qsh

libra_py.workflows.nbra.qsh.compute_freqs(H_vib, params)[source]

Compute a matrix of frequencies for each matrix element

Parameters

  • H_vib (list of CMATRIX objects) – the vibronic Hamiltonian for all time-points H_vib[istep].get(i,j) - i,j matrix element for the step istep

  • params (dictionary) –

    the parameters that control the execution of this function

    SeeAlso: influence_spectrum.compute_mat_elt for the description of other parameters:

    • filename

    • logname

    • nfreqs

    SeeAlso: influence_spectrum.recipe1(data, params) for the description of other parameters:

    • dt

    • wspan

    • dw

    • do_output

    • acf_filename

    • spectrum_filename

    • do_center

    • acf_type

    • data_type

Returns

(freqs, dev), where:

SeeAlso: influence_spectrum.compute_mat_elt for the description of the output freqs

dev ( list of lists of double ):

dev[i][j] is the standard deviation the QSH terms (sum over frequencies)

Return type

tuple

libra_py.workflows.nbra.qsh.compute_qs_Hvib(Nfreqs, freqs, t, H_vib_re_ave, H_vib_re_std, dw_Hvib_re, up_Hvib_re, H_vib_im_ave, H_vib_im_std, dw_Hvib_im, up_Hvib_im, dev)[source]

Compute the QSH Hamiltonians

Parameters

  • Nfreqs (int) – the number of frequencies we want to use in the QSH calculations (upper limit, the actual number could be smaller)

  • freqs (list of lists of doubles) – contains the spectral info for various matrix elements of the sampled Hvib SeeAlso: influence_spectrum.compute_mat_elt for the description of the output freqs

  • t (double) – time at which we want to reconstruct the QSH [ units: a.u. ]

  • H_vib_re_ave (MATRIX(nstates, nstates)) – average of energies for direct Hamiltonian

  • H_vib_im_ave (MATRIX(nstates, nstates)) – average of couplings for direct Hamiltonian

  • H_vib_re_std (MATRIX(nstates, nstates)) – std of energies for direct Hamiltonian

  • H_vib_im_std (MATRIX(nstates, nstates)) – std of couplings for direct Hamiltonian

  • up_Hvib_re (MATRIX(nstates, nstates)) – maximum value of energies for direct Hamiltonian

  • up_Hvib_im (MATRIX(nstates, nstates)) – maximum value of couplings for direct Hamiltonian

  • dw_Hvib_re (MATRIX(nstates, nstates)) – minimal value of energies for direct Hamiltonian

  • dw_Hvib_im (MATRIX(nstates, nstates)) – minimal value of couplings for direct Hamiltonian

  • dev (list of lists of doubles, nstates x nstates) – std for direct Hamiltonian SeeAlso: compute_freqs for the description of the output dev

Returns

contains QSH vibronic Hamiltonian at a given time

Return type

CMATRIX(nstates, nstates)

libra_py.workflows.nbra.qsh.run(H_vib, params)[source]

The procedure to convert the results of QE/model Hvib calculations to longer timescales using the QSH approach

Parameters

  • H_vib (list of lists of CMATRIX) –

    the vibronic Hamiltonian for all data sets and all time-points

    Such that H_vib[idata][istep].get(i,j) is the i,j matrix element for the data set `idata` and step in that data set `istep`

  • params (dictionary) –

    controls the present and all underlying level calculations

    • params[“dt”] ( double ): nuclear dynamics integration time step

      this is also the spacing between initial data points [ units: a.u. of time, default: 41.0]

    • params[“nfreqs”] ( int ): maximal number of frequencies to use to reconstruct all the matrix elements [ default: 1]

    • params[“nsteps”] ( int ): how many time-steps of QSH to generate [ default: 10]

    • params[“do_QSH_output”] ( Boolean ): the flag that determines whether to generate the

      output files containing the QSH Hamiltonians. [ default : False]

    • params[“output_set_paths”] ( list of strings ):

      Directories where the resulting QSH Hvib files will be printed out. These directories should already exist [default: QSH_#_of_data_set, e.g. QSH_0, QSH_1, etc.]

    • params[“qsh_Hvib_re_prefix”] ( string ): prefixes of the output files with real part

      of the QSH vibronic Hamiltonian at time t

    • params[“qsh_Hvib_re_suffix”] ( string ): suffixes of the output files with real part

      of the QSH vibronic Hamiltonian at time t

    • params[“qsh_Hvib_im_prefix”] ( string ): prefixes of the output files with imaginary part

      of the QSH vibronic Hamiltonian at time t

    • params[“qsh_Hvib_im_suffix”] ( string ): suffixes of the output files with imaginary part

      of the QSH vibronic Hamiltonian at time t

Returns

qsh_H_vib, such as

qsh_H_vib[idata][istep] - is a CMATRIX(nstates, nstates) object representing a vibronic Hamiltonian predicted for the time step istep using the training dataset idata

Return type

( list of lists )