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
SS = H.diagonalize()
H.undiagonalize()
print("\nHamiltonian in internal units")
print(H)
print("\nTransformation matrix")
print(SS)
print("\nAll states")
k = 0
for st in ag.allstates(mult=mult, save_indices=True):
print(st[0], ag.elsigs[k])
k += 1
sbi = ag.get_SystemBathInteraction()
cfm = sbi.CC
print("\nReorganization energies")
for ic in range(cfm.nof):
with energy_units("1/cm"):
print(ic, cfm.cfuncs[ic+1].get_reorganization_energy())
print("\nSBI:")
print(sbi)
print(ag)
print(ag.which_band)
print(ag.vibindices)
#plt.title('aggregate: 12 perylenes, linear dense zigzag ')
#plt.savefig('L12per_pbl_spec.pdf')
plt.show()
with energy_units("1/cm"):
aAnth.plot(axis=[10000,15000,0.0,1.1])
# Redfield Tensor
print("Calculating relaxation tensor ...")
start = tm.time()
# System bath interaction
#sbi = AG.get_system_bath_coupling()
sbi = AG.get_SystemBathInteraction()
# Hamiltonian
HH = AG.get_Hamiltonian()
# Relaxation tensor
RT = RedfieldRelaxationTensor(HH,sbi)
#RT = TDRedfieldRelaxationTensor(HH,sbi)
RT.secularize()
print("... done in ",tm.time()-start)
#for n in range(4):
# print(numpy.real(RT.data[n,n,5,5]))
#
#RR = RedfieldRateMatrix(HH,sbi)
#for n in range(4):
# print(numpy.real(RR.data[n,5]))
print(D.data[0, 3, :])
SS = H.diagonalize()
H.undiagonalize()
print("\nHamiltonian in internal units")
print(H)
print("\nTransformation matrix")
print(SS)
print("\nAll states")
k = 0
for st in ag.allstates(mult=mult, save_indices=True):
print(st[0], ag.elsigs[k])
k += 1
sbi = ag.get_SystemBathInteraction()
cfm = sbi.CC
print("\nReorganization energies")
for ic in range(cfm.nof):
with energy_units("1/cm"):
print(ic, cfm.cfuncs[ic + 1].get_reorganization_energy())
print("\nSBI:")
print(sbi)
print(ag)
print(ag.which_band)
print(ag.vibindices)
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([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
