def test_fluor_calculator(self):
"""Testing some basic methods of the FluorSpectrumCalculator class
"""
#Calculations for monomer are already performed. Now testing that
#fluorescence spectrum can be calculated for an aggregate.
try:
mol1 = Molecule(elenergies=[0.0, 12000.0])
mol2 = Molecule(elenergies=[0.0, 12000.0])
params = dict(ftype="OverdampedBrownian",
reorg=20,
cortime=100,
T=300)
mol1.set_dipole(0, 1, [0.0, 1.0, 0.0])
mol2.set_dipole(0, 1, [0.0, 1.0, 0.0])
cf = CorrelationFunction(self.ta, params)
mol1.set_transition_environment((0, 1), cf)
mol2.set_transition_environment((0, 1), cf)
agg = Aggregate(name="tester_dim", molecules=[mol1, mol2])
agg.build()
HH = agg.get_Hamiltonian()
fluor_calc = FluorSpectrumCalculator(self.ta,
system=agg,
dynamics="secular",
relaxation_tensor=None,
rate_matrix=None,
effective_hamiltonian=HH,
temperature=300)
fluor_calc.bootstrap(rwa=12000)
fluor_calc = fluor_calc.calculate()
except:
raise Exception('Fluorescence not calculatable for aggregate')
# FIXME: temporary fix for version 0.0.34 # Manager().gen_conf.legacy_relaxation = True # # PURELY ELECTRONIC Aggregate of two molecules # from quantarhei import Molecule m1 = Molecule([0.0, 1.0]) m2 = Molecule([0.0, 1.1]) m3 = Molecule([0.0, 1.2]) from quantarhei import Aggregate agg = Aggregate([m1, m2, m3]) agg.build() # # Operator describing relaxation # from quantarhei.qm import Operator HH = agg.get_Hamiltonian() K = Operator(dim=HH.dim, real=True) K.data[1, 2] = 1.0 # # System bath interaction with prescribed rate # from quantarhei.qm import SystemBathInteraction
gamma=1.0 / 10000.0)
with energy_units('1/cm'):
cf2 = CorrelationFunction(tsbi, params2)
cf.add_to_data(cf2)
#
# Set system-bath interaction
#
mol1.set_transition_environment((0, 1), cf)
mol2.set_transition_environment((0, 1), cf)
#
# Creating aggregate
#
agg = Aggregate("Dimer", molecules=[mol1, mol2])
agg.set_coupling_by_dipole_dipole()
with energy_units("1/cm"):
print(agg.get_resonance_coupling(0, 1))
agg.build(mult=2)
with energy_units("1/cm"):
rwa_cm = agg.get_RWA_suggestion()
rwa = agg.get_RWA_suggestion()
#
# Prepare for calculation of 2D spectra
#
# TimeAxis for t2 waiting time
def redfield_tensor(self):
print("Redfield tensor calculation")
#
# Correlation function
#
params = {
"ftype": world.ctype,
"reorg": world.reorg,
"cortime": world.ctime,
"T": world.temp,
"matsubara": world.mats
}
# FIXME: also time_units, temperature_units
with energy_units(world.e_units):
cf = CorrelationFunction(world.ta, params)
#
# Homodimer
#
with energy_units(world.h_units):
en = world.senergy
m1 = Molecule("mol1", [0.0, en])
m2 = Molecule("mol2", [0.0, en])
m1.set_egcf((0, 1), cf)
m2.set_egcf((0, 1), cf)
agg = Aggregate("Homodimer")
agg.add_Molecule(m1)
agg.add_Molecule(m2)
# m = Manager()
##
# with energy_units("1/cm"):
# Hm = m1.get_Hamiltonian()
# print(Hm)
# print(m.convert_energy_2_current_u(Hm._data))
with energy_units(world.r_units):
agg.set_resonance_coupling(0, 1, world.r_coupl)
agg.build()
H = agg.get_Hamiltonian()
world.HH = H
##
# with energy_units("1/cm"):
# print(H)
# print(m.convert_energy_2_current_u(H._data))
sbi = agg.get_SystemBathInteraction()
H.protect_basis()
with eigenbasis_of(H):
RRT = RedfieldRelaxationTensor(H, sbi)
dim = H.dim
rates_T = numpy.zeros(dim * dim)
k = 0
world.K12 = numpy.real(RRT.data[1, 1, 2, 2])
for i in range(dim):
for j in range(dim):
rates_T[k] = numpy.real(RRT.data[i, i, j, j])
k += 1
world.rates_T = rates_T
tsbi = TimeAxis(0.0, 3 * Nr, 10.0)
params = dict(ftype="OverdampedBrownian", T=300, reorg=30.0, cortime=50.0)
with energy_units('1/cm'):
cf = CorrelationFunction(tsbi, params)
mol1.set_transition_environment((0, 1), cf)
mol2.set_transition_environment((0, 1), cf)
mol3.set_transition_environment((0, 1), cf)
mol4.set_transition_environment((0, 1), cf)
#
# Creating aggregate
#
agg = Aggregate(molecules=molecules)
#agg = Aggregate("Dimer", molecules=[mol1, mol2, mol3])
if True:
with energy_units("1/cm"):
agg.set_resonance_coupling(0, 1, 60.0)
agg.set_resonance_coupling(1, 2, 60.0)
agg.set_resonance_coupling(0, 2, 30.0)
agg.set_resonance_coupling(1, 3, 30.0)
pass
#agg.set_coupling_by_dipole_dipole()
agg.build(mult=2)
with energy_units("1/cm"):
tsbi = TimeAxis(0.0, 3 * Nr, 2.0)
params = dict(ftype="OverdampedBrownian", T=300, reorg=50.0, cortime=100.0)
with energy_units('1/cm'):
cf = CorrelationFunction(tsbi, params)
mol1.set_transition_environment((0, 1), cf)
mol2.set_transition_environment((0, 1), cf)
mol3.set_transition_environment((0, 1), cf)
mol4.set_transition_environment((0, 1), cf)
#
# Creating aggregate
#
agg = Aggregate("Dimer", molecules=[mol1, mol2, mol3, mol4])
#agg = Aggregate("Dimer", molecules=[mol1, mol2, mol3])
with energy_units("1/cm"):
agg.set_resonance_coupling(0, 1, 60.0)
agg.set_resonance_coupling(1, 2, 60.0)
agg.set_resonance_coupling(0, 2, 30.0)
agg.set_resonance_coupling(1, 3, 30.0)
pass
#agg.set_coupling_by_dipole_dipole()
agg.build(mult=2)
with energy_units("1/cm"):
rwa_cm = agg.get_RWA_suggestion()
# -*- coding: utf-8 -*-
_show_plots_ = False
from quantarhei import Molecule, Aggregate
#from quantarhei import energy_units
en = [0.0, 1.0]
m1 = Molecule(name="Mol1", elenergies=en)
m2 = Molecule(name="Mol2", elenergies=en)
ag = Aggregate(name="Homodimer")
ag.add_Molecule(m1)
ag.add_Molecule(m2)
ag.set_resonance_coupling(0, 1, 0.1)
ag.build(mult=1)
H = ag.get_Hamiltonian()
#with energy_units("1/cm"):
# print(H)
the we create electronic Lindblad form for a system with vibrational
levels
"""
#
# PURELY ELECTRONIC Aggregate of two molecules
#
from quantarhei import Molecule
m1 = Molecule([0.0, 1.0])
m2 = Molecule([0.0, 1.1])
m3 = Molecule([0.0, 1.2])
from quantarhei import Aggregate
agg = Aggregate([m1, m2, m3])
agg.build()
#
# Operator describing relaxation
#
from quantarhei.qm import Operator
HH = agg.get_Hamiltonian()
K = Operator(dim=HH.dim,real=True)
K.data[1,2] = 1.0
#
# System bath interaction with prescribed rate
#
from quantarhei.qm import SystemBathInteraction
# -*- coding: utf-8 -*-
from quantarhei import Molecule, Aggregate
from quantarhei import energy_units
en = [0.0, 1.0]
m1 = Molecule("Mol1", en)
m2 = Molecule("Mol2", en)
ag = Aggregate("Homodimer", maxband=1)
ag.add_Molecule(m1)
ag.add_Molecule(m2)
ag.set_resonance_coupling(0, 1, 0.1)
ag.build()
H = ag.get_Hamiltonian()
with energy_units("1/cm"):
print(H)
import matplotlib.pyplot as plt
plt.plot(time.data, sm)
plt.axis([0.0, 100.0, 0.0, 1.1])
plt.show()
#
# Molecular dimer without vibrations
#
from quantarhei import Aggregate
mol1 = Molecule("Mol 1", [0.0, 1.0])
mol2 = Molecule("Mol 2", [0.0, 1.0])
agg = Aggregate("Dimer")
agg.add_Molecule(mol1)
agg.add_Molecule(mol2)
agg.set_resonance_coupling(0, 1, 0.01)
agg.build()
H = agg.get_Hamiltonian()
print(H)
psi = StateVector(3)
psi.data[2] = 1.0
dimer_propagator = StateVectorPropagator(time, H)
def redfield_relaxation(self):
print("Redfield rate calculation")
#
# Correlation function
#
params = {
"ftype": world.ctype,
"reorg": world.reorg,
"cortime": world.ctime,
"T": world.temp,
"matsubara": world.mats
}
# FIXME: also time_units, temperature_units
with energy_units(world.e_units):
cf = CorrelationFunction(world.ta, params)
#
# Homodimer
#
with energy_units(world.h_units):
en = world.senergy
m1 = Molecule([0.0, en], "mol1")
m2 = Molecule([0.0, en], "mol2")
# m3 = Molecule("mol2", [0.0, en])
m1.set_egcf((0, 1), cf)
m2.set_egcf((0, 1), cf)
# m3.set_egcf((0,1), cf)
agg = Aggregate(name="Homodimer")
agg.add_Molecule(m1)
agg.add_Molecule(m2)
# agg.add_Molecule(m3)
# with energy_units("1/cm"):
# Hm = m1.get_Hamiltonian()
# print(Hm)
# print(m.convert_energy_2_current_u(Hm._data))
with energy_units(world.r_units):
agg.set_resonance_coupling(0, 1, world.r_coupl)
# agg.set_resonance_coupling(1,2,world.r_coupl)
agg.build()
H = agg.get_Hamiltonian()
# with energy_units("1/cm"):
# print(H)
# print(m.convert_energy_2_current_u(H._data))
sbi = agg.get_SystemBathInteraction()
RRM = RedfieldRateMatrix(H, sbi)
world.K12 = numpy.real(RRM.data[1, 2])
dim = H.dim
rates_M = numpy.zeros(dim * dim)
k = 0
for i in range(dim):
for j in range(dim):
rates_M[k] = RRM.data[i, j]
k += 1
world.rates_M = rates_M
"A377": "BChl7",
"A378": "BChl8"
}
for name in names:
for m in molecules:
if m.name == name:
m.set_name(naming_map[name])
# all except for 378 go into aggregate
if name != "378":
for_aggregate.append(m)
#
# Create an new aggregate of the Bacteriochlorophylls without BChl8
#
agg = Aggregate(name="FMO", molecules=for_aggregate)
# Setting site energies according to literature
#
with energy_units("1/cm"):
m = agg.get_Molecule_by_name("BChl1")
m.set_energy(1, 12468.0)
m = agg.get_Molecule_by_name("BChl2")
m.set_energy(1, 12466.0)
m = agg.get_Molecule_by_name("BChl3")
m.set_energy(1, 12129.0)
m = agg.get_Molecule_by_name("BChl4")
m.set_energy(1, 12410.0)
m = agg.get_Molecule_by_name("BChl5")
m.set_energy(1, 12320.0)
m = agg.get_Molecule_by_name("BChl6")
m1.set_transition_environment((0,1),cfce2)
m2.set_transition_environment((0,1),cfce1)
m3.set_transition_environment((0,1),cfce1)
m4.set_transition_environment((0,1),cfce2)
m5.set_transition_environment((0,1),cfce1)
m6.set_transition_environment((0,1),cfce2)
m7.set_transition_environment((0,1),cfce1)
m8.set_transition_environment((0,1),cfce1)
m9.set_transition_environment((0,1),cfce2)
m10.set_transition_environment((0,1),cfce2)
m11.set_transition_environment((0,1),cfce2)
m12.set_transition_environment((0,1),cfce1)
# create an aggregate
AG = Aggregate("TestAggregate")
if explicit_mapping:
AG.set_egcf_matrix(cm)
# fill the cluster with monomers
AG.add_Molecule(m1)
AG.add_Molecule(m2)
AG.add_Molecule(m3)
AG.add_Molecule(m4)
AG.add_Molecule(m5)
AG.add_Molecule(m6)
AG.add_Molecule(m7)
AG.add_Molecule(m8)
AG.add_Molecule(m9)
AG.add_Molecule(m10)
#
en = [0.0, 1.0]
m1 = Molecule("Mol1", en)
m2 = Molecule("Mol2", en)
m3 = Molecule("Mol3", en)
m1.set_dipole(0, 1, [1.0, 0.0, 0.0])
time = TimeAxis(0.0, 1000, 1.0)
bath_params = dict(ftype="OverdampedBrownian", T=300, cortime=100, reorg=30.0)
with energy_units("1/cm"):
cf = CorrelationFunction(time, bath_params)
m1.set_transition_environment((0, 1), cf)
m2.set_transition_environment((0, 1), cf)
m3.set_transition_environment((0, 1), cf)
ag = Aggregate("Homodimer")
ag.add_Molecule(m1)
ag.add_Molecule(m2)
ag.add_Molecule(m3)
ag.set_resonance_coupling(0, 1, 0.1)
mult = 2
ag.build(mult=mult, sbi_for_higher_ex=False)
#
# Look at its various components
#
H = ag.get_Hamiltonian()
print("Shape of the operators")
def get_Aggregate(self, name="dimer-1"):
if name == "dimer-1":
agg = Aggregate(name=name)
elif name == "trimer-1":
agg = Aggregate(name=name)
with energy_units("1/cm"):
m1 = Molecule("Mol 1", [0.0, 10100.0])
m2 = Molecule("Mol 2", [0.0, 10050.0])
m3 = Molecule("Mol 3", [0.0, 10000.0])
m1.position = [0.0, 0.0, 0.0]
m2.position = [15.0, 0.0, 0.0]
m3.position = [10.0, 10.0, 0.0]
m1.set_dipole(0, 1, [5.8, 0.0, 0.0])
m2.set_dipole(0, 1, [5.8, 0.0, 0.0])
m3.set_dipole(0, 1, [numpy.sqrt(12.0), 0.0, 0.0])
agg.add_Molecule(m1)
agg.add_Molecule(m2)
agg.add_Molecule(m3)
self.molecules = [m1, m2, m3]
# m4 = Molecule("Mol 4", [0.0, 11000.0])
# m5 = Molecule("Mol 5", [0.0, 11000.0])
# m4.position = [15.0, 15.0, 0.0]
# m5.position = [15.0, 10.0, 0.0]
# m4.set_dipole(0,1,[5.8, 0.0, 0.0])
# m5.set_dipole(0,1,[5.8, 0.0, 0.0])
# agg.add_Molecule(m4)
# agg.add_Molecule(m5)
agg.set_coupling_by_dipole_dipole()
elif name == "pentamer-1":
agg = Aggregate(name=name)
with energy_units("1/cm"):
m1 = Molecule("Mol 1", [0.0, 10100.0])
m2 = Molecule("Mol 2", [0.0, 10050.0])
m3 = Molecule("Mol 3", [0.0, 10000.0])
m4 = Molecule("Mol 4", [0.0, 10200.0])
m5 = Molecule("Mol 5", [0.0, 10070.0])
m1.position = [0.0, 0.0, 0.0]
m2.position = [15.0, 0.0, 0.0]
m3.position = [10.0, 10.0, 0.0]
m4.position = [15.0, 15.0, 0.0]
m5.position = [0, 10.0, 10.0]
m1.set_dipole(0, 1, [5.8, 0.0, 0.0])
m2.set_dipole(0, 1, [5.8, 0.0, 0.0])
m3.set_dipole(0, 1, [numpy.sqrt(12.0), 0.0, 0.0])
m4.set_dipole(0, 1, [5.8, 0.0, 0.0])
m5.set_dipole(0, 1, [5.8, 0.0, 0.0])
agg.add_Molecule(m1)
agg.add_Molecule(m2)
agg.add_Molecule(m3)
agg.add_Molecule(m4)
agg.add_Molecule(m5)
self.molecules = [m1, m2, m3, m4, m5]
agg.set_coupling_by_dipole_dipole()
else:
raise Exception("Unknown model name %s" % name)
return agg
