos[2] = 0.4
assert all(abs(a.pos - [0.2, 0.3, 0.4]) < 1e-8)
def test_fail_init():
""" Test failures during initialization. """
from pytest import raises
from pylada import error
with raises(error.TypeError):
a = Atom(0.1, 0.1, 0.1, 'Au', type='Au')
with raises(error.TypeError):
a = Atom(0.1, 0.1, 0.1, pos=[0.1, 0.1, 0.1])
def test_copy():
""" Test copy and deep copy. """
from copy import copy, deepcopy
b = Atom(0, 0, 0, 'Au', m=0)
a = copy(b)
b.type = 'Pd'
assert a.pos is b.pos
assert a.type == 'Au'
a = deepcopy(b)
b.type = 'Au'
b.pos += 1
del b.m
assert a.type == "Pd"
assert all(abs(a.pos - 0.0) < 1e-8)
assert len(a.__dict__) == 3
assert getattr(a, 'm', 1) == 0
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_copy():
""" Test copy and deep copy. """
from copy import copy, deepcopy
b = Atom(0, 0, 0, "Au", m=0)
a = copy(b)
b.type = "Pd"
assert a.pos is b.pos
assert a.type == "Au"
a = deepcopy(b)
b.type = "Au"
b.pos += 1
del b.m
assert a.type == "Pd"
assert all(abs(a.pos - 0.0) < 1e-8)
assert len(a.__dict__) == 3
assert getattr(a, "m", 1) == 0
def test_pickle():
""" Test pickling. """
from pickle import loads, dumps
a = Atom(pos=[0, 1, 2], type="Au", m=6)
b = loads(dumps(a))
assert b.__class__ is a.__class__
assert all(abs(b.pos - [0, 1, 2]) < 1e-12)
assert b.type == 'Au'
assert len(b.__dict__) == 3
assert b.__dict__.get('m', 0) == 6
b = loads(dumps((a, a)))
assert b[0] is b[1]
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_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_repr():
""" Test representability. """
actual = repr(Atom(type='Au', pos=[1, 1, 1], m=1, dtype='int64'))
assert actual == "{0.__name__}(1, 1, 1, 'Au', dtype='int64', m=1)".format(Atom)
actual = str(Atom(type='Au', pos=[1., 1, 1], site=1))
assert actual == "{0.__name__}(1.0, 1.0, 1.0, 'Au', site=1)".format(Atom)
def test_init():
""" Test atom initialization. """
from numpy import all, abs, array
# Try correct initialization. Check for garbage collection.
a = Atom()
assert a.type is None and all(abs(a.pos) < 1e-8) and len(a.__dict__) == 2
assert a.type is None and all(abs(a.pos) < 1e-8) and len(a.__dict__) == 2
a = Atom(0.1, 0.1, 0.1, 'Au')
assert a.type == "Au"
assert all(abs(a.pos - 0.1) < 1e-8)
assert len(a.__dict__) == 2
a = Atom(0.1, 0.1, 0.1, type=['Au', 'Pd'])
assert a.type == ["Au", 'Pd']
assert all(abs(a.pos - 0.1) < 1e-8)
assert len(a.__dict__) == 2
a = Atom(type='Au', pos=[0.1, 0.1, 0.1])
assert a.type == "Au" and all(
abs(a.pos - 0.1) < 1e-8) and len(a.__dict__) == 2
a = Atom(type='Au', pos=[0.1, 0.1, 0.1], m=5)
assert a.type == "Au" and all(
abs(a.pos - 0.1) < 1e-8) and len(a.__dict__) == 3 and getattr(a, 'm', 3) == 5
a = Atom(0.1, 0.1, 0.1, 0.1, 0.1)
assert all(abs(array(a.type) - 0.1) < 1e-8) and all(abs(a.pos - 0.1)
< 1e-8) and len(a.__dict__) == 2
l = [None]
a = Atom(0.1, 0.1, 0.1, l)
assert a.type is l
assert all(abs(a.pos - 0.1) < 1e-8) and len(a.__dict__) == 2
a.pos[0] = 0.2
a.pos[1] = 0.3
a.pos[2] = 0.4
assert all(abs(a.pos - [0.2, 0.3, 0.4]) < 1e-8)
def test_todict():
""" Test to_dict member. """
a = Atom(0, 0, 0, 'Au', m=0)
a = a.to_dict()
assert a['type'] == "Au" and all(a['pos'] == 0) and a['m'] == 0
def test_todict():
""" Test to_dict member. """
a = Atom(0, 0, 0, "Au", m=0)
a = a.to_dict()
assert a["type"] == "Au" and all(a["pos"] == 0) and a["m"] == 0