def test_complex_multiorbital_hamiltonian():
def checkerboard_lattice(delta, t):
lat = pb.Lattice(a1=[1, 0], a2=[0, 1])
lat.add_sublattices(('A', [0, 0], -delta),
('B', [1 / 2, 1 / 2], delta))
lat.add_hoppings(
([0, 0], 'A', 'B', t),
([0, -1], 'A', 'B', t),
([-1, 0], 'A', 'B', t),
([-1, -1], 'A', 'B', t),
)
return lat
hopp_t = np.array([[2 + 2j, 3 + 3j], [4 + 4j,
5 + 5j]]) # multi-orbital hopping
onsite_en = np.array([[1, 1j], [-1j, 1]]) # onsite energy
model = pb.Model(checkerboard_lattice(onsite_en, hopp_t),
pb.translational_symmetry(True, True))
h = model.hamiltonian.toarray()
assert model.system.num_sites == 2
assert h.shape[0] == 4
assert pytest.fuzzy_equal(h, h.T.conjugate()) # check if Hermitian
assert pytest.fuzzy_equal(
h[:2, :2], -h[-2:, -2:]) # onsite energy on A and B is opposite
assert pytest.fuzzy_equal(h[:2, 2:4],
4 * hopp_t) # hopping A <-> B is 4 * hopp_t
def assert_state(name, **kwargs):
state, x, y, z, nearest = capture[name]
assert state.shape == kwargs["shape"]
assert pytest.fuzzy_equal(state, kwargs["state"])
assert x.shape == kwargs["shape"]
assert pytest.fuzzy_equal(x, kwargs["x"])
assert pytest.fuzzy_equal(y, kwargs["y"])
assert pytest.fuzzy_equal(z, kwargs["z"])
assert np.all(nearest == kwargs["nearest"])
def assert_positions(name, **kwargs):
x, y, z, nearest = capture[name]
assert x.shape == kwargs["shape"]
assert y.shape == kwargs["shape"]
assert z.shape == kwargs["shape"]
assert pytest.fuzzy_equal(x, kwargs["x"])
assert pytest.fuzzy_equal(y, kwargs["y"])
assert pytest.fuzzy_equal(z, kwargs["z"])
assert np.all(nearest == kwargs["nearest"])
def test_builder():
"""Builder pattern methods"""
lattice = pb.Lattice([1, 0], [0, 1])
copy = lattice.with_offset([0, 0.5])
assert pytest.fuzzy_equal(copy.offset, [0, 0.5, 0])
assert pytest.fuzzy_equal(lattice.offset, [0, 0, 0])
copy = lattice.with_min_neighbors(5)
assert copy.min_neighbors == 5
assert lattice.min_neighbors == 1
def assert_onsite(name, **expected):
energy, x, y, z = capture[name]
assert energy.shape == expected["shape"]
expected_energy = np.array(expected["energy"])
for index in np.ndindex(*expected_energy.shape):
expected_slice = np.full(energy.shape[-1], expected_energy[index])
assert pytest.fuzzy_equal(energy[index], expected_slice)
assert pytest.fuzzy_equal(x, expected["x"])
assert pytest.fuzzy_equal(y, expected["y"])
assert pytest.fuzzy_equal(z, expected["z"])
def test_ldos(kpm, baseline, plot_if_fails):
energy = np.linspace(0, 2, 25)
results = [k.calc_ldos(energy, broadening=0.15, position=(0, 0)) for k in kpm]
expected = pb.results.LDOS(energy, baseline(results[0].ldos.astype(np.float32)))
for i in range(len(results)):
plot_if_fails(results[i], expected, 'plot', label=i)
assert pytest.fuzzy_equal(results[0], expected, rtol=1e-4, atol=1e-6)
assert pytest.fuzzy_equal(results[1], expected, rtol=1e-4, atol=1e-6)
assert pytest.fuzzy_equal(results[2], expected, rtol=1e-4, atol=1e-6)
assert pytest.fuzzy_equal(results[3], expected, rtol=1e-4, atol=1e-6)
def test_site_position():
@pb.site_position_modifier
def mod(x, y, z):
return x + 1, y + 1, z + 1
assert (one, ) * 3 == mod(zero, zero, zero)
assert (one, ) * 3 == mod.apply(zero, zero, zero, one)
capture = {}
@pb.site_position_modifier
def check_args(x, y, z, sub_id, sites):
capture[sub_id] = [v.copy() for v in (x, y, z)]
capture[sub_id].append(sites.argsort_nearest([0, graphene.a_cc / 2]))
return x, y, z
def assert_positions(name, **kwargs):
x, y, z, nearest = capture[name]
assert x.shape == kwargs["shape"]
assert y.shape == kwargs["shape"]
assert z.shape == kwargs["shape"]
assert pytest.fuzzy_equal(x, kwargs["x"])
assert pytest.fuzzy_equal(y, kwargs["y"])
assert pytest.fuzzy_equal(z, kwargs["z"])
assert np.all(nearest == kwargs["nearest"])
model = build_model(check_args, pb.primitive(1, 2))
assert model.hamiltonian.dtype == np.float32
assert_positions("A",
shape=(2, ),
nearest=[1, 0],
x=[-graphene.a / 2, 0],
y=[-2 * graphene.a_cc, -graphene.a_cc / 2],
z=[0, 0])
assert_positions("B",
shape=(2, ),
nearest=[1, 0],
x=[-graphene.a / 2, 0],
y=[-graphene.a_cc, graphene.a_cc / 2],
z=[0, 0])
@pb.site_position_modifier
def shift(x, y, z):
return x + 1, y + 1, z + 1
model = build_model(check_args, shift)
assert pytest.fuzzy_equal(model.system.x, [1, 1])
assert pytest.fuzzy_equal(model.system.y,
[1 - graphene.a_cc / 2, 1 + graphene.a_cc / 2])
assert pytest.fuzzy_equal(model.system.z, [1, 1])
def test_lapack(baseline, plot_if_fails):
model = pb.Model(graphene.monolayer(), pb.translational_symmetry())
solver = pb.solver.lapack(model)
assert pytest.fuzzy_equal(solver.eigenvalues, [-3*abs(graphene.t), 3*abs(graphene.t)])
from math import pi, sqrt
g = [0, 0]
k1 = [-4*pi / (3*sqrt(3) * graphene.a_cc), 0]
m = [0, 2*pi / (3 * graphene.a_cc)]
k2 = [2*pi / (3*sqrt(3) * graphene.a_cc), 2*pi / (3 * graphene.a_cc)]
bands = solver.calc_bands(k1, g, m, k2, step=3)
expected = baseline(bands)
plot_if_fails(bands, expected, 'plot')
assert pytest.fuzzy_equal(bands, expected, 2.e-2, 1.e-6)
def test_ldos(kpm, baseline, plot_if_fails):
energy = np.linspace(0, 2, 25)
results = [
k.calc_ldos(energy, broadening=0.15, position=(0, 0)) for k in kpm
]
expected = pb.results.LDOS(energy,
baseline(results[0].ldos.astype(np.float32)))
for i in range(len(results)):
plot_if_fails(results[i], expected, 'plot', label=i)
assert pytest.fuzzy_equal(results[0], expected, rtol=1e-4, atol=1e-6)
assert pytest.fuzzy_equal(results[1], expected, rtol=1e-4, atol=1e-6)
assert pytest.fuzzy_equal(results[2], expected, rtol=1e-4, atol=1e-6)
assert pytest.fuzzy_equal(results[3], expected, rtol=1e-4, atol=1e-6)
def test_structure_map(model):
system = model.system
zeros = np.zeros_like(system.x)
spatial_map = pb.results.SpatialMap(zeros, system.positions, system.sublattices)
structure_map = system.with_data(zeros)
assert pytest.fuzzy_equal(spatial_map.data, structure_map.spatial_map.data)
assert pytest.fuzzy_equal(spatial_map.positions, structure_map.spatial_map.positions)
assert pytest.fuzzy_equal(spatial_map.sublattices, structure_map.spatial_map.sublattices)
tmp = structure_map[structure_map.x < 0.05]
assert structure_map.hoppings.nnz == 41
assert tmp.hoppings.nnz == 21
assert tmp.hoppings.tocsr().data.mapping == model.lattice.impl.hop_name_map
def test_site_generator():
"""Generated some disordered sites"""
@pb.site_generator("New", energy=0.4)
def site_gen():
x = [10, 20, 30]
y = [1, 2, 3]
z = [0, -1, -2]
return x, y, z
model = pb.Model(graphene.monolayer(), graphene.hexagon_ac(1), site_gen)
s = model.system[model.system.x >= 10]
assert s.num_sites == 3
assert pytest.fuzzy_equal(s.x, [10, 20, 30])
assert pytest.fuzzy_equal(s.y, [1, 2, 3])
assert pytest.fuzzy_equal(s.z, [0, -1, -2])
def test_expected(lattice, baseline, plot_if_fails):
expected = baseline(lattice)
plot_if_fails(lattice, expected, 'plot')
assert lattice.sub_name_map == expected.sub_name_map
assert lattice.hop_name_map == expected.hop_name_map
assert pytest.fuzzy_equal(lattice, expected)
def test_dos(params, baseline, plot_if_fails):
configurations = [
{
'matrix_format': "ELL",
'optimal_size': False,
'interleaved': False
},
{
'matrix_format': "ELL",
'optimal_size': True,
'interleaved': True
},
]
model = pb.Model(*params)
kernel = pb.lorentz_kernel()
strategies = [
pb.kpm(model, kernel=kernel, silent=True, **c) for c in configurations
]
energy = np.linspace(0, 2, 25)
results = [kpm.calc_dos(energy, broadening=0.15) for kpm in strategies]
expected = results[0].with_data(
baseline(results[0].data.astype(np.float32)))
for i in range(len(results)):
plot_if_fails(results[i], expected, 'plot', label=i)
for result in results:
assert pytest.fuzzy_equal(result, expected, rtol=1e-3, atol=1e-6)
def test_brillouin_zone():
from math import pi, sqrt
lat = pb.Lattice(a1=1)
assert pytest.fuzzy_equal(lat.brillouin_zone(), [-pi, pi])
lat = pb.Lattice(a1=[0, 1], a2=[0.5, 0.5])
assert pytest.fuzzy_equal(
lat.brillouin_zone(),
[[0, -2 * pi], [2 * pi, 0], [0, 2 * pi], [-2 * pi, 0]])
# Identical lattices represented using acute and obtuse angles between primitive vectors
acute = pb.Lattice(a1=[1, 0], a2=[1 / 2, 1 / 2 * sqrt(3)])
obtuse = pb.Lattice(a1=[1 / 2, 1 / 2 * sqrt(3)],
a2=[1 / 2, -1 / 2 * sqrt(3)])
assert pytest.fuzzy_equal(acute.brillouin_zone(), obtuse.brillouin_zone())
def test_hopping_generator():
"""Generated next-nearest hoppings should produce the same result as the builtin lattice"""
from scipy.spatial import cKDTree
@pb.hopping_generator("tnn_test", energy=graphene.t_nn)
def next_nearest(x, y, z):
pos = np.stack([x, y, z], axis=1)
dmin = graphene.a * 0.95
dmax = graphene.a * 1.05
kdtree = cKDTree(pos)
coo = kdtree.sparse_distance_matrix(kdtree, dmax).tocoo()
idx = coo.data > dmin
return coo.row[idx], coo.col[idx]
@pb.onsite_energy_modifier
def onsite_offset(energy):
return energy + 3 * graphene.t_nn
model = pb.Model(graphene.monolayer(), next_nearest, onsite_offset,
graphene.hexagon_ac(1))
expected = pb.Model(graphene.monolayer(2), graphene.hexagon_ac(1))
assert pytest.fuzzy_equal(model.hamiltonian, expected.hamiltonian)
@pb.hopping_generator("t_new", energy=1.0)
def bad_generator():
"""Different array lengths"""
return [0, 1, 2], [0, 1]
model = pb.Model(graphene.monolayer(), pb.primitive(3, 3), bad_generator)
with pytest.raises(RuntimeError) as excinfo:
model.eval()
assert "the number of `from` and `to` indices must be equal" in str(
excinfo.value)
def test_ldos_sublattice():
"""LDOS for A and B sublattices should be antisymmetric for graphene with a mass term"""
model = pb.Model(graphene.monolayer(), graphene.hexagon_ac(10), graphene.mass_term(1))
kpm = pb.greens.kpm(model)
a, b = (kpm.calc_ldos(np.linspace(-5, 5, 50), 0.1, [0, 0], sub) for sub in ('A', 'B'))
assert pytest.fuzzy_equal(a.ldos, b.ldos[::-1], rtol=1e-3, atol=1e-6)
def test_ldos_sublattice():
"""LDOS for A and B sublattices should be antisymmetric for graphene with a mass term"""
model = pb.Model(graphene.monolayer(), graphene.hexagon_ac(10), graphene.mass_term(1))
kpm = pb.chebyshev.kpm(model)
a, b = (kpm.calc_ldos(np.linspace(-5, 5, 50), 0.1, [0, 0], sub) for sub in ('A', 'B'))
assert pytest.fuzzy_equal(a.ldos, b.ldos[::-1], rtol=1e-3, atol=1e-6)
def test_expected(lattice, baseline, plot_if_fails):
expected = baseline(lattice)
plot_if_fails(lattice, expected, 'plot')
assert lattice.sub_name_map == expected.sub_name_map
assert lattice.hop_name_map == expected.hop_name_map
assert pytest.fuzzy_equal(lattice, expected)
def test_pickle_round_trip(lattice, tmpdir):
file_name = str(tmpdir.join('file.npz'))
pb.save(lattice, file_name)
from_file = pb.load(file_name)
assert lattice.sub_name_map == from_file.sub_name_map
assert lattice.hop_name_map == from_file.hop_name_map
assert pytest.fuzzy_equal(lattice, from_file)
def test_dos(solver, baseline, plot_if_fails):
energy = np.linspace(0, 0.075, 15)
result = solver.calc_dos(energy, 0.01)
expected = pb.results.DOS(energy, baseline(result.dos))
plot_if_fails(result, expected, 'plot')
assert pytest.fuzzy_equal(result, expected, rtol=2e-2, atol=1e-5)
def test_pickle_round_trip(lattice, tmpdir):
file_name = str(tmpdir.join('file.npz'))
pb.save(lattice, file_name)
from_file = pb.load(file_name)
assert lattice.sub_name_map == from_file.sub_name_map
assert lattice.hop_name_map == from_file.hop_name_map
assert pytest.fuzzy_equal(lattice, from_file)
def test_add_multiorbital_sublattice():
lat = pb.Lattice([1, 0], [0, 1])
lat.add_one_sublattice("A", [0, 0])
assert lat.nsub == 1
lat.add_one_sublattice("B", [0, 0], [1, 2, 3])
assert pytest.fuzzy_equal(lat.sublattices["B"].energy,
[[1, 0, 0], [0, 2, 0], [0, 0, 3]])
lat.add_one_sublattice("C", [0, 0], [[1, 2, 3], [0, 4, 5], [0, 0, 6]])
assert pytest.fuzzy_equal(lat.sublattices["C"].energy,
[[1, 2, 3], [2, 4, 5], [3, 5, 6]])
lat.add_one_sublattice("D", [0, 0], [[1, 2j, 3], [0, 4, 5j], [0, 0, 6]])
assert pytest.fuzzy_equal(lat.sublattices["D"].energy,
[[1, 2j, 3], [-2j, 4, 5j], [3, -5j, 6]])
lat.add_one_sublattice("E", [0, 0], [[1, 2, 3], [2, 4, 5], [3, 5, 6]])
assert pytest.fuzzy_equal(lat.sublattices["E"].energy,
[[1, 2, 3], [2, 4, 5], [3, 5, 6]])
assert lat.nsub == 5
with pytest.raises(RuntimeError) as excinfo:
lat.add_one_sublattice("zero-dimensional", [0, 0], [])
assert "can't be zero-dimensional" in str(excinfo.value)
with pytest.raises(RuntimeError) as excinfo:
lat.add_one_sublattice("complex onsite energy", [0, 0], [1j, 2j, 3j])
assert "must be a real vector or a square matrix" in str(excinfo.value)
with pytest.raises(RuntimeError) as excinfo:
lat.add_one_sublattice("not square", [0, 0], [[1, 2, 3], [4, 5, 6]])
assert "must be a real vector or a square matrix" in str(excinfo.value)
with pytest.raises(RuntimeError) as excinfo:
lat.add_one_sublattice("not square", [0, 0],
[[1j, 2, 3], [2, 4j, 5], [3, 5, 6j]])
assert "The main diagonal of the onsite hopping term must be real" in str(
excinfo.value)
with pytest.raises(RuntimeError) as excinfo:
lat.add_one_sublattice("not Hermitian", [0, 0],
[[1, 2, 3], [4, 5, 6], [7, 8, 9]])
assert "The onsite hopping matrix must be upper triangular or Hermitian" in str(
excinfo.value)
def test_expected(model, baseline):
model.attach_lead(1, [0, -1], [0, 1])
model.attach_lead(-1, [0, -1], [0, 1])
model.attach_lead(2, [-1, -5], [1, -5])
model.attach_lead(-2, [-1, 5], [1, 5])
ports = model.system.ports
expected = baseline(ports)
assert pytest.fuzzy_equal(ports, expected, 1.e-4, 1.e-6)
def test_expected(model, baseline):
model.attach_lead(1, [0, -1], [0, 1])
model.attach_lead(-1, [0, -1], [0, 1])
model.attach_lead(2, [-1, -5], [1, -5])
model.attach_lead(-2, [-1, 5], [1, 5])
ports = model.system.ports
expected = baseline(ports)
assert pytest.fuzzy_equal(ports, expected, 1.e-4, 1.e-6)
def test_kwant():
"""Create the same model using kwant and pybinding and solve with kwant.smatrix"""
energy = 1
vs = np.linspace(-2, 0, 5)
system = make_wire_with_flat_potential()
kwant_result = np.array([calc_transmission(system, energy, v) for v in vs])
pb_result = np.array([calc_transmission(pb_model(v).tokwant(), energy) for v in vs])
assert pytest.fuzzy_equal(pb_result, kwant_result)
def test_freeform(baseline, plot_if_fails):
def donut(inner_radius, outer_radius):
def contains(x, y, _):
r = np.sqrt(x**2 + y**2)
return np.logical_and(inner_radius < r, r < outer_radius)
return pb.FreeformShape(contains,
width=[2 * outer_radius, 2 * outer_radius])
assert pytest.fuzzy_equal(
donut(0.5, 1).vertices,
[[-1, -1, 0], [1, -1, 0], [-1, 1, 0], [1, 1, 0]] * 2)
shape = donut(0.6, 1.1)
model = pb.Model(graphene.monolayer(), shape)
expected = baseline(model.system)
plot_if_fails(model.system, expected, 'plot')
plot_if_fails(shape, shape, 'plot')
assert pytest.fuzzy_equal(model.system, expected, 1.e-4, 1.e-6)
def test_hamiltonian(model):
"""Must be in the correct format and point to memory allocated in C++ (no copies)"""
h = model.hamiltonian
assert isinstance(h, csr_matrix)
assert h.dtype == np.float32
assert h.shape == (2, 2)
assert pytest.fuzzy_equal(h.data, [graphene.t] * 2)
assert pytest.fuzzy_equal(h.indices, [1, 0])
assert pytest.fuzzy_equal(h.indptr, [0, 1, 2])
assert h.data.flags['OWNDATA'] is False
assert h.data.flags['WRITEABLE'] is False
with pytest.raises(ValueError) as excinfo:
h.data += 1
assert "read-only" in str(excinfo.value)
h2 = model.hamiltonian
assert h2.data is not h.data
assert point_to_same_memory(h2.data, h.data)
def test_kpm_reuse():
"""KPM should return the same result when a single object is used for multiple calculations"""
model = pb.Model(graphene.monolayer(), graphene.hexagon_ac(10))
kpm = pb.chebyshev.kpm(model)
energy = np.linspace(-5, 5, 50)
broadening = 0.1
for position in [0, 0], [6, 0]:
actual = kpm.calc_ldos(energy, broadening, position)
expected = pb.chebyshev.kpm(model).calc_ldos(energy, broadening, position)
assert pytest.fuzzy_equal(actual, expected, rtol=1e-3, atol=1e-6)
def test_kpm_reuse():
"""KPM should return the same result when a single object is used for multiple calculations"""
model = pb.Model(graphene.monolayer(), graphene.hexagon_ac(10))
kpm = pb.greens.kpm(model)
energy = np.linspace(-5, 5, 50)
broadening = 0.1
for position in [0, 0], [6, 0]:
actual = kpm.calc_ldos(energy, broadening, position)
expected = pb.greens.kpm(model).calc_ldos(energy, broadening, position)
assert pytest.fuzzy_equal(actual, expected, rtol=1e-3, atol=1e-6)
def test_freeform(baseline, plot_if_fails):
def donut(inner_radius, outer_radius):
def contains(x, y, _):
r = np.sqrt(x**2 + y**2)
return np.logical_and(inner_radius < r, r < outer_radius)
return pb.FreeformShape(contains, width=[2 * outer_radius, 2 * outer_radius])
assert pytest.fuzzy_equal(
donut(0.5, 1).vertices,
[[ 1, 1, 0], [ 1, 1, 0], [ 1, -1, 0], [ 1, -1, 0],
[-1, 1, 0], [-1, 1, 0], [-1, -1, 0], [-1, -1, 0]]
)
shape = donut(0.6, 1.1)
model = pb.Model(graphene.monolayer(), shape)
expected = baseline(model.system)
plot_if_fails(model.system, expected, 'plot')
plot_if_fails(shape, shape, 'plot')
assert pytest.fuzzy_equal(model.system, expected, 1.e-4, 1.e-6)
def test_hamiltonian(model):
"""Must be in the correct format and point to memory allocated in C++ (no copies)"""
h = model.hamiltonian
assert isinstance(h, csr_matrix)
assert h.dtype == np.float32
assert h.shape == (2, 2)
assert pytest.fuzzy_equal(h.data, [graphene.t] * 2)
assert pytest.fuzzy_equal(h.indices, [1, 0])
assert pytest.fuzzy_equal(h.indptr, [0, 1, 2])
assert h.data.flags['OWNDATA'] is False
assert h.data.flags['WRITEABLE'] is False
with pytest.raises(ValueError) as excinfo:
h.data += 1
assert "read-only" in str(excinfo.value)
h2 = model.hamiltonian
assert h2.data is not h.data
assert point_to_same_memory(h2.data, h.data)
def test_spatial_ldos(solver, baseline, plot_if_fails):
ldos_map = solver.calc_spatial_ldos(energy=0.05, broadening=0.01)
x_max = solver.system.x.max()
y_max = solver.system.y.max()
ldos_map = ldos_map.cropped(x=(x_max - 1, x_max + 1), y=(y_max - 1, y_max + 1))
expected = ldos_map.with_data(baseline(ldos_map.data))
plot_if_fails(ldos_map, expected, "plot")
assert pytest.fuzzy_equal(ldos_map, expected, rtol=1e-2, atol=1e-5)
def test_ldos(solver, plot_if_fails):
"""Compare an LDOS sum at every position with directly calculated DOS"""
energy = np.linspace(0, 0.075, 15)
broadening = 0.01
expected = solver.calc_dos(energy, broadening)
ldos = np.stack([solver.calc_ldos(energy, broadening, position).ldos
for position in zip(*solver.system.positions)])
result = pb.results.DOS(energy, np.sum(ldos, axis=0))
plot_if_fails(result, expected, 'plot')
assert pytest.fuzzy_equal(result, expected)
def test_kwant():
"""Create the same model using kwant and pybinding and solve with kwant.smatrix"""
energy = 1
vs = np.linspace(-2, 0, 5)
system = make_wire_with_flat_potential()
kwant_result = np.array(
[calc_transmission(system, energy, v) for v in vs])
pb_result = np.array(
[calc_transmission(pb_model(v).tokwant(), energy) for v in vs])
assert pytest.fuzzy_equal(pb_result, kwant_result)
def test_add_sublattice(capsys):
lat = pb.Lattice(1)
assert lat.nsub == 0
lat.add_one_sublattice("A", 0.0)
assert lat.nsub == 1
lat.add_sublattices(("B", 0.1), ("C", 0.2))
assert lat.nsub == 3
subs = lat.sublattices
assert len(subs) == 3
assert all(v in subs for v in ("A", "B", "C"))
assert pytest.fuzzy_equal(subs["A"].position, [0, 0, 0])
assert subs["A"].energy == 0
assert subs["A"].unique_id == 0
assert subs["A"].alias_id == 0
assert pytest.fuzzy_equal(subs["B"].position, [0.1, 0, 0])
assert subs["B"].energy == 0
assert subs["B"].unique_id == 1
assert subs["B"].alias_id == 1
assert pytest.fuzzy_equal(subs["C"].position, [0.2, 0, 0])
assert subs["C"].energy == 0
assert subs["C"].unique_id == 2
assert subs["C"].alias_id == 2
with pytest.raises(RuntimeError) as excinfo:
lat.add_one_sublattice("", 0)
assert "Sublattice name can't be blank" in str(excinfo.value)
with pytest.raises(RuntimeError) as excinfo:
lat.add_one_sublattice("A", 0)
assert "Sublattice 'A' already exists" in str(excinfo.value)
with pytest.warns(LoudDeprecationWarning):
assert lat["A"] == "A"
capsys.readouterr()
def test_structure_map(model):
system = model.system
zeros = np.zeros_like(system.x)
spatial_map = pb.results.SpatialMap.from_system(zeros, system)
structure_map = pb.results.StructureMap.from_system(zeros, system)
assert pytest.fuzzy_equal(spatial_map, structure_map.spatial_map)
tmp = structure_map[structure_map.x < 0.05]
assert structure_map.hoppings.nnz == 41
assert tmp.hoppings.nnz == 21
assert tmp.hoppings.data.mapping == model.lattice.impl.hop_name_map
def test_structure_map(model):
system = model.system
zeros = np.zeros_like(system.positions.x)
spatial_map = pb.results.SpatialMap.from_system(zeros, system)
structure_map = pb.results.StructureMap.from_system(zeros, system)
assert pytest.fuzzy_equal(spatial_map, structure_map.spatial_map)
tmp = structure_map.copy()
tmp.filter(tmp.pos.x < 0.05)
assert structure_map.hoppings.nnz == 41
assert tmp.hoppings.nnz == 21
def test_add_sublattice():
lat = pb.Lattice(1)
assert lat.nsub == 0
lat.add_one_sublattice("A", 0.0)
assert lat.nsub == 1
lat.add_sublattices(("B", 0.1), ("C", 0.2))
assert lat.nsub == 3
subs = lat.sublattices
assert len(subs) == 3
assert all(v in subs for v in ("A", "B", "C"))
assert pytest.fuzzy_equal(subs["A"].position, [0, 0, 0])
assert subs["A"].energy == 0
assert subs["A"].unique_id == 0
assert subs["A"].alias_id == 0
assert pytest.fuzzy_equal(subs["B"].position, [0.1, 0, 0])
assert subs["B"].energy == 0
assert subs["B"].unique_id == 1
assert subs["B"].alias_id == 1
assert pytest.fuzzy_equal(subs["C"].position, [0.2, 0, 0])
assert subs["C"].energy == 0
assert subs["C"].unique_id == 2
assert subs["C"].alias_id == 2
with pytest.raises(RuntimeError) as excinfo:
lat.add_one_sublattice("", 0)
assert "Sublattice name can't be blank" in str(excinfo.value)
with pytest.raises(RuntimeError) as excinfo:
lat.add_one_sublattice("A", 0)
assert "Sublattice 'A' already exists" in str(excinfo.value)
pytest.deprecated_call(lat.__getitem__, "A")
def assert_positions(name, **expected):
_, x1, y1, z1, x2, y2, z2 = capture[name]
assert pytest.fuzzy_equal(x1.squeeze(), expected["x1"])
assert pytest.fuzzy_equal(y1.squeeze(), expected["y1"])
assert pytest.fuzzy_equal(z1.squeeze(), expected["z1"])
assert pytest.fuzzy_equal(x2.squeeze(), expected["x2"])
assert pytest.fuzzy_equal(y2.squeeze(), expected["y2"])
assert pytest.fuzzy_equal(z1.squeeze(), expected["z2"])
def test_kpm_multiple_indices(model):
"""KPM can take a vector of column indices and return the Green's function for all of them"""
kpm = pb.greens.kpm(model)
num_sites = model.system.num_sites
i, j = num_sites // 2, num_sites // 4
energy = np.linspace(-0.3, 0.3, 10)
broadening = 0.8
cols = [j, j + 1, j + 2]
gs = kpm(i, cols, energy, broadening)
assert len(gs) == len(cols)
g = kpm(j, i, energy, broadening)
assert pytest.fuzzy_equal(gs[0], g)
def test_wrapper_return():
"""Make sure the boost python wrapper return type conversion is working"""
@pb.hopping_energy_modifier
def mul(energy):
"""Returning a non-contiguous view will force the wrapper to create a copy"""
energy = np.concatenate([energy, energy])
energy *= 3
return energy[::2]
lattice = pb.Lattice([1, 0])
lattice.add_sublattices(("A", [0, 0]), ("B", [0, 0]))
lattice.add_one_hopping([0], "A", "B", 1.0)
model = pb.Model(lattice, mul, pb.primitive(2))
assert pytest.fuzzy_equal(model.hamiltonian.data, [3, 3, 3, 3])
def test_make_lattice():
a, t = 1, 1
lat1 = pb.Lattice([a, 0], [0, a])
lat1.add_one_sublattice('s', (0, 0))
lat1.add_hoppings([(0, 1), 's', 's', t],
[(1, 0), 's', 's', t])
lat1.min_neighbors = 2
lat2 = pb.make_lattice(
vectors=[[a, 0], [0, a]],
sublattices=[['s', (0, 0)]],
hoppings=[[(0, 1), 's', 's', t],
[(1, 0), 's', 's', t]],
min_neighbors=2
)
assert pytest.fuzzy_equal(lat1, lat2)
def test_ndsweep(baseline):
@pb.parallelize(v1=np.linspace(0, 0.1, 5), v2=np.linspace(-0.2, 0.2, 4))
def factory(v1, v2, energy=np.linspace(0, 0.1, 10)):
model = pb.Model(
graphene.monolayer(),
graphene.hexagon_ac(side_width=15),
pb.constant_potential(v1),
pb.constant_potential(v2)
)
kpm = pb.greens.kpm(model)
return kpm.deferred_ldos(energy, broadening=0.15, position=[0, 0])
silence_parallel_output(factory)
result = pb.parallel.ndsweep(factory)
expected = baseline(result)
assert pytest.fuzzy_equal(result, expected, rtol=1e-4, atol=1e-6)
def test_sweep(baseline, plot_if_fails):
@pb.parallelize(v=np.linspace(0, 0.1, 10))
def factory(v, energy=np.linspace(0, 0.1, 10)):
model = pb.Model(
graphene.monolayer(),
graphene.hexagon_ac(side_width=15),
pb.constant_potential(v)
)
kpm = pb.greens.kpm(model)
return kpm.deferred_ldos(energy, broadening=0.15, position=[0, 0])
silence_parallel_output(factory)
labels = dict(title="test sweep", x="V (eV)", y="E (eV)", data="LDOS")
result = pb.parallel.sweep(factory, labels=labels)
expected = baseline(result)
plot_if_fails(result, expected, 'plot')
assert pytest.fuzzy_equal(result, expected, rtol=1e-4, atol=1e-6)
def test_hopping_generator():
"""Generated next-nearest hoppings should produce the same result as the builtin lattice"""
from scipy.spatial import cKDTree
@pb.hopping_generator("tnn_test", energy=graphene.t_nn)
def next_nearest(x, y, z):
pos = np.stack([x, y, z], axis=1)
dmin = graphene.a * 0.95
dmax = graphene.a * 1.05
kdtree = cKDTree(pos)
coo = kdtree.sparse_distance_matrix(kdtree, dmax).tocoo()
idx = coo.data > dmin
return coo.row[idx], coo.col[idx]
@pb.onsite_energy_modifier
def onsite_offset(energy):
return energy + 3 * graphene.t_nn
model = pb.Model(graphene.monolayer(), next_nearest, onsite_offset, graphene.hexagon_ac(1))
expected = pb.Model(graphene.monolayer(2), graphene.hexagon_ac(1))
assert pytest.fuzzy_equal(model.hamiltonian, expected.hamiltonian)
def test_expected(model, baseline, plot_if_fails):
system = model.system
expected = baseline(system)
plot_if_fails(system, expected, 'plot')
assert pytest.fuzzy_equal(system, expected, 1.e-4, 1.e-6)
def test_pickle_round_trip(model, tmpdir):
file_name = str(tmpdir.join('file.npz'))
pb.save(model.system, file_name)
from_file = pb.load(file_name)
assert pytest.fuzzy_equal(model.system, from_file)
def test_polygon(polygon, baseline, plot_if_fails):
model = pb.Model(graphene.monolayer(), polygon)
expected = baseline(model.system)
plot_if_fails(model.system, expected, 'plot')
plot_if_fails(polygon, polygon, 'plot')
assert pytest.fuzzy_equal(model.system, expected, 1.e-4, 1.e-6)