def init_func_and_attrs(self, request, siesta_test_files):
name = request.param
if name.startswith("siesta_PDOS_file"):
spin_type = name.split("_")[-1]
n_spin, filename = {
"unpolarized": (1, "SrTiO3.PDOS"),
"polarized": (2, "SrTiO3_polarized.PDOS"),
"noncollinear": (4, "SrTiO3_noncollinear.PDOS")
}[spin_type]
init_func = sisl.get_sile(siesta_test_files(filename)).plot
attrs = {
"na": 5,
"no": 72,
"n_spin": n_spin,
"species": ('Sr', 'Ti', 'O')
}
elif name.startswith("sisl_H"):
gr = sisl.geom.graphene()
H = sisl.Hamiltonian(gr)
H.construct([(0.1, 1.44), (0, -2.7)])
spin_type = name.split("_")[-1]
n_spin, H = {
"unpolarized": (1, H),
"polarized": (2, H.transform(spin=sisl.Spin.POLARIZED)),
"noncolinear": (4, H.transform(spin=sisl.Spin.NONCOLINEAR)),
"spinorbit": (4, H.transform(spin=sisl.Spin.SPINORBIT))
}[spin_type]
init_func = partial(H.plot.pdos, Erange=[-5, 5])
attrs = {"na": 2, "no": 2, "n_spin": n_spin, "species": ('C', )}
elif name == "wfsx_file":
# From a siesta .WFSX file
# Since there is no hamiltonian for bi2se3_3ql.fdf, we create a dummy one
wfsx = sisl.get_sile(siesta_test_files("bi2se3_3ql.bands.WFSX"))
geometry = sisl.get_sile(
siesta_test_files("bi2se3_3ql.fdf")).read_geometry()
geometry = sisl.Geometry(geometry.xyz, atoms=wfsx.read_basis())
H = sisl.Hamiltonian(geometry, dim=4)
init_func = partial(H.plot.pdos,
wfsx_file=wfsx,
entry_points_order=["wfsx file"])
attrs = {"na": 15, "no": 195, "n_spin": 4, "species": ('Bi', 'Se')}
return init_func, attrs
def test_gf_write_read(sisl_tmp, sisl_system):
tb = sisl.Hamiltonian(sisl_system.gtb)
f = sisl_tmp('file.TSGF', _dir)
bz = sisl.MonkhorstPack(tb, [3, 3, 1])
E = np.linspace(-2, 2, 20) + 1j * 1e-4
S = np.eye(len(tb), dtype=np.complex128)
gf = sisl.io.get_sile(f)
gf.write_header(E, bz, tb)
for i, (write_hs, k, e) in enumerate(gf):
Hk = tb.Hk(k, format='array')
if write_hs and i % 2 == 0:
gf.write_hamiltonian(Hk)
elif write_hs:
gf.write_hamiltonian(Hk, S)
gf.write_self_energy(S * e - Hk)
no_u, k, E_file = gf.read_header()
assert np.allclose(E, E_file)
assert np.allclose(k, bz.k)
for i, (write_hs, k, e) in enumerate(gf):
Hk = tb.Hk(k, format='array')
if write_hs and i % 2 == 0:
Hk_file, _ = gf.read_hamiltonian()
elif write_hs:
Hk_file, Sk_file = gf.read_hamiltonian()
assert np.allclose(S, Sk_file)
assert np.allclose(Hk, Hk_file)
SE_file = gf.read_self_energy()
assert np.allclose(SE_file, S * e - Hk)
def init_func_and_attrs(self, request, siesta_test_files):
name = request.param
if name.startswith("sisl_H"):
gr = sisl.geom.graphene()
H = sisl.Hamiltonian(gr)
H.construct([(0.1, 1.44), (0, -2.7)])
spin_type = name.split("_")[-1]
n_spin, H = {
"unpolarized": (1, H),
"polarized": (2, H.transform(spin=sisl.Spin.POLARIZED)),
"noncolinear": (1, H.transform(spin=sisl.Spin.NONCOLINEAR)),
"spinorbit": (1, H.transform(spin=sisl.Spin.SPINORBIT))
}.get(spin_type)
n_states = 2
if H.spin.is_spinorbit or H.spin.is_noncolinear:
n_states *= 2
# Directly creating a BandStructure object
bz = sisl.BandStructure(H, [[0, 0, 0], [2/3, 1/3, 0], [1/2, 0, 0]], 6, ["Gamma", "M", "K"])
init_func = bz.plot.fatbands
attrs = {
"bands_shape": (6, n_spin, n_states) if H.spin.is_polarized else (6, n_states),
"weights_shape": (n_spin, 6, n_states, 2) if H.spin.is_polarized else (6, n_states, 2),
"ticklabels": ["Gamma", "M", "K"],
"tickvals": [0., 1.70309799, 2.55464699],
"gap": 0,
"spin_texture": not H.spin.is_diagonal,
"spin": H.spin
}
return init_func, attrs
def dispatch(self,
t=(-2.414, -0.168),
beta=(-1.847, -3.077),
a=1.42,
orthogonal=False):
distance = self._obj.distance
da = 0.0005
R = (distance(0, a) + da, distance(1, a) + da, distance(2, a) + da)
def construct(H, ia, atoms, atoms_xyz=None):
idx_t012, rij_t012 = H.geometry.close(ia,
R=R,
atoms=atoms,
atoms_xyz=atoms_xyz,
ret_rij=True)
H[ia, idx_t012[0]] = 0.
H[ia, idx_t012[1]] = t[0] * np.exp(beta[0] * (rij_t012[1] - R[1]))
H[ia, idx_t012[2]] = t[1] * np.exp(beta[1] * (rij_t012[2] - R[2]))
# Define the graphene lattice
C = si.Atom(6, si.AtomicOrbital(n=2, l=1, m=0, R=R[-1]))
graphene = si.geom.graphene(a, C, orthogonal=orthogonal)
# Define the Hamiltonian
H = si.Hamiltonian(graphene)
H.construct(construct)
return H
def dispatch(self, t=-2.7, a=1.42, orthogonal=False):
# Define the graphene lattice
da = 0.0005
C = si.Atom(6, si.AtomicOrbital(n=2, l=1, m=0, R=a + da))
graphene = si.geom.graphene(a, C, orthogonal=orthogonal)
# Define the Hamiltonian
H = si.Hamiltonian(graphene)
H.construct([(da, a + da), (0, t)])
return H
def dispatch(self, a=1.42, orthogonal=False):
distance = self._obj.distance
da = 0.0005
R = (distance(0, a) + da, distance(1, a) + da, distance(2, a) + da,
distance(3, a) + da)
# Define the graphene lattice
C = si.Atom(6, si.AtomicOrbital(n=2, l=1, m=0, R=R[-1]))
graphene = si.geom.graphene(a, C, orthogonal=orthogonal)
# Define the Hamiltonian
H = si.Hamiltonian(graphene, orthogonal=False)
t = [(-0.45, 1), (-2.78, 0.117), (-0.15, 0.004), (-0.095, 0.002)]
H.construct([R, t])
return H
def dispatch(self, set='A', a=1.42, orthogonal=False):
distance = self._obj.distance
da = 0.0005
H_orthogonal = True
#U = 2.0
R = tuple(distance(i, a) + da for i in range(4))
if set == 'A':
# same as simple
t = (0, -2.7)
#U = 0.
elif set == 'B':
# same as simple
t = (0, -2.7)
elif set == 'C':
t = (0, -2.7, -0.2)
elif set == 'D':
t = (0, -2.7, -0.2, -0.18)
elif set == 'E':
# same as D, but specific for GNR
t = (0, -2.7, -0.2, -0.18)
elif set == 'F':
# same as D, but specific for GNR
t = [(0, 1), (-2.7, 0.11), (-0.09, 0.045), (-0.27, 0.065)]
H_orthogonal = False
elif set == 'G':
# same as D, but specific for GNR
t = [(0, 1), (-2.97, 0.073), (-0.073, 0.018), (-0.33, 0.026)]
#U = 0.
H_orthogonal = False
else:
raise ValueError(
f"Set specification for {self.doi} does not exist, should be one of [A-G]"
)
# Reduce size of R
R = R[:len(t)]
# Currently we do not carry over U, since it is not specified for the
# sisl objects....
# Define the graphene lattice
C = si.Atom(6, si.AtomicOrbital(n=2, l=1, m=0, R=R[-1]))
graphene = si.geom.graphene(a, C, orthogonal=orthogonal)
graphene.optimize_nsc([0, 1])
# Define the Hamiltonian
H = si.Hamiltonian(graphene, orthogonal=H_orthogonal)
H.construct([R, t])
return H
def test_tshs_spin_orbit(sisl_tmp):
H1 = sisl.Hamiltonian(sisl.geom.graphene(), spin=sisl.Spin('SO'))
H1.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]]))
f1 = sisl_tmp('tmp1.TSHS', _dir)
f2 = sisl_tmp('tmp2.TSHS', _dir)
H1.write(f1)
H1.finalize()
H2 = sisl.get_sile(f1).read_hamiltonian()
H2.write(f2)
H3 = sisl.get_sile(f2).read_hamiltonian()
assert H1._csr.spsame(H2._csr)
assert np.allclose(H1._csr._D, H2._csr._D)
assert H1._csr.spsame(H3._csr)
assert np.allclose(H1._csr._D, H3._csr._D)
def test_gf_write(sisl_tmp, sisl_system):
tb = sisl.Hamiltonian(sisl_system.gtb)
f = sisl_tmp('file.TSGF', _dir)
gf = sisl.io.get_sile(f)
bz = sisl.MonkhorstPack(tb, [3, 3, 1])
E = np.linspace(-2, 2, 20) + 1j * 1e-4
S = np.eye(len(tb), dtype=np.complex128)
gf.write_header(E, bz, tb)
for i, (write_hs, k, e) in enumerate(gf):
Hk = tb.Hk(k, format='array')
if write_hs and i % 2 == 0:
gf.write_hamiltonian(Hk)
elif write_hs:
gf.write_hamiltonian(Hk, S)
gf.write_self_energy(S * e - Hk)
def get_bond_order(self, format='csr', midgap=0.):
""" Compute Huckel bond order
Parameters
----------
format: {'csr', 'array', 'dense', 'coo', ...}
the returned format of the matrix, defaulting to the `scipy.sparse.csr_matrix`,
however if one always requires operations on dense matrices, one can always
return in `numpy.ndarray` (`'array'`) or `numpy.matrix` (`'dense'`).
midgap: float, optional
energy value that separates filled states (lower energy) from empty states (higher energy)
Returns
-------
the Huckel bond-order matrix object
"""
g = self.geometry
BO = sisl.Hamiltonian(g)
R = [0.1, 1.6]
for w, k in zip(self.mp.weight, self.mp.k):
# spin-up first
ev, evec = self.eigh(k=k, eigvals_only=False, spin=0)
ev -= midgap
idx = np.where(ev < 0.)[0]
bo = np.dot(np.conj(evec[:, idx]), evec[:, idx].T)
# add spin-down
ev, evec = self.eigh(k=k, eigvals_only=False, spin=1)
ev -= midgap
idx = np.where(ev < 0.)[0]
bo += np.dot(np.conj(evec[:, idx]), evec[:, idx].T)
for ix in (-1, 0, 1):
for iy in (-1, 0, 1):
for iz in (-1, 0, 1):
r = (ix, iy, iz)
phase = np.exp(-2.j * np.pi * np.dot(k, r))
for ia in g:
for ja in g.close_sc(ia, R=R, isc=r)[1]:
bor = bo[ia, ja] * phase
BO[ia, ja] += w * bor.real
# Add sigma bond at the end
for ia in g:
idx = g.close(ia, R=R)
BO[ia, idx[1]] += 1.
return BO.Hk(format=format) # Fold to Gamma
def test_tshs_missing_diagonal(sisl_tmp):
H1 = sisl.Hamiltonian(sisl.geom.graphene())
H1.construct(([0.1, 1.44], [0., -2.7]))
# remove diagonal component here
del H1[0, 0]
f1 = sisl_tmp('tmp1.TSHS', _dir)
H1.write(f1)
f2 = sisl_tmp('tmp2.TSHS', _dir)
H2 = sisl.get_sile(f1).read_hamiltonian()
H2.write(f2)
H3 = sisl.get_sile(f2).read_hamiltonian()
H1.finalize()
assert not H1._csr.spsame(H2._csr)
assert H2._csr.spsame(H3._csr)
assert np.allclose(H2._csr._D, H3._csr._D)
H1[0, 0] = 0.
H1.finalize()
assert H1._csr.spsame(H2._csr)
def test_lspgeom_sislconvert():
Hs = si.Hamiltonian(si.geom.graphene(),
orthogonal=True,
spin=si.Spin.POLARIZED)
dim = Hs.dim
assert dim == 2
Hs.set_nsc((7, 7, 1))
Hs.construct([[0.1, 1.5, 3, 5, 9], [-2, 1, 0.1, 0.01, 0.001]])
Hs = Hs.tile(4, 0).tile(4, 1)
Hs.finalize()
LHs = LSpGeom(Hs)
Hs2 = LHs.tosisl()
assert all(_allclose_csr(Hs.tocsr(i), Hs2.tocsr(i)) for i in range(dim))
assert Hs.geometry.equal(Hs2.geometry)
LHs += LHs * 0.3
Hs += Hs * 0.3
Hs2 = LHs.tosisl()
assert all(_allclose_csr(Hs.tocsr(i), Hs2.tocsr(i)) for i in range(dim))
assert Hs.geometry.equal(Hs2.geometry)
def test_gf_write_read_spin(sisl_tmp, sisl_system):
f = sisl_tmp('file.TSGF', _dir)
tb = sisl.Hamiltonian(sisl_system.gtb, spin=sisl.Spin('P'))
tb.construct([(0.1, 1.5), ([0.1, -0.1], [2.7, 1.6])])
bz = sisl.MonkhorstPack(tb, [3, 3, 1])
E = np.linspace(-2, 2, 3) + 1j * 1e-4
S = np.eye(len(tb), dtype=np.complex128)
gf = sisl.io.get_sile(f)
gf.write_header(bz, E)
for i, (ispin, write_hs, k, e) in enumerate(gf):
Hk = tb.Hk(k, spin=ispin, format='array')
if write_hs and i % 2 == 0:
gf.write_hamiltonian(Hk)
elif write_hs:
gf.write_hamiltonian(Hk, S)
gf.write_self_energy(S * e - Hk)
# Check it isn't opened
assert not gf._fortran_is_open()
nspin, no_u, k, E_file = gf.read_header()
assert nspin == 2
assert np.allclose(E, E_file)
assert np.allclose(k, bz.k)
for i, (ispin, write_hs, k, e) in enumerate(gf):
Hk = tb.Hk(k, spin=ispin, format='array')
if write_hs and i % 2 == 0:
Hk_file, _ = gf.read_hamiltonian()
elif write_hs:
Hk_file, Sk_file = gf.read_hamiltonian()
assert np.allclose(S, Sk_file)
assert np.allclose(Hk, Hk_file)
SE_file = gf.read_self_energy()
assert np.allclose(SE_file, S * e - Hk)
def test_tshs_spin_orbit_tshs2nc2tshs(sisl_tmp):
H1 = sisl.Hamiltonian(sisl.geom.graphene(), spin=sisl.Spin('SO'))
H1.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]]))
fdf_file = sisl_tmp('RUN.fdf', _dir)
f1 = sisl_tmp('tmp1.TSHS', _dir)
f2 = sisl_tmp('tmp1.nc', _dir)
H1.write(f1)
H1.finalize()
H2 = sisl.get_sile(f1).read_hamiltonian()
H2.write(f2)
H3 = sisl.get_sile(f2).read_hamiltonian()
open(fdf_file, 'w').writelines(["SystemLabel tmp1"])
fdf = sisl.get_sile(fdf_file)
assert np.allclose(
fdf.read_supercell(order='nc').cell,
fdf.read_supercell(order='TSHS').cell)
assert H1._csr.spsame(H2._csr)
assert np.allclose(H1._csr._D, H2._csr._D)
assert H1._csr.spsame(H3._csr)
assert np.allclose(H1._csr._D, H3._csr._D)
def dispatch(self, t=-2.7, a=1.42, orthogonal=False):
distance = self._obj.distance
da = 0.0005
R = (distance(0, a) + da, distance(1, a) + da)
def construct(H, ia, atoms, atoms_xyz=None):
idx_t01, rij_t01 = H.geometry.close(ia,
R=R,
atoms=atoms,
atoms_xyz=atoms_xyz,
ret_rij=True)
H[ia, idx_t01[0]] = 0.
H[ia, idx_t01[1]] = t * (a / rij_t01[1])**2
# Define the graphene lattice
C = si.Atom(6, si.AtomicOrbital(n=2, l=1, m=0, R=R[-1]))
graphene = si.geom.graphene(a, C, orthogonal=orthogonal)
# Define the Hamiltonian
H = si.Hamiltonian(graphene)
H.construct(construct)
return H
def init_func_and_attrs(self, request, siesta_test_files):
name = request.param
if name.startswith("siesta_PDOS_file"):
spin_type = name.split("_")[-1]
n_spin, filename = {
"unpolarized": (1, "SrTiO3.PDOS"),
"polarized": (2, "SrTiO3_polarized.PDOS"),
"noncollinear": (4, "SrTiO3_noncollinear.PDOS")
}[spin_type]
init_func = sisl.get_sile(siesta_test_files(filename)).plot
attrs = {
"na": 5,
"no": 72,
"n_spin": n_spin,
"species": ('Sr', 'Ti', 'O')
}
elif name.startswith("sisl_H"):
gr = sisl.geom.graphene()
H = sisl.Hamiltonian(gr)
H.construct([(0.1, 1.44), (0, -2.7)])
spin_type = name.split("_")[-1]
n_spin, H = {
"unpolarized": (1, H),
"polarized": (2, H.transform(spin=sisl.Spin.POLARIZED)),
"noncolinear": (4, H.transform(spin=sisl.Spin.NONCOLINEAR)),
"spinorbit": (4, H.transform(spin=sisl.Spin.SPINORBIT))
}[spin_type]
init_func = partial(H.plot.pdos, Erange=[-5, 5])
attrs = {"na": 2, "no": 2, "n_spin": n_spin, "species": ('C', )}
return init_func, attrs
def test_lspgeom_sameassisl():
Hs = si.Hamiltonian(si.geom.graphene(),
orthogonal=True,
spin=si.Spin.POLARIZED)
dim = Hs.dim
assert dim == 2
Hs.set_nsc((7, 7, 1))
Hs.construct([[0.1, 1.5, 3, 5, 9], [-2, 1, 0.1, 0.01, 0.001]])
Hs = Hs.tile(4, 0).tile(4, 1)
Hs.finalize()
LHs = LSpGeom(Hs)
HS2 = Hs + Hs
LHs2 = LHs + LHs
assert all(_allclose_csr(HS2.tocsr(i), LHs2[i]) for i in range(dim))
Hzero = Hs - Hs
LHszero = LHs - LHs
assert all(_allclose_csr(Hzero.tocsr(i), LHszero[i]) for i in range(dim))
Hzero.eliminate_zeros(atol=1e-3)
LHszero.eliminate_zeros(atol=1e-3)
assert all(_allclose_csr(Hzero.tocsr(i), LHszero[i]) for i in range(dim))
Hnz = Hs - 0.5 * Hs
Hnz2 = Hnz.copy()
LHsnz = LHs - 0.5 * LHs
LHsnz2 = LHsnz.copy()
assert all(_allclose_csr(Hnz.tocsr(i), LHsnz[i]) for i in range(dim))
Hnz.eliminate_zeros(atol=1e-2)
LHsnz.eliminate_zeros(atol=1e-2)
assert all(_allclose_csr(Hnz.tocsr(i), LHsnz[i]) for i in range(dim))
diff1 = Hnz2 - Hnz
diff2 = LHsnz2 - LHsnz
assert all(
_allclose_csr(diff1.tocsr(i), diff2[i], rtol=1e-10)
for i in range(dim))
g = geom.zgnr(W, atoms=C)
# Add another atom to have heterogeneous number of orbitals per atoms
C2 = sisl.Atom(6, orbitals=[pz])
G_C2 = sisl.Geometry(g.xyz[0], atoms=C2)
g = g.replace(0, G_C2)
# Identify index for atoms
idx = g.a2o(range(len(g)))
# Build U for each orbital in each atom
#U = np.zeros(g.no)
#U[idx] = 3.
# Build TB Hamiltonian, zeroes for non-pz orbitals
TBham = sisl.Hamiltonian(g, spin='polarized')
for ia in g:
ib = g.close(ia, R=[0, 1.42 + 0.1])
io_a = g.a2o(ia, all=True)
for iib in ib[1]:
io_b = g.a2o(iib, all=True)
TBham[io_a[0], io_b[0]] = -2.7
# HubbardHamiltonian object and converge
HH = HubbardHamiltonian(TBham, U=None, nkpt=[100, 1, 1])
HH.set_polarization([0], dn=[g.a2o(13)])
HH.converge(density.calc_n, print_info=True, tol=1e-10, steps=3)
# Print spin-densities difference compared to sing-orbital case
print(
'\n ** Difference between spin densities for single and multi-orbital cases **'
def sp2(ext_geom,
t1=2.7,
t2=0.2,
t3=0.18,
eB=3.,
eN=-3.,
s0=1.0,
s1=0,
s2=0,
s3=0,
dq=0,
dim=2):
""" Function to create a Tight Binding Hamiltoninan for sp2 Carbon systems
It takes advantage of the `sisl` class for building sparse Hamiltonian matrices,
`sisl.physics.Hamiltonian`
It obtains the Hamiltonian for ``ext_geom`` (which must be a `sisl.Geometry` instance)
with the parameters for first, second and third nearest neighbors (``t1``, ``t2``, ``t3``).
One can also use a non-orthogonal basis of atomic orbitals by passing the parameters for the
overlap matrix between first, second and third nearest neighbors (``s1``, ``s2``, ``s3``).
The function will also take into account the possible presence of Boron or Nitrogen atoms,
for which one would need to specify the on-site energy for those atoms (``eB`` and ``eN``)
Returns
-------
H: sisl.physics.Hamiltonian
tight-binding Hamiltonian for the sp2 structure of ``dim=2`` (for the two spin channels)
"""
# Determine pz sites
aux = []
sp3 = []
for ia, atom in enumerate(ext_geom.atoms.iter()):
# Append non C-type atoms in aux list
if atom.Z not in [5, 6, 7]:
aux.append(ia)
idx = ext_geom.close(ia, R=[0.1, 1.6])
if len(idx[1]) == 4: # Search for atoms with 4 neighbors
if atom.Z == 6:
sp3.append(ia)
# Remove all sites not carbon-type
pi_geom = ext_geom.remove(aux + sp3)
pi_geom.reduce()
# Iterate over atomic species to set initial charge
maxR = 20
r = np.linspace(0, maxR, 700)
# In Slater-type orbitals (Hydrogen-like atom solution), the radial function is ~exp(-Zr/2a)
# where a=0.529 \AA is the Bohr radius and Z is the atomic number.
# We use the effective nuclear charge instead, which for Carbon atoms is approximately Zeff~3.
func = np.exp(-3 * r)
for atom, _ in pi_geom.atoms.iter(True):
pz = sisl.AtomicOrbital('pz', (r, func), R=maxR, q0=atom.Z - 5 + dq)
atom.orbitals[0] = pz
# Construct Hamiltonian
if s1 != 0:
orthogonal = False
else:
orthogonal = True
H = sisl.Hamiltonian(pi_geom, orthogonal=orthogonal, dim=dim)
# Radii defining 1st, 2nd, and 3rd neighbors
R = [0.1, 1.6, 2.6, 3.1]
# Build hamiltonian for backbone
for ia in pi_geom:
idx = pi_geom.close(ia, R=R)
# NB: I found that ':' is necessary in the following lines, but I don't understand why...
if pi_geom.atoms[ia].Z == 5:
H[ia, ia, :] = eB # set onsite for B sites
elif pi_geom.atoms[ia].Z == 7:
H[ia, ia, :] = eN # set onsite for N sites
# set hoppings
H[ia, idx[1], :] = -t1
if t2 != 0:
H[ia, idx[2], :] = -t2
if t3 != 0:
H[ia, idx[3], :] = -t3
if not H.orthogonal:
H.S[ia, ia] = s0
H.S[ia, idx[1]] = s1
H.S[ia, idx[2]] = s2
H.S[ia, idx[3]] = s3
return H
def test_gf_write_read_direct(sisl_tmp, sisl_system):
f = sisl_tmp('file.TSGF', _dir)
tb = sisl.Hamiltonian(sisl_system.gtb, spin=sisl.Spin('P'))
tb.construct([(0.1, 1.5), ([0.1, -0.1], [2.7, 1.6])])
bz = sisl.MonkhorstPack(tb, [3, 3, 1])
E = np.linspace(-2, 2, 3) + 1j * 1e-4
S = np.eye(len(tb), dtype=np.complex128)
gf = sisl.io.get_sile(f)
gf.write_header(bz, E)
for i, (ispin, write_hs, k, e) in enumerate(gf):
Hk = tb.Hk(k, spin=ispin, format='array')
if write_hs and i % 2 == 0:
gf.write_hamiltonian(Hk)
elif write_hs:
gf.write_hamiltonian(Hk, S)
gf.write_self_energy(S * e - Hk)
# ensure it is not opened
assert not gf._fortran_is_open()
# First try from beginning
for e in [0, 1, E[1], 0, E[0]]:
ie = gf.Eindex(e)
SE1 = gf.self_energy(e, bz.k[2, :])
assert gf._state == 1
assert gf._ik == 2
assert gf._iE == ie
assert gf._ispin == 0
assert gf._is_read == 1
SE2 = gf.self_energy(e, bz.k[2, :], spin=1)
assert gf._state == 1
assert gf._ik == 2
assert gf._iE == ie
assert gf._ispin == 1
assert gf._is_read == 1
assert not np.allclose(SE1, SE2)
# In the middle we read some hamiltonians
H1, S1 = gf.HkSk(bz.k[2, :], spin=0)
assert gf._state == 0
assert gf._ik == 2
assert gf._iE == 0
assert gf._ispin == 0
assert gf._is_read == 1
assert np.allclose(S, S1)
H2, S1 = gf.HkSk(bz.k[2, :], spin=1)
assert gf._state == 0
assert gf._ik == 2
assert gf._iE == 0
assert gf._ispin == 1
assert gf._is_read == 1
assert np.allclose(S, S1)
assert not np.allclose(H1, H2)
assert not np.allclose(H1, SE1)
H2, S1 = gf.HkSk(bz.k[2, :], spin=0)
assert gf._state == 0
assert gf._ik == 2
assert gf._iE == 0
assert gf._ispin == 0
assert gf._is_read == 1
assert np.allclose(S, S1)
assert np.allclose(H1, H2)
# Now read self-energy
SE2 = gf.self_energy(e, bz.k[2, :], spin=0)
assert gf._state == 1
assert gf._ik == 2
assert gf._iE == ie
assert gf._ispin == 0
assert gf._is_read == 1
assert np.allclose(SE1, SE2)
def init_func_and_attrs(self, request, siesta_test_files):
name = request.param
if name.startswith("sisl_H"):
gr = sisl.geom.graphene()
H = sisl.Hamiltonian(gr)
H.construct([(0.1, 1.44), (0, -2.7)])
spin_type = name.split("_")[2]
n_spin, H = {
"unpolarized": (1, H),
"polarized": (2, H.transform(spin=sisl.Spin.POLARIZED)),
"noncolinear": (1, H.transform(spin=sisl.Spin.NONCOLINEAR)),
"spinorbit": (1, H.transform(spin=sisl.Spin.SPINORBIT))
}.get(spin_type)
n_states = 2
if H.spin.is_spinorbit or H.spin.is_noncolinear:
n_states *= 2
# Directly creating a BandStructure object
if name.endswith("jump"):
names = ["Gamma", "M", "M", "K"]
bz = sisl.BandStructure(H, [[0, 0, 0], [2 / 3, 1 / 3, 0], None,
[2 / 3, 1 / 3, 0], [1 / 2, 0, 0]],
6, names)
nk = 7
tickvals = [0., 1.70309799, 1.83083034, 2.68237934]
else:
names = ["Gamma", "M", "K"]
bz = sisl.BandStructure(
H, [[0, 0, 0], [2 / 3, 1 / 3, 0], [1 / 2, 0, 0]], 6, names)
nk = 6
tickvals = [0., 1.70309799, 2.55464699]
init_func = bz.plot.fatbands
attrs = {
"bands_shape":
(nk, n_spin, n_states) if H.spin.is_polarized else
(nk, n_states),
"weights_shape":
(n_spin, nk, n_states, 2) if H.spin.is_polarized else
(nk, n_states, 2),
"ticklabels":
names,
"tickvals":
tickvals,
"gap":
0,
"spin_texture":
not H.spin.is_diagonal,
"spin":
H.spin
}
elif name == "wfsx file":
# From a siesta bands.WFSX file
# Since there is no hamiltonian for bi2se3_3ql.fdf, we create a dummy one
wfsx = sisl.get_sile(siesta_test_files("bi2se3_3ql.bands.WFSX"))
geometry = sisl.get_sile(
siesta_test_files("bi2se3_3ql.fdf")).read_geometry()
geometry = sisl.Geometry(geometry.xyz, atoms=wfsx.read_basis())
H = sisl.Hamiltonian(geometry, dim=4)
init_func = partial(H.plot.fatbands,
wfsx_file=wfsx,
E0=-51.68,
entry_points_order=["wfsx file"])
attrs = {
"bands_shape": (16, 8),
"weights_shape": (16, 8, 195),
"ticklabels": None,
"tickvals": None,
"gap": 0.0575,
"spin_texture": False,
"spin": sisl.Spin("nc")
}
return init_func, attrs
import plotly.graph_objs as go
import numpy as np
import sisl
r = np.linspace(0, 3.5, 50)
f = np.exp(-r)
orb = sisl.AtomicOrbital('2pzZ', (r, f))
geom = sisl.geom.graphene(orthogonal=True, atoms=sisl.Atom(6, orb))
geom = geom.move([0, 0, 5])
H = sisl.Hamiltonian(geom)
H.construct([(0.1, 1.44), (0, -2.7)], )
def test_eigenstate_wf():
plot = H.eigenstate()[0].plot.wavefunction(geometry=H.geometry)
assert len(plot.data) > 0
assert isinstance(plot.data[0], go.Isosurface)
def test_hamiltonian_wf():
# Check if it works for 3D plots
plot = H.plot.wavefunction(2)
assert isinstance(plot.data[0], go.Isosurface)
# Check that setting plot geom to True adds data traces
plot.update_settings(plot_geom=False)
#final_H_pertb = sisl.Hamiltonian(fdf.read_geometry(), dtype = np.complex128)
##print(np.shape(H_perturbation[:,0,0].reshape((5022,1))))
##final_H_pertb = sparse.csr_matrix((H_perturbation[:,:,0].reshape(5022*5022*9,1), (H_perturbation[:,0,0].reshape((5022,1)),H_perturbation[0,:,0].reshape((5022*9,1)))), shape=(5022,5022*9))
#print(np.shape(final_H_pertb))
#final_H_pertb = final_H_pertb.fromsp(fdf.read_geometry(),test_csr)
#print(final_H_pertb)
#dH.write_delta(final_H_pertb, E = energies)#, K=[0,0,0])
# Let's jsut assume the general case in which there are no enegy and K dipendency.
multiE = '' # 'multiE'
multiK = '' # 'multiK'
dH = sisl.get_sile(
'{}/photocurrent/deltaH{}{}_{}.dH.nc'.format(path_wd, multiE, multiK,
bias), 'w')
final_H_pertb = sisl.Hamiltonian(fdf.read_geometry(), dtype=np.complex128)
#print(np.shape(H_perturbation[:,0,0].reshape((5022,1))))
#final_H_pertb = sparse.csr_matrix((H_perturbation[:,:,0].reshape(5022*5022*9,1), (H_perturbation[:,0,0].reshape((5022,1)),H_perturbation[0,:,0].reshape((5022*9,1)))), shape=(5022,5022*9))
print(np.shape(final_H_pertb))
print(fdf.read_geometry())
final_H_pertb = final_H_pertb.fromsp(fdf.read_geometry(), test_csr)
print(final_H_pertb)
## Energy and kpoint dependent perturbation Hamiltonian
#for energies in np.linspace(-0.1, photon_energy+0.1, 301):
##print('*********************'+str(energies)+'*********************')
#for kpoints in np.linspace(0, 0.5, 5):
##print('*********************'+str(kpoints)+'*********************')
#dH.write_delta(final_H_pertb, E = energies, k = [kpoints,0,0])
# Energy dependent perturbation Hamiltonian
"""
y0: center of channel
y: coordinates to apply the potential too
y_length: y0 - y_length / 2 -- y0 + y_length / 2 is the channel position
"""
tanhL = np.tanh((y - y0 - y_length * 0.5) / relax)
tanhR = np.tanh(-(y - y0 + y_length * 0.5) / relax)
return 0.5 * (tanhL + tanhR)
def potential(H, ia, idxs, idxs_xyz=None):
# Retrieve all atoms close to ia
idx = H.geometry.close(ia, R=[0.1, 1.44], idx=idxs, idx_xyz=idxs_xyz)
H[ia, idx[0]] = onsite_y(
H.geometry.center(what='cell')[1], H.geometry.xyz[idx[0], 1], 50, 5)
H[ia, idx[1]] = -2.7
graphene = si.geom.graphene(orthogonal=True).tile(200, 1)
H = si.Hamiltonian(graphene)
H.construct(potential)
# Extract the diagonal (on-site terms of the Hamiltonian)
diag = H.Hk().diagonal()
plt.plot(H.geometry.xyz[:, 1], diag)
plt.xlabel('y [Ang]')
plt.ylabel('Onsite [eV]')
plt.show()
def CAP(geometry, side, dz_CAP=30, write_xyz=True, zaxis=2):
# Determine orientation
if zaxis == 2:
xaxis, yaxis = 0, 1
elif zaxis == 0:
xaxis, yaxis = 1, 2
elif zaxis == 1:
xaxis, yaxis = 0, 2
# Natural units (see "http://superstringtheory.com/unitsa.html")
hbar = 1
m = 0.511e6 # eV
c = 2.62
print('\nSetting up CAP regions: {}'.format(side))
print('Width of absorbing walls = {} Angstrom'.format(dz_CAP))
Wmax = 100
dH_CAP = si.Hamiltonian(geometry, dtype='complex128')
CAP_list = []
### EDGES
if 'right' in side:
print('Setting at right')
z, y = geometry.xyz[:, xaxis], geometry.xyz[:, yaxis]
z2 = np.max(geometry.xyz[:, xaxis]) + 1.
z1 = z2 - dz_CAP
idx = np.where(np.logical_and(z1 <= z, z < z2))[0]
fz = (4 / (c**2)) * ((dz_CAP / (z2 - 2 * z1 + z[idx]))**2 +
(dz_CAP / (z2 - z[idx]))**2 - 2)
Wz = ((hbar**2) / (2 * m)) * (2 * np.pi / (dz_CAP / 2000))**2 * fz
orbs = dH_CAP.geom.a2o(
idx) # if you have just 1 orb per atom, then orb = ia
for orb, wz in zip(orbs, Wz):
dH_CAP[orb, orb] = complex(0, -wz)
CAP_list.append(idx)
#print(list2range_TBTblock(idx))
if 'left' in side:
print('Setting at left')
z, y = geometry.xyz[:, xaxis], geometry.xyz[:, yaxis]
z2 = np.min(geometry.xyz[:, xaxis]) - 1.
z1 = z2 + dz_CAP
idx = np.where(np.logical_and(z2 < z, z <= z1))[0]
fz = (4 / (c**2)) * ((dz_CAP / (z2 - 2 * z1 + z[idx]))**2 +
(dz_CAP / (z2 - z[idx]))**2 - 2)
Wz = ((hbar**2) / (2 * m)) * (2 * np.pi / (dz_CAP / 2000))**2 * fz
orbs = dH_CAP.geom.a2o(
idx) # if you have just 1 orb per atom, then orb = ia
for orb, wz in zip(orbs, Wz):
dH_CAP[orb, orb] = complex(0, -wz)
CAP_list.append(idx)
#print(list2range_TBTblock(idx))
if 'top' in side:
print('Setting at top')
z, y = geometry.xyz[:, xaxis], geometry.xyz[:, yaxis]
y2 = np.max(geometry.xyz[:, yaxis]) + 1.
y1 = y2 - dz_CAP
idx = np.where(np.logical_and(y1 <= y, y < y2))[0]
fz = (4 / (c**2)) * ((dz_CAP / (y2 - 2 * y1 + y[idx]))**2 +
(dz_CAP / (y2 - y[idx]))**2 - 2)
Wz = ((hbar**2) / (2 * m)) * (2 * np.pi / (dz_CAP / 2000))**2 * fz
orbs = dH_CAP.geom.a2o(
idx) # if you have just 1 orb per atom, then orb = ia
for orb, wz in zip(orbs, Wz):
dH_CAP[orb, orb] = complex(0, -wz)
CAP_list.append(idx)
#print(list2range_TBTblock(idx))
if 'bottom' in side:
print('Setting at bottom')
z, y = geometry.xyz[:, xaxis], geometry.xyz[:, yaxis]
y2 = np.min(geometry.xyz[:, yaxis]) - 1.
y1 = y2 + dz_CAP
idx = np.where(np.logical_and(y2 < y, y <= y1))[0]
fz = (4 / (c**2)) * ((dz_CAP / (y2 - 2 * y1 + y[idx]))**2 +
(dz_CAP / (y2 - y[idx]))**2 - 2)
Wz = ((hbar**2) / (2 * m)) * (2 * np.pi / (dz_CAP / 2000))**2 * fz
orbs = dH_CAP.geom.a2o(
idx) # if you have just 1 orb per atom, then orb = ia
for orb, wz in zip(orbs, Wz):
dH_CAP[orb, orb] = complex(0, -wz)
CAP_list.append(idx)
#print(list2range_TBTblock(idx))
CAP_list = np.concatenate(CAP_list).ravel().tolist()
if write_xyz:
# visualize CAP regions
visualize = geometry.copy()
visualize.atom[CAP_list] = si.Atom(8, R=[1.44])
visualize.write('CAP.xyz')
return dH_CAP
def init_func_and_attrs(self, request, siesta_test_files):
name = request.param
if name == "siesta_output":
# From a siesta .bands file
init_func = sisl.get_sile(siesta_test_files("SrTiO3.bands")).plot
attrs = {
"bands_shape": (150, 72),
"ticklabels": ('Gamma', 'X', 'M', 'Gamma', 'R', 'X'),
"tickvals":
[0.0, 0.429132, 0.858265, 1.465149, 2.208428, 2.815313],
"gap": 1.677,
"spin_texture": False,
"spin": sisl.Spin("")
}
elif name.startswith("sisl_H"):
gr = sisl.geom.graphene()
H = sisl.Hamiltonian(gr)
H.construct([(0.1, 1.44), (0, -2.7)])
spin_type = name.split("_")[-1]
n_spin, H = {
"unpolarized": (0, H),
"polarized": (2, H.transform(spin=sisl.Spin.POLARIZED)),
"noncolinear": (0, H.transform(spin=sisl.Spin.NONCOLINEAR)),
"spinorbit": (0, H.transform(spin=sisl.Spin.SPINORBIT))
}.get(spin_type)
n_states = 2
if not H.spin.is_diagonal:
n_states *= 2
# Let's create the same graphene bands plot using the hamiltonian
# from two different prespectives
if name.startswith("sisl_H_path"):
# Passing a list of points (as if we were interacting from a GUI)
path = [{
"active": True,
"x": x,
"y": y,
"z": z,
"divisions": 3,
"name": tick
} for tick, (x, y, z) in zip(
["Gamma", "M", "K"], [[0, 0, 0], [2 / 3, 1 /
3, 0], [1 / 2, 0, 0]])]
init_func = partial(H.plot.bands, band_structure=path)
else:
# Directly creating a BandStructure object
bz = sisl.BandStructure(
H, [[0, 0, 0], [2 / 3, 1 / 3, 0], [1 / 2, 0, 0]], 6,
["Gamma", "M", "K"])
init_func = bz.plot
attrs = {
"bands_shape": (6, n_spin, n_states) if n_spin != 0 else
(6, n_states),
"ticklabels": ["Gamma", "M", "K"],
"tickvals": [0., 1.70309799, 2.55464699],
"gap":
0,
"spin_texture":
not H.spin.is_diagonal,
"spin":
H.spin
}
return init_func, attrs
#!/usr/bin/env python
# This benchmark creates a very large graphene flake and uses construct
# to create it.
# This benchmark may be called using:
#
# python -m cProfile -o $0.profile $0
#
# and it may be post-processed using
#
# python stats.py $0.profile
#
import sys
import sisl
import numpy as np
if len(sys.argv) > 1:
N = int(sys.argv[1])
else:
N = 200
print("N = {}".format(N))
gr = sisl.geom.graphene(orthogonal=True).tile(N, 0).tile(N, 1)
H = sisl.Hamiltonian(gr)
H.construct([(0.1, 1.44), (0., -2.7)], method='cube', eta=True)
import sisl
graphene = sisl.geom.graphene()
H = sisl.Hamiltonian(graphene)
for ia, io in H:
idx = H.geometry.close(ia, R=[0.1, 1.43])
H[io, idx[0]] = 0.
H[io, idx[1]] = -2.7
print(H.eigh(k=[0., 0.5, 0.]))