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 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 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 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 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()
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"):
rwa_cm = agg.get_RWA_suggestion()
rwa = agg.get_RWA_suggestion()
#
# Calculate 2D spectra
# -*- 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.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)
#dat = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.01], [0.0, 0.01, 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) #dat = [[0.0, 0.0, 0.0], [0.0, 1.0, 0.01], [0.0, 0.01, 1.1]]
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")
print(H.data.shape)
with energy_units("1/cm"):
print(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
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 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
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
