def read_energy_density_matrix(self, **kwargs):
""" Returns the energy density matrix from the siesta.DM file """
# Now read the sizes used...
spin, no, nsc, nnz = _siesta.read_tsde_sizes(self.file)
_bin_check(self, 'read_energy_density_matrix',
'could not read energy density matrix sizes.')
ncol, col, dEDM = _siesta.read_tsde_edm(self.file, spin, no, nsc, nnz)
_bin_check(self, 'read_energy_density_matrix',
'could not read energy density matrix.')
# Try and immediately attach a geometry
geom = kwargs.get('geometry', kwargs.get('geom', None))
if geom is None:
# We truly, have no clue,
# Just generate a boxed system
xyz = [[x, 0, 0] for x in range(no)]
sc = SuperCell([no, 1, 1], nsc=nsc)
geom = Geometry(xyz, Atom(1), sc=sc)
if nsc[0] != 0 and np.any(geom.nsc != nsc):
# We have to update the number of supercells!
geom.set_nsc(nsc)
if geom.no != no:
raise SileError(
str(self) + '.read_energy_density_matrix could '
'not use the passed geometry as the number of atoms or orbitals '
'is inconsistent with DM file.')
# Create the energy density matrix container
EDM = EnergyDensityMatrix(geom,
spin,
nnzpr=1,
dtype=np.float64,
orthogonal=False)
# Create the new sparse matrix
EDM._csr.ncol = ncol.astype(np.int32, copy=False)
EDM._csr.ptr = np.insert(np.cumsum(ncol, dtype=np.int32), 0, 0)
# Correct fortran indices
EDM._csr.col = col.astype(np.int32, copy=False) - 1
EDM._csr._nnz = len(col)
EDM._csr._D = np.empty([nnz, spin + 1], np.float64)
EDM._csr._D[:, :spin] = dEDM[:, :]
# EDM file does not contain overlap matrix... so neglect it for now.
EDM._csr._D[:, spin] = 0.
# Convert the supercells to sisl supercells
if nsc[0] != 0 or geom.no_s >= col.max():
_csr_from_siesta(geom, EDM._csr)
else:
warn(
str(self) + '.read_energy_density_matrix may '
'result in a wrong sparse pattern!')
return EDM
def read_energy_density_matrix(self, **kwargs):
""" Returns the energy density matrix from the siesta.DM file """
# Now read the sizes used...
spin, no, nnz = _siesta.read_tsde_sizes(self.file)
ncol, col, dEDM = _siesta.read_tsde_edm(self.file, spin, no, nnz)
# Try and immediately attach a geometry
geom = kwargs.get('geometry', kwargs.get('geom', None))
if geom is None:
# We truly, have no clue,
# Just generate a boxed system
xyz = [[x, 0, 0] for x in range(no)]
geom = Geometry(xyz, Atom(1), sc=[no, 1, 1])
if geom.no != no:
raise ValueError(
"Reading EDM files requires the input geometry to have the "
"correct number of orbitals.")
# Create the energy density matrix container
EDM = EnergyDensityMatrix(geom,
spin,
nnzpr=1,
dtype=np.float32,
orthogonal=False)
# Create the new sparse matrix
EDM._csr.ncol = ncol.astype(np.int32, copy=False)
EDM._csr.ptr = np.insert(np.cumsum(ncol, dtype=np.int32), 0, 0)
# Correct fortran indices
EDM._csr.col = col.astype(np.int32, copy=False) - 1
EDM._csr._nnz = len(col)
EDM._csr._D = np.empty([nnz, spin + 1], np.float32)
EDM._csr._D[:, :spin] = dEDM[:, :]
# EDM file does not contain overlap matrix... so neglect it for now.
EDM._csr._D[:, spin] = 0.
return EDM