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