def calculate_band_energy(self, band='d', atomtype=None, atomindex=None,
exclude=None, include=None):
if (atomtype is not None) and (atomindex is not None):
raise RuntimeError('atomtype and atomindex are mutually exclusive!')
if (atomtype is None) and (atomindex is None):
print 'Analyzing the %s-band for the whole system' % band.lower()
atomtype = 'all'
if (atomtype is not 'all') and (not self.pdos):
raise RuntimeError('Cannot analyze %s atom(s), PDOS data not found.' % atomtype)
atomlist = convert2list(atomtype)
excludelist = convert2list(exclude)
includelist = convert2list(include)
allowed_bands = ['s', 'p', 'd'] # List of allowed bands
nbands = len(band) # nbands is the number of bands to be analyzed
bandlist = list() # List of bands to be analyzed
for ban in band:
if (ban.lower() not in allowed_bands):
raise RuntimeError('Unknown band type: %s' % ban)
else:
bandlist.append(ban.lower())
statesum = 0.0 # stores the sum of the states
esum = 0.0 # stores the sum of the energy weighted by the number of states
if (atomtype == 'all'):
energy, dos = self.get_total_dos()
esum, statesum = self.calculate_weighted_average(energy, dos, band)
else:
if (not atomlist) and (not includelist):
raise RuntimeError('No atoms specified!')
elif (not atomlist) and (includelist):
dos = self.get_total_atom_dos(atomtype=None, exclude=excludelist,
include=includelist)
es, ss = self.calculate_weighted_average(dos, band)
esum += es
statesum += ss
else:
for atom in atomlist:
dos = self.get_total_atom_dos(atomtype=atom, exclude=excludelist,
include=includelist)
es, ss = self.calculate_weighted_average(dos, band)
esum += es
statesum += ss
# print 'Total:', esum, statesum
return esum / statesum
def __dos_integrate(self, band='d', atomtype=None, exclude=None,
include=None, erange=None, rank=0):
labels = {'s': 0, 'p': 1, 'd': 2}
spinlabels = {'s': [0, 1], 'p': [2, 3], 'd': [4, 5]}
allowed_bands = ['s', 'p', 'd'] # List of allowed bands
bandlist = list() # List of bands to be analyzed
if (self.spin):
totaldos = np.zeros((self.npoints, 6))
elif (not self.spin):
totaldos = np.zeros((self.npoints, 3))
dosband = np.zeros((self.npoints))
atomlist = convert2list(atomtype)
excludelist = convert2list(exclude)
includelist = convert2list(include)
for ban in band:
if (ban.lower() not in allowed_bands):
raise RuntimeError('Unknown band type: %s' % ban)
else:
bandlist.append(ban.lower())
# Here we get the totaldos for each atom in the system
for label in self.atom_labels:
for atom in atomlist:
if ((atom in label) or (label in includelist)) and (label not in excludelist):
totaldos += self.get_total_atom_dos(atomtype=atom,
exclude=excludelist,
include=includelist)
if (erange == None):
emin = self.energies[0]
emax = self.energies[-1]
elif (erange == 'fermi'):
emin = self.energies[0]
emax = 0.0
else:
emin = erange[0]
emax = erange[1]
energylist = list()
indexlist = list()
for n,e in enumerate(self.energies):
if (e > emin) and (e < emax):
energylist.append(e)
indexlist.append(n)
start = indexlist[0]
finish = indexlist[-1]
if (self.spin):
for b in band:
colup = spinlabels[b][0]
coldown = spinlabels[b][1]
dosband += (totaldos[:, colup] + totaldos[:, coldown])
elif (not self.spin):
for b in band:
col = labels[b]
dosband += totaldos[:, col]
if (rank == 0):
trimdos = dosband[start:finish+1]
elif (rank == 1):
trimdos = dosband[start:finish+1] * energylist
elif (rank == 2):
trimdos = dosband[start:finish+1] * energylist *energylist
else:
raise RuntimeError('Rank %i not recognized' % rank)
return integrate(grid=energylist, data=trimdos)
def dosplot(filename=None, energies=list(), dos=list(), plottype='chemist',
legend=list(), location=1, erange=list(), staterange=list(), add_plot=False):
"""
Wrapper for plotting the DOS with Matplotlib
For the legend location guide, see:
http://matplotlib.org/users/legend_guide.html#legend-location
"""
doslist = convert2list(dos)
legendlist = convert2list(legend)
if (len(doslist) != len(legendlist)):
print 'Number of DOS: ', len(doslist)
print 'Number of legends: ', len(legendlist)
raise RuntimeError('Number of legends does not match number of lines')
if (plottype == 'chemist'):
x = energies
plt.xlabel('Energy (eV)')
plt.ylabel('States (ab. units)')
plotlist = list()
for i in range(len(doslist)):
tmp = plt.plot(x, doslist[i], label=legendlist[i])
plotlist.append(tmp)
if (erange):
plt.xlim(erange)
minimum = erange[0]
maximum = erange[1]
else:
minimum = math.ceil(energies.min())
maximum = math.ceil(energies.max())
if (staterange):
plt.ylim(staterange)
ticks = np.arange(minimum, maximum+1, 2)
plt.xticks(ticks)
elif (plottype == 'physicist'):
y = energies
plt.xlabel('States (ab. units)')
plt.ylabel('Energy (eV)')
plotlist = list()
for i in range(len(doslist)):
tmp = plt.plot(doslist[i], y, label=legendlist[i])
plotlist.append(tmp)
if (erange):
plt.ylim(erange)
if (staterange):
plt.xlim(staterange)
plt.legend(loc=location)
plt.savefig(filename)
if (not add_plot):
plt.close()
def get_band_width(self, band='d', atomtype=None, exclude=None,
include=None, erange=None):
# Yes I'm lazy, sue me.
labels = {'s': 0, 'p': 1, 'd': 2}
spinlabels = {'s': [0, 1], 'p': [2, 3], 'd': [4, 5]}
allowed_bands = ['s', 'p', 'd'] # List of allowed bands
bandlist = list() # List of bands to be analyzed
if (self.spin):
totaldos = np.zeros((self.npoints, 6))
elif (not self.spin):
totaldos = np.zeros((self.npoints, 3))
dosband = np.zeros((self.npoints))
atomlist = convert2list(atomtype)
excludelist = convert2list(exclude)
includelist = convert2list(include)
for ban in band:
if (ban.lower() not in allowed_bands):
raise RuntimeError('Unknown band type: %s' % ban)
else:
bandlist.append(ban.lower())
# Here we get the totaldos for each atom in the system
for label in self.atom_labels:
for atom in atomlist:
if ((atom in label) or (label in includelist)) and (label not in excludelist):
totaldos += self.get_total_atom_dos(atomtype=atom,
exclude=excludelist,
include=includelist)
if (erange == None):
# print 'Integrating over whole range up to the Fermi level.'
emin = self.energies[0]
emax = 0.0
elif (erange[1] == 'fermi'):
emin = erange[0]
emax = 0.0
else:
emin = erange[0]
emax = erange[1]
energylist = list()
indexlist = list()
for n,e in enumerate(self.energies):
if (e > emin) and (e < emax):
energylist.append(e)
indexlist.append(n)
start = indexlist[0]
finish = indexlist[-1]
if (self.spin):
for b in band:
colup = spinlabels[b][0]
coldown = spinlabels[b][1]
dosband += (totaldos[:, colup] + totaldos[:, coldown])
elif (not self.spin):
for b in band:
col = labels[b]
dosband += totaldos[:, col]
trimdos = dosband[start:finish+1] * energylist * energylist
filling = self.get_band_filling(band=band, atomtype=atomtype,
include=include, exclude=exclude, erange=erange)
return math.sqrt(integrate(grid=energylist, data=trimdos) / filling)
