def set_cor_func(for_agg, params, ax_len = 10000):
ax_length = ax_len
# Needs to have small step for the dynamics to converge
t_ax_sd = qr.TimeAxis(0.0, ax_length, 1)
db = SpectralDensityDB()
# Parameters for spectral density. ODBO, Renger or Silbey
params = params
with qr.energy_units('1/cm'):
sd_low_freq = qr.SpectralDensity(t_ax_sd, params)
reorg = qr.convert(sd_low_freq.measure_reorganization_energy(), "int", "1/cm")
print("spectral density reorg -", reorg)
# Adding the high freq modes
sd_high_freq = db.get_SpectralDensity(t_ax_sd, "Wendling_JPCB_104_2000_5825")
ax = sd_low_freq.axis
sd_high_freq.axis = ax
sd_tot = sd_low_freq + sd_high_freq
cf = sd_tot.get_CorrelationFunction(temperature=params['T'], ta=t_ax_sd)
# Assigning the correlation function to the list of molecules
for mol in for_agg:
mol.set_transition_environment((0,1),cf)
def assign_spec_dens(self, sd_type = 'OverdampedBrownian', high_freq = True):
t_ax_sd = qr.TimeAxis(0.0, 10000, 1)
db = SpectralDensityDB()
# Parameters for spectral density. ODBO, Renger or Silbey
params = {
"ftype": sd_type,
"alternative_form": True,
"reorg": self.reorg,
"T": self.temp,
"cortime": self.cor_time
}
with qr.energy_units('1/cm'):
sd_low_freq = qr.SpectralDensity(t_ax_sd, params)
if high_freq:
# Adding the high freq modes
sd_high_freq = db.get_SpectralDensity(t_ax_sd, "Wendling_JPCB_104_2000_5825")
ax = sd_low_freq.axis
sd_high_freq.axis = ax
sd_tot = sd_low_freq + sd_high_freq
cf = sd_tot.get_CorrelationFunction(temperature=self.temp, ta=t_ax_sd)
# Assigning the correlation function to the list of molecules
else:
cf = sd_low_freq.get_CorrelationFunction(temperature=self.temp, ta=t_ax_sd)
for mol in self.mol_list:
mol.set_transition_environment((0,1),cf)
# Needs to have small step for the dynamics to converge
t_ax_sd = qr.TimeAxis(0.0, 10000, 1)
db = SpectralDensityDB()
# Parameters for spectral density. ODBO, Renger or Silbey
params = {
"ftype": "OverdampedBrownian",
#"ftype": "B777",
"alternative_form": True,
"reorg": reorganisation,
"T": temperature,
"cortime": cor_time
}
with qr.energy_units('1/cm'):
sd_low_freq = qr.SpectralDensity(t_ax_sd, params)
# Adding the high freq modes
sd_high_freq = db.get_SpectralDensity(t_ax_sd, "Wendling_JPCB_104_2000_5825")
ax = sd_low_freq.axis
sd_high_freq.axis = ax
sd_tot = sd_low_freq + sd_high_freq
cf = sd_tot.get_CorrelationFunction(temperature=temperature, ta=t_ax_sd)
# Assigning the correlation function to the list of molecules
for mol in for_agg:
mol.set_transition_environment((0, 1), cf)
if _test_:
with qr.energy_units("1/cm"):
sd_tot.plot(show=True, axis=[0, 2000, 0.0, np.max(sd_tot.data)])