Averaging over non-adiabatic couplings for a pair of states in MD trajectory

[Hamid Mehdipour]

Dear PYXAID users,

I would be very thankful if anyone here share their knowledge of averaging over a a pair of state's non-adiabatic coupling for a MD trajectory. Does pyxaid have any script that could perform such averaging? or one has to make a python script for that?

All the best

Hamid

[brendanqhd]

Hi Hamid,

In step3, at the end of the file "py-scr3.py", there should be the following:

average.average(params["namdtime"],Nstates,params["iconds"],opt,MS,inp_dir,res_dir)

This should calculate the average NACs associated with your initial conditions.

Best,
Brendan

[Hamid Mehdipour]

Hi Brendan,

Great!

Do appreciate your very fast response to my question.

Best

Hamid

[Hamid Mehdipour]

Dear Brenden,

To be honest I do not know where exactly the values of NACs (for each pair of states) is written? the only output I get are decoherence_rate, spectral density, dephasing function, energy and populations. Does one has to set params["debug_flag"] at 1 or 2 ...?

Best

Hamid

[Alexey Akimov]

Dear Hamid,

Yes, there is such a script - see for instance here: https://github.com/Quantum-Dynamics-Hub/pyxaid2/blob/master/code_level3/py-scr6.py 

The lines like

excitation_spectrum.ham_map("res/0_Ham_", tmin,tmax,"_re" ,opt,scl1,"spectr1/ave_Ham_re.dat")

Will compute the trajectory-average over the vibronic Hamiltonian matrices (real part of those, that is the energies). The line

excitation_spectrum.ham_map("res/0_Ham_", tmin,tmax,"_im" ,opt,scl1,"spectr1/ave_Ham_im.dat")

will do the same for the imaginary parts, that is for the couplings.

opt = 1

selects an averaging of the absolute values of couplings |d_ij|.

Best,

Alexey

[Hamid Mehdipour]

Really appreciated