params["Hvib_im_prefix"] = "hvib_"
params["Hvib_im_suffix"] = "_im"
# General simulaiton parameters
params["T"] = 300.0 # Temperature, K
params[
"dt"] = 1.0 * units.fs2au # Nuclear dynamics integration timestep, in a.u.
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
print("\nGathering data from MD ")
absolute_path = os.getcwd()
params = {}
params["data_set_paths"] = []
params["data_set_paths"].append(absolute_path + "/../../../step3/res_mb_sp/")
params["Hvib_re_prefix"] = "Hvib_ci_"
params["Hvib_re_suffix"] = "_re"
params["Hvib_im_prefix"] = "Hvib_ci_"
params["Hvib_im_suffix"] = "_im"
params["nfiles"] = 1800
params["nstates"] = 151 # total number of electronic states
params["init_times"] = [0]
params["active_space"] = list(range(1,
params["nstates"])) # indexing is from 0!
# Include H**O and up to the last electronic state
hvib_mb = step4.get_Hvib2(params)
hvib_mb[0][-1].show_matrix()
print("Length of hvib_mb is: ", len(hvib_mb[0]))
#sys.exit(0)
# For the SD (SP) case
print("\nGathering data from MD ")
absolute_path = os.getcwd()
params = {}
params["data_set_paths"] = []
params["data_set_paths"].append(absolute_path + "/../../../step3/res_mb_sp/")
params["Hvib_re_prefix"] = "Hvib_sd_"
params["Hvib_re_suffix"] = "_re"
params["Hvib_im_prefix"] = "Hvib_sd_"
params["Hvib_im_suffix"] = "_im"
params["nfiles"] = 1800
params["data_set_paths"].append(
"/budgetdata/academic/alexeyak/brendan/Si_QD/F_capped/1nm/step2_F1/traj0/res/"
)
params["Hvib_re_prefix"] = "hvib_"
params["Hvib_re_suffix"] = "_re"
params["Hvib_im_prefix"] = "hvib_"
params["Hvib_im_suffix"] = "_im"
params["nfiles"] = 5000
params["nstates"] = 30
params["init_times"] = [0]
params["active_space"] = range(30)
times = [5000]
for t in times:
params["nsteps"] = t
Hvib = step4.get_Hvib2(params)
# Compute energy gaps for states i,j in trajectory of length "t"
dE = decoherence_times.energy_gaps_ave(Hvib, [params["init_times"][0]],
params["nsteps"])
# For computing influence spectra
params2 = {}
params2["dt"] = 1.0 # MD timestep in fs
params2["wspan"] = 16384.0 # cm^-1
params2["dw"] = 1.0 # cm^-1
params2["do_output"] = False
params2["do_center"] = True
params2["acf_type"] = 1
params2["data_type"] = 0
states = range(len(params["active_space"]))
absolute_path = os.getcwd()
params = {}
params["data_set_paths"] = []
params["data_set_paths"].append(absolute_path + "/namd_data/")
#params["data_set_paths"].append(absolute_path+"/../dftbp_check/step3/res_mb_sp/")
params["Hvib_re_prefix"] = "Hvib_ks_"
params["Hvib_re_suffix"] = "_re"
params["Hvib_im_prefix"] = "Hvib_ks_"
params["Hvib_im_suffix"] = "_im"
params["nfiles"] = 2000
params["nstates"] = 2 # total number of electronic states
params["init_times"] = [10000]
params["active_space"] = range(2) # indexing is from 0!
#params["active_space"] = range(0,int(params["nstates"]/2)) # indexing is from 0!
# Include H**O and up to the last electronic state
Hvib_ks = step4.get_Hvib2(params)
Hvib_ks[0][-1].show_matrix()
print("Length of hvib is: ", len(Hvib_ks[0]))
#sys.exit(0)
def compute_state_energies_vs_time(hvib):
"""
Computes the states energies vs time for a given hvib.
hvib ( list of list of matrices ): The vibronic hamiltonian for all timesteps
returns: a list of energies vs time for all states in hvib
"""
nsteps = len(hvib)
nstates = hvib[0].num_of_rows
energies = []
for state in [0, 1]:
print("\nGathering data from MD ")
absolute_path = os.getcwd()
params = {}
params["data_set_paths"] = []
params["data_set_paths"].append(absolute_path +
"/../../step3/mixed_electron_hole/_res")
params["Hvib_re_prefix"] = "Hvib_ci_"
params["Hvib_re_suffix"] = "_re"
params["Hvib_im_prefix"] = "Hvib_ci_"
params["Hvib_im_suffix"] = "_im"
params["nfiles"] = 4000
params["nstates"] = 31 # total number of electronic states
params["init_times"] = [0]
params["active_space"] = list(range(params["nstates"])) # indexing is from 0!
# Include H**O and up to the last electronic state
hvib_mb = step4.get_Hvib2(params)
hvib_mb[0][-1].show_matrix()
print("Length of hvib_mb is: ", len(hvib_mb[0]))
#sys.exit(0)
print("\nGathering data from MD ")
absolute_path = os.getcwd()
params = {}
params["data_set_paths"] = []
params["data_set_paths"].append(absolute_path +
"/../../step3/mixed_electron_hole/_res")
params["Hvib_re_prefix"] = "Hvib_sd_"
params["Hvib_re_suffix"] = "_re"
params["Hvib_im_prefix"] = "Hvib_sd_"
params["Hvib_im_suffix"] = "_im"
params["nfiles"] = 4000