def plot_exciton_spectrum(en, T, M, broadening=0.005, units="nm"):
"""
plot absorption and circular dichroism spectra on top of each other
Parameters
----------
en: numpy array with shape (Nst), excitation energies in Hartree
T : numpy array with shape (3,Nst), electric transition dipoles
M : numpy array with shape (3,Nst), magnetic transition dipoles
"""
# oscillator strengths and rotational strength
nst = len(en)
f = np.zeros(nst)
R = np.zeros(nst)
angleEM = np.zeros(nst)
for i in range(0, nst):
f[i] = 2.0/3.0 * en[i] * np.dot(T[:,i].conjugate(), T[:,i])
# Im{ T_(0->i) * M[i->0] }
R[i] = np.dot(T[:,i], M[:,i])
import matplotlib.pyplot as plt
from DFTB.Analyse.absorption_spectrum import broadened_spectrum, convert_energy
ens, ab_spec = broadened_spectrum(en, f, broadening)
ens, cd_spec = broadened_spectrum(en, R, broadening)
ax_cd = plt.subplot(211)
ax_ab = plt.subplot(212, sharex = ax_cd)
# convert energies from Hartree to nm
ens = convert_energy(ens, "Hartree", units)
fs = 18.0 # fontsize
ax_cd.set_xlabel("Energy / %s" % units, fontsize=fs)
# circular dichroism spectrum
ax_cd.plot(ens, cd_spec)
ax_cd.set_ylabel("Rotational Strength / arb. units", fontsize=fs)
# absorption spectrum
ax_ab.plot(ens, ab_spec)
ax_cd.set_ylabel("Oscillator Strength / arb. units", fontsize=fs)
plt.show()
def plotDOS(self):
self.figDOS.clf()
ax = self.figDOS.add_subplot(111)
units = self.energyUnits.itemText(self.energyUnits.currentIndex())
broadening = abs(float(self.broadening.text()))
ax.set_title("Density of States (DOS)")
ax.set_xlabel("Kohn-Sham Energy / %s" % units, fontsize=15)
ax.set_ylabel("DOS / arbitrary units", fontsize=15)
ens = self.tddftb.dftb2.getKSEnergies()
dos = 1.0 * np.ones(ens.shape)
# stick spectrum
ens_out = convert_energy(ens, "Hartree", units)
ax.vlines(ens_out,
np.zeros(ens_out.shape),
dos,
lw=2,
color="black",
picker=5)
# selected states are highlighted
selected = self.tableMOs.selectionModel().selectedRows()
for s in selected:
i = s.row()
ax.vlines(ens_out[i], [0.0], dos[i], lw=3, color="green")
ax.text(ens_out[i], dos[i], "%s %s" % (i + 1, self.mo_names[i]))
def onpick(event):
self.tableMOs.setCurrentCell(event.ind[0], 0)
self.figDOS.canvas.mpl_connect('pick_event', onpick)
if broadening > 0.0:
ens_broadened, spec = broadened_spectrum(ens, dos, broadening)
ens_broadened_out = convert_energy(ens_broadened, "Hartree", units)
scale = spec.max() / dos.max() / 1.1
x, y = ens_broadened_out, spec / scale
ax.plot(x, y, lw=1, color="blue")
x_occ = x[x <= ens_out[self.H**O]]
y_occ = y[x <= ens_out[self.H**O]]
x_virt = x[x >= ens_out[self.LUMO]]
y_virt = y[x >= ens_out[self.LUMO]]
ax.fill_between(x_occ, 0, y_occ, alpha=0.5, color="blue")
ax.fill_between(x_virt, 0, y_virt, alpha=0.5, color="red")
ax.annotate('',
xy=(ens_out[self.H**O], 1.1),
xycoords='data',
xytext=(ens_out[self.LUMO], 1.1),
textcoords='data',
arrowprops={'arrowstyle': '<->'})
ax.annotate(
'gap = %4.3f' % (ens_out[self.LUMO] - ens_out[self.H**O]),
xy=((ens_out[self.H**O] + ens_out[self.LUMO]) / 2.0, 1.1),
xycoords='data',
xytext=(0, 5),
textcoords='offset points')
self.canvasDOS.draw()
self.showMullikenCharges()
if len(selected) > 0:
i = selected[0].row()
self.moLabel.setText("Molecular Orbital: %s %s" %
(i + 1, self.mo_names[i]))
if i in self.mo_cubes:
mo_cube = self.mo_cubes[i]
self.molecularOrbitalViewer.setCubes([mo_cube])
else:
print("No cube for molecular orbital %d" % (i + 1))
def plotSpectrum(self):
self.figSpectrum.clf()
ax = self.figSpectrum.add_subplot(111)
units = self.energyUnits.itemText(self.energyUnits.currentIndex())
broadening = abs(float(self.broadening.text()))
ax.set_title("Absorption Spectrum")
ax.set_xlabel("Excitation Energy / %s" % units, fontsize=15)
ax.set_ylabel("Oscillator strength", fontsize=15)
ens = self.tddftb.Omega
osz = self.tddftb.oscillator_strength
# stick spectrum
ens_out = convert_energy(ens, "Hartree", units)
ax.vlines(ens_out,
np.zeros(ens_out.shape),
osz,
lw=2,
color="black",
picker=5)
# selected states are highlighted
selected = self.tableStates.selectionModel().selectedRows()
for s in selected:
I = s.row()
ax.vlines(ens_out[I], [0.0], osz[I], lw=3, color="green")
ax.text(
ens_out[I], osz[I], "%s (%s$_{%d}$)" %
(self.tddftb.Irreps[I], self.tddftb.multiplicity, I + 1))
def onpick(event):
self.tableStates.setCurrentCell(event.ind[0], 0)
self.figSpectrum.canvas.mpl_connect('pick_event', onpick)
if broadening > 0.0:
ens_broadened, spec = broadened_spectrum(ens, osz, broadening)
ens_broadened_out = convert_energy(ens_broadened, "Hartree", units)
scale = spec.max() / osz.max() / 1.1
ax.plot(ens_broadened_out, spec / scale, lw=1, color="blue")
self.canvasSpectrum.draw()
if len(selected) > 0:
I = selected[0].row()
self.tdenseLabel.setText(
"Excited State: %s (%s%d)" %
(self.tddftb.Irreps[I], self.tddftb.multiplicity, I + 1))
self.showPartialCharges(I)
if I in self.tdense_cubes:
tdense_cube = self.tdense_cubes[I]
self.transitionDensityViewer.setCubes([tdense_cube])
difdense_cube = self.difdense_cubes[I]
self.differenceDensityViewer.setCubes([difdense_cube])
else:
print(
"No cube for transition and difference density of state %d"
% (I + 1))
# transition densities in occ-virt plane
self.plotExcitationCoefficients2D(I)
self.canvasExvec.draw()