def test_build_min_neighbors():
latt = Lattice(np.eye(2))
latt.add_atom()
latt.add_connections()
shape = Circle([0, 0], radius=5)
latt.build(shape, min_neighbors=2)
assert_array_equal(latt.data.get_limits(), [[-4.0, -4.0], [4.0, 4.0]])
def test_hash():
latt = Lattice(np.eye(2))
latt.add_atom(atom=atom)
latt.add_connections()
latt.build((5, 5))
hash1 = latt.__hash__()
latt.build((6, 5))
assert latt.__hash__() != hash1
def test_superindex_from_position():
latt = Lattice(np.eye(2))
latt.add_atom()
latt.add_connections()
latt.build((4, 4), primitive=False)
for i in range(latt.num_sites):
pos = latt.position(i)
assert latt.superindex_from_pos(pos) == i
def test_superindex_from_index():
latt = Lattice(np.eye(2))
latt.add_atom()
latt.add_connections()
latt.build((4, 4), primitive=False)
for i in range(latt.num_sites):
ind = latt.indices[i]
assert latt.superindex_from_index(ind) == i
def test_append():
latt = Lattice(np.eye(2))
latt.add_atom()
latt.add_connections()
latt.build((4, 4), primitive=False)
latt2 = latt.copy()
latt.append(latt2)
assert_elements_equal1d(latt.nearest_neighbors(20), [15, 21, 25])
assert_elements_equal1d(latt.nearest_neighbors(21), [16, 20, 22, 26])
assert_elements_equal1d(latt.nearest_neighbors(22), [17, 21, 23, 27])
assert_elements_equal1d(latt.nearest_neighbors(23), [18, 22, 24, 28])
assert_elements_equal1d(latt.nearest_neighbors(24), [19, 23, 29])
def test_position():
latt = Lattice(np.eye(2))
latt.add_atom([0.0, 0.0], "A")
latt.add_atom([0.5, 0.5], "B")
latt.add_connection("A", "A", 1)
latt.add_connection("A", "B", 1)
latt.analyze()
latt.build((4, 4), primitive=False)
assert_array_equal(latt.position(0), [0.0, 0.0])
assert_array_equal(latt.position(1), [0.5, 0.5])
assert_array_equal(latt.position(2), [0.0, 1.0])
assert_array_equal(latt.position(3), [0.5, 1.5])
def test_atom():
latt = Lattice(np.eye(2))
at1 = latt.add_atom([0.0, 0.0], "A")
at2 = latt.add_atom([0.5, 0.5], "B")
latt.add_connection("A", "A", 1)
latt.add_connection("A", "B", 1)
latt.analyze()
latt.build((4, 4), primitive=False)
assert latt.atom(0) == at1
assert latt.atom(1) == at2
assert latt.atom(2) == at1
assert latt.atom(3) == at2
def test_alpha():
latt = Lattice(np.eye(2))
latt.add_atom([0.0, 0.0], "A")
latt.add_atom([0.5, 0.5], "B")
latt.add_connection("A", "A", 1)
latt.add_connection("A", "B", 1)
latt.analyze()
latt.build((4, 4), primitive=False)
assert latt.alpha(0) == 0
assert latt.alpha(1) == 1
assert latt.alpha(2) == 0
assert latt.alpha(3) == 1
def test_to_dict():
latt = Lattice(np.eye(2))
latt.add_atom()
latt.add_connections()
latt.build((5, 5))
d = latt.todict()
expected = [[1.0, 0.0], [0.0, 1.0]]
assert_array_equal(d["vectors"], expected)
expected = [[0.0, 0.0]]
assert_array_equal(d["positions"], expected)
expected = [[1]]
assert_array_equal(d["connections"], expected)
expected = [5.0, 5.0]
assert_array_equal(d["shape"], expected)
def _benchmark_build_periodic(latt: lp.Lattice, sizes, runs, **kwargs):
profiler = Profiler()
data = np.zeros((len(sizes), 4))
for i, size in enumerate(sizes):
t, mem, per = 0.0, 0.0, 0.0
for _ in range(runs):
profiler.start()
latt.build(np.ones(latt.dim) * size, **kwargs)
t += profiler.seconds
mem += profiler.memory
profiler.start()
latt.set_periodic(True)
per += profiler.seconds
data[i, 0] = latt.num_sites
data[i, 1] = t / runs
data[i, 2] = mem / runs
data[i, 3] = per / runs
return data
def test_build_exceptions():
latt = Lattice(np.eye(2))
latt.add_atom()
with pytest.raises(NoConnectionsError):
latt.build((5, 5))
latt.add_connections(analyze=False)
with pytest.raises(NotAnalyzedError):
latt.build((5, 5))
latt.analyze()
with pytest.raises(ValueError):
latt.build((5, 5, 5))
def test_compute_connections():
latt = Lattice(np.eye(2))
latt.add_atom()
latt.add_connections()
latt.build((4, 4), primitive=False)
latt2 = Lattice(np.eye(2))
latt2.add_atom()
latt2.add_connections()
latt2.build((4, 4), pos=(5, 0), primitive=False)
pairs, dists = latt.compute_connections(latt2)
expected = [[20, 0], [21, 1], [22, 2], [23, 3], [24, 4]]
assert_array_equal(pairs, expected)
assert np.all(dists) == 1
latt2.build((4, 4), pos=(5, 1), primitive=False)
pairs, dists = latt.compute_connections(latt2)
expected = [[21, 0], [22, 1], [23, 2], [24, 3]]
assert_array_equal(pairs, expected)
assert np.all(dists) == 1
def test_volume():
latt = Lattice(np.eye(2))
latt.add_atom()
latt.add_connections()
latt.build((4, 4), primitive=False)
assert latt.volume() == 25