def test_nc_DM_non_colinear(sisl_tmp):
DM1 = DensityMatrix(sisl.geom.graphene(), spin=sisl.Spin('NC'))
DM1.construct(([0.1, 1.44],
[[0.1, 0.2, 0.3, 0.4],
[0.2, 0.3, 0.4, 0.5]]))
f1 = sisl_tmp('DM1.nc', _dir)
f2 = sisl_tmp('DM2.nc', _dir)
DM1.write(f1)
DM1.finalize()
DM2 = sisl.get_sile(f1).read_density_matrix()
DM2.write(f2)
DM3 = sisl.get_sile(f2).read_density_matrix()
assert DM1._csr.spsame(DM2._csr)
assert DM1._csr.spsame(DM3._csr)
# DM1 is finalized, but DM2 is not finalized
assert np.allclose(DM1._csr._D, DM2._csr._D)
# DM2 and DM3 are the same
assert np.allclose(DM2._csr._D, DM3._csr._D)
DM2.finalize()
assert np.allclose(DM1._csr._D, DM2._csr._D)
def test_spin_rotate_nc(self, setup):
bond = 1.42
sq3h = 3.**.5 * 0.5
sc = SuperCell(np.array(
[[1.5, sq3h, 0.], [1.5, -sq3h, 0.], [0., 0., 10.]], np.float64) *
bond,
nsc=[3, 3, 1])
orb = AtomicOrbital('px', R=bond * 1.001)
C = Atom(6, orb)
g = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) * bond,
atoms=C,
sc=sc)
D = DensityMatrix(g, spin=Spin('nc'))
D.construct([[0.1, bond + 0.01],
[(1., 0.5, 0.01, 0.01), (0.1, 0.2, 0.1, 0.1)]])
D_mull = D.mulliken()
d = D.spin_rotate([45, 60, 90], rad=False)
d_mull = d.mulliken()
assert not np.allclose(D_mull, d_mull)
assert np.allclose(D_mull[:, 0], d_mull[:, 0])
def test_rho_fail_p(self, setup):
bond = 1.42
sq3h = 3.**.5 * 0.5
sc = SuperCell(np.array(
[[1.5, sq3h, 0.], [1.5, -sq3h, 0.], [0., 0., 10.]], np.float64) *
bond,
nsc=[3, 3, 1])
n = 60
rf = np.linspace(0, bond * 1.01, n)
rf = (rf, rf)
orb = SphericalOrbital(1, rf, 2.)
C = Atom(6, orb)
g = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) * bond,
atom=C,
sc=sc)
D = DensityMatrix(g, spin=Spin('P'))
D.construct([[0.1, bond + 0.01], [(1., 0.5), (0.1, 0.1)]])
grid = Grid(0.2, geometry=D.geom)
D.density(grid, [1., -1, 0.])
def test_read_write_density_matrix(self, sisl_tmp, sisl_system, sile):
G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :])
DM = DensityMatrix(G, orthogonal=True)
DM.construct([[0.1, 1.45], [0.1, -2.7]])
f = sisl_tmp("test_read_write_density_matrix.win", _dir)
# Write
with sile(f, mode='w') as s:
s.write_density_matrix(DM)
# Read 1
try:
with sile(f, mode='r') as s:
dm = s.read_density_matrix(geometry=DM.geometry)
assert DM.spsame(dm)
except UnicodeDecodeError as e:
pass
# Read 2
try:
with sile(f, mode='r') as s:
dm = DensityMatrix.read(s, geometry=DM.geometry)
assert DM.spsame(dm)
except UnicodeDecodeError as e:
pass
def test_spin_align_pol(self, setup):
bond = 1.42
sq3h = 3.**.5 * 0.5
sc = SuperCell(np.array([[1.5, sq3h, 0.],
[1.5, -sq3h, 0.],
[0., 0., 10.]], np.float64) * bond, nsc=[3, 3, 1])
orb = AtomicOrbital('px', R=bond * 1.001)
C = Atom(6, orb)
g = Geometry(np.array([[0., 0., 0.],
[1., 0., 0.]], np.float64) * bond,
atoms=C, sc=sc)
D = DensityMatrix(g, spin=Spin('p'))
D.construct([[0.1, bond + 0.01], [(1., 0.5), (0.1, 0.2)]])
D_mull = D.mulliken()
v = np.array([1, 2, 3])
d = D.spin_align(v)
d_mull = d.mulliken()
assert D_mull.shape == (len(D), 2)
assert d_mull.shape == (len(D), 4)
assert not np.allclose(-np.diff(D_mull, axis=1), d_mull[:, 3])
assert np.allclose(D_mull.sum(1), d_mull[:, 0])
def test_spin_align_so(self, setup):
bond = 1.42
sq3h = 3.**.5 * 0.5
sc = SuperCell(np.array(
[[1.5, sq3h, 0.], [1.5, -sq3h, 0.], [0., 0., 10.]], np.float64) *
bond,
nsc=[3, 3, 1])
orb = AtomicOrbital('px', R=bond * 1.001)
C = Atom(6, orb)
g = Geometry(np.array([[0., 0., 0.], [1., 0., 0.]], np.float64) * bond,
atom=C,
sc=sc)
D = DensityMatrix(g, spin=Spin('SO'))
D.construct([[0.1, bond + 0.01],
[(1., 0.5, 0.01, 0.01, 0.01, 0.01, 0.2, 0.2),
(0.1, 0.2, 0.1, 0.1, 0., 0.1, 0.2, 0.3)]])
D_mull = D.mulliken()
v = np.array([1, 2, 3])
d = D.spin_align(v)
d_mull = d.mulliken()
assert not np.allclose(D_mull, d_mull)
assert np.allclose(D_mull[:, 0], d_mull[:, 0])
