ICSS plots

jok42bm · 2022-12-09 09:15:34

Hello,

I tried to create an ICSS plot as described in the manual (plane map of magnetic shielding value). It somehow did not work as I wished as you can hopefully see in the attached picture. Thank you for your help.

jok42bm · 2022-12-09 12:19:18

I also just noticed when I use e.g. NICSnptlim = 8000 that in the last (17th for benzene) input file are only 6184 atoms and in the other input files are the requested 8000.
I also tried 6000 grid points once, then the last input shows again less atoms with a number of only 2256 atoms. I do not know if that is an issue.

sobereva · 2022-12-10 05:14:57

Did you change "iuserfunc" in settings.ini and reboot Multiwfn as mentioned in Multiwfn manual? If you didn't do that, the "100 User-defined function" will correspond to a constant and evidently you will not obtain ICSS plane map by selecting it as the function to be plotted.

Please do not worry about the phenomenon you mentioned in #2, it is quite normal. This is because the total number of integration grid points is not a multiple of 8000 or 6000.

jok42bm · 2022-12-10 09:30:29

sobereva wrote:

Did you change "iuserfunc" in settings.ini and reboot Multiwfn as mentioned in Multiwfn manual? If you didn't do that, the "100 User-defined function" will correspond to a constant and evidently you will not obtain ICSS plane map by selecting it as the function to be plotted.
Please do not worry about the phenomenon you mentioned in #2, it is quite normal. This is because the total number of integration grid points is not a multiple of 8000 or 6000.

Hi, thank you for your help. I think I changed "iuserfunc" to -3 after the calculations of the necessary outputs. Or is it necessary to change this value before generating the inputs?

For the second thing with the grid points, I get this error when I stay with the value of 8000 after I put in the output files that contain the 8000 atoms:.

When I change the grid value to a lower value this error does not appear. But I do not know if it makes sense to change the grid value after I generated the inputs with another grid value so that I have two different grid values ?

jok42bm · 2022-12-10 09:33:18

jok42bm wrote:

sobereva wrote:
Did you change "iuserfunc" in settings.ini and reboot Multiwfn as mentioned in Multiwfn manual? If you didn't do that, the "100 User-defined function" will correspond to a constant and evidently you will not obtain ICSS plane map by selecting it as the function to be plotted.
Please do not worry about the phenomenon you mentioned in #2, it is quite normal. This is because the total number of integration grid points is not a multiple of 8000 or 6000.
Hi, thank you for your help. I think I changed "iuserfunc" to -3 after the calculations of the necessary outputs. Or is it necessary to change this value before generating the inputs?
For the second thing with the grid points, I get this error when I stay with the value of 8000 after I put in the output files that contain the 8000 atoms:.

https://i.postimg.cc/KkMgTRmC/IMG-20221209-125634.jpg

When I change the grid value to a lower value this error does not appear. But I do not know if it makes sense to change the grid value after I generated the inputs with another grid value so that I have two different grid values ?

And the next thing is that the generated cube file contains many zeros so that e.g. gaussview cannot plot any surface.
So I think that maybe the main thing is that I do something wrong before I am doing the plot that is described in the manual.

jok42bm · 2022-12-11 13:37:47

Hi again,

a colleague now wrote me that he also tried to make an ICSS-Plot but he had the same problem that the cube file has only zeros in it, so it is empty. ?

sobereva · 2022-12-12 08:36:21

Please make sure that you can normally plot ICSS isosurface map first. As shown in Section 4.200.4 of Multiwfn manual, http://sobereva.com/multiwfn/extrafiles … e_ICSS.rar contains all .out files for benzene. Please try to first reproduce the isosurface map given in the manual using these .out files. If you can normally view the ICSS isosurface map, the exported cube file should not only contain zero values. I don't find any problem in reproducing result of this example using the latest version of Multiwfn.

jok42bm · 2022-12-12 12:59:25

sobereva wrote:

Please make sure that you can normally plot ICSS isosurface map first. As shown in Section 4.200.4 of Multiwfn manual, http://sobereva.com/multiwfn/extrafiles … e_ICSS.rar contains all .out files for benzene. Please try to first reproduce the isosurface map given in the manual using these .out files. If you can normally view the ICSS isosurface map, the exported cube file should not only contain zero values. I don't find any problem in reproducing result of this example using the latest version of Multiwfn.

Thank you again. When I use the downloaded output-files, I get a cube-file like this for the ZZ-term:

Generated by Multiwfn
Totally -2147483647 grid points
1************************************
***** -Infinity 0.000000 0.000000
***** 0.000000 -Infinity 0.000000
***** 0.000000 0.000000 -Infinity
1 1.000000 0.000000 0.000000 0.000000

When I did the calculation myself, the cube-file looks like this:

Generated by Multiwfn
Totally 132750 grid points
6184 -16.046996 -28.673071 -24.000001
45 0.991512 0.000000 0.000000
59 0.000000 0.991512 0.000000
50 0.000000 0.000000 0.991512
6 6.000000 0.000000 2.628208 0.000000
6 6.000000 2.276094 1.314104 0.000000
6 6.000000 2.276094 -1.314104 0.000000
6 6.000000 0.000000 -2.628208 0.000000
6 6.000000 -2.276094 -1.314104 0.000000
6 6.000000 -2.276094 1.314104 0.000000
1 1.000000 0.000000 4.673070 0.000000
1 1.000000 4.046996 2.336535 0.000000
1 1.000000 4.046996 -2.336535 0.000000
1 1.000000 0.000000 -4.673070 0.000000
1 1.000000 -4.046996 -2.336535 0.000000
1 1.000000 -4.046996 2.336535 0.000000
0 0.000000 14.638055 -0.740448 -10.819806
0 0.000000 14.638055 -0.740448 -10.229709
0 0.000000 14.638055 -0.740448 -9.639612
0 0.000000 14.638055 -0.740448 -9.049515
0 0.000000 14.638055 -0.740448 -8.459418
0 0.000000 14.638055 -0.740448 -7.869320
0 0.000000 14.638055 -0.740448 -7.279223
0 0.000000 14.638055 -0.740448 -6.689126
0 0.000000 14.638055 -0.740448 -6.099029
0 0.000000 14.638055 -0.740448 -5.508931
0 0.000000 14.638055 -0.740448 -4.918834
0 0.000000 14.638055 -0.740448 -4.328737
0 0.000000 14.638055 -0.740448 -3.738640
0 0.000000 14.638055 -0.740448 -3.148543
0 0.000000 14.638055 -0.740448 -2.558445
0 0.000000 14.638055 -0.740448 -1.968348
0 0.000000 14.638055 -0.740448 -1.378251
0 0.000000 14.638055 -0.740448 -0.788154
0 0.000000 14.638055 -0.740448 -0.198057
0 0.000000 14.638055 -0.740448 0.392041
0 0.000000 14.638055 -0.740448 0.982138
0 0.000000 14.638055 -0.740448 1.572235
0 0.000000 14.638055 -0.740448 2.162330
0 0.000000 14.638055 -0.740448 2.752428
0 0.000000 14.638055 -0.740448 3.342525
0 0.000000 14.638055 -0.740448 3.932622
0 0.000000 14.638055 -0.740448 4.522719
0 0.000000 14.638055 -0.740448 5.112817
0 0.000000 14.638055 -0.740448 5.702914
0 0.000000 14.638055 -0.740448 6.293011
0 0.000000 14.638055 -0.740448 6.883108
0 0.000000 14.638055 -0.740448 7.473205
0 0.000000 14.638055 -0.740448 8.063303
0 0.000000 14.638055 -0.740448 8.653400
0 0.000000 14.638055 -0.740448 9.243497
0 0.000000 14.638055 -0.740448 9.833594
0 0.000000 14.638055 -0.740448 10.423692
0 0.000000 14.638055 -0.740448 11.013789
0 0.000000 14.638055 -0.740448 11.603886
0 0.000000 14.638055 -0.740448 12.193983
0 0.000000 14.638055 -0.150350 -12.000001
0 0.000000 14.638055 -0.150350 -11.409904
0 0.000000 14.638055 -0.150350 -10.819806
0 0.000000 14.638055 -0.150350 -10.229709
0 0.000000 14.638055 -0.150350 -9.639612
0 0.000000 14.638055 -0.150350 -9.049515
0 0.000000 14.638055 -0.150350 -8.459418
0 0.000000 14.638055 -0.150350 -7.869320
0 0.000000 14.638055 -0.150350 -7.279223
0 0.000000 14.638055 -0.150350 -6.689126
0 0.000000 14.638055 -0.150350 -6.099029
0 0.000000 14.638055 -0.150350 -5.508931
0 0.000000 14.638055 -0.150350 -4.918834
0 0.000000 14.638055 -0.150350 -4.328737
0 0.000000 14.638055 -0.150350 -3.738640
0 0.000000 14.638055 -0.150350 -3.148543

...
...
...

0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000
0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000 0.00000E+000

...
...
...

I do not know what I did wrong, maybe I have to try again something

sobereva · 2022-12-14 02:09:42

Generated by Multiwfn
Totally -2147483647 grid points
1************************************
***** -Infinity 0.000000 0.000000
***** 0.000000 -Infinity 0.000000
***** 0.000000 0.000000 -Infinity
1 1.000000 0.000000 0.000000 0.000000

The definition of grid is evidently wrong. Perhaps you loaded incorrect file when Multiwfn boots up, or selected a wrong option to define grid. Please copy all information from Multiwfn window to a .txt file and upload it, so that I can check all details. (still, performing the ICSS analysis based on the output files of benzene as example).

jok42bm · 2022-12-15 14:39:33

sobereva wrote:

Generated by Multiwfn
Totally -2147483647 grid points
1************************************
***** -Infinity 0.000000 0.000000
***** 0.000000 -Infinity 0.000000
***** 0.000000 0.000000 -Infinity
1 1.000000 0.000000 0.000000 0.000000
The definition of grid is evidently wrong. Perhaps you loaded incorrect file when Multiwfn boots up, or selected a wrong option to define grid. Please copy all information from Multiwfn window to a .txt file and upload it, so that I can check all details. (still, performing the ICSS analysis based on the output files of benzene as example).

Sure, here it is. Let me know if you anything else. Thank you
(Can I upload the text-file?)

Multiwfn -- A Multifunctional Wavefunction Analyzer
Version 3.8(dev), release date: 2022-Dec-1
Developer: Tian Lu (Beijing Kein Research Center for Natural Sciences)
Below paper ***MUST BE CITED*** if Multiwfn is utilized in your work:
Tian Lu, Feiwu Chen, J. Comput. Chem., 33, 580-592 (2012)
See "How to cite Multiwfn.pdf" in Multiwfn binary package for more information
Multiwfn official website: http://sobereva.com/multiwfn
Multiwfn English forum: http://sobereva.com/wfnbbs
Multiwfn Chinese forum: http://bbs.keinsci.com/wfn

( Number of parallel threads: 4 Current date: 2022-12-15 Time: 15:33:33 )

Input file path, for example E:\Kan_Colle\Kongou.wfn
(Supported: .mwfn/wfn/wfx/fch/molden/31/chg/pdb/xyz/mol/mol2/cif/cub, etc.)
Hint: Press ENTER button directly can select file in a GUI window. To reload the file last time used, simply input the letter "o". Input such as ?miku.fch can open the miku.fch in the same folder as the file last time used.
E:\Calculus\ICSS_test\OutputDownloaded\benzene_ICSS\benzene\NICS0017.out
Please wait...
Trying to load geometry from this file...
Note: Unable to load geometry in input orientation, trying to load geometry in standard orientation instead
Warning: Failed to load geometry in standard orientation from this file
Number of alpha/beta/total electrons: 21 21 42

Loaded E:\Calculus\ICSS_test\OutputDownloaded\benzene_ICSS\benzene\NICS0017.out successfully!

"q": Exit program gracefully "r": Load a new file
************ Main function menu ************
0 Show molecular structure and view orbitals
1 Output all properties at a point 2 Topology analysis
3 Output and plot specific property in a line
4 Output and plot specific property in a plane
5 Output and plot specific property within a spatial region (calc. grid data)
6 Check & modify wavefunction
7 Population analysis and calculation of atomic charges
8 Orbital composition analysis 9 Bond order analysis
10 Plot total DOS, partial DOS, OPDOS, local DOS and photoelectron spectrum
11 Plot IR/Raman/UV-Vis/ECD/VCD/ROA/NMR spectrum
12 Quantitative analysis of molecular surface
13 Process grid data (No grid data is presented currently)
14 Adaptive natural density partitioning (AdNDP) analysis
15 Fuzzy atomic space analysis
16 Charge decomposition analysis (CDA) and plot orbital interaction diagram
17 Basin analysis 18 Electron excitation analysis
19 Orbital localization analysis 20 Visual study of weak interaction
21 Energy decomposition analysis 22 Conceptual DFT (CDFT) analysis
23 ETS-NOCV analysis 24 (Hyper)polarizability analysis
25 Electron delocalization and aromaticity analyses
100 Other functions (Part 1) 200 Other functions (Part 2)
300 Other functions (Part 3)
200

============ Other functions (Part 2) ============
0 Return
1 Calculate core-valence bifurcation (CVB) index and related quantities
2 Calculate atomic and bond dipole moments in Hilbert space
3 Generate cube file for multiple orbital wavefunctions
4 Generate iso-chemical shielding surfaces (ICSS) and related quantities
5 Plot radial distribution function for a real space function
6 Analyze correspondence between orbitals in two wavefunctions
7 Parse output of (hyper)polarizability task of Gaussian
8 Study (hyper)polarizability by sum-over-states (SOS) method
9 Calculate average bond length and average coordinate number
10 Output various kinds of integral between orbitals
11 Calculate center, first/second moments and radius of gyration of a function
12 Calculate energy index (EI) or bond polarity index (BPI)
13 Evaluate orbital contributions to density difference or other grid data
14 Domain analysis (Obtaining properties within isosurfaces of a function)
15 Calculate electron correlation index (PCCP, 18, 24015)
16 Generate natural orbitals based on the density matrix in .fch/.fchk file
17 Calculate Coulomb and exchange integrals between two orbitals
18 Calculate bond length/order alternation (BLA/BOA)
19 Calculate spatial delocalization index (SDI) for orbitals or a function
20 Bond order density (BOD) and natural adaptive orbital (NAdO) analyses
4
Citation of ICSS: J. Chem. Soc. Perkin Trans. 2, 2001, 1893
Citation of ICSS_XX/YY/ZZ and ICSS_ani:
Carbon, 165, 468 (2020) DOI: 10.1016/j.carbon.2020.04.099

Please select a method to set up grid
-10 Set extension distance of grid range for mode 1~4, current: 12.000 Bohr
1 Low quality grid, covering whole system, about 125000 points in total
2 Medium quality grid, covering whole system, about 512000 points in total
3 High quality grid, covering whole system, about 1728000 points in total
4 Input the number of points or grid spacing in X,Y,Z, covering whole system
5 Input original point, grid spacings, and the number of points
6 Input center coordinate, number of points and extension distance
7 The same as 6, but input two atoms, the midpoint will be defined as center
8 Use grid setting of another cube file
10 Set box of grid data visually using a GUI window
11 Select a set of atoms, set extension distance around them and grid spacing
1
Coordinate of origin in X,Y,Z is ************************************ Bohr
Coordinate of end point in X,Y,Z is Infinity Infinity Infinity Bohr
Grid spacing in X,Y,Z is -Infinity -Infinity -Infinity Bohr
Number of points in X,Y,Z is*************** Total: -2147483647
The number of Bq per batch: 8000
The number of center per file (NICSnptlim in settings.ini): 8000

If skip generating Gaussian input file of NMR task? (y/n)
y
Now please run these input files by Gaussian

Input the path of Gaussian output file of NMR task
Assume that you input "C:\ltwd\NICS", then C:\ltwd\NICS0001.out, C:\ltwd\NICS0002.out, C:\ltwd\NICS0003.out... will be loaded (.log suffix is also allowed)
E:\Calculus\ICSS_test\OutputDownloaded\benzene_ICSS\benzene\NICS
Load which term?
1: Isotropic 2: Anisotropy 3: XX component 4: YY component 5: ZZ component
5
Loading finished!

-1 Load another ICSS form
0 Return to main menu
1 Visualize ZZ-chemical shielding surface
2 Export the grid data to ICSSZZ.cub current folder
2
Note: Current system has no atom, in order to maximize compatibility of the generated .cub file, a hydrogen atom is added to 0,0,0

The cube file has been exported to current folder

-1 Load another ICSS form
0 Return to main menu
1 Visualize ZZ-chemical shielding surface
2 Export the grid data to ICSSZZ.cub current folder

sobereva · 2022-12-16 05:55:56

You loaded a wrong file when Multiwfn boots up. You should load "examples\ICSS\benzene.gjf" as mentioned in Section 4.200.4 of multiwfn manual rather than NICS0017.out.

jok42bm · 2022-12-17 09:27:03

sobereva wrote:

You loaded a wrong file when Multiwfn boots up. You should load "examples\ICSS\benzene.gjf" as mentioned in Section 4.200.4 of multiwfn manual rather than NICS0017.out.

Hi, it works now. Thank you very much for your help.

sankeerthana · 2023-12-07 08:58:05

I want to try 3D ICSS plot of molecules. Can you please tell me how to do the calculation? I have done 2D ICSS plot. But I don't have any idea to do 3D plot.

Last edited by sankeerthana (2023-12-07 09:07:03)

sobereva · 2023-12-07 11:54:55

sankeerthana wrote:

I want to try 3D ICSS plot of molecules. Can you please tell me how to do the calculation? I have done 2D ICSS plot. But I don't have any idea to do 3D plot.

Please check Section 3.28.3 in Multiwfn manual for introduction and Section 4.25.3 for example.

sankeerthana · 2023-12-08 09:51:11

I have selected an isotropic and visualised isosurface. Is this 3D ICSS plotting, or should I choose any other option?

I would like to plot the 3D ICSS plot as shown in the figure b.
Kindly help me with my doubt.

sobereva · 2023-12-08 09:58:45

Perhaps you didn't properly specify a proper isovalue (too small currently), thus obtaining a very ugly isosurface map.

Please try to reproduce the ICSS example in Multiwfn manual first to understand how to correctly use this function.

Multiwfn forum

#1 2022-12-09 09:15:34

ICSS plots

#2 2022-12-09 12:19:18

Re: ICSS plots

#3 2022-12-10 05:14:57

Re: ICSS plots

#4 2022-12-10 09:30:29

Re: ICSS plots

#5 2022-12-10 09:33:18

Re: ICSS plots

#6 2022-12-11 13:37:47

Re: ICSS plots

#7 2022-12-12 08:36:21

Re: ICSS plots

#8 2022-12-12 12:59:25

Re: ICSS plots

#9 2022-12-14 02:09:42

Re: ICSS plots

#10 2022-12-15 14:39:33

Re: ICSS plots

#11 2022-12-16 05:55:56

Re: ICSS plots

#12 2022-12-17 09:27:03

Re: ICSS plots

#13 2023-12-07 08:58:05

Re: ICSS plots

#14 2023-12-07 11:54:55

Re: ICSS plots

#15 2023-12-08 09:51:11

Re: ICSS plots

#16 2023-12-08 09:58:45

Re: ICSS plots

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