def dos(self):
energies = self.dos_total['energies'] - self.fermi
total = []
for ispin in self.dos_total:
if ispin == 'energies':
continue
total.append(self.dos_total[ispin])
# total = np.array(total).T
return DensityOfStates(
energies=energies,
total=total,
projected=self.dos_projected,
interpolation_factor=self.dos_interpolation_factor)
def dos_parametric(self, atoms=None, orbitals=None, spin=None, title=None):
"""
This function sums over the list of atoms and orbitals given
for example dos_paramateric(atoms=[0,1,2],orbitals=[1,2,3],spin=[0,1])
will sum all the projections of atoms 0,1,2 and all the orbitals of 1,2,3 (px,py,pz)
and return separatly for the 2 spins as a DensityOfStates object from pychemia.visual.DensityofStates
:param atoms: list of atom index needed to be sumed over. count from zero with the same
order as POSCAR
:param orbitals: list of orbitals needed to be sumed over
| s || py || pz || px || dxy || dyz || dz2 || dxz ||x2-y2||
| 0 || 1 || 2 || 3 || 4 || 5 || 6 || 7 || 8 ||
:param spin: which spins to be included. count from 0
There are no sum over spins
"""
projected = self.dos_projected
dos_projected, labelsInfo = self._get_dos_projected()
self.availiableOrbitals = list(labelsInfo.keys())
self.availiableOrbitals.pop(0)
if atoms == None:
atoms = arange(self.nions, dtype=int)
if spin == None:
spin = [0, 1]
if orbitals == None:
orbitals = arange((len(projected[0].labels) - 1) // 2, dtype=int)
if title == None:
title = 'Sum'
orbitals = array(orbitals)
if len(spin) == 2:
labels = ['Energy', 'Spin-Up', 'Spin-Down']
new_orbitals = []
for ispin in spin:
new_orbitals.append(
list(orbitals + ispin *
(len(projected[0].labels) - 1) // 2))
orbitals = new_orbitals
else:
for x in orbitals:
if (x + 1 > (len(projected[0].labels) - 1) // 2):
print('listed wrong amount of orbitals')
print('Only use one or more of the following ' + str(
arange((len(projected[0].labels) - 1) //
2, dtype=int)))
print('Only use one or more of the following ' + str(
arange((len(projected[0].labels) - 1) //
2, dtype=int)))
print('They correspond to the following orbitals : ' +
str(self.availiableOrbitals))
print('Again do not trust the plot that was just produced')
if spin[0] == 0:
labels = ['Energy', 'Spin-Up']
elif spin[0] == 1:
labels = ['Energy', 'Spin-Down']
ret = zeros(shape=(len(projected[0].energies), len(spin) + 1))
ret[:, 0] = projected[0].energies
for iatom in atoms:
if len(spin) == 2:
ret[:, 1:] += self.dos_projected[iatom].values[:,
orbitals].sum(
axis=2)
elif len(spin) == 1:
ret[:, 1] += self.dos_projected[iatom].values[:, orbitals].sum(
axis=1)
return DensityOfStates(table=ret, title=title, labels=labels)