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_add_connection():
latt = Lattice(np.eye(2))
latt.add_atom([0.0, 0.0], atom="A")
latt.add_atom([0.5, 0.5], atom="B")
latt.add_connection("A", "A", 1)
latt.add_connection("A", "B", 1)
latt.analyze()
# Assert neighbor atom index is right
assert all(latt.get_neighbors(alpha=0, distidx=0)[:, -1] == 1)
assert all(latt.get_neighbors(alpha=0, distidx=1)[:, -1] == 0)
assert all(latt.get_neighbors(alpha=1, distidx=0)[:, -1] == 0)
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_analyze_exceptions():
latt = Lattice(np.eye(2))
with pytest.raises(NoAtomsError):
latt.analyze()
latt.add_atom()
with pytest.raises(NoConnectionsError):
latt.analyze()
def test_get_alpha():
latt = Lattice(np.eye(2))
at1 = latt.add_atom([0.0, 0.0], atom="A")
at2 = latt.add_atom([0.5, 0.5], atom="B")
assert latt.get_alpha("A") == [0]
assert latt.get_alpha(at1) == 0
assert latt.get_alpha("B") == [1]
assert latt.get_alpha(at2) == 1
latt = Lattice(np.eye(2))
latt.add_atom([0.0, 0.0], atom="A")
latt.add_atom([0.5, 0.5], atom="A")
assert latt.get_alpha("A") == [0, 1]
def test_fromdict(latt):
d = latt.todict()
latt2 = Lattice.fromdict(d)
assert_array_equal(latt.vectors, latt2.vectors)
assert_array_equal(latt.atom_positions, latt2.atom_positions)
assert_array_equal(latt._connections, latt2._connections)
assert_array_equal(latt.num_neighbors, latt2.num_neighbors)
def test_brillouin_zone():
latt = Lattice.square()
bz = latt.brillouin_zone()
expected = [[-1.0, -1.0], [1.0, -1.0], [-1.0, 1.0], [1.0, 1.0]]
assert_array_equal(bz.vertices / np.pi, expected)
expected = [[0, 1], [0, 2], [1, 3], [2, 3]]
assert_array_equal(bz.edges, expected)
def test_add_atom(dim):
latt = Lattice(np.eye(dim))
latt.add_atom()
assert_array_equal(latt.atom_positions[0], np.zeros(dim))
with pytest.raises(SiteOccupiedError):
latt.add_atom()
with pytest.raises(ValueError):
latt.add_atom(np.zeros(4))
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_get_atom():
latt = Lattice(np.eye(2))
at1 = latt.add_atom([0.0, 0.0], atom="A")
at2 = latt.add_atom([0.5, 0.5], atom="B")
assert latt.get_atom("A") == at1
assert latt.get_atom(0) == at1
assert latt.get_atom("B") == at2
assert latt.get_atom(1) == at2
def test_get_base_atom_dict():
latt = Lattice(np.eye(2))
ata = latt.add_atom([0, 0], atom="A")
atb = latt.add_atom([0.5, 0], atom="B")
latt.add_atom([0.5, 0.5], atom="B")
result = latt.get_base_atom_dict()
assert len(result) == 2
assert_array_equal(result[ata], [[0, 0]])
assert_array_equal(result[atb], [[0.5, 0.0], [0.5, 0.5]])
def test_get_position(nvec, alpha):
latt = Lattice(np.eye(2))
latt.add_atom([0.0, 0.0], atom="A")
latt.add_atom([0.5, 0.5], atom="B")
pos = latt.translate(nvec, latt.atom_positions[alpha])
assert_allclose(latt.get_position(nvec, alpha), pos)
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 test_get_positions(nvecs, alpha):
latt = Lattice(np.eye(2))
latt.add_atom([0.0, 0.0], atom="A")
latt.add_atom([0.5, 0.5], atom="B")
indices = np.array([[*nvec, alpha] for nvec in nvecs])
results = latt.get_positions(indices)
for res, nvec in zip(results, nvecs):
pos = latt.translate(nvec, latt.atom_positions[alpha])
assert_allclose(res, pos)
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_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_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_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))
SiteOccupiedError,
NoAtomsError,
NoConnectionsError,
NotAnalyzedError,
)
from lattpy import Lattice, Circle, Atom
import lattpy as lp
settings.load_profile("lattpy")
atom = Atom()
PI = np.pi
TWOPI = 2 * np.pi
chain = Lattice.chain(a=1.0)
rchain = Lattice(TWOPI)
square = Lattice.square(a=1.0)
rsquare = Lattice(TWOPI * np.eye(2))
rect = Lattice.rectangular(a1=2.0, a2=1.0)
rrect = Lattice(PI * np.array([[1, 0], [0, 2]]))
hexagonal = Lattice.hexagonal(a=1)
rhexagonal = Lattice(
np.array([[+2.0943951, +3.62759873], [+2.0943951, -3.62759873]]))
sc = Lattice.sc(a=1.0)
rsc = Lattice(TWOPI * np.eye(3))
fcc = Lattice.fcc(a=1.0)
def test_neighbor_pairs_unique(latt: lp.Lattice):
pairs, distindices = latt.neighbor_pairs(unique=True)
for (i, j), distidx in zip(pairs, distindices): # noqa
assert i < j
neighbors = latt.neighbors(i, distidx=distidx)
assert j in neighbors
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_volume():
latt = Lattice(np.eye(2))
latt.add_atom()
latt.add_connections()
latt.build((4, 4), primitive=False)
assert latt.volume() == 25
def test_neighbor_pairs(latt: lp.Lattice):
pairs, distindices = latt.neighbor_pairs()
for (i, j), distidx in zip(pairs, distindices): # noqa
neighbors = latt.neighbors(i, distidx=distidx)
assert j in neighbors
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_adjacency_matrix(latt: lp.Lattice):
adjmat = latt.adjacency_matrix()
for i in range(latt.num_sites):
for distidx, neighbors in latt.iter_neighbors(i):
for j in neighbors:
assert adjmat[i, j] == distidx + 1
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])