NUCIND: Difference between revisions
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{{TAGDEF|NUCIND|.TRUE. {{!}} .FALSE. | .FALSE. }} | {{TAGDEF|NUCIND|.TRUE. {{!}} .FALSE. | .FALSE. }} | ||
Description: Allows the | Description: Allows the nucleus-independent chemical shielding (NICS) to be calculated. | ||
---- | ---- | ||
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{{not released}} | {{not released}} | ||
In conjunction with {{TAGO|LCHIMAG|True}}, {{TAG|NUCIND}} calculates the chemical shielding tensor <math>\sigma_{ij}</math> at positions off-nucleus, hence | In conjunction with {{TAGO|LCHIMAG|True}}, {{TAG|NUCIND}} calculates the chemical shielding tensor <math>\sigma_{ij}(\mathbf{R})</math> at positions <math>\textbf{R}</math> off-nucleus, hence nucleus-independent chemical shielding (NICS) {{Cite|schleyer:1996}}{{Cite|chen:schleyer:2005}}. VASP calculates only from the plane wave | ||
grid, there is no one-center augmentation. | |||
It is also written to {{FILE|vaspout.h5}}, if compiled with [[Makefile.include#Customize|HDF5 support]]. You can find the data groups | When {{TAGO|NUCIND|True}}, by default these are calculated on the fine FFT grid {{TAG|NGXF}} x {{TAG|NGYF}} x {{TAG|NGZF}} in ppm. The output is written to {{FILE|NICS}}. | ||
It is also written to {{FILE|vaspout.h5}}, if compiled with [[Makefile.include#Customize|HDF5 support]]. You can find the data groups: | |||
<pre> | <pre> | ||
/results/nics Group | /results/nics Group | ||
| Line 33: | Line 36: | ||
calc.nics.plot() | calc.nics.plot() | ||
</syntaxhighlight> | </syntaxhighlight> | ||
to select the isotropic chemical shielding <math>\sigma_{iso}</math> in 3D space. It will produce an isosurface of the shielding (positive) and deshielding (negative) over the crystal structure. | to select the isotropic chemical shielding <math>\sigma_{iso}</math> in 3D space {{Cite|klod:kleinpeter:2001}}{{Cite|kleinpeter:klod:koch:2007}}. It will produce an isosurface of the shielding (positive) and deshielding (negative) over the crystal structure. | ||
Alternatively, produce a 2D contour plot of the NICS in a plane: | Alternatively, produce a 2D contour plot of the NICS in a plane {{Cite|karadakov:horner:2013}}: | ||
<syntaxhighlight lang="python"> | <syntaxhighlight lang="python"> | ||
import py4vasp as pv | import py4vasp as pv | ||
| Line 50: | Line 53: | ||
* <code>"skew"</code> - plot the skew <math>\kappa</math> | * <code>"skew"</code> - plot the skew <math>\kappa</math> | ||
Alternatively, if the {{FILE|POSNICS}} file is present, then the positions defined within that file will be used. These chemical shielding tensors are printed in the {{FILE|OUTCAR}} file as follows: | == POSNICS == | ||
Alternatively, if the {{FILE|POSNICS}} file is present, then the positions defined within that file will be used. The calculation takes longer as each point is calculated in serial and not in parallel as for the grid. However, there is far greater flexibility for defining physically relevant positions, e.g., hydrogen bonds, close to nuclei, or chemical bonds. These chemical shielding tensors are printed in the {{FILE|OUTCAR}} file as follows, e.g., for the 100th NICS point: | |||
<pre> | <pre> | ||
nics 100 | nics 100 | ||
| Line 57: | Line 62: | ||
-0.000000 -0.000000 -0.326272 | -0.000000 -0.000000 -0.326272 | ||
</pre> | </pre> | ||
It is also written to {{FILE|vaspout.h5}}, if compiled with [[Makefile.include#Customize|HDF5 support]]. You can find the data groups: | |||
<pre> | |||
/results/posnics Group | |||
/results/posnics/label Dataset {SCALAR} | |||
/results/posnics/positions Dataset {3, 10000} | |||
/results/posnics/values Dataset {10000, 3, 3} | |||
</pre> | |||
and use {{py4vasp}} to access these, e.g., using | |||
<syntaxhighlight lang="python"> | |||
import py4vasp as pv | |||
calc = pv.Calculation.from_path(".") | |||
calc.nics.read() | |||
</syntaxhighlight> | |||
to read the NICS values for the positions defined in {{FILE|POSNICS}}. Since the grid is not necessarily regular, you will need to plot these yourself. | |||
== Related tags and articles == | == Related tags and articles == | ||
| Line 63: | Line 84: | ||
== References == | == References == | ||
[[Category:INCAR tag]][[Category:NMR]] | |||
Latest revision as of 14:20, 21 March 2025
NUCIND = .TRUE. | .FALSE.
Default: NUCIND = .FALSE.
Description: Allows the nucleus-independent chemical shielding (NICS) to be calculated.
Warning: Not yet released!
This page contains information about a feature that will be available in a future release of VASP. In other words, currently you cannot use it even with the latest version of VASP. The information may change significantly until it is released.
In conjunction with LCHIMAG = True, NUCIND calculates the chemical shielding tensor at positions off-nucleus, hence nucleus-independent chemical shielding (NICS) [1][2]. VASP calculates only from the plane wave
grid, there is no one-center augmentation.
When NUCIND = True, by default these are calculated on the fine FFT grid NGXF x NGYF x NGZF in ppm. The output is written to NICS.
It is also written to vaspout.h5, if compiled with HDF5 support. You can find the data groups:
/results/nics Group
/results/nics/grid Dataset {3}
/results/nics/structure Group
/results/nics/structure/position Group
/results/nics/structure/position/direct_coordinates Dataset {SCALAR}
/results/nics/structure/position/ion_sha256 Dataset {2}
/results/nics/structure/position/ion_types Dataset {2}
/results/nics/structure/position/lattice_vectors Dataset {3, 3}
/results/nics/structure/position/number_ion_types Dataset {2}
/results/nics/structure/position/position_ions Dataset {8, 3}
/results/nics/structure/position/scale Dataset {SCALAR}
/results/nics/structure/position/system Dataset {SCALAR}
/results/nics/values Dataset {9, 108, 108, 108}
and use py4vasp to access these, e.g., using
import py4vasp as pv
calc = pv.Calculation.from_path(".")
calc.nics.plot()
to select the isotropic chemical shielding in 3D space [3][4]. It will produce an isosurface of the shielding (positive) and deshielding (negative) over the crystal structure.
Alternatively, produce a 2D contour plot of the NICS in a plane [5]:
import py4vasp as pv
calc = pv.Calculation.from_path(".")
calc.nics.to_contour(a=0.5)
It will result in a contour plot showing the isotropic chemical shielding in the selected plane. The plane is selected as a fraction x of the lattice vector. Here, x=0.5 corresponds to half of the primary lattice vector . For the other lattice vectors use b=x or c=x.
For both the 2D and 3D plots, the isotropic chemical shielding is used by default. You can alternatively select the other properties (see LCHIMAG for details. Herzfeld-Berger convention is followed [6]) by inputting them as arguments into the functions, e.g., calc.nics.plot("anisotropic") or calc.nics.to_contour("span", a=0.5):
"isotropic"(default) - plot the isotropic chemical shielding"anisotropic"- plot the anisotropic chemical shielding"span"- plots the span"skew"- plot the skew
POSNICS
Alternatively, if the POSNICS file is present, then the positions defined within that file will be used. The calculation takes longer as each point is calculated in serial and not in parallel as for the grid. However, there is far greater flexibility for defining physically relevant positions, e.g., hydrogen bonds, close to nuclei, or chemical bonds. These chemical shielding tensors are printed in the OUTCAR file as follows, e.g., for the 100th NICS point:
nics 100
1.187143 -0.003408 -0.000000
-0.002977 -1.893648 -0.000000
-0.000000 -0.000000 -0.326272
It is also written to vaspout.h5, if compiled with HDF5 support. You can find the data groups:
/results/posnics Group
/results/posnics/label Dataset {SCALAR}
/results/posnics/positions Dataset {3, 10000}
/results/posnics/values Dataset {10000, 3, 3}
and use py4vasp to access these, e.g., using
import py4vasp as pv
calc = pv.Calculation.from_path(".")
calc.nics.read()
to read the NICS values for the positions defined in POSNICS. Since the grid is not necessarily regular, you will need to plot these yourself.
Related tags and articles
LCHIMAG, NICS, LNICSALL, LPOSNICS, POSNICS
References
- ↑ P. von Ragué Schleyer, C. Maerker, A. Dransfeld, H. Jiao, N. J. R. van Eikema Hommes, Nucleus-Independent Chemical Shifts: A Simple and Efficient Aromaticity Probe, J. Am. Chem. Soc. 118, 6317 (1996).
- ↑ Z. Chen, C. S. Wannere, C. Corminboeuf, R. Puchta. P. von Ragué Schleyer, Nucleus-Independent Chemical Shifts (NICS) as an Aromaticity Criterion, Chem. Rev. 10, 105, 3842–3888 (2005).
- ↑ S. Klod, E. Kleinpeter, Ab initio calculation of the anisotropy effect of multiple bonds and the ring current effect of arenes—application in conformational and configurational analysis, J. Chem. Soc., Perkin Trans. 2, 1893-1898 (2001).
- ↑ E. Kleinpeter, S. Klod, A. Koch, Visualization of through space NMR shieldings of aromatic and anti-aromatic molecules and a simple means to compare and estimate aromaticity, J. Mol. Struct. THEOCHEM 811, 45-60 (2007).
- ↑ P. Karadakov, K. Horner, Magnetic Shielding in and around Benzene and Cyclobutadiene: A Source of Information about Aromaticity, Antiaromaticity, and Chemical Bonding, J. Phys. Chem. A, 117, 518-523 (2013).
- ↑ J. Mason, Conventions for the reporting of nuclear magnetic shielding (or shift) tensors suggested by participants in the NATO ARW on NMR shielding constants at the University of Maryland, College Park, July 1992, Solid State Nucl. Magn. Reson. 2, 285 (1993).