NMR Shielding Tensor Tutorial
Performing a parallel relativistic NMR shielding tensor calculation in ReSpect requires the following sequence of steps
SCF(4c) → NMR
where the initial SCF(4c) step represents the self-consistent field (SCF) procedure. The actual NMR shielding tensors are evaluated in the second step (NMR), starting from the relativistic molecular orbitals obtained in the previous SCF(4c).
To perform the SCF(4c) calculation, execute the command
respect --scf --inp=my-input-file --nt=4 --scratch=/path/to/scratch/directory
where arguments mandatory to
starts the SCF procedure;
specifies a name of the input file;
specifies the number of physical cores required for parallel execution;
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
cs: with some CS-specific keywords. A comprehensive list of all SCF keywords can be found here. A simple example of my-input-file.inp looks like
#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: 1.0e-5
Having the SCF(4c) calculation finished successfully, let's perform the final NMR step by running the command
respect --cs --inp=my-input-file --nt=4 --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:valuepair, 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: How to scale the speed of light in NMR calculations?
Set the cscale option in the SCF calculation. The scaling value is then automatically transferred to the CS calculation.
Q: Is it possible to scale spin-orbit interaction in NMR calculations?
No. Currently one can only turn off SO interaction by setting soscale option to zero in the SCF calculation. This setting is then automatically transferred to the CS calculation.
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 both the file and the command line argument exist, then ReSpect takes the scratch directory setting from the command line.
Q: I want to run a multiple cs calculations starting from the same four-component molecular orbitals. Is there a way to avoid recalculating the 4c scf job multiple times?
Yes, one can run the cs calculation with command
/path/to/ReSpect/respect --cs --inp=cs-input --start-data=4c
where the cs-input.inp file contains only the
cs: input block
cs: maxiterations: 30 gauge: giao convergence: 1.0e-5
The above command will take the initial data from 4c.50 and performs the cs calculation according to the input in cs-input.inp. 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 always starting from the same SCF(4c).
Department of Chemistry
UiT The Arctic University of Norway
Tromsø, NO-9037 Norway