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 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 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 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
# -*- 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)
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)
psi_t = dimer_propagator.propagate(psi)
psi_t.plot(ptype="square", show=False)
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
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(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)
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()
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)
AG.add_Molecule(m11)
AG.add_Molecule(m12)
print(AG._has_egcf_matrix)
print(AG._has_system_bath_interaction)
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
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
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
