def test_lattice_old_interface():
with pytest.warns(FutureWarning):
_ = Lattice(basis_vectors=[[1.0]], atoms_coord=[[0.0], [0.5]], extent=[4])
def check_alternative(method, alternative):
with pytest.warns(FutureWarning):
result = method()
np.testing.assert_almost_equal(alternative(), result)
for g in graphs + symmetric_graphs:
if not isinstance(g, Lattice):
continue
check_alternative(lambda: g.atom_label(0), lambda: g.basis_coords[0, -1])
check_alternative(lambda: g.site_to_vector(0), lambda: g.basis_coords[0, :-1])
check_alternative(lambda: g.site_to_coord(0), lambda: g.positions[0])
*cell1, label1 = g.basis_coords[1]
check_alternative(
lambda: g.vector_to_site(cell1),
lambda: g.id_from_basis_coords([*cell1, 0]),
)
check_alternative(
lambda: g.vector_to_coord(cell1, label1),
lambda: g.position_from_basis_coords([*cell1, label1]),
)
check_alternative(lambda: g.coordinates, lambda: g.positions)
check_alternative(lambda: g.atoms_coord, lambda: g.site_offsets)
def test_duplicate_atoms():
lattice = Lattice(
basis_vectors=[[1.0, 0.0], [1.0 / 2.0, math.sqrt(3) / 2.0]],
extent=[10, 10],
pbc=[False, False],
site_offsets=[[0, 0], [0, 0]],
)
np.testing.assert_almost_equal(lattice.site_offsets, np.array([[0, 0]]))
def test_lattice_site_lookup():
g = Lattice([[1]], [2])
pos = [[0.0], [1.0]]
ids = g.id_from_position(pos)
np.testing.assert_almost_equal(ids, [0, 1])
with pytest.raises(_lattice.InvalidSiteError):
g.id_from_position([[0.5]])
with pytest.raises(_lattice.InvalidSiteError):
g.id_from_position([0.5])
with pytest.raises(_lattice.InvalidSiteError):
pos = g.position_from_basis_coords([2])
with pytest.raises(_lattice.InvalidSiteError):
pos = g.position_from_basis_coords([[2]])
pytestmark = common.skipif_mpi
graphs = [
# star and tree
Graph.from_igraph(ig.Graph.Star(5)),
Graph.from_igraph(ig.Graph.Tree(n=3, children=2)),
# Grid graphs
Hypercube(length=10, n_dim=1, pbc=True),
Hypercube(length=4, n_dim=2, pbc=True),
Hypercube(length=5, n_dim=1, pbc=False),
Grid([2, 2], pbc=False),
Grid([4, 2], pbc=[True, False]),
# lattice graphs
Lattice(
basis_vectors=[[1.0, 0.0], [1.0 / 2.0, math.sqrt(3) / 2.0]],
extent=[3, 3],
pbc=[False, False],
site_offsets=[[0, 0]],
),
Lattice(
basis_vectors=[[1.5, math.sqrt(3) / 2.0], [0, math.sqrt(3)]],
extent=[3, 5],
site_offsets=[[0, 0], [1, 1]],
),
Lattice(
basis_vectors=[
[1.0, 0.0, 0.0],
[1.0 / 2.0, math.sqrt(3) / 2.0, 0.0],
[0.0, 0.0, 1.0],
],
extent=[2, 3, 4],
site_offsets=[[0, 0, 0]],