def test_abs_calculator(self):
"""Testing some basic methods of the AbsSpectrumCalculator class
"""
#Calculations for monomer are already performed. Now testing that
#absorption 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()
abs_calc = AbsSpectrumCalculator(self.ta,
system=agg,
dynamics="secular",
relaxation_tensor=None,
rate_matrix=None)
abs_calc.bootstrap(rwa=12000)
abs_calc = abs_calc.calculate()
except:
raise Exception('Absorption not calculatable for aggregate')
def build_aggregate_2(settings):
"""Example function for building aggregate no. 2"""
mol_l = []
mod_l = []
with qr.energy_units("1/cm"):
for ind in range(settings["Nmol"]):
mol = Molecule([0.0, settings["E1"]])
# mol1.set_dipole(0,1,[1.0, 0.0, 0.0])
# mol1.set_transition_width((0,1), width)
mod = Mode(settings["omega"])
mol.add_Mode(mod)
mod.set_nmax(0, settings["Nvib_0"])
mod.set_nmax(1, settings["Nvib_1"])
mod.set_HR(1, settings["HR"])
mol_l.append(mol)
mod_l.append(mod)
agg = Aggregate(molecules=mol_l)
for ind in range(settings["Nmol"] - 1):
agg.set_resonance_coupling(ind, ind + 1, settings["JJ"])
# agg.set_resonance_coupling(settings["Nmol"]-1, 0, settings["JJ"])
agg.build(mult=1)
return agg
def test_abs_calculator(self):
"""Testing some basic methods of the AbsSpectrumCalculator class
"""
#Calculations for monomer are already performed. Now testing that
#absorption 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()
abs_calc = AbsSpectrumCalculator(self.ta,
system=agg,
dynamics="secular",
relaxation_tensor=None,
rate_matrix=None)
abs_calc.bootstrap(rwa=12000)
abs_calc = abs_calc.calculate()
except:
raise Exception('Absorption not calculatable for aggregate')
def homochain_aggregate(self):
molecules = []
time = world.time #TimeAxis(0.0, 10000, 1.0)
k = 0
couplings = []
temp = 0.0
for row in self.hashes:
tenergy = float(row['tr_energy'])
coupling = float(row['neighbor_coupling'])
ftype_abbv = row['corfce']
if ftype_abbv == "OB":
ftype = "OverdampedBrownian"
reorg = float(row['reorg'])
e_units = row['e_units']
ctime = float(row['ctime'])
tempp = float(row['temperature'])
matsu = int(row['matsubara'])
if temp == 0.0:
temp = tempp
else:
if temp != tempp:
raise Exception(
"Temperatures must be the same for all molecules")
params = dict(ftype=ftype,
cortime=ctime,
reorg=reorg,
T=temp,
matsubara=matsu)
with energy_units(e_units):
m = Molecule(name="", elenergies=[0.0, tenergy])
cf = CorrelationFunction(time, params)
m.set_transition_environment((0, 1), cf)
molecules.append(m)
couplings.append(coupling)
k += 1
agg = Aggregate(name="", molecules=molecules)
with energy_units("1/cm"):
for i in range(k):
if i + 1 < k:
agg.set_resonance_coupling(i, i + 1, couplings[i])
else:
agg.set_resonance_coupling(i, 0, couplings[i])
agg.build()
world.temperature = temp
world.aggregate = agg
world.time = time
world.N = k + 1
def setUp(self,verbose=False):
self.verbose = verbose
#
# PURE ELECTRONIC AGGREGATE
#
m1 = Molecule([0.0, 1.0])
m2 = Molecule([0.0, 1.0])
agg = Aggregate(molecules=[m1, m2])
agg.set_resonance_coupling(0,1, 0.1)
agg.build()
self.ham = agg.get_Hamiltonian()
KK12 = ProjectionOperator(1, 2, dim=self.ham.dim)
KK21 = ProjectionOperator(2, 1, dim=self.ham.dim)
self.rates = (1.0/100.0, 1.0/200.0)
self.sbi = SystemBathInteraction([KK12,KK21],
rates=self.rates)
self.sbi.set_system(agg)
#
# VIBRONIC AGGREGATE
#
vm1 = Molecule([0.0, 1.0])
vm2 = Molecule([0.0, 1.0])
mod1 = Mode(0.01)
mod2 = Mode(0.01)
vm1.add_Mode(mod1)
vm2.add_Mode(mod2)
mod1.set_nmax(0, 3)
mod1.set_nmax(1, 3)
mod2.set_nmax(0, 3)
mod2.set_nmax(1, 3)
vagg = Aggregate(molecules=[vm1, vm2])
vagg.set_resonance_coupling(0, 1, 0.1)
vagg.build()
self.vham = vagg.get_Hamiltonian()
self.vsbi = SystemBathInteraction([KK12, KK21], rates=self.rates)
self.vsbi.set_system(vagg)
def setUp(self, verbose=False):
self.verbose = verbose
#
# PURE ELECTRONIC AGGREGATE
#
m1 = Molecule([0.0, 1.0])
m2 = Molecule([0.0, 1.0])
agg = Aggregate(molecules=[m1, m2])
agg.set_resonance_coupling(0, 1, 0.1)
agg.build()
self.ham = agg.get_Hamiltonian()
KK12 = ProjectionOperator(1, 2, dim=self.ham.dim)
KK21 = ProjectionOperator(2, 1, dim=self.ham.dim)
self.rates = (1.0 / 100.0, 1.0 / 200.0)
self.sbi = SystemBathInteraction([KK12, KK21], rates=self.rates)
self.sbi.set_system(agg)
#
# VIBRONIC AGGREGATE
#
vm1 = Molecule([0.0, 1.0])
vm2 = Molecule([0.0, 1.0])
mod1 = Mode(0.01)
mod2 = Mode(0.01)
vm1.add_Mode(mod1)
vm2.add_Mode(mod2)
mod1.set_nmax(0, 3)
mod1.set_nmax(1, 3)
mod2.set_nmax(0, 3)
mod2.set_nmax(1, 3)
vagg = Aggregate(molecules=[vm1, vm2])
vagg.set_resonance_coupling(0, 1, 0.1)
vagg.build()
self.vham = vagg.get_Hamiltonian()
self.vsbi = SystemBathInteraction([KK12, KK21], rates=self.rates)
self.vsbi.set_system(vagg)
def absorption_spectrum_trimer(self):
dd1 = [0.0, 3.0, 0.0]
dd2 = [0.0, 1.0, 2.0]
dd3 = [0.0, 1.0, 1.0]
cf = world.cf
with energy_units("1/cm"):
m1 = Molecule([0.0, 12100])
m1.set_dipole(0, 1, dd1)
m1.set_transition_environment((0, 1), cf)
m2 = Molecule([0.0, 11800])
m2.set_dipole(0, 1, dd2)
m2.set_transition_environment((0, 1), cf)
m3 = Molecule([0.0, 12500])
m3.set_dipole(0, 1, dd3)
m3.set_transition_environment((0, 1), cf)
m1.position = [0.0, 0.0, 0.0]
m2.position = [5.0, 0.0, 0.0]
m3.position = [0.0, 5.0, 0.0]
AG = Aggregate(name="TestAggregate")
AG.add_Molecule(m1)
AG.add_Molecule(m2)
AG.add_Molecule(m3)
AG.set_coupling_by_dipole_dipole(epsr=3.0)
AG.build()
(RRr,
hamr) = AG.get_RelaxationTensor(world.ta,
relaxation_theory="standard_Redfield",
time_dependent=True)
ac = AbsSpectrumCalculator(world.ta,
AG,
relaxation_tensor=RRr,
effective_hamiltonian=hamr)
with energy_units("1/cm"):
ac.bootstrap(rwa=12000)
a1 = ac.calculate()
with energy_units("1/cm"):
world.abs = numpy.zeros((len(a1.data), 2))
for kk in range(len(a1.data)):
world.abs[kk, 0] = a1.axis.data[kk] #frequency[kk]
world.abs[kk, 1] = a1.data[kk]
def absorption_spectrum_trimer(self):
dd1 = [0.0,3.0,0.0]
dd2 = [0.0,1.0,2.0]
dd3 = [0.0,1.0,1.0]
cf = world.cf
with energy_units("1/cm"):
m1 = Molecule([0.0, 12100])
m1.set_dipole(0,1,dd1)
m1.set_transition_environment((0,1), cf)
m2 = Molecule([0.0, 11800])
m2.set_dipole(0,1,dd2)
m2.set_transition_environment((0,1), cf)
m3 = Molecule([0.0, 12500])
m3.set_dipole(0,1,dd3)
m3.set_transition_environment((0,1), cf)
m1.position = [0.0,0.0,0.0]
m2.position = [5.0,0.0,0.0]
m3.position = [0.0,5.0,0.0]
AG = Aggregate(name="TestAggregate")
AG.add_Molecule(m1)
AG.add_Molecule(m2)
AG.add_Molecule(m3)
AG.set_coupling_by_dipole_dipole(epsr=3.0)
AG.build()
(RRr,hamr) = AG.get_RelaxationTensor(world.ta,
relaxation_theory="standard_Redfield",
time_dependent=True)
ac = AbsSpectrumCalculator(world.ta,AG,
relaxation_tensor=RRr,
effective_hamiltonian=hamr)
with energy_units("1/cm"):
ac.bootstrap(rwa=12000)
a1 = ac.calculate(raw=True)
with energy_units("1/cm"):
world.abs = numpy.zeros((len(a1.data),2))
for kk in range(len(a1.data)):
world.abs[kk,0] = a1.axis.data[kk] #frequency[kk]
world.abs[kk,1] = a1.data[kk]
def homochain_aggregate(self):
molecules = []
time = world.time #TimeAxis(0.0, 10000, 1.0)
k = 0
couplings = []
temp = 0.0
for row in self.hashes:
tenergy = float(row['tr_energy'])
coupling = float(row['neighbor_coupling'])
ftype_abbv = row['corfce']
if ftype_abbv == "OB":
ftype = "OverdampedBrownian"
reorg = float(row['reorg'])
e_units = row['e_units']
ctime = float(row['ctime'])
tempp = float(row['temperature'])
matsu = int(row['matsubara'])
if temp == 0.0:
temp = tempp
else:
if temp != tempp:
raise Exception("Temperatures must be the same for all molecules")
params = dict(ftype=ftype, cortime=ctime,
reorg=reorg, T=temp, matsubara=matsu)
with energy_units(e_units):
m = Molecule([0.0, tenergy])
cf = CorrelationFunction(time, params)
m.set_transition_environment((0,1), cf)
molecules.append(m)
couplings.append(coupling)
k += 1
agg = Aggregate(molecules=molecules)
with energy_units("1/cm"):
for i in range(k):
if i+1 < k:
agg.set_resonance_coupling(i,i+1,couplings[i])
else:
agg.set_resonance_coupling(i,0,couplings[i])
agg.build()
world.temperature = temp
world.aggregate = agg
world.time = time
world.N = k+1
def absorption_spectrum_dimer(self):
dd1 = [0.0,3.0,0.0]
dd2 = [0.0,1.0,1.0]
cf = world.cf
#cm = CorrelationFunctionMatrix(world.ta,2,1)
#cm.set_correlation_function(cf,[(1,1),(0,0)])
with energy_units("1/cm"):
m1 = Molecule([0.0, 12100])
m1.set_dipole(0,1,dd1)
m1.set_transition_environment((0,1), cf)
m2 = Molecule([0.0, 12000])
m2.set_dipole(0,1,dd2)
m2.set_transition_environment((0,1), cf)
#m1.set_egcf([0,1],cf)
#m2.set_egcf([0,1],cf)
#m1.set_egcf_mapping((0,1),cm,0)
#m2.set_egcf_mapping((0,1),cm,1)
m1.position = [0.0,0.0,0.0]
m2.position = [5.0,0.0,0.0]
AG = Aggregate(name="TestAggregate")
#AG.set_egcf_matrix(cm)
AG.add_Molecule(m1)
AG.add_Molecule(m2)
AG.set_coupling_by_dipole_dipole()
AG.build()
ac = AbsSpectrumCalculator(world.ta,AG)
with energy_units("1/cm"):
ac.bootstrap(rwa=12000)
a1 = ac.calculate(raw=True)
with energy_units("1/cm"):
world.abs = numpy.zeros((len(a1.data),2))
for kk in range(len(a1.data)):
world.abs[kk,0] = a1.axis.data[kk] #frequency[kk]
world.abs[kk,1] = a1.data[kk]
def build_testing_aggregate():
"""Testing aggregate for unit tests."""
# Number of molecules
Nmol = 2
# energy of molecule one
E1 = 12500.0
# energy gap to molecule two
Edelta = 100.0
# coupling between the two molecules
JJ = 30.0
# frequency of the vibrational mode
omega = 110.0
# Huan-Rhys factor
HR = 0.01
# transition width
width = 80
# max nvib states
Nvib_0 = 3
Nvib_1 = 3
mol_l = []
mod_l = []
with qr.energy_units("1/cm"):
for ind in range(Nmol):
mol = Molecule([0.0, E1])
mol.set_dipole(0, 1, [1.0, 0.0, 0.0])
mol.set_transition_width((0, 1), width)
mod = Mode(omega)
mol.add_Mode(mod)
mod.set_nmax(0, Nvib_0)
mod.set_nmax(1, Nvib_1)
mod.set_HR(1, HR)
mol_l.append(mol)
mod_l.append(mod)
agg = Aggregate(molecules=mol_l)
for ind in range(Nmol - 1):
agg.set_resonance_coupling(ind, ind + 1, JJ)
agg.set_resonance_coupling(Nmol - 1, 0, JJ)
agg.build(mult=1)
return agg
def setUp(self, verbose=False):
lindichs = LinDichSpectrumBase()
with energy_units("1/cm"):
f = FrequencyAxis(10000.0, 2000, 1.0)
a = self._spectral_shape(f, [1.0, 11000.0, 100.0])
lindichs.axis = f
lindichs.data = a
self.lindichs = lindichs
self.axis = lindichs.axis
#make a single-molecule system
time = TimeAxis(0.0, 1000, 1.0)
self.ta = time
with energy_units("1/cm"):
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(time, params)
mol1.set_transition_environment((0, 1), cf)
mol2.set_transition_environment((0, 1), cf)
mol1.position = [0, 0, 0]
mol2.position = [10, 10, 10]
agg = Aggregate(name="tester_dim", molecules=[mol1, mol2])
agg.build()
lindich_calc = LinDichSpectrumCalculator(time, system=agg, \
vector_perp_to_membrane=numpy.array((0,1,0)))
lindich_calc.bootstrap(rwa=12000)
lindich1 = lindich_calc.calculate()
self.lindich1 = lindich1
def hamiltonian_is_created(self):
#
# Homodimer
#
with energy_units(world.h_units):
en = world.senergy
m1 = Molecule([0.0, en], "mol1")
m2 = Molecule([0.0, en], "mol2")
agg = Aggregate(name="Homodimer")
agg.add_Molecule(m1)
agg.add_Molecule(m2)
with energy_units(world.r_units):
agg.set_resonance_coupling(0,1,world.r_coupl)
agg.build()
world.HH = agg.get_Hamiltonian()
def hamiltonian_is_created(self):
#
# Homodimer
#
with energy_units(world.h_units):
en = world.senergy
m1 = Molecule([0.0, en], "mol1")
m2 = Molecule([0.0, en], "mol2")
agg = Aggregate(name="Homodimer")
agg.add_Molecule(m1)
agg.add_Molecule(m2)
with energy_units(world.r_units):
agg.set_resonance_coupling(0, 1, world.r_coupl)
agg.build()
world.HH = agg.get_Hamiltonian()
def setUp(self,verbose=False):
lindichs = LinDichSpectrumBase()
with energy_units("1/cm"):
f = FrequencyAxis(10000.0,2000, 1.0)
a = self._spectral_shape(f, [1.0, 11000.0, 100.0])
lindichs.axis = f
lindichs.data = a
self.lindichs = lindichs
self.axis = lindichs.axis
#make a single-molecule system
time = TimeAxis(0.0,1000,1.0)
self.ta = time
with energy_units("1/cm"):
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(time, params)
mol1.set_transition_environment((0,1),cf)
mol2.set_transition_environment((0,1),cf)
mol1.position = [0, 0, 0]
mol2.position = [10, 10, 10]
agg = Aggregate(name="tester_dim", molecules=[mol1, mol2])
agg.build()
lindich_calc = LinDichSpectrumCalculator(time, system=agg, \
vector_perp_to_membrane=numpy.array((0,1,0)))
lindich_calc.bootstrap(rwa=12000)
lindich1 = lindich_calc.calculate()
self.lindich1 = lindich1
# 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
# -*- 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)
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
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")
print(H.data.shape)
with energy_units("1/cm"):
print(H)
D = ag.get_TransitionDipoleMoment()
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(name="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
t2s = TimeAxis(0.0, 5, 20.0)
#
# Set up calculator
# -*- coding: utf-8 -*-
#<remove>
_show_plots_ = False
#</remove>
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)
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
t2s = TimeAxis(0.0, 5, 20.0)
#
# Set up calculator
# # Molecular dimer without vibrations # from quantarhei import Aggregate mol1 = Molecule(name="Mol 1", elenergies=[0.0, 1.0]) mol2 = Molecule(name="Mol 2", elenergies=[0.0, 1.0]) agg = Aggregate(name="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) psi_t = dimer_propagator.propagate(psi) psi_t.plot(ptype="square", show=False) #dat = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.01], [0.0, 0.01, 1.1]] H._data[2,2] = 1.2 #dat
class TestAggregate(unittest.TestCase):
"""Tests for the Manager class
"""
def setUp(self):
m1 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m2 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
time = TimeAxis(0.0, 1000, 1.0)
params = dict(ftype="OverdampedBrownian", reorg=20, cortime=100, T=300)
with energy_units("1/cm"):
fc = CorrelationFunction(time, params)
m1.set_transition_environment((0,1), fc)
m1.position = [0.0, 0.0, 0.0]
m1.set_dipole(0,1,[10.0, 0.0, 0.0])
m2.set_transition_environment((0,1), fc)
m2.position = [10.0, 0.0, 0.0]
m2.set_dipole(0,1,[10.0, 0.0, 0.0])
self.agg = Aggregate(name="TestAgg", molecules=[m1,m2])
self.agg.set_coupling_by_dipole_dipole()
self.agg.build()
m3 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m4 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
m3.add_Mode(Mode(0.01))
m4.add_Mode(Mode(0.01))
mod3 = m3.get_Mode(0)
mod4 = m4.get_Mode(0)
mod3.set_nmax(0, 4)
mod3.set_nmax(1, 4)
mod3.set_HR(1, 0.1)
mod4.set_nmax(0, 4)
mod4.set_nmax(1, 4)
mod4.set_HR(1, 0.3)
self.vagg = Aggregate(molecules=[m3, m4])
self.vagg.build()
def test_saving_of_aggregate(self):
"""Testing the saving capability of the Aggregate class
"""
use_temporary_file = True
if use_temporary_file:
drv = "core"
bcs = False
with h5py.File('tempfile.hdf5',
driver=drv,
backing_store=bcs) as f:
self.agg.save(f,report_unsaved=True)
# reread it
agg = Aggregate()
agg.load(f)
else:
with h5py.File('tempfile.hdf5') as f:
self.agg.save(f)
with h5py.File('tempfile.hdf5') as f:
agg = Aggregate()
agg.load(f)
self.assertEqual(self.agg.nmono, agg.nmono)
self.assertEqual(self.agg.mult, agg.mult)
self.assertEqual(self.agg.sbi_mult, agg.sbi_mult)
self.assertEqual(self.agg.name, agg.name)
self.assertEqual(self.agg._has_egcf_matrix, agg._has_egcf_matrix)
self.assertEqual(self.agg._has_system_bath_interaction,
agg._has_system_bath_interaction)
self.assertEqual(self.agg.coupling_initiated, agg.coupling_initiated)
self.assertEqual(self.agg._has_relaxation_tensor,
agg._has_relaxation_tensor)
self.assertEqual(self.agg._relaxation_theory, agg._relaxation_theory)
self.assertEqual(self.agg._built, agg._built)
self.assertEqual(self.agg.Nel,agg.Nel)
self.assertEqual(self.agg.Ntot,agg.Ntot)
numpy.testing.assert_array_equal(self.agg.Nb,agg.Nb)
for key in agg.mnames.keys():
self.assertEqual(self.agg.mnames[key],agg.mnames[key])
numpy.testing.assert_array_equal(self.agg.resonance_coupling,
agg.resonance_coupling)
mnames = ["Molecule 1", "Molecule 2"]
for k in range(agg.nmono):
m = agg.monomers[k]
self.assertIn(m.name, mnames)
mnames.remove(m.name)
def test_trace_over_vibrations(self):
"""Testing trace over vibrational DOF
"""
agg = self.vagg
ham = agg.get_Hamiltonian()
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[5, 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=7)
N = agg.Nb[0]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N+5, N+5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=3)
N = agg.Nb[1]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N+5, N+5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=2)
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")
print(H.data.shape)
with energy_units("1/cm"):
print(H)
D = ag.get_TransitionDipoleMoment()
with eigenbasis_of(H):
with energy_units("1/cm"):
print(H)
class AggregateTest(unittest.TestCase):
"""Tests for the Manager class
"""
def setUp(self):
m1 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m2 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
time = TimeAxis(0.0, 1000, 1.0)
params = dict(ftype="OverdampedBrownian", reorg=20, cortime=100, T=300)
with energy_units("1/cm"):
fc = CorrelationFunction(time, params)
m1.set_transition_environment((0, 1), fc)
m1.position = [0.0, 0.0, 0.0]
m1.set_dipole(0, 1, [10.0, 0.0, 0.0])
m2.set_transition_environment((0, 1), fc)
m2.position = [10.0, 0.0, 0.0]
m2.set_dipole(0, 1, [10.0, 0.0, 0.0])
self.agg = Aggregate(name="TestAgg", molecules=[m1, m2])
self.agg.set_coupling_by_dipole_dipole()
self.agg.build()
m3 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m4 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
m3.add_Mode(Mode(0.01))
m4.add_Mode(Mode(0.01))
mod3 = m3.get_Mode(0)
mod4 = m4.get_Mode(0)
mod3.set_nmax(0, 4)
mod3.set_nmax(1, 4)
mod3.set_HR(1, 0.1)
mod4.set_nmax(0, 4)
mod4.set_nmax(1, 4)
mod4.set_HR(1, 0.3)
self.vagg = Aggregate(molecules=[m3, m4])
self.vagg.build()
#########################################################################
#
# TESTS
#
#########################################################################
def test_saving_of_aggregate(self):
"""(Aggregate) Testing its saving capability
"""
use_temporary_file = True
if use_temporary_file:
#drv = "core"
#bcs = False
#with h5py.File('tempfile.hdf5',
# driver=drv,
# backing_store=bcs) as f:
with tempfile.TemporaryFile() as f:
self.agg.save(f, test=True) #,report_unsaved=True)
# reread it
agg = Aggregate()
agg = agg.load(f, test=True)
else:
#with h5py.File('tempfile.hdf5') as f:
with open('tempfile.qrp', 'wb') as f:
self.agg.save(f)
#with h5py.File('tempfile.hdf5') as f:
with open('tempfile.qrp', 'rb') as f:
agg = Aggregate()
agg.load(f)
self.assertEqual(self.agg.nmono, agg.nmono)
self.assertEqual(self.agg.mult, agg.mult)
self.assertEqual(self.agg.sbi_mult, agg.sbi_mult)
self.assertEqual(self.agg.name, agg.name)
self.assertEqual(self.agg._has_egcf_matrix, agg._has_egcf_matrix)
self.assertEqual(self.agg._has_system_bath_interaction,
agg._has_system_bath_interaction)
self.assertEqual(self.agg.coupling_initiated, agg.coupling_initiated)
self.assertEqual(self.agg._has_relaxation_tensor,
agg._has_relaxation_tensor)
self.assertEqual(self.agg._relaxation_theory, agg._relaxation_theory)
self.assertEqual(self.agg._built, agg._built)
self.assertEqual(self.agg.Nel, agg.Nel)
self.assertEqual(self.agg.Ntot, agg.Ntot)
numpy.testing.assert_array_equal(self.agg.Nb, agg.Nb)
for key in agg.mnames.keys():
self.assertEqual(self.agg.mnames[key], agg.mnames[key])
numpy.testing.assert_array_equal(self.agg.resonance_coupling,
agg.resonance_coupling)
mnames = ["Molecule 1", "Molecule 2"]
for k in range(agg.nmono):
m = agg.monomers[k]
self.assertIn(m.name, mnames)
mnames.remove(m.name)
def test_trace_over_vibrations(self):
"""(Aggregate) Testing trace over vibrational DOF
"""
agg = self.vagg
ham = agg.get_Hamiltonian()
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[5, 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data),
1.0,
decimal=7)
N = agg.Nb[0]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N + 5, N + 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data),
1.0,
decimal=3)
N = agg.Nb[1]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N + 5, N + 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data),
1.0,
decimal=2)
def test_get_Density_Matrix_thermal(self):
"""(Aggregate) Testing the get_Densitymatrix method with `thermal` condition type
"""
from quantarhei.core.units import kB_intK
vagg = self.vagg
H = vagg.get_Hamiltonian()
N = H.data.shape[0]
# zero temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal")
tst0 = numpy.zeros((N, N), dtype=qr.COMPLEX)
tst0[0, 0] = 1.0
numpy.testing.assert_almost_equal(rho0.data, tst0)
# room temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal",
temperature=300)
# cannonical balance between neighboring states is tested
kbT = kB_intK * 300.0
for k in range(N - 1):
E2 = H.data[k + 1, k + 1]
E1 = H.data[k, k]
ratio = numpy.exp(-(E2 - E1) / kbT)
numpy.testing.assert_almost_equal(
ratio, rho0.data[k + 1, k + 1] / rho0.data[k, k])
def test_get_Density_Matrix_thermal_excited(self):
"""(Aggregate) Testing the get_Densitymatrix method with `thermal_excited_state` condition type
"""
from quantarhei.core.units import kB_intK
vagg = self.vagg
H = vagg.get_Hamiltonian()
N = H.data.shape[0]
Nb0 = vagg.Nb[0]
# zero temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal_excited_state")
tst0 = numpy.zeros((N, N), dtype=qr.COMPLEX)
tst0[Nb0, Nb0] = 1.0
numpy.testing.assert_almost_equal(rho0.data, tst0)
# room temperature
kbT = kB_intK * 300.0
H = self.agg.get_Hamiltonian()
N = H.data.shape[0]
Nb0 = self.agg.Nb[0]
with qr.eigenbasis_of(H):
rho0 = self.agg.get_DensityMatrix(
condition_type="thermal_excited_state", temperature=300)
tst0 = numpy.zeros((N, N), dtype=qr.COMPLEX)
with qr.eigenbasis_of(H):
ssum = 0.0
for i in range(Nb0, N):
tst0[i,
i] = numpy.exp(-(H.data[i, i] - H.data[Nb0, Nb0]) / kbT)
ssum += tst0[i, i]
tst0 = tst0 / ssum
numpy.testing.assert_almost_equal(rho0.data, tst0)
# ssum = 0.0
# for i in range(N):
# tst0[i,i] = numpy.exp(-H.data[i,i]/kbT)
# ssum += tst0[i,i]
# tst0 = tst0/ssum
#
# DD = vagg.TrDMOp.data
# # abs value of the transition dipole moment
# dabs = numpy.sqrt(DD[:,:,0]**2 + \
# DD[:,:,1]**2 + DD[:,:,2]**2)
# # excitation from bra and ket
# tst0 = numpy.dot(dabs, numpy.dot(tst0,dabs))
#
# numpy.testing.assert_almost_equal(rho0.data, tst0)
def test_get_temperature(self):
"""(Aggregate) Testing temperature retrieval
"""
agg = self.agg
T = agg.get_temperature()
numpy.testing.assert_almost_equal(T, 300.0)
def test_init_coupling_matrix(self):
"""(Aggregate) Testing coupling matrix initialization
"""
agg = TestAggregate(name="dimer-2-env")
self.assertFalse(agg.coupling_initiated)
agg.init_coupling_matrix()
self.assertTrue(agg.coupling_initiated)
self.assertAlmostEqual(0.0, agg.resonance_coupling[0, 1])
def test_set_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling setting with different units
"""
agg = TestAggregate(name="dimer-2-env")
agg.init_coupling_matrix()
agg.set_resonance_coupling(0, 1, 1.0)
self.assertAlmostEqual(1.0, agg.resonance_coupling[0, 1])
self.assertAlmostEqual(1.0, agg.resonance_coupling[1, 0])
with qr.energy_units("1/cm"):
agg.set_resonance_coupling(0, 1, 100.0)
self.assertAlmostEqual(qr.convert(100.0, "1/cm", "int"),
agg.resonance_coupling[0, 1])
self.assertAlmostEqual(qr.convert(100.0, "1/cm", "int"),
agg.resonance_coupling[1, 0])
def test_get_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling retrieval in different units
"""
agg = TestAggregate(name="dimer-2-env")
agg.init_coupling_matrix()
agg.set_resonance_coupling(0, 1, 1.0)
coup = agg.get_resonance_coupling(1, 0)
self.assertAlmostEqual(coup, 1.0)
with qr.energy_units("1/cm"):
coup = agg.get_resonance_coupling(1, 0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "1/cm"))
with qr.energy_units("eV"):
coup = agg.get_resonance_coupling(1, 0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "eV"))
with qr.energy_units("THz"):
coup = agg.get_resonance_coupling(1, 0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "THz"))
def test_set_resonance_coupling_matrix(self):
"""(Aggregate) Testing setting the whole resonance coupling matrix
"""
agg = TestAggregate(name="dimer-2-env")
mat = [[0.0, 1.0], [1.0, 0.0]]
agg.set_resonance_coupling_matrix(mat)
self.assertAlmostEqual(agg.resonance_coupling[1, 0], 1.0)
self.assertAlmostEqual(agg.resonance_coupling[0, 1], 1.0)
self.assertAlmostEqual(agg.resonance_coupling[0, 0], 0.0)
self.assertAlmostEqual(agg.resonance_coupling[1, 1], 0.0)
mat = ((0.0, 500.0), (500.0, 0.0))
with qr.energy_units("1/cm"):
agg.set_resonance_coupling_matrix(mat)
inint = qr.convert(500, "1/cm", "int")
self.assertAlmostEqual(agg.resonance_coupling[1, 0], inint)
self.assertAlmostEqual(agg.resonance_coupling[0, 1], inint)
self.assertAlmostEqual(agg.resonance_coupling[0, 0], 0.0)
self.assertAlmostEqual(agg.resonance_coupling[1, 1], 0.0)
def test_dipole_dipole_coupling(self):
"""(Aggregate) Testing dipole-dipole coupling calculation
"""
agg = TestAggregate(name="dimer-2-env")
coup1 = agg.dipole_dipole_coupling(0, 1)
coup2 = agg.dipole_dipole_coupling(0, 1, epsr=2.0)
self.assertAlmostEqual(coup1, coup2 * 2.0)
with qr.energy_units("1/cm"):
coup = agg.dipole_dipole_coupling(0, 1)
self.assertAlmostEqual(qr.convert(coup1, "int", "1/cm"), coup)
def test_set_coupling_by_dipole_dipole(self):
"""(Aggregate) Testing dipole-dipole coupling calculation for the whole agregate
"""
agg = TestAggregate(name="dimer-2-env")
agg.set_coupling_by_dipole_dipole()
coup1 = agg.dipole_dipole_coupling(0, 1)
self.assertAlmostEqual(coup1, agg.resonance_coupling[0, 1])
with qr.energy_units("1/cm"):
agg.set_coupling_by_dipole_dipole()
coup1 = agg.dipole_dipole_coupling(0, 1)
self.assertAlmostEqual(coup1, agg.resonance_coupling[0, 1])
def test_calculate_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling calculation by various methods
"""
agg = TestAggregate(name="dimer-2-env")
agg.calculate_resonance_coupling(method="dipole-dipole")
coup1 = agg.dipole_dipole_coupling(0, 1)
self.assertEqual(coup1, agg.resonance_coupling[1, 0])
with qr.energy_units("1/cm"):
agg.calculate_resonance_coupling(method="dipole-dipole")
self.assertEqual(coup1, agg.resonance_coupling[1, 0])
def test_add_Molecule(self):
"""(Aggregate) Testing add_Molecule() method
"""
agg = TestAggregate(name="dimer-2-env")
mol = qr.Molecule(elenergies=[0.0, 1.0])
nmols1 = agg.nmono
agg.add_Molecule(mol)
nmols2 = agg.nmono
self.assertEqual(nmols1 + 1, nmols2)
self.assertEqual(len(agg.monomers), nmols2)
self.assertLessEqual(len(agg.mnames), nmols2)
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
class AggregateTest(unittest.TestCase):
"""Tests for the Manager class
"""
def setUp(self):
m1 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m2 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
time = TimeAxis(0.0, 1000, 1.0)
params = dict(ftype="OverdampedBrownian", reorg=20, cortime=100, T=300)
with energy_units("1/cm"):
fc = CorrelationFunction(time, params)
m1.set_transition_environment((0,1), fc)
m1.position = [0.0, 0.0, 0.0]
m1.set_dipole(0,1,[10.0, 0.0, 0.0])
m2.set_transition_environment((0,1), fc)
m2.position = [10.0, 0.0, 0.0]
m2.set_dipole(0,1,[10.0, 0.0, 0.0])
self.agg = Aggregate(name="TestAgg", molecules=[m1,m2])
self.agg.set_coupling_by_dipole_dipole()
self.agg.build()
m3 = Molecule(name="Molecule 1", elenergies=[0.0, 1.0])
m4 = Molecule(name="Molecule 2", elenergies=[0.0, 1.0])
m3.add_Mode(Mode(0.01))
m4.add_Mode(Mode(0.01))
mod3 = m3.get_Mode(0)
mod4 = m4.get_Mode(0)
mod3.set_nmax(0, 4)
mod3.set_nmax(1, 4)
mod3.set_HR(1, 0.1)
mod4.set_nmax(0, 4)
mod4.set_nmax(1, 4)
mod4.set_HR(1, 0.3)
self.vagg = Aggregate(molecules=[m3, m4])
self.vagg.build()
#########################################################################
#
# TESTS
#
#########################################################################
def test_saving_of_aggregate(self):
"""(Aggregate) Testing its saving capability
"""
use_temporary_file = True
if use_temporary_file:
#drv = "core"
#bcs = False
#with h5py.File('tempfile.hdf5',
# driver=drv,
# backing_store=bcs) as f:
with tempfile.TemporaryFile() as f:
self.agg.save(f, test=True) #,report_unsaved=True)
# reread it
agg = Aggregate()
agg = agg.load(f, test=True)
else:
#with h5py.File('tempfile.hdf5') as f:
with open('tempfile.qrp','wb') as f:
self.agg.save(f)
#with h5py.File('tempfile.hdf5') as f:
with open('tempfile.qrp','rb') as f:
agg = Aggregate()
agg.load(f)
self.assertEqual(self.agg.nmono, agg.nmono)
self.assertEqual(self.agg.mult, agg.mult)
self.assertEqual(self.agg.sbi_mult, agg.sbi_mult)
self.assertEqual(self.agg.name, agg.name)
self.assertEqual(self.agg._has_egcf_matrix, agg._has_egcf_matrix)
self.assertEqual(self.agg._has_system_bath_interaction,
agg._has_system_bath_interaction)
self.assertEqual(self.agg.coupling_initiated, agg.coupling_initiated)
self.assertEqual(self.agg._has_relaxation_tensor,
agg._has_relaxation_tensor)
self.assertEqual(self.agg._relaxation_theory, agg._relaxation_theory)
self.assertEqual(self.agg._built, agg._built)
self.assertEqual(self.agg.Nel,agg.Nel)
self.assertEqual(self.agg.Ntot,agg.Ntot)
numpy.testing.assert_array_equal(self.agg.Nb,agg.Nb)
for key in agg.mnames.keys():
self.assertEqual(self.agg.mnames[key],agg.mnames[key])
numpy.testing.assert_array_equal(self.agg.resonance_coupling,
agg.resonance_coupling)
mnames = ["Molecule 1", "Molecule 2"]
for k in range(agg.nmono):
m = agg.monomers[k]
self.assertIn(m.name, mnames)
mnames.remove(m.name)
def test_trace_over_vibrations(self):
"""(Aggregate) Testing trace over vibrational DOF
"""
agg = self.vagg
ham = agg.get_Hamiltonian()
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[5, 5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=7)
N = agg.Nb[0]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N+5, N+5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=3)
N = agg.Nb[1]
rho = ReducedDensityMatrix(dim=ham.dim)
rho._data[N+5, N+5] = 1.0
redr = agg.trace_over_vibrations(rho)
numpy.testing.assert_almost_equal(numpy.trace(redr._data), 1.0,
decimal=2)
def test_get_Density_Matrix_thermal(self):
"""(Aggregate) Testing the get_Densitymatrix method with `thermal` condition type
"""
from quantarhei.core.units import kB_intK
vagg = self.vagg
H = vagg.get_Hamiltonian()
N = H.data.shape[0]
# zero temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal")
tst0 = numpy.zeros((N,N),dtype=qr.COMPLEX)
tst0[0,0] = 1.0
numpy.testing.assert_almost_equal(rho0.data, tst0)
# room temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal",
temperature=300)
# cannonical balance between neighboring states is tested
kbT = kB_intK*300.0
for k in range(N-1):
E2 = H.data[k+1,k+1]
E1 = H.data[k,k]
ratio = numpy.exp(-(E2-E1)/kbT)
numpy.testing.assert_almost_equal(ratio,
rho0.data[k+1,k+1]/rho0.data[k,k])
def test_get_Density_Matrix_thermal_excited(self):
"""(Aggregate) Testing the get_Densitymatrix method with `thermal_excited_state` condition type
"""
from quantarhei.core.units import kB_intK
vagg = self.vagg
H = vagg.get_Hamiltonian()
N = H.data.shape[0]
Nb0 = vagg.Nb[0]
# zero temperature
rho0 = vagg.get_DensityMatrix(condition_type="thermal_excited_state")
tst0 = numpy.zeros((N,N),dtype=qr.COMPLEX)
tst0[Nb0,Nb0] = 1.0
numpy.testing.assert_almost_equal(rho0.data, tst0)
# room temperature
kbT = kB_intK*300.0
H = self.agg.get_Hamiltonian()
N = H.data.shape[0]
Nb0 = self.agg.Nb[0]
with qr.eigenbasis_of(H):
rho0 = self.agg.get_DensityMatrix(condition_type="thermal_excited_state",
temperature=300)
tst0 = numpy.zeros((N,N),dtype=qr.COMPLEX)
with qr.eigenbasis_of(H):
ssum = 0.0
for i in range(Nb0, N):
tst0[i,i] = numpy.exp(-(H.data[i,i]-H.data[Nb0,Nb0])/kbT)
ssum += tst0[i,i]
tst0 = tst0/ssum
numpy.testing.assert_almost_equal(rho0.data, tst0)
# ssum = 0.0
# for i in range(N):
# tst0[i,i] = numpy.exp(-H.data[i,i]/kbT)
# ssum += tst0[i,i]
# tst0 = tst0/ssum
#
# DD = vagg.TrDMOp.data
# # abs value of the transition dipole moment
# dabs = numpy.sqrt(DD[:,:,0]**2 + \
# DD[:,:,1]**2 + DD[:,:,2]**2)
# # excitation from bra and ket
# tst0 = numpy.dot(dabs, numpy.dot(tst0,dabs))
#
# numpy.testing.assert_almost_equal(rho0.data, tst0)
def test_get_temperature(self):
"""(Aggregate) Testing temperature retrieval
"""
agg = self.agg
T = agg.get_temperature()
numpy.testing.assert_almost_equal(T, 300.0)
def test_init_coupling_matrix(self):
"""(Aggregate) Testing coupling matrix initialization
"""
agg = TestAggregate(name="dimer-2-env")
self.assertFalse(agg.coupling_initiated)
agg.init_coupling_matrix()
self.assertTrue(agg.coupling_initiated)
self.assertAlmostEqual(0.0, agg.resonance_coupling[0,1])
def test_set_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling setting with different units
"""
agg = TestAggregate(name="dimer-2-env")
agg.init_coupling_matrix()
agg.set_resonance_coupling(0, 1, 1.0)
self.assertAlmostEqual(1.0, agg.resonance_coupling[0,1])
self.assertAlmostEqual(1.0, agg.resonance_coupling[1,0])
with qr.energy_units("1/cm"):
agg.set_resonance_coupling(0, 1, 100.0)
self.assertAlmostEqual(qr.convert(100.0, "1/cm", "int"),
agg.resonance_coupling[0,1])
self.assertAlmostEqual(qr.convert(100.0, "1/cm", "int"),
agg.resonance_coupling[1,0])
def test_get_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling retrieval in different units
"""
agg = TestAggregate(name="dimer-2-env")
agg.init_coupling_matrix()
agg.set_resonance_coupling(0, 1, 1.0)
coup = agg.get_resonance_coupling(1,0)
self.assertAlmostEqual(coup, 1.0)
with qr.energy_units("1/cm"):
coup = agg.get_resonance_coupling(1,0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "1/cm"))
with qr.energy_units("eV"):
coup = agg.get_resonance_coupling(1,0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "eV"))
with qr.energy_units("THz"):
coup = agg.get_resonance_coupling(1,0)
self.assertAlmostEqual(coup, qr.convert(1.0, "int", "THz"))
def test_set_resonance_coupling_matrix(self):
"""(Aggregate) Testing setting the whole resonance coupling matrix
"""
agg = TestAggregate(name="dimer-2-env")
mat = [[0.0, 1.0],
[1.0, 0.0]]
agg.set_resonance_coupling_matrix(mat)
self.assertAlmostEqual(agg.resonance_coupling[1,0], 1.0)
self.assertAlmostEqual(agg.resonance_coupling[0,1], 1.0)
self.assertAlmostEqual(agg.resonance_coupling[0,0], 0.0)
self.assertAlmostEqual(agg.resonance_coupling[1,1], 0.0)
mat = ((0.0, 500.0),
(500.0, 0.0))
with qr.energy_units("1/cm"):
agg.set_resonance_coupling_matrix(mat)
inint = qr.convert(500, "1/cm", "int")
self.assertAlmostEqual(agg.resonance_coupling[1,0], inint)
self.assertAlmostEqual(agg.resonance_coupling[0,1], inint)
self.assertAlmostEqual(agg.resonance_coupling[0,0], 0.0)
self.assertAlmostEqual(agg.resonance_coupling[1,1], 0.0)
def test_dipole_dipole_coupling(self):
"""(Aggregate) Testing dipole-dipole coupling calculation
"""
agg = TestAggregate(name="dimer-2-env")
coup1 = agg.dipole_dipole_coupling(0,1)
coup2 = agg.dipole_dipole_coupling(0,1, epsr=2.0)
self.assertAlmostEqual(coup1, coup2*2.0)
with qr.energy_units("1/cm"):
coup = agg.dipole_dipole_coupling(0,1)
self.assertAlmostEqual(qr.convert(coup1,"int","1/cm"), coup)
def test_set_coupling_by_dipole_dipole(self):
"""(Aggregate) Testing dipole-dipole coupling calculation for the whole agregate
"""
agg = TestAggregate(name="dimer-2-env")
agg.set_coupling_by_dipole_dipole()
coup1 = agg.dipole_dipole_coupling(0,1)
self.assertAlmostEqual(coup1, agg.resonance_coupling[0,1])
with qr.energy_units("1/cm"):
agg.set_coupling_by_dipole_dipole()
coup1 = agg.dipole_dipole_coupling(0,1)
self.assertAlmostEqual(coup1, agg.resonance_coupling[0,1])
def test_calculate_resonance_coupling(self):
"""(Aggregate) Testing resonance coupling calculation by various methods
"""
agg = TestAggregate(name="dimer-2-env")
agg.calculate_resonance_coupling(method="dipole-dipole")
coup1 = agg.dipole_dipole_coupling(0,1)
self.assertEqual(coup1, agg.resonance_coupling[1,0])
with qr.energy_units("1/cm"):
agg.calculate_resonance_coupling(method="dipole-dipole")
self.assertEqual(coup1, agg.resonance_coupling[1,0])
def test_add_Molecule(self):
"""(Aggregate) Testing add_Molecule() method
"""
agg = TestAggregate(name="dimer-2-env")
mol = qr.Molecule(elenergies=[0.0, 1.0])
nmols1 = agg.nmono
agg.add_Molecule(mol)
nmols2 = agg.nmono
self.assertEqual(nmols1 + 1, nmols2)
self.assertEqual(len(agg.monomers), nmols2)
self.assertLessEqual(len(agg.mnames), nmols2)
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
# -*- 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)
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
AG.add_Molecule(m12)
print(AG._has_egcf_matrix)
print(AG._has_system_bath_interaction)
# setting coupling by dipole-dipole formula
AG.set_coupling_by_dipole_dipole(prefac=0.0147520827152)
print (AG.resonance_coupling[1,2]/cm2int)
# building aggregate
print("Building aggregate... ")
start = tm.time()
AG.build()
print("...done in ",tm.time()-start)
with energy_units("1/cm"):
anth = Molecule("Anth",[0.0,11380]) #*cm2int],[d0,d1])
anth.set_dipole(0,1,d1)
anth.set_egcf((0,1),cfce1)
# FIXME: use with construct
aAnth = AbsSpect(time,anth)
aAnth.calculate(12000*cm2int)
aAnth.normalize2()
a1 = AbsSpect(time,AG)
a1.calculate(12000*cm2int)
a1.normalize2()
# 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
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([0.0, en], "mol1")
m2 = Molecule([0.0, en], "mol2")
m1.set_egcf((0,1), cf)
m2.set_egcf((0,1), cf)
agg = Aggregate(name="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