params["nsteps"] = params["nfiles"] # The length of the NA-MD trajectory params["init_times"] = [0] # starting points for sub-trajectories params["do_output"] = True # request to print the results into a file params[ "do_return"] = False # request to not store the date in the operating memory # For running NA-MD start = time.time() Hvib = step4.get_Hvib2( params) # get the Hvib for all data sets, Hvib is a lists of lists init_time = params["init_times"][0] end = time.time() print("Time to read / assemble data = ", end - start) # Compute average decoherence time over entire trajectory tau, rates = decoherence_times.decoherence_times_ave( Hvib, [init_time], params["nfiles"] - init_time, 0) avg_deco = tau / units.fs2au avg_deco.show_matrix() """ #====================== One case ===================== # Looking on the "SH" populations - NBRA-TSH approach params["gap_min_exception"] = 0 params["Boltz_opt"] = 1 # Option for the frustrated hops acceptance/rejection params["Boltz_opt_BL"] = 0 # Option to incorporate hte frustrated hops into BL probabilities params["outfile"] = "_out_TSH_.txt" # output file params["evolve_Markov"] = False # don't propagate Markov params["evolve_TSH"] = True # Rely on propagating trajectories params["ntraj"] = 100 # how many stochastic trajectories start = time.time() res = lz.run(Hvib, params) end = time.time()
data_conv.scissor( Hvib, 2, -0.40 / 27.2114 ) # energies of 2 and 3 SD states are lowered more by -0.33 eV as a result of lowering energies of ZnPc's L and L+1 states by -0.33 eV # """ # to switch on and off the shifting/rescaling # Compute tNAC map opt = 2 Hvib_ave = data_stat.cmat_stat2(Hvib[0], opt) data_outs.show_matrix_splot((1000.0 / units.ev2Ha) * Hvib_ave.imag(), "_tnac_61_pc1sr1.txt", set_diag_to_zero=0) # calculations of the decoherence times tau, rates = decoherence_times.decoherence_times_ave(Hvib, [0], params["fsnap"], 0) avg_deco = tau * units.au2fs avg_deco.show_matrix() # Compute average band gap: # avg_gap = decoherence_times.energy_gaps_ave(Hvib, [0], nsteps) # 5. Nonadiabatic Dynamics params = {} params["nfiles"] = 5997 # ex # of Hvib files to read for a given traj for i in [0, 2, 3]: for j in [2, 3]: params[