NMR Shielding Tensor Tutorial

Performing the relativistic NMR shielding tensor calculations in ReSpect requires the following sequence of steps

SCF(1c) → SCF(4c) → NMR

where the initial SCF(1c) step represents the self-consistent field (SCF) procedure based on a scalar-relativistic, one-component (1c) Hamiltonian and this step is primarily meant to provide a very good guess of initial molecular orbitals for subsequent fully relativistic calculations, where both scalar- and spin-orbit corrections are included variationally. In the second SCF(4c) step, the actual relativistic molecular orbitals are determined by means of SCF with the relativistic four-component (4c) Dirac—Coulomb Hamiltonian. Finally, the NMR shielding tensor is evaluated in the last step, starting from the relativistic molecular orbitals obtained in SCF(4c).

To perform the SCF(1c) calculation, execute the command

/path/to/ReSpect/respect --scf --inp=1c --scratch=/path/to/scratch/directory

where arguments mandatory to respect mean

  • --scf
    starts the SCF procedure;

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

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

A simple example of the input file 1c.inp for a scalar relativistic one-component DFT calculation of HBr with the Douglas–Kroll–Hess Hamiltonian looks like

#scf procedure with 1c scalar DKH2 Hamiltonian
scf:

    geometry:
       H      1.41400    0.00000    0.00000
       Br     0.00000    0.00000    0.00000

    method: ks-dkh2/pbe0
    basis:
            H:  upcS-1
            Br: dyall-vdz

    charge:        0
    multiplicity:  1
    maxiterations: 30
    nc-model:      point

Note that a comprehensive list of all SCF keywords can be found here.

Having the initial SCF(1c) step finished, let's move on to the next SCF(4c) step. In order to have the 1c molecular orbitals ready for a restart, we execute the linux command first

ln  -sf  1c.50  4c.50

which soft-links the ReSpect checkpoint file 1c.50 generated in the previous SCF(1c) calculation to a new checkpoint file 4c.50. Now, we can perform the second SCF(4c) step

/path/to/ReSpect/respect --restart --scf --inp=4c --scratch=/path/to/scratch/directory

where the additional argument --restart enforces respect to search for the initial molecular orbitals in the checkpoint file 4c.50. An example of the input file 4c.inp is

#4c SCF Dirac-Kohn-Sham DFT calculation of HBr 
#molecule with the Dirac--Coulomb Hamiltonian
scf:

    geometry:
       H      1.41400    0.00000    0.00000
       Br     0.00000    0.00000    0.00000

    method: mdks/pbe0
    basis:
            H:  upcS-1
            Br: dyall-vdz

    charge:        0
    multiplicity:  1
    maxiterations: 30
    nc-model:      gauss
    convergence:   1.0e-6


#NMR shielding tensor calculation with RMB-GIAO 
cs:

    maxiterations: 30
    gauge:         giao
    convergence:   1.0d-5

Here, we replaced the 1c DKH2 Hamiltonian method:ks-dkh2/dft-functional by the 4c Dirac—Coulomb Hamiltonian method:mdks/dft-functional.

Having the SCF(4c) calculation finished successfully, let's perform the final NMR step by running the command

/path/to/ReSpect/respect --cs --inp=4c --scratch=/path/to/scratch/directory

where the input block cs: takes control of the setup for the NMR shielding tensor calculation. A comprehensive list of all NMR shielding tensor keywords can be found here.

As a final note, 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 SCF and NMR 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 SCF and NMR 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 SCF or NMR job reads

/path/to/ReSpect/respect --nt=N --scf --inp=my-input-file
/path/to/ReSpect/respect --nt=N --cs  --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: I want to run multiple cs calculations for the same four-component molecular orbitals. Is there a way to avoid running expensive 4c scf job multiple times?

Yes, in the above example one can run the cs calculation with command

/path/to/ReSpect/respect --cs --inp=cs-input --start-data=4c

where cs-input.inp file contains cs input section

cs:

    maxiterations: 30
    gauge:         giao
    convergence:   1.0d-5

The above command will take 4c.50 data and run cs calculation with cs-input.inp input data. After successful end of the cs job, the final output data will be stored in the file 4c-cs-input.out_cs. This step can be repeated multiple times with different cs input files but the same SCF(4c) output data.


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