def read_overlap(self, **kwargs):
""" Returns the overlap matrix from the TranSiesta file """
tshs_g = self.read_geometry()
geom = _geometry_align(tshs_g, kwargs.get('geometry', tshs_g),
self.__class__, 'read_overlap')
# read the sizes used...
sizes = _siesta.read_tshs_sizes(self.file)
_bin_check(self, 'read_overlap', 'could not read sizes.')
isc = _siesta.read_tshs_cell(self.file, sizes[3])[2].T
_bin_check(self, 'read_overlap', 'could not read cell.')
no = sizes[2]
nnz = sizes[4]
ncol, col, dS = _siesta.read_tshs_s(self.file, no, nnz)
_bin_check(self, 'read_overlap', 'could not read overlap matrix.')
# Create the Hamiltonian container
S = Overlap(geom, nnzpr=1)
# Create the new sparse matrix
S._csr.ncol = ncol.astype(np.int32, copy=False)
S._csr.ptr = np.insert(np.cumsum(ncol, dtype=np.int32), 0, 0)
# Correct fortran indices
S._csr.col = col.astype(np.int32, copy=False) - 1
S._csr._nnz = len(col)
S._csr._D = _a.emptyd([nnz, 1])
S._csr._D[:, 0] = dS[:]
# Convert to sisl supercell
_csr_from_sc_off(S.geometry, isc, S._csr)
return S
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])
n = 60
rf = np.linspace(0, bond * 1.01, n)
rf = (rf, rf)
orb = SphericalOrbital(1, rf, 2.)
C = Atom(6, orb.toAtomicOrbital())
self.g = Geometry(np.array([[0., 0., 0.],
[1., 0., 0.]], np.float64) * bond,
atoms=C, sc=self.sc)
self.S = Overlap(self.g)
def read_overlap(self, **kwargs):
""" Returns the overlap matrix from the siesta.HSX file """
# Now read the sizes used...
Gamma, spin, no, no_s, nnz = _siesta.read_hsx_sizes(self.file)
_bin_check(self, 'read_overlap',
'could not read overlap matrix sizes.')
ncol, col, dS = _siesta.read_hsx_s(self.file, Gamma, spin, no, no_s,
nnz)
_bin_check(self, 'read_overlap', 'could not read overlap matrix.')
geom = kwargs.get('geometry', kwargs.get('geom', None))
if geom is None:
warn(self.__class__.__name__ +
".read_overlap requires input geometry to assign S")
if geom.no != no:
raise SileError(
str(self) + '.read_overlap could not use the '
'passed geometry as the number of atoms or orbitals is '
'inconsistent with HSX file.')
# Create the Hamiltonian container
S = Overlap(geom, nnzpr=1)
# Create the new sparse matrix
S._csr.ncol = ncol.astype(np.int32, copy=False)
S._csr.ptr = np.insert(np.cumsum(ncol, dtype=np.int32), 0, 0)
# Correct fortran indices
S._csr.col = col.astype(np.int32, copy=False) - 1
S._csr._nnz = len(col)
S._csr._D = _a.emptyf([nnz, 1])
S._csr._D[:, 0] = dS[:]
# Convert the supercells to sisl supercells
if no_s // no == np.product(geom.nsc):
_csr_from_siesta(geom, S._csr)
return S
def test_fromsp(self, setup):
S = setup.S.copy()
csr = S.tocsr()
S2 = Overlap.fromsp(S.geometry, csr)
assert np.allclose(csr.data, S2.tocsr().data)