def read_basis(self):
""" Returns data associated with the ion.xml file """
# Get the element-tree
ET = ElementTree(None, self.file)
root = ET.getroot()
# Get number of orbitals
label = root.find('label').text.strip()
Z = int(root.find('z').text) # atomic number
mass = float(root.find('mass').text)
# Read in the PAO's
paos = root.find('paos')
# Now loop over all orbitals
orbital = []
# All orbital data
Bohr2Ang = unit_convert('Bohr', 'Ang')
for orb in paos:
n = int(orb.get('n'))
l = int(orb.get('l'))
z = int(orb.get('z')) # zeta
q0 = float(orb.get('population'))
P = not int(orb.get('ispol')) == 0
# Radial components
rad = orb.find('radfunc')
npts = int(rad.find('npts').text)
# Grid spacing in Bohr (conversion is done later
# because the normalization is easier)
delta = float(rad.find('delta').text)
# Read in data to a list
dat = list(map(float, rad.find('data').text.split()))
# Since the readed data has fewer significant digits we
# might as well re-create the table of the radial component.
r = aranged(npts) * delta
# To get it per Ang**3
# TODO, check that this is correct.
# The fact that we have to have it normalized means that we need
# to convert psi /sqrt(Bohr**3) -> /sqrt(Ang**3)
# \int psi^\dagger psi == 1
psi = arrayd(dat[1::2]) * r**l / Bohr2Ang**(3. / 2.)
# Create the sphericalorbital and then the atomicorbital
sorb = SphericalOrbital(l, (r * Bohr2Ang, psi), q0)
# This will be -l:l (this is the way siesta does it)
orbital.extend(sorb.toAtomicOrbital(n=n, Z=z, P=P))
# Now create the atom and return
return Atom(Z, orbital, mass=mass, tag=label)
def read_data(self, as_dataarray=False):
r""" Returns data associated with the PDOS file
For spin-polarized calculations the returned values are up/down, orbitals, energy.
For non-collinear calculations the returned values are sum/x/y/z, orbitals, energy.
Parameters
----------
as_dataarray: bool, optional
If True the returned PDOS is a `xarray.DataArray` with energy, spin
and orbital information as coordinates in the data.
The geometry, unit and Fermi level are stored as attributes in the
DataArray.
Returns
-------
geom : Geometry instance with positions, atoms and orbitals. The
orbitals of these atoms are `AtomicOrbital` instances.
E : the energies at which the PDOS has been evaluated at (if the Fermi-level is present the energies
are shifted to :math:`E - E_F = 0`, this will *only* be done from Siesta 4.0.2 and later).
PDOS : an array of DOS, for non-polarized calculations it has dimension ``(atom.no, len(E))``,
else it has dimension ``(nspin, atom.no, len(E))``.
DataArray : if `as_dataarray` is True, only this data array is returned, in this case
all data can be post-processed using the `xarray` selection routines.
"""
# Get the element-tree
ET = ElementTree('pdos', self.file)
root = ET.getroot()
# Get number of orbitals
nspin = int(root.find('nspin').text)
# Try and find the fermi-level
Ef = root.find('fermi_energy')
E = arrayd(list(map(float, root.find('energy_values').text.split())))
if Ef is not None:
Ef = float(Ef.text)
E -= Ef
ne = len(E)
# All coordinate, atoms and species data
xyz = []
atoms = []
atom_species = []
def ensure_size(ia):
while len(atom_species) <= ia:
atom_species.append(None)
xyz.append(None)
def ensure_size_orb(ia, i):
while len(atoms) <= ia:
atoms.append([])
while len(atoms[ia]) <= i:
atoms[ia].append(None)
if nspin == 4:
def process(D):
tmp = np.empty(D.shape[0], D.dtype)
tmp[:] = D[:, 3]
D[:, 3] = D[:, 0] - D[:, 1]
D[:, 0] = D[:, 0] + D[:, 1]
D[:, 1] = D[:, 2]
D[:, 2] = tmp[:]
return D
else:
def process(D):
return D
if as_dataarray:
import xarray as xr
if nspin == 1:
spin = ['sum']
elif nspin == 2:
spin = ['up', 'down']
elif nspin == 4:
spin = ['sum', 'x', 'y' 'z']
# Dimensions of the PDOS data-array
dims = ['E', 'spin', 'n', 'l', 'm', 'zeta', 'polarization']
shape = (ne, nspin, 1, 1, 1, 1, 1)
def to(o, DOS):
# Coordinates for this dataarray
coords = [E, spin, [o.n], [o.l], [o.m], [o.Z], [o.P]]
return xr.DataArray(data=process(DOS).reshape(shape),
dims=dims,
coords=coords,
name='PDOS')
else:
def to(o, DOS):
return process(DOS)
D = []
for orb in root.findall('orbital'):
# Short-hand function to retrieve integers for the attributes
def oi(name):
return int(orb.get(name))
# Get indices
ia = oi('atom_index') - 1
i = oi('index') - 1
species = orb.get('species')
# Create the atomic orbital
try:
Z = oi('Z')
except:
try:
Z = PeriodicTable().Z(species)
except:
# Unknown
Z = -1
try:
P = orb.get('P') == 'true'
except:
P = False
ensure_size(ia)
xyz[ia] = list(map(float, orb.get('position').split()))
atom_species[ia] = Z
# Construct the atomic orbital
O = AtomicOrbital(n=oi('n'), l=oi('l'), m=oi('m'), Z=oi('z'), P=P)
# We know that the index is far too high. However,
# this ensures a consecutive orbital
ensure_size_orb(ia, i)
atoms[ia][i] = O
# it is formed like : spin-1, spin-2 (however already in eV)
DOS = arrayd(list(map(float,
orb.find('data').text.split()))).reshape(
-1, nspin)
if as_dataarray:
if len(D) == 0:
D = to(O, DOS)
else:
D = D.combine_first(to(O, DOS))
else:
D.append(process(DOS))
# Now we need to parse the data
# First reduce the atom
atoms = [[o for o in a if o] for a in atoms]
atoms = Atoms([Atom(Z, os) for Z, os in zip(atom_species, atoms)])
geom = Geometry(arrayd(xyz) * Bohr2Ang, atoms)
if as_dataarray:
# Add attributes
D.attrs['geometry'] = geom
D.attrs['units'] = '1/eV'
if Ef is None:
D.attrs['Ef'] = 'Unknown'
else:
D.attrs['Ef'] = Ef
return D
return geom, E, np.moveaxis(np.stack(D, axis=0), 2, 0)
