def test_spin2(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)],
Atom(6, R=1.01),
sc=SuperCell(100, nsc=[3, 3, 1]))
H = Hamiltonian(g, dtype=np.int32, spin=Spin.POLARIZED)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H[0, j] = (i, i * 2)
H2 = Hamiltonian(g, 2, dtype=np.int32)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H2[0, j] = (i, i * 2)
assert H.spsame(H2)
H2 = Hamiltonian(g, Spin(Spin.POLARIZED), dtype=np.int32)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H2[0, j] = (i, i * 2)
assert H.spsame(H2)
H2 = Hamiltonian(g, Spin('polarized'), dtype=np.int32)
for i in range(10):
j = range(i * 2, i * 2 + 3)
H2[0, j] = (i, i * 2)
assert H.spsame(H2)
def test_spin1():
for val in ['unpolarized', '', Spin.UNPOLARIZED,
'polarized', 'p', Spin.POLARIZED,
'non-collinear', 'nc', Spin.NONCOLINEAR,
'spin-orbit', 'so', Spin.SPINORBIT]:
s = Spin(val)
str(s)
s1 = s.copy()
assert s == s1
def test_spin1(self):
for val in ['unpolarized', '',
'polarized', 'p',
'non-colinear', 'nc',
'spin-orbit', 'so']:
s = Spin(val)
repr(s)
s1 = s.copy()
assert_equal(s, s1)
def test_sparse_orbital_bz_spin_orbit_warns_hermitian():
M = SparseOrbitalBZSpin(geom.graphene(), spin=Spin('SO'))
with pytest.warns(SislWarning, match='Hermitian'):
M.construct(([0.1, 1.44],
[[0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8],
[0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]]))
def test_pickle():
import pickle as p
S = Spin('nc')
n = p.dumps(S)
s = p.loads(n)
assert S == s
def test_sparse_orbital_bz_spin_orbit():
M = SparseOrbitalBZSpin(geom.graphene(), spin=Spin('SO'))
M.construct(([0.1, 1.44], [[0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8],
[0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]]))
new = (M + M.transpose(True)) / 2
assert np.abs((M - new)._csr._D).sum() == 0
def test_rho2(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)
D.construct([[0.1, bond + 0.01], [1., 0.1]])
grid = Grid(0.2, geometry=D.geom)
D.density(grid)
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)
D.density(grid, [1., -1])
D.density(grid, 0)
D.density(grid, 1)
D = DensityMatrix(g, spin=Spin('NC'))
D.construct([[0.1, bond + 0.01],
[(1., 0.5, 0.01, 0.01), (0.1, 0.1, 0.1, 0.1)]])
grid = Grid(0.2, geometry=D.geom)
D.density(grid)
D.density(grid, [[1., 0.], [0., -1]])
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., 0.),
(0.1, 0.1, 0.1, 0.1, 0., 0., 0., 0.)]])
grid = Grid(0.2, geometry=D.geom)
D.density(grid)
D.density(grid, [[1., 0.], [0., -1]])
D.density(grid, Spin.X)
D.density(grid, Spin.Y)
D.density(grid, Spin.Z)
def test_non_colinear_non_orthogonal(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g,
dtype=np.float64,
orthogonal=False,
spin=Spin.NONCOLINEAR)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
if i > 0:
H[i, i - 1, 0] = 1.
H[i, i - 1, 1] = 1.
if i < 9:
H[i, i + 1, 0] = 1.
H[i, i + 1, 1] = 1.
H.S[i, i] = 1.
eig1 = H.eigh()
# Check TimeSelector
for i in range(4):
assert np.allclose(H.eigh(), eig1)
assert len(eig1) == len(H)
H1 = Hamiltonian(g,
dtype=np.float64,
orthogonal=False,
spin=Spin('non-collinear'))
for i in range(10):
j = range(i * 4, i * 4 + 3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i - 1, 0] = 1.
H1[i, i - 1, 1] = 1.
if i < 9:
H1[i, i + 1, 0] = 1.
H1[i, i + 1, 1] = 1.
H1.S[i, i] = 1.
assert H1.spsame(H)
eig1 = H1.eigh()
# Check TimeSelector
for i in range(4):
assert np.allclose(H1.eigh(), eig1)
assert np.allclose(H.eigh(), H1.eigh())
es = H1.eigenstate()
assert np.allclose(es.eig, eig1)
es.spin_moment()
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_fermi_level_spin(self, setup):
R, param = [0.1, 1.5], [(1., 1.), (2.1, 0.1)]
H = Hamiltonian(setup.g.copy(), spin=Spin('P'))
H.construct([R, param])
bz = MonkhorstPack(H, [10, 10, 1])
q = 1.1
Ef = H.fermi_level(bz, q=q)
assert np.asarray(Ef).ndim == 0
H.shift(-Ef)
assert H.fermi_level(bz, q=q) == pytest.approx(0., abs=1e-6)
def test_fermi_level_spin_separate(self, setup):
R, param = [0.1, 1.5], [(1., 1.), (2.1, 0.1)]
H = Hamiltonian(setup.g.copy(), spin=Spin('P'))
H.construct([R, param])
bz = MonkhorstPack(H, [10, 10, 1])
q = [0.5, 0.3]
Ef = H.fermi_level(bz, q=q)
assert len(Ef) == 2
H.shift(-Ef)
assert np.allclose(H.fermi_level(bz, q=q), 0.)
def test_sparse_orbital_bz_non_colinear():
M = SparseOrbitalBZSpin(geom.graphene(), spin=Spin('NC'))
M.construct(([0.1, 1.44], [[0.1, 0.2, 0.3, 0.4], [0.2, 0.3, 0.4, 0.5]]))
MT = M.transpose()
MH = M.transpose(True)
assert np.abs((M - MT)._csr._D).sum() != 0
assert np.abs((M - MH)._csr._D).sum() != 0
assert np.abs((MT - MH)._csr._D).sum() != 0
def test_shift3(self, setup):
R, param = [0.1, 1.5], [(1., -1., 1.), (0.1, 0.1, 0.1)]
H = Hamiltonian(setup.g.copy(), spin=Spin('P'), orthogonal=False)
H.construct([R, param])
eig0_0 = H.eigh(spin=0)[0]
eig1_0 = H.eigh(spin=1)[0]
H.shift(0.2)
assert H.eigh(spin=0)[0] == pytest.approx(eig0_0 + 0.2)
assert H.eigh(spin=1)[0] == pytest.approx(eig1_0 + 0.2)
H.shift([0, -0.2])
assert H.eigh(spin=0)[0] == pytest.approx(eig0_0 + 0.2)
assert H.eigh(spin=1)[0] == pytest.approx(eig1_0)
def test_pickle_non_orthogonal_spin():
import pickle as p
gr = _get()
sp = SparseOrbitalBZSpin(gr, spin=Spin('p'), orthogonal=False)
sp[0, 0, :] = 0.5
sp[1, 1, :] = 0.5
sp.S[0, 0] = 1.
sp.S[1, 1] = 1.
s = p.dumps(sp)
SP = p.loads(s)
assert sp.spsame(SP)
assert np.allclose(sp.eigh(), SP.eigh())
def test_sparse_orbital_bz_spin_orbit():
M = SparseOrbitalBZSpin(geom.graphene(), spin=Spin('SO'))
M.construct(([0.1, 1.44], [[0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8],
[0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]]))
MT = M.transpose()
MH = M.transpose(True)
assert np.abs((M - MT)._csr._D).sum() != 0
assert np.abs((M - MH)._csr._D).sum() != 0
assert np.abs((MT - MH)._csr._D).sum() != 0
def test_so1(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.float64, spin=Spin.SPINORBIT)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
H[i, i, 4] = 0.1
H[i, i, 5] = 0.1
H[i, i, 6] = 0.1
H[i, i, 7] = 0.1
if i > 0:
H[i, i - 1, 0] = 1.
H[i, i - 1, 1] = 1.
if i < 9:
H[i, i + 1, 0] = 1.
H[i, i + 1, 1] = 1.
eig1 = H.eigh()
# Check TimeSelector
for i in range(2):
assert np.allclose(H.eigh(), eig1)
assert len(H.eigh()) == len(H)
H1 = Hamiltonian(g, dtype=np.float64, spin=Spin('spin-orbit'))
for i in range(10):
j = range(i * 4, i * 4 + 3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i - 1, 0] = 1.
H1[i, i - 1, 1] = 1.
if i < 9:
H1[i, i + 1, 0] = 1.
H1[i, i + 1, 1] = 1.
assert H1.spsame(H)
eig1 = H1.eigh()
# Check TimeSelector
for i in range(2):
assert np.allclose(H1.eigh(), eig1)
assert np.allclose(H.eigh(), H1.eigh())
es = H.eigenstate()
assert np.allclose(es.eig, eig1)
es.spin_moment()
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_wavefunction_eta():
N = 50
o1 = SphericalOrbital(0, (np.linspace(0, 2, N), np.exp(-np.linspace(0, 100, N))))
G = Geometry([[1] * 3, [2] * 3], Atom(6, o1), sc=[4, 4, 4])
H = Hamiltonian(G, spin=Spin('nc'))
R, param = [0.1, 1.5], [[0., 0., 0.1, -0.1],
[1., 1., 0.1, -0.1]]
H.construct([R, param])
ES = H.eigenstate()
# Plot in the full thing
grid = Grid(0.1, dtype=np.complex128, sc=SuperCell([2, 2, 2], origo=[-1] * 3))
grid.fill(0.)
ES.sub(0).wavefunction(grid, eta=True)
def test_sparse_orbital_bz_non_colinear():
M = SparseOrbitalBZSpin(geom.graphene(), spin=Spin('NC'))
M.construct(([0.1, 1.44], [[0.1, 0.2, 0.3, 0.4], [0.2, 0.3, 0.4, 0.5]]))
MT = M.transpose()
MH = M.transpose(True)
assert np.abs((M - MT)._csr._D).sum() != 0
# For a non-collinear with construct we don't take
# into account the imaginary parts... :(
# This should be fixed
assert np.abs((M - MH)._csr._D).sum() == 0
assert np.abs((MT - MH)._csr._D).sum() != 0
def test_so1(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=SuperCell(100, nsc=[3, 3, 1]))
H = Hamiltonian(g, dtype=np.float64, spin=Spin.SPINORBIT)
for i in range(10):
j = range(i*2, i*2+3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
H[i, i, 4] = 0.1
H[i, i, 5] = 0.1
H[i, i, 6] = 0.1
H[i, i, 7] = 0.1
if i > 0:
H[i, i-1, 0] = 1.
H[i, i-1, 1] = 1.
if i < 9:
H[i, i+1, 0] = 1.
H[i, i+1, 1] = 1.
eig1 = H.eigh(dtype=np.complex64)
assert np.allclose(H.eigh(dtype=np.complex128), eig1)
assert len(H.eigh()) == len(H)
H1 = Hamiltonian(g, dtype=np.float64, spin=Spin('spin-orbit'))
for i in range(10):
j = range(i*2, i*2+3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i-1, 0] = 1.
H1[i, i-1, 1] = 1.
if i < 9:
H1[i, i+1, 0] = 1.
H1[i, i+1, 1] = 1.
assert H1.spsame(H)
eig1 = H1.eigh(dtype=np.complex64)
assert np.allclose(H1.eigh(dtype=np.complex128), eig1)
assert np.allclose(H.eigh(dtype=np.complex64), H1.eigh(dtype=np.complex128))
es = H.eigenstate(dtype=np.complex128)
assert np.allclose(es.eig, eig1)
sm = es.spin_moment()
om = es.spin_orbital_moment()
assert np.allclose(sm, om.sum(1))
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_sparse_orbital_bz_non_colinear_trs_kramers_theorem():
M = SparseOrbitalBZSpin(geom.graphene(), spin=Spin('NC'))
M.construct(([0.1, 1.44], [[0.1, 0.2, 0.3, 0.4], [0.2, 0.3, 0.4, 0.5]]))
M = (M + M.transpose(True)) * 0.5
MTRS = (M + M.trs()) * 0.5
# This will in principle also work for M since the above parameters preserve
# TRS
k = np.array([0.1, 0.1, 0])
eig1 = MTRS.eigh(k=k)
eig2 = MTRS.eigh(k=-k)
assert np.allclose(eig1, eig2)
def test_non_colinear_non_orthogonal(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=SuperCell(100, nsc=[3, 3, 1]))
H = Hamiltonian(g, dtype=np.float64, orthogonal=False, spin=Spin.NONCOLINEAR)
for i in range(10):
j = range(i*2, i*2+3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
if i > 0:
H[i, i-1, 0] = 1.
H[i, i-1, 1] = 1.
if i < 9:
H[i, i+1, 0] = 1.
H[i, i+1, 1] = 1.
H.S[i, i] = 1.
eig1 = H.eigh(dtype=np.complex64)
assert np.allclose(H.eigh(dtype=np.complex128), eig1)
assert len(eig1) == len(H)
H1 = Hamiltonian(g, dtype=np.float64, orthogonal=False, spin=Spin('non-collinear'))
for i in range(10):
j = range(i*2, i*2+3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i-1, 0] = 1.
H1[i, i-1, 1] = 1.
if i < 9:
H1[i, i+1, 0] = 1.
H1[i, i+1, 1] = 1.
H1.S[i, i] = 1.
assert H1.spsame(H)
eig1 = H1.eigh(dtype=np.complex64)
assert np.allclose(H1.eigh(dtype=np.complex128), eig1)
assert np.allclose(H.eigh(dtype=np.complex64), H1.eigh(dtype=np.complex128))
es = H1.eigenstate(dtype=np.complex128)
assert np.allclose(es.eig, eig1)
sm = es.spin_moment()
om = es.spin_orbital_moment()
assert np.allclose(sm, om.sum(1))
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_spin2(self):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.int32, spin=2)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[0, j] = (i, i * 2)
H2 = Hamiltonian(g, 2, dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H2[0, j] = (i, i * 2)
assert_true(H.spsame(H2))
H2 = Hamiltonian(g, Spin(2), dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H2[0, j] = (i, i * 2)
assert_true(H.spsame(H2))
H2 = Hamiltonian(g, Spin('polarized'), dtype=np.int32)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H2[0, j] = (i, i * 2)
assert_true(H.spsame(H2))
def test_sparse_orbital_bz_non_colinear():
M = SparseOrbitalBZSpin(geom.graphene(), spin=Spin('NC'))
M.construct(([0.1, 1.44], [[0.1, 0.2, 0.3, 0.4], [0.2, 0.3, 0.4, 0.5]]))
M.finalize()
MT = M.transpose()
MH = M.transpose(True)
assert np.abs((M - MT)._csr._D).sum() != 0
# For a non-collinear with construct we don't take
# into account the imaginary parts... :(
# Transposing and Hermitian transpose are the same for NC
# There are only 1 imaginary part which will change sign regardless
assert np.abs((MT - MH)._csr._D).sum() != 0
assert np.abs((M - MH)._csr._D).sum() == 0
def test_orbital_momentum(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('SO'))
D.construct([[0.1, bond + 0.01], [(1., 0.5, 0.01, 0.01, 0.01, 0.01, 0., 0.), (0.1, 0.1, 0.1, 0.1, 0., 0., 0., 0.)]])
D.orbital_momentum("atom")
D.orbital_momentum("orbital")
def test_non_colinear1(self, setup):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.float64, spin=Spin.NONCOLINEAR)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
if i > 0:
H[i, i - 1, 0] = 1.
H[i, i - 1, 1] = 1.
if i < 9:
H[i, i + 1, 0] = 1.
H[i, i + 1, 1] = 1.
eig1 = H.eigh(dtype=np.complex64)
assert np.allclose(H.eigh(dtype=np.complex128), eig1)
assert np.allclose(H.eigh(gauge='r', dtype=np.complex128), eig1)
assert len(eig1) == len(H)
H1 = Hamiltonian(g, dtype=np.float64, spin=Spin('non-collinear'))
for i in range(10):
j = range(i * 4, i * 4 + 3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i - 1, 0] = 1.
H1[i, i - 1, 1] = 1.
if i < 9:
H1[i, i + 1, 0] = 1.
H1[i, i + 1, 1] = 1.
assert H1.spsame(H)
eig1 = H1.eigh(dtype=np.complex64)
assert np.allclose(H1.eigh(dtype=np.complex128), eig1)
assert np.allclose(H.eigh(), H1.eigh())
es = H1.eigenstate(dtype=np.complex128)
assert np.allclose(es.eig, eig1)
es.spin_moment()
PDOS = es.PDOS(np.linspace(-1, 1, 100))
DOS = es.DOS(np.linspace(-1, 1, 100))
assert np.allclose(PDOS.sum(1)[0, :], DOS)
def test_so1(self):
g = Geometry([[i, 0, 0] for i in range(10)], Atom(6, R=1.01), sc=[100])
H = Hamiltonian(g, dtype=np.float64, spin=8)
for i in range(10):
j = range(i * 4, i * 4 + 3)
H[i, i, 0] = 0.
H[i, i, 1] = 0.
H[i, i, 2] = 0.1
H[i, i, 3] = 0.1
H[i, i, 4] = 0.1
H[i, i, 5] = 0.1
H[i, i, 6] = 0.1
H[i, i, 7] = 0.1
if i > 0:
H[i, i - 1, 0] = 1.
H[i, i - 1, 1] = 1.
if i < 9:
H[i, i + 1, 0] = 1.
H[i, i + 1, 1] = 1.
eig1 = H.eigh()
# Check TimeSelector
for i in range(2):
assert_true(np.allclose(H.eigh(), eig1))
assert_true(len(H.eigh()) == len(H))
H1 = Hamiltonian(g, dtype=np.float64, spin=Spin('spin-orbit'))
for i in range(10):
j = range(i * 4, i * 4 + 3)
H1[i, i, 0] = 0.
H1[i, i, 1] = 0.
H1[i, i, 2] = 0.1
H1[i, i, 3] = 0.1
if i > 0:
H1[i, i - 1, 0] = 1.
H1[i, i - 1, 1] = 1.
if i < 9:
H1[i, i + 1, 0] = 1.
H1[i, i + 1, 1] = 1.
assert_true(H1.spsame(H))
eig1 = H1.eigh()
# Check TimeSelector
for i in range(2):
assert_true(np.allclose(H1.eigh(), eig1))
assert_true(np.allclose(H.eigh(), H1.eigh()))
def test_spin_rotate_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,
atoms=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()
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 update_options(self, spin, only_if_polarized=None):
"""
Updates the options of the spin selector.
It does so according to the type of spin that the plot is handling.
Parameters
-----------
spin: sisl.Spin, str or int
It is used to indicate the kind of spin.
only_if_polarized: bool, optional
If set to `True`, the options can only be either [UP, DOWN] or [].
That is, no extra options for non collinear and spin orbit calculations.
If not provided the initialization value of `only_if_polarized` will be used.
See also
---------
sisl.physics.Spin
"""
if not isinstance(spin, Spin):
spin = Spin(spin)
# Use the default for this input field if only_if_polarized is not provided.
if only_if_polarized is None:
only_if_polarized = self._only_if_polarized
# Determine what are the new options
if only_if_polarized:
if spin.is_polarized:
options = self._options[Spin.POLARIZED]
else:
options = self._options[Spin.UNPOLARIZED]
else:
options = self._options[spin.kind]
# Update them
self.modify("inputField.params.options", options)
return self
def test_rho_fail_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])
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,
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, 0.1, 0.1, 0.1)]])
grid = Grid(0.2, geometry=D.geometry)
with pytest.raises(ValueError):
D.density(grid, [1., 0.])
def test_spin_align_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,
atom=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()
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])
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])
