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)
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)])
cf.plot(show=True)
#######################################################################
# "reorg": reorganisation,
# "T":temperature,
# "cortime":cTime}
#with qr.energy_units("1/cm"):
# sdLowFreq = qr.SpectralDensity(timeSD, paramsReng)
'''
# Over Damped Brownian Oscillaotr
params = {"ftype":"OverdampedBrownian",
"T":temperature,
"reorg":reorganisation,
"cortime":cTime}
with qr.energy_units('1/cm'):
sdLowFreq = qr.SpectralDensity(timeSD, params)
'''
# Silbey form of spec dens
sdLowFreq = db.get_SpectralDensity(timeSD, "Renger_JCP_2002")
# Adding the high freq modes
sdWend = db.get_SpectralDensity(timeSD, "Wendling_JPCB_104_2000_5825")
ax = sdLowFreq.axis
sdWend.axis = ax
sdTot = sdLowFreq + sdWend
cf = sdTot.get_CorrelationFunction(temperature=temperature, ta=timeSD)
if _show_:
with qr.energy_units("1/cm"):
sdTot.plot(show=True, axis=[0, 2000, 0.0, np.max(sdTot.data)])
cf.plot(show=True)
#######################################################################
# Creation of the aggregate ring
# -*- coding: utf-8 -*-
import numpy
from quantarhei.models.spectdens import SpectralDensityDB
#from quantarhei.models.spectdens import CorrelationFunctionDB
from quantarhei import SpectralDensity
from quantarhei import TimeAxis, energy_units
_show_plots_ = True
axis = TimeAxis(0.0, 10000, 1.0)
db = SpectralDensityDB(verbose=True)
sdw = db.get_SpectralDensity(axis, "Wendling_JPCB_104_2000_5825")
#sdw = db.get_SpectralDensity(axis, "Renger_JCP_2002")
params = dict(ftype="OverdampedBrownian", reorg=300.0, cortime=100.0)
with energy_units("1/cm"):
sdob = SpectralDensity(axis, params)
ax = sdw.axis
sdob.axis = ax
sd_tot = sdob + sdw
with energy_units("1/cm"):
if _show_plots_:
sd_tot.plot(axis=[0, 1300, 0.0, numpy.max(sd_tot.data)])
# here we get correlation function at a given temperature in K
# -*- coding: utf-8 -*-
import numpy
from quantarhei.models.spectdens import SpectralDensityDB
#from quantarhei.models.spectdens import CorrelationFunctionDB
from quantarhei import SpectralDensity
from quantarhei import TimeAxis, energy_units
axis = TimeAxis(0.0, 10000, 1.0)
db = SpectralDensityDB(verbose=True)
#sdw = db.get_SpectralDensity(axis, "Wendling_JPCB_104_2000_5825")
sdw = db.get_SpectralDensity(axis, "Renger_JCP_2002")
params = dict(ftype="OverdampedBrownian", reorg=300.0, cortime=100.0)
with energy_units("1/cm"):
sdob = SpectralDensity(axis, params)
ax = sdw.axis
sdob.axis = ax
sd_tot = sdob + sdw
with energy_units("1/cm"):
sd_tot.plot(axis=[0, 1300, 0.0, numpy.max(sd_tot.data)])
cf = sd_tot.get_CorrelationFunction(300.0)
print(db.get_status_string())
cf.plot()