def calcTwoD(loopNum):
''' Caculates a 2d spectrum for both perpendicular and parael lasers
using aceto bands and accurate lineshapes'''
container = []
agg = qr.Aggregate(molecules=forAggregate)
with qr.energy_units('1/cm'):
for i in range(len(forAggregate)):
agg.monomers[i].set_energy(1, random.gauss(energy, staticDis))
agg.set_coupling_by_dipole_dipole(epsr=1.21)
agg.build(mult=2)
agg.diagonalize()
tcalc_para = qr.TwoDResponseCalculator(t1axis=t13, t2axis=t2s, t3axis=t13, system=agg)
tcalc_para.bootstrap(rwa, pad=padding, verbose=True, lab=labPara, printEigen=False, printResp='paraResp')#, printResp='paraResp'
twods_para = tcalc_para.calculate()
paraContainer = twods_para.get_TwoDSpectrumContainer()
container.append(paraContainer)
tcalc_perp = qr.TwoDResponseCalculator(t1axis=t13, t2axis=t2s, t3axis=t13, system=agg)
tcalc_perp.bootstrap(rwa, pad=padding, verbose=True, lab=labPerp, printEigen=False)#, printResp='perpResp'
twods_perp = tcalc_perp.calculate()
perpContainer = twods_perp.get_TwoDSpectrumContainer()
container.append(perpContainer)
return container
def test_TwoDResponseCalculator(self):
"""Testing basic functions of the TwoDSpectrumCalculator class
"""
t1 = qr.TimeAxis(0.0, 1000, 1.0)
t3 = qr.TimeAxis(0.0, 1000, 1.0)
t2 = qr.TimeAxis(30, 10, 10.0)
twod_calc = qr.TwoDResponseCalculator(t1, t2, t3)
def twod_setup(self, ax2, ax13):
self.resp_calc = qr.TwoDResponseCalculator(
t1axis=ax13,
t2axis=ax2,
t3axis=ax13,
system=self.agg
)
self.t1axis = ax13
self.t2axis = ax2
def calcTwoD(n_loopsum): #
''' Caculates a 2d spectrum for both perpendicular and parael lasers
using aceto bands and accurate lineshapes'''
container = []
#energies0 = [energy - (100 * num_mol / 2) + i * 100 for i in range(num_mol)]
#energies0 = [energy] * num_mol
# Giving random energies to the moleucles according to a gauss dist
with qr.energy_units("1/cm"):
for i, mol in enumerate(for_agg):
mol.set_energy(1, random.gauss(energy, static_dis))
#mol.set_energy(1, energies0[i])
agg = qr.Aggregate(molecules=for_agg)
agg.set_coupling_by_dipole_dipole(epsr=1.21)
agg.build(mult=2)
print(np.diagonal(agg.HH[1:num_mol + 1, 1:num_mol + 1]))
agg.diagonalize()
rwa = agg.get_RWA_suggestion()
print(np.diagonal(agg.HH[1:num_mol + 1, 1:num_mol + 1]))
# Initialising the twod response calculator for the paralell laser
resp_calc_temp = qr.TwoDResponseCalculator(t1axis=t13_ax,
t2axis=t2_ax,
t3axis=t13_ax,
system=agg)
# Bootstrap is the place to add 0-padding to the response signal
# printEigen=True prints eigenvalues, printResp='string' prints response
# Response is calculated Converted into spectrum Stored in a container
for lab in labs:
resp_calc = copy.deepcopy(resp_calc_temp)
resp_calc.bootstrap(rwa, pad=padding, lab=lab)
resp_cont = resp_calc.calculate()
spec_cont = resp_cont.get_TwoDSpectrumContainer()
container.append(spec_cont)
return container
def calcTwoD(n_loopsum): #
''' Caculates a 2d spectrum for both perpendicular and parael lasers
using aceto bands and accurate lineshapes'''
resp_container = []
#energies0 = [energy - (100 * num_mol / 2) + i * 100 for i in range(num_mol)]
#energies0 = [energy] * num_mol
# Giving random energies to the moleucles according to a gauss dist
with qr.energy_units("1/cm"):
for i, mol in enumerate(for_agg):
mol.set_energy(1, random.gauss(energy, static_dis))
#mol.set_energy(1, energies0[i])
agg = qr.Aggregate(molecules=for_agg)
agg_rates = copy.deepcopy(agg)
agg_rates.set_coupling_by_dipole_dipole(epsr=1.21)
agg_rates.build(mult=2)
if _forster_:
KK = agg_rates.get_FoersterRateMatrix()
else:
KK = agg_rates.get_RedfieldRateMatrix()
agg.set_coupling_by_dipole_dipole(epsr=1.21)
agg.build(mult=2)
rwa = agg.get_RWA_suggestion()
HH = agg_rates.get_Hamiltonian()
pig_ens = np.diagonal(HH.data[1:num_mol+1,1:num_mol+1])\
/ (2.0*const.pi*const.c*1.0e-13)
en_order = np.argsort(pig_ens)
SS = HH.diagonalize()
eig_vecs = np.transpose(SS[1:num_mol + 1, 1:num_mol + 1])
state_ens = np.diagonal(HH.data[1:num_mol+1,1:num_mol+1])\
/ (2.0*const.pi*const.c*1.0e-13)
agg_rates.diagonalize()
dips = agg_rates.D2[0][1:num_mol + 1]
dip_order = np.flip(np.argsort(dips))
# Initialising the twod response calculator for the paralell laser
resp_calc_temp = qr.TwoDResponseCalculator(t1axis=t13_ax,
t2axis=t2_ax,
t3axis=t13_ax,
system=agg,
rate_matrix=KK)
# keep_resp saves the reponse int he object. write_resp writes to numpy
# Response is calculated Converted into spectrum Stored in a container
for i, lab in enumerate(labs):
resp_calc = copy.deepcopy(resp_calc_temp)
resp_calc.bootstrap(
rwa, lab=lab, verbose=False,
keep_resp=True) #write_resp = save_dir + las_pol[i] + '_resp',
resp_cont = resp_calc.calculate()
resp_container.append(resp_calc.responses)
state_data = {
'pig_ens': pig_ens,
'en_order': en_order,
'eig_vecs': eig_vecs,
'state_ens': state_ens,
'dips': dips,
'dip_order': dip_order,
'rwa': rwa
}
return resp_container, state_data
agg_2D.diagonalize()
# laboratory settings
lab = qr.LabSetup()
lab.set_polarizations(pulse_polarizations=(X, X, X), detection_polarization=X)
#
#
#
#
#
#from quantarhei.spectroscopy.mocktwodcalculator \
# import MockTwoDResponseCalculator as TwoDResponseCalculator
#
#calc = TwoDResponseCalculator(t1_axis, t2_axis, t3_axis)
calc = qr.TwoDResponseCalculator(t1_axis, t2_axis, t3_axis, system=agg_2D)
with qr.energy_units("1/cm"):
calc.bootstrap(rwa=12100.0, pad=Npad)
#calc.bootstrap(rwa=qr.convert(12100.0,"1/cm","int"), pad=1000)
print("Calculating", Nt2, "spectra")
tcont = calc.calculate()
qr.done_in(True)
tcont = tcont.get_TwoDSpectrumContainer()
T2 = 3 * dt2
twod = tcont.get_spectrum(T2)
### short test of addition of data
rwa = agg.get_RWA_suggestion()
#agg.diagonalize()
#
# Prepare for calculation of 2D spectra
#
# TimeAxis for t2 waiting time
t2s = qr.TimeAxis(0.0, 10, 20.0)
#
# Set up calculator
#
tcalc = qr.TwoDResponseCalculator(t1axis=ta, t2axis=t2s, t3axis=ta,
system=agg)
tcalc.bootstrap(rwa, verbose=True, lab=lab)
#
# Calculate 2D spectra, display and save them
#
w1_min = rwa_cm - 700.0
w1_max = rwa_cm + 700.0
w3_min = rwa_cm - 700.0
w3_max = rwa_cm + 700.0
window_2D = [w1_min, w1_max, w3_min, w3_max]
t_start = time.time()
agg = qr.Aggregate(molecules=for_agg)
agg.set_coupling_by_dipole_dipole(epsr=1.21)
agg.build(mult=2)
# Can save the hamiltoniam diag matrix, diaged hamiltonian and dipoles
if _save_:
myFuncs.save_eigen_data(agg=agg, file=eigen_file)
agg.diagonalize()
rwa = agg.get_RWA_suggestion()
with qr.energy_units('1/cm'):
print(agg.get_Hamiltonian())
# Initialising the twod response calculator for the paralell laser
resp_cal_para = qr.TwoDResponseCalculator(t1axis=t13_ax,
t2axis=t2_ax,
t3axis=t13_ax,
system=agg)
# Copying the response calculator for the perpendicular laser
resp_cal_perp = copy.deepcopy(resp_cal_para)
# Bootstrap is the place to add 0-padding to the response signal
# printEigen=True prints eigenvalues, printResp='string' prints response
# Response is calculated Converted into spectrum Stored in a container
resp_cal_para.bootstrap(rwa,
verbose=True,
pad=padding,
printResp=para_resp_dir,
lab=lab_para)
resp_para_cont = resp_cal_para.calculate()
spec_cont_para = resp_para_cont.get_TwoDSpectrumContainer()