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 setUp(self, verbose=False):
self.verbose = verbose
time = TimeAxis(0.0, 1000, 1.0)
with energy_units("1/cm"):
params = {
"ftype": "OverdampedBrownian",
"reorg": 30.0,
"T": 300.0,
"cortime": 100.0
}
cf1 = CorrelationFunction(time, params)
cf2 = CorrelationFunction(time, params)
sd = SpectralDensity(time, params)
cm1 = CorrelationFunctionMatrix(time, 2, 1)
cm1.set_correlation_function(cf1, [(0, 0), (1, 1)])
cm2 = CorrelationFunctionMatrix(time, 2, 1)
cm2.set_correlation_function(cf2, [(0, 0), (1, 1)])
K11 = numpy.array([[1.0, 0.0], [0.0, 0.0]], dtype=numpy.float)
K21 = numpy.array([[1.0, 0.0], [0.0, 0.0]], dtype=numpy.float)
K12 = K11.copy()
K22 = K21.copy()
KK11 = Operator(data=K11)
KK21 = Operator(data=K21)
KK12 = Operator(data=K12)
KK22 = Operator(data=K22)
self.sbi1 = SystemBathInteraction([KK11, KK21], cm1)
self.sbi2 = SystemBathInteraction([KK12, KK22], cm2)
with energy_units("1/cm"):
h1 = [[0.0, 100.0], [100.0, 0.0]]
h2 = [[0.0, 100.0], [100.0, 0.0]]
self.H1 = Hamiltonian(data=h1)
self.H2 = Hamiltonian(data=h2)
#sd.convert_2_spectral_density()
with eigenbasis_of(self.H1):
de = self.H1.data[1, 1] - self.H1.data[0, 0]
self.c_omega_p = sd.at(de, approx="spline") #interp_data(de)
self.c_omega_m = sd.at(-de, approx="spline") #interp_data(-de)
def setUp(self, verbose=False):
self.verbose = verbose
K12 = numpy.array([[0.0, 1.0], [0.0, 0.0]], dtype=numpy.float)
K21 = numpy.array([[0.0, 0.0], [1.0, 0.0]], dtype=numpy.float)
KK12 = Operator(data=K12)
KK21 = Operator(data=K21)
self.KK12 = KK12
self.KK21 = KK21
self.rates = (1.0 / 100.0, 1.0 / 200.0)
self.sbi1 = SystemBathInteraction([KK12, KK21], rates=self.rates)
self.sbi2 = SystemBathInteraction([KK12, KK21], rates=self.rates)
with energy_units("1/cm"):
h1 = [[100.0, 0.0], [0.0, 0.0]]
h2 = [[100.0, 0.0], [0.0, 0.0]]
self.H1 = Hamiltonian(data=h1)
self.H2 = Hamiltonian(data=h2)
# # 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 sbi = SystemBathInteraction(sys_operators=[K], rates=(1.0 / 100, )) agg.set_SystemBathInteraction(sbi) # # Corresponding Lindblad form # from quantarhei.qm import LindbladForm LF = LindbladForm(HH, sbi, as_operators=False) print(LF.data[1, 1, 2, 2]) print(LF.data[1, 2, 1, 2]) # # We can get it also from the aggregate #
def setUp(self, verbose=False):
self.verbose = verbose
#
# Lindblad projection operators
#
K12 = numpy.array([[0.0, 1.0], [0.0, 0.0]], dtype=numpy.float)
K21 = numpy.array([[0.0, 0.0], [1.0, 0.0]], dtype=numpy.float)
KK12 = Operator(data=K12)
KK21 = Operator(data=K21)
self.KK12 = KK12
self.KK21 = KK21
#
# Linbdlad rates
#
self.rates = (1.0 / 100.0, 1.0 / 200.0)
#
# System-bath interaction using operators and rates in site basis
#
self.sbi1 = SystemBathInteraction([KK12, KK21], rates=self.rates)
self.sbi2 = SystemBathInteraction([KK12, KK21], rates=self.rates)
#
# Test Hamiltonians
#
with energy_units("1/cm"):
h1 = [[100.0, 0.0], [0.0, 0.0]]
h2 = [[100.0, 0.0], [0.0, 0.0]]
self.H1 = Hamiltonian(data=h1)
self.H2 = Hamiltonian(data=h2)
h3 = [[100.0, 20.0], [20.0, 0.0]]
self.H3 = Hamiltonian(data=h3)
# less trivial Hamiltonian
h4 = [[100.0, 200.0, 30.0], [200.0, 50.0, -100.0],
[30.0, -100.0, 0.0]]
self.H4 = Hamiltonian(data=h4)
h4s = [[100.0, 0.0, 0.0], [0.0, 50.0, 0.0], [0.0, 0.0, 0.0]]
self.H4s = Hamiltonian(data=h4s)
#
# Projection operators in eigenstate basis
#
with eigenbasis_of(self.H3):
K_12 = ProjectionOperator(0, 1, dim=2)
K_21 = ProjectionOperator(1, 0, dim=2)
self.K_12 = K_12
self.K_21 = K_21
with eigenbasis_of(self.H4):
Ke_12 = ProjectionOperator(0, 1, dim=3)
Ke_21 = ProjectionOperator(1, 0, dim=3)
Ke_23 = ProjectionOperator(1, 2, dim=3)
Ke_32 = ProjectionOperator(2, 1, dim=3)
Ks_12 = ProjectionOperator(0, 1, dim=3)
Ks_21 = ProjectionOperator(1, 0, dim=3)
Ks_23 = ProjectionOperator(1, 2, dim=3)
Ks_32 = ProjectionOperator(2, 1, dim=3)
self.rates4 = [1.0 / 100, 1.0 / 200, 1.0 / 150, 1.0 / 300]
#
# System-bath operators defined in exciton basis
#
self.sbi3 = SystemBathInteraction([K_12, K_21], rates=self.rates)
self.sbi4e = SystemBathInteraction([Ke_12, Ke_21, Ke_23, Ke_32],
rates=self.rates4)
self.sbi4s = SystemBathInteraction([Ks_12, Ks_21, Ks_23, Ks_32],
rates=self.rates4)
class TestElectronicLindblad(unittest.TestCase):
"""Tests for the ElectronicLindbladForm class
"""
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 test_comparison_of_rates_in_electronic(self):
"""Testing that ElectronicLindblad and rate matrix are compatible
This is for the case that everything is electronic
"""
dim = self.ham.dim
KT = numpy.zeros((dim, dim), dtype=numpy.float64)
KM = numpy.zeros((dim, dim), dtype=numpy.float64)
LT = ElectronicLindbladForm(self.ham, self.sbi, as_operators=False)
for n in range(dim):
for m in range(dim):
KT[n, m] = numpy.real(LT.data[n, n, m, m])
KM = numpy.zeros((dim, dim))
KM[1, 1] = -self.rates[1]
KM[2, 2] = -self.rates[0]
KM[1, 2] = self.rates[0]
KM[2, 1] = self.rates[1]
#print("KT = ", KT)
#print("KM = ", KM)
#print("LT = ", LT.data)
numpy.testing.assert_allclose(KT, KM, rtol=1.0e-2)
def test_construction_electronic_lindblad(self):
"""Testing construction of electronic Lindblad form for vibronic system
"""
LT = ElectronicLindbladForm(self.vham, self.vsbi, as_operators=False)
dim = self.vham.dim
zer = numpy.zeros((dim, dim, dim, dim), dtype=numpy.float64)
numpy.testing.assert_array_equal(LT._data - LT._data, zer)
def test_comparison_with_and_without_vib(self):
"""Testing ElectronicLindbladForm in propagation
"""
# Lindblad forms
LT = ElectronicLindbladForm(self.ham, self.sbi, as_operators=False)
vLT = ElectronicLindbladForm(self.vham, self.vsbi, as_operators=False)
# Propagators
time = TimeAxis(0.0, 1000, 1.0)
el_prop = ReducedDensityMatrixPropagator(time, self.ham, LT)
vib_prop = ReducedDensityMatrixPropagator(time, self.vham, vLT)
# electronic initial condition
rho0 = ReducedDensityMatrix(dim=self.ham.dim)
rho0.data[2, 2] = 1.0
# vibronic intial condition
vrho0 = ReducedDensityMatrix(dim=self.vham.dim)
agg = self.vsbi.system
Nin = agg.vibindices[2][0]
vrho0.data[Nin, Nin] = 1.0
# propagations
rhot = el_prop.propagate(rho0)
vrhot = vib_prop.propagate(vrho0)
# averaging over vibrational level at t=0
Nel = agg.Nel
aver_vrhot0 = agg.trace_over_vibrations(vrho0)
# Test
numpy.testing.assert_allclose(rhot._data[0, :, :], rho0._data)
numpy.testing.assert_allclose(rhot._data[0, :, :], aver_vrhot0._data)
aver_vrhot10 = agg.trace_over_vibrations(vrhot, 10)
numpy.testing.assert_allclose(rhot._data[10, :, :], aver_vrhot10._data)
aver_vrhot800 = agg.trace_over_vibrations(vrhot, 800)
numpy.testing.assert_allclose(rhot._data[800, :, :],
aver_vrhot800._data)
# # 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 sbi = SystemBathInteraction(sys_operators=[K], rates=(1.0/100,)) agg.set_SystemBathInteraction(sbi) # # Corresponding Lindblad form # from quantarhei.qm import LindbladForm LF = LindbladForm(HH, sbi, as_operators=False) print(LF.data[1,1,2,2]) print(LF.data[1,2,1,2]) # # We can get it also from the aggregate #
def test_LindbladWithVibrations_dynamics_comp(self):
"""Compares Lindblad dynamics of a system with vibrations calculated from propagator and superoperator
"""
# Aggregate
import quantarhei as qr
time = qr.TimeAxis(0.0, 1000, 1.0)
# create a model
with qr.energy_units("1/cm"):
me1 = qr.Molecule([0.0, 12100.0])
me2 = qr.Molecule([0.0, 12000.0])
me3 = qr.Molecule([0.0, 12900.0])
agg_el = qr.Aggregate([me1, me2, me3])
agg_el.set_resonance_coupling(0, 1, qr.convert(150, "1/cm", to="int"))
agg_el.set_resonance_coupling(1, 2, qr.convert(50, "1/cm", to="int"))
m1 = qr.Molecule([0.0, 12100.0])
m2 = qr.Molecule([0.0, 12000.0])
m3 = qr.Molecule([0.0, 12900.0])
mod1 = qr.Mode(frequency=qr.convert(100, "1/cm", "int"))
m1.add_Mode(mod1)
mod1.set_HR(1, 0.01)
agg = qr.Aggregate([m1, m2, m3])
agg.set_resonance_coupling(0, 1, qr.convert(150, "1/cm", to="int"))
agg.set_resonance_coupling(1, 2, qr.convert(50, "1/cm", to="int"))
agg_el.build()
agg.build()
hame = agg_el.get_Hamiltonian()
ham = agg.get_Hamiltonian()
# calculate relaxation tensor
with qr.eigenbasis_of(hame):
#
# Operator describing relaxation
#
K = qr.qm.ProjectionOperator(1, 2, dim=hame.dim)
#
# System bath interaction with prescribed rate
#
from quantarhei.qm import SystemBathInteraction
sbi = SystemBathInteraction(sys_operators=[K], rates=(1.0/100.0,))
sbi.set_system(agg) #agg.set_SystemBathInteraction(sbi)
with qr.eigenbasis_of(ham):
#
# Corresponding Lindblad form
#
from quantarhei.qm import ElectronicLindbladForm
LF = ElectronicLindbladForm(ham, sbi, as_operators=True)
#
# Evolution of reduced density matrix
#
prop = qr.ReducedDensityMatrixPropagator(time, ham, LF)
#
# Evolution by superoperator
#
eSO = qr.qm.EvolutionSuperOperator(time, ham, LF)
eSO.set_dense_dt(5)
eSO.calculate()
# compare the two propagations
pairs = [(5,4), (5,5), (6,5), (7,5)]
for p in pairs:
rho_i1 = qr.ReducedDensityMatrix(dim=ham.dim)
rho_i1.data[p[0],p[1]] = 1.0
rho_t1 = prop.propagate(rho_i1)
exp_rho_t2 = eSO.data[:,:,:,p[0],p[1]]
#import matplotlib.pyplot as plt
#plt.plot(rho_t1.TimeAxis.data, numpy.real(rho_t1.data[:,p[0],p[1]]), "-r")
#plt.plot(rho_t1.TimeAxis.data, numpy.real(exp_rho_t2[:,p[0],p[1]]), "--g")
#plt.show()
#for kk in range(rho_t1.TimeAxis.length):
# print(kk, numpy.real(rho_t1.data[kk,p[0],p[1]]),numpy.real(exp_rho_t2[kk,p[0],p[1]]))
#numpy.testing.assert_allclose(RRT.data, rtd)
numpy.testing.assert_allclose(numpy.real(rho_t1.data[:,:,:]),
numpy.real(exp_rho_t2[:,:,:]),
rtol=5.0e-2,
atol=1.0e-3)
m3v.add_Mode(mod3)
mod3.set_nmax(0, Nvib)
mod3.set_nmax(1, Nvib)
mod3.set_HR(1, 0.3)
vagg = Aggregate(molecules=[m1v, m2v, m3v])
vagg.build()
from quantarhei.qm import ProjectionOperator
K12 = ProjectionOperator(1, 2, dim=4)
K23 = ProjectionOperator(2, 3, dim=4)
ops = [K12, K23]
rates = [1.0/100.0, 1.0/150.0]
vsbi = SystemBathInteraction(sys_operators=ops, rates=rates)
vsbi.set_system(vagg)
from quantarhei.qm import ElectronicLindbladForm
ham = vagg.get_Hamiltonian()
print("Hamiltonian dimension: ", ham.dim)
print("Constructing electronic Lindblad form")
eLF = ElectronicLindbladForm(ham, vsbi, as_operators=True)
print("...done")
time = TimeAxis(0.0, 1000, 1.0)
from quantarhei.qm import ReducedDensityMatrixPropagator
vibprop = ReducedDensityMatrixPropagator(time, ham, eLF)
def test_Lindblad_dynamics_comp(self):
"""Compares Lindblad dynamics calculated from propagator and superoperator
"""
# Aggregate
import quantarhei as qr
import quantarhei.models.modelgenerator as mgen
time = qr.TimeAxis(0.0, 1000, 1.0)
# create a model
mg = mgen.ModelGenerator()
agg = mg.get_Aggregate(name="trimer-1")
agg.build()
ham = agg.get_Hamiltonian()
# calculate relaxation tensor
with qr.eigenbasis_of(ham):
#
# Operator describing relaxation
#
from quantarhei.qm import Operator
K = Operator(dim=ham.dim, real=True)
K.data[1, 2] = 1.0
#
# System bath interaction with prescribed rate
#
from quantarhei.qm import SystemBathInteraction
sbi = SystemBathInteraction(sys_operators=[K],
rates=(1.0 / 100.0, ))
agg.set_SystemBathInteraction(sbi)
#
# Corresponding Lindblad form
#
from quantarhei.qm import LindbladForm
LF = LindbladForm(ham, sbi, as_operators=False)
#
# Evolution of reduced density matrix
#
prop = qr.ReducedDensityMatrixPropagator(time, ham, LF)
#
# Evolution by superoperator
#
eSO = qr.qm.EvolutionSuperOperator(time, ham, LF)
eSO.set_dense_dt(5)
eSO.calculate()
# compare the two propagations
pairs = [(1, 3), (3, 2), (3, 3)]
for p in pairs:
rho_i1 = qr.ReducedDensityMatrix(dim=ham.dim)
rho_i1.data[p[0], p[1]] = 1.0
rho_t1 = prop.propagate(rho_i1)
exp_rho_t2 = eSO.data[:, :, :, p[0], p[1]]
#import matplotlib.pyplot as plt
#plt.plot(rho_t1.TimeAxis.data, numpy.real(rho_t1.data[:,p[0],p[1]]))
#plt.plot(rho_t1.TimeAxis.data, numpy.real(exp_rho_t2[:,p[0],p[1]]))
#plt.show()
#numpy.testing.assert_allclose(RRT.data, rtd)
numpy.testing.assert_allclose(numpy.real(rho_t1.data[:, :, :]),
numpy.real(exp_rho_t2[:, :, :]),
rtol=1.0e-7,
atol=1.0e-6)
def test_LindbladWithVibrations_dynamics_comp(self):
"""Compares Lindblad dynamics of a system with vibrations calculated from propagator and superoperator
"""
# Aggregate
import quantarhei as qr
time = qr.TimeAxis(0.0, 1000, 1.0)
# create a model
with qr.energy_units("1/cm"):
me1 = qr.Molecule([0.0, 12100.0])
me2 = qr.Molecule([0.0, 12000.0])
me3 = qr.Molecule([0.0, 12900.0])
agg_el = qr.Aggregate([me1, me2, me3])
agg_el.set_resonance_coupling(0, 1,
qr.convert(150, "1/cm", to="int"))
agg_el.set_resonance_coupling(1, 2, qr.convert(50,
"1/cm",
to="int"))
m1 = qr.Molecule([0.0, 12100.0])
m2 = qr.Molecule([0.0, 12000.0])
m3 = qr.Molecule([0.0, 12900.0])
mod1 = qr.Mode(frequency=qr.convert(100, "1/cm", "int"))
m1.add_Mode(mod1)
mod1.set_HR(1, 0.01)
agg = qr.Aggregate([m1, m2, m3])
agg.set_resonance_coupling(0, 1, qr.convert(150, "1/cm", to="int"))
agg.set_resonance_coupling(1, 2, qr.convert(50, "1/cm", to="int"))
agg_el.build()
agg.build()
hame = agg_el.get_Hamiltonian()
ham = agg.get_Hamiltonian()
# calculate relaxation tensor
with qr.eigenbasis_of(hame):
#
# Operator describing relaxation
#
K = qr.qm.ProjectionOperator(1, 2, dim=hame.dim)
#
# System bath interaction with prescribed rate
#
from quantarhei.qm import SystemBathInteraction
sbi = SystemBathInteraction(sys_operators=[K],
rates=(1.0 / 100.0, ))
sbi.set_system(agg) #agg.set_SystemBathInteraction(sbi)
with qr.eigenbasis_of(ham):
#
# Corresponding Lindblad form
#
from quantarhei.qm import ElectronicLindbladForm
LF = ElectronicLindbladForm(ham, sbi, as_operators=True)
#
# Evolution of reduced density matrix
#
prop = qr.ReducedDensityMatrixPropagator(time, ham, LF)
#
# Evolution by superoperator
#
eSO = qr.qm.EvolutionSuperOperator(time, ham, LF)
eSO.set_dense_dt(5)
eSO.calculate()
# compare the two propagations
pairs = [(5, 4), (5, 5), (6, 5), (7, 5)]
for p in pairs:
rho_i1 = qr.ReducedDensityMatrix(dim=ham.dim)
rho_i1.data[p[0], p[1]] = 1.0
rho_t1 = prop.propagate(rho_i1)
exp_rho_t2 = eSO.data[:, :, :, p[0], p[1]]
#import matplotlib.pyplot as plt
#plt.plot(rho_t1.TimeAxis.data, numpy.real(rho_t1.data[:,p[0],p[1]]), "-r")
#plt.plot(rho_t1.TimeAxis.data, numpy.real(exp_rho_t2[:,p[0],p[1]]), "--g")
#plt.show()
#for kk in range(rho_t1.TimeAxis.length):
# print(kk, numpy.real(rho_t1.data[kk,p[0],p[1]]),numpy.real(exp_rho_t2[kk,p[0],p[1]]))
#numpy.testing.assert_allclose(RRT.data, rtd)
numpy.testing.assert_allclose(numpy.real(rho_t1.data[:, :, :]),
numpy.real(exp_rho_t2[:, :, :]),
rtol=5.0e-2,
atol=1.0e-3)
class TestElectronicLindblad(unittest.TestCase):
"""Tests for the ElectronicLindbladForm class
"""
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 test_comparison_of_rates_in_electronic(self):
"""Testing that ElectronicLindblad and rate matrix are compatible
This is for the case that everything is electronic
"""
dim = self.ham.dim
KT = numpy.zeros((dim,dim), dtype=numpy.float64)
KM = numpy.zeros((dim,dim), dtype=numpy.float64)
LT = ElectronicLindbladForm(self.ham, self.sbi, as_operators=False)
for n in range(dim):
for m in range(dim):
KT[n,m] = numpy.real(LT.data[n,n,m,m])
KM = numpy.zeros((dim,dim))
KM[1,1] = -self.rates[1]
KM[2,2] = -self.rates[0]
KM[1,2] = self.rates[0]
KM[2,1] = self.rates[1]
#print("KT = ", KT)
#print("KM = ", KM)
#print("LT = ", LT.data)
numpy.testing.assert_allclose(KT,KM, rtol=1.0e-2)
def test_construction_electronic_lindblad(self):
"""Testing construction of electronic Lindblad form for vibronic system
"""
LT = ElectronicLindbladForm(self.vham, self.vsbi, as_operators=False)
dim = self.vham.dim
zer = numpy.zeros((dim, dim, dim, dim), dtype=numpy.float64)
numpy.testing.assert_array_equal(LT._data-LT._data, zer)
def test_comparison_with_and_without_vib(self):
"""Testing ElectronicLindbladForm in propagation
"""
# Lindblad forms
LT = ElectronicLindbladForm(self.ham, self.sbi, as_operators=False)
vLT = ElectronicLindbladForm(self.vham, self.vsbi, as_operators=False)
# Propagators
time = TimeAxis(0.0, 1000, 1.0)
el_prop = ReducedDensityMatrixPropagator(time, self.ham, LT)
vib_prop = ReducedDensityMatrixPropagator(time, self.vham, vLT)
# electronic initial condition
rho0 = ReducedDensityMatrix(dim=self.ham.dim)
rho0.data[2,2] = 1.0
# vibronic intial condition
vrho0 = ReducedDensityMatrix(dim=self.vham.dim)
agg = self.vsbi.system
Nin = agg.vibindices[2][0]
vrho0.data[Nin, Nin] = 1.0
# propagations
rhot = el_prop.propagate(rho0)
vrhot = vib_prop.propagate(vrho0)
# averaging over vibrational level at t=0
Nel = agg.Nel
aver_vrhot0 = agg.trace_over_vibrations(vrho0)
# Test
numpy.testing.assert_allclose(rhot._data[0,:,:], rho0._data)
numpy.testing.assert_allclose(rhot._data[0,:,:], aver_vrhot0._data)
aver_vrhot10 = agg.trace_over_vibrations(vrhot, 10)
numpy.testing.assert_allclose(rhot._data[10,:,:],
aver_vrhot10._data)
aver_vrhot800 = agg.trace_over_vibrations(vrhot, 800)
numpy.testing.assert_allclose(rhot._data[800,:,:],
aver_vrhot800._data)