RT-TDSCF Tutorial

Running a RT-TDSCF simulation is a simple two-step process

/path/to/ReSpect/respect --scf   --inp=my-input-file --scratch=/path/to/scratch/directory
/path/to/ReSpect/respect --tdscf --inp=my-input-file --scratch=/path/to/scratch/directory

The first call of respect with the argument --scf starts a time-independent SCF calculation, which is a necessary prerequisite for the following RT-TDSCF calculation. The second call of respect with the argument --tdscf actually starts the RT-TDSCF simulation, the result of which can be further post-processed and visualized by a script spectrum.py provided with the ReSpect installation (see text below for more details).

The other arguments mandatory to respect are

  • --inp
    specifies a name of the input file;

  • --scratch
    specifies a path to the scratch directory.

The input file my-input-file.inp should contain an input block scf: with some SCF-specific keywords and an input block tdscf: with some TDSCF-specific keywords. A comprehensive list of all keywords for SCF can be found here and for TDSCF here. A simple example of my-input-file.inp looks like

#non-relativistic 1c Hartree-Fock calculation of H2O molecule
scf:

    geometry:
        O    0.000000    0.000000    0.000000
        H    0.000000    0.000000    0.940000
        H    0.903870    0.000000   -0.258105

    method: hf
    basis:  ucc-pvdz

    charge:        0
    multiplicity:  1
    nc-model:      point
    maxiterations: 30
    convergence:   1.0e-7


#RT-TDSCF calculation with a delta-type external field
#of amplitude 0.001 [a.u.] and x-direction
tdscf:
       spectroscopy:     eas
       time-steps:       2000 x 0.5
       field:
             model:      delta
             amplitude:  0.001
             direction:  1.0 0.0 0.0

There are several important aspects associated with the RT-TDSCF simulations, namely

  • it is necessary to perform three indipendent RT-TDSCF simulations with the external field oriented along three perpendicular Cartesian directions
    The easiest way to accomplish this requirement is to set the keyword direction: in the input block tdscf: to an unit vector along the x-axis as

  • direction:  1.0  0.0  0.0

    or to an unit vector along the y-axis as

    direction:  0.0  1.0  0.0

    or to an unit vector along the z-axis as

    direction:  0.0  0.0  1.0

    and rerun the RT-TDSCF simulation for each direction. Importantly, save the TDSCF output files with specific suffixes -- _x.out_tdscf for x-direction, _y.out_tdscf for y-direction, and _z.out_tdscf for z-direction. These name-specific files are required for a final post-processing of the time-domain signal and visualisation of spectra (see next point).

  • final post-processing of time-domain signals and visualisation of spectra using the script spectrum.py
    After having the three TDSCF outputs files, for instance named as my-output_x.out_tdscf, my-output_y.out_tdscf, and my-output_z.out_tdscf, the final electron absorption spectrum (eas) can be obtained by running

  • /path/to/ReSpect/spectrum.py --files=my-output --spectroscopy=eas --plot

    In addition to the spectral plot, the script will also generate two files; my-output.out_spectrum_eas containing all datapoints of the frequency domain spectrum and my-output.out_peaks_eas containing datapoints above the threshold 10-7 and information about the post-processing settings, relevant physical constants, and spectral resolution. All arguments to the script spectrum.py can be listed by the command

    /path/to/ReSpect/spectrum.py --help

There are several important and worth-to-remember aspects associated with the input syntax, namely

  • the input is case-insensitive
    This means that the program does not distinguish between uppercase and lowercase letters.

  • the input is insensitive to the number of blank lines and/or comment lines
    All comments begin with the number sign (#), can start anywhere on a line and continue until the end of the line.

  • the input is compliant with the dictionary syntax of the YAML markup language
    This means that each input line is represented either by a single block: statement or by a simple keyword:value pair, such as

  • block1:
        keyword1: value1 
        keyword2: value2  
        ...
        block2: 
          keyword3: value3
          keyword4: value4
          ...
        block3: 
               keyword5: value5
               keyword6: value6
               ...
    

    It is essential to remember that all members of one block: are lines beginning at the same indentation level. Whitespace indentation is used to denote the block structure; however, tab characters are never allowed as indentation. The only exception to the YAML-based input syntax is the block geometry: which utilizes a simple xyz format for the molecular geometry specification.


TIPS & TRICKS

Q: Is there a way to launch RT-TDSCF calculations without the need to explicitly setup the scratch path by "--scratch=/path/to/scratch/directory"?

Yes, the argument "--scratch=/path/to/scratch/directory" can be saved to the file .respectrc in your home directory. If the file and the argument exist, then ReSpect takes the scratch directory setting from the file.

Q: How to set the number of processors for parallel RT-TDSCF calculations?

For OpenMP parallel calculations, the number of processors can be controlled from the command line by the argument --nt=N, where N ideally refers to the total number of physical cores of a machine. Thus, the command line for launching an OpenMP parallel RT-TDSCF job reads

/path/to/ReSpect/respect --nt=N --tdscf --inp=my-input-file

Note, however, we have assumed here that the scratch path is setup through the file .respectrc (see the previous discussion).

Q: How to restart a RT-TDSCF calculation?

RT-TDSCF calculations can be restarted simply be adding an extra argument --restart to the command line

/path/to/ReSpect/respect --tdscf --inp=my-input-file --restart

The restart process collects and prints to the output file my-input-file.out_tdscf all relevant RT-TDSCF data generated in a previous run.


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Hylleraas Centre
Department of Chemistry
UiT The Arctic University of Norway
Tromsø, NO-9037 Norway
Email: info@respectprogram.eu