def __init__(self):
bond = 1.42
sq3h = 3.**.5 * 0.5
self.sc = SuperCell(
np.array([[1.5, sq3h, 0.], [1.5, -sq3h, 0.], [0., 0., 10.]],
np.float64) * bond,
nsc=[3, 3, 1])
C = Atom(Z=6, R=[bond * 1.01] * 3)
self.g = Geometry(
np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) * bond,
atoms=C,
sc=self.sc)
self.E = EnergyDensityMatrix(self.g)
self.ES = EnergyDensityMatrix(self.g, orthogonal=False)
def func(E, ia, idxs, idxs_xyz):
idx = E.geometry.close(ia,
R=(0.1, 1.44),
atoms=idxs,
atoms_xyz=idxs_xyz)
ia = ia * 3
i0 = idx[0] * 3
i1 = idx[1] * 3
# on-site
p = 1.
E.E[ia, i0] = p
E.E[ia + 1, i0 + 1] = p
E.E[ia + 2, i0 + 2] = p
# nn
p = 0.1
# on-site directions
E.E[ia, ia + 1] = p
E.E[ia, ia + 2] = p
E.E[ia + 1, ia] = p
E.E[ia + 1, ia + 2] = p
E.E[ia + 2, ia] = p
E.E[ia + 2, ia + 1] = p
E.E[ia, i1 + 1] = p
E.E[ia, i1 + 2] = p
E.E[ia + 1, i1] = p
E.E[ia + 1, i1 + 2] = p
E.E[ia + 2, i1] = p
E.E[ia + 2, i1 + 1] = p
self.func = func
def test_nc_EDM_non_colinear(sisl_tmp):
EDM1 = EnergyDensityMatrix(sisl.geom.graphene(), spin=sisl.Spin('NC'))
EDM1.construct(([0.1, 1.44], [0.1, 0.2, 0.3, 0.4]))
f1 = sisl_tmp('EDM1.nc', _dir)
f2 = sisl_tmp('EDM2.nc', _dir)
EDM1.write(f1)
EDM1.finalize()
EDM2 = sisl.get_sile(f1).read_energy_density_matrix()
EDM2.write(f2)
EDM3 = sisl.get_sile(f2).read_energy_density_matrix()
assert EDM1._csr.spsame(EDM2._csr)
assert np.allclose(EDM1._csr._D, EDM2._csr._D)
assert EDM1._csr.spsame(EDM3._csr)
assert np.allclose(EDM1._csr._D, EDM3._csr._D)
def test_nc_EDM_non_colinear(sisl_tmp):
EDM1 = EnergyDensityMatrix(sisl.geom.graphene(), spin=sisl.Spin('NC'))
EDM1.construct(([0.1, 1.44], [[0.1, 0.2, 0.3, 0.4], [0.2, 0.3, 0.4, 0.5]]))
f1 = sisl_tmp('EDM1.nc', _dir)
f2 = sisl_tmp('EDM2.nc', _dir)
EDM1.write(f1, sort=False)
EDM1.finalize()
EDM2 = sisl.get_sile(f1).read_energy_density_matrix(sort=False)
EDM2.write(f2, sort=False)
EDM3 = sisl.get_sile(f2).read_energy_density_matrix(sort=False)
assert EDM1._csr.spsame(EDM2._csr)
assert EDM1._csr.spsame(EDM3._csr)
# EDM1 is finalized, but EDM2 is not finalized
assert not np.allclose(EDM1._csr._D, EDM2._csr._D)
# EDM2 and EDM3 are the same
assert np.allclose(EDM2._csr._D, EDM3._csr._D)
EDM2.finalize()
assert np.allclose(EDM1._csr._D, EDM2._csr._D)
def test_read_write_energy_density_matrix(self, sisl_tmp, sisl_system, sile):
G = sisl_system.g.rotatec(-30)
EDM = EnergyDensityMatrix(G, orthogonal=True)
EDM.construct([[0.1, 1.45], [0.1, -2.7]])
f = sisl_tmp('test_read_write_energy_density_matrix.win', _dir)
# Write
sile(f, mode='w').write_energy_density_matrix(EDM)
# Read 1
try:
edm = sile(f, mode='r').read_energy_density_matrix(geometry=EDM.geom)
assert EDM.spsame(edm)
except UnicodeDecodeError as e:
pass
# Read 2
try:
edm = EnergyDensityMatrix.read(sile(f, mode='r'), geometry=EDM.geom)
assert EDM.spsame(edm)
except UnicodeDecodeError as e:
pass
def test_spin(self, setup):
g = setup.g.copy()
EnergyDensityMatrix(g)
EnergyDensityMatrix(g, spin=Spin('P'))
EnergyDensityMatrix(g, spin=Spin('NC'))
EnergyDensityMatrix(g, spin=Spin('SO'))