Posts by sobereva

sobereva · Multiwfn and wavefunction analysis

Hello,

If you choose two atomic nuclei to define the line to be plot in Multiwfn, then the value of X-axis will corresponds to the distance from starting point, which is irrelevant to Cartesian coordinate of the atoms.

sobereva · Multiwfn and wavefunction analysis

Hello,

The color transition methods are hard-coded, you cannot change it without modifying source code. Please look at plot.f90 in source code package, in which "subroutine setcolortable" contains the code for defining the coloring transitions.

sobereva · Multiwfn and wavefunction analysis

Change the last line to: $NBO AONAO DMNAO $END

sobereva · Multiwfn and wavefunction analysis

alessiomacorano wrote:

Dear Prof. Tian Lu,
Thank you very much for your clear answer. So, for a set of different molecules that have the same nucleophilic reactive group, for example -SH (as in my case), can I also use Hirshfeld atomic charges or the Fukui function to evaluate the nucleophilicity of sulfur S between different molecules and make a rank between the molecules from the most nucleophile to the less one right ?
my best
Alessio

Dear Alessio,

Fukui function cannot be used to evaluate relative nucleophilicity between different molecules, but local softness can, which includes global softness on the top of Fukui function. Hirshfeld charges can also be compared between different molecules.

Tian

sobereva · Quantum Chemistry

This depends on your practical purpose. I suggest reading original paper of Seminario (International Journal of Quantum Chemistry: Quantum Chemistry Symposium 30, 1271 -1277 (1996)), and review of relaxed force constant (Chem. Soc. Rev., 2008, 37, 1558–1567).

sobereva · Quantum Chemistry

Bond force constant can be calculated by my code Sobtop (http://sobereva.com/soft/Sobtop) based on Gaussian .fch file produced by freq task (namely this .fch file contains Hessian), Seminario and modified Seminario methods are supported in Sobtop for this purpose.

If you need relaxed force constant, you can use http://www.oc.tu-bs.de/Grunenberg/compliance.html

This is no other post about AIMD.

sobereva · Multiwfn and wavefunction analysis

Without detailed information, including ORCA input and output files, input file for Multiwfn, and all commands you inputted in Multiwfn, I cannot easily answer this question.

sobereva · Multiwfn and wavefunction analysis

No. The ESP code in current version of Multiwfn is much faster than orca_plot, see comparison of speed (Table 1): Phys. Chem. Chem. Phys., 23, 20323–20328 (2021)

sobereva · Multiwfn and wavefunction analysis

Dear Alessio,

1 In principle, considering implicit solvent should be more rigorous, but it doesn't necessarily improve fitting quality. So you can try both cases, with and without implicit solvation model.

2 Nucleophilicity index should only be calculated for reactant molecule, protonated amine NH3 should be ignored. Nucleophilic index is not necessarily limited to neutral species, though you can simultaneously consider other descriptors, such as Hirshfeld atomic charge of key atom(s), average local ionization energy (ALIE), etc.

Best regards,

Tian

sobereva · Multiwfn and wavefunction analysis

Perhaps you loaded a wrong file. You should use Gaussian output file rather than fch file as input file in this analysis, as illustrated in Section 4.9.4 of Multiwfn manual.

sobereva · Multiwfn and wavefunction analysis

Today a Multiwfn user asked me how to generate wavefunction file of excited state calculated by ORCA, my reply is given below, which may also be useful for other people:

Run the following task, assume that input file is H2CO.inp and output file is H2CO.out
! PBE0 def2-SVP
%tddft
tprint 1E-8
end
*xyz 0 1
C 0.00000000 0.00000000 -0.52887900
H 0.00000000 0.93777000 -1.12367000
O 0.00000000 0.00000000 0.67757700
H 0.00000000 -0.93777000 -1.12367000
*

Then run this command to obtain H2CO.molden.input:
orca_2mkl H2CO -molden

Load H2CO.molden.input into Multiwfn, and input
18
13
H2CO.out
1 //The excited state of interest
Now you have NO_0001.mwfn in current folder, which records natural orbitals of S1 state, and can be used as input file of Multiwfn for wavefunction analysis on the S1 state.
If you want to convert it to .wfx format, boot up Multiwfn and load NO_0001.mwfn, then input
100
2
4
S1.wfx
Now you have S1.wfx in current folder, which may be used in other code to perform wavefunction analysis for S1 state.

sobereva · Multiwfn and wavefunction analysis

Note that using SDD for B is not good, 6-31+G(d,p) should also be applied to B. In addition, as you already specified genecp, pseudo=read is redundant.

Using revised input file, I performed calculation using G16, the output file is attached: a.out

and I didn't encounter the same problem when using the FiPC-NICS analysis in latest version of Multiwfn. Full output information is shown below for your check:

 Multiwfn -- A Multifunctional Wavefunction Analyzer
 Version 3.8(dev), update date: 2025-Aug-14
 Developer: Tian Lu (Beijing Kein Research Center for Natural Sciences)
 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:  16  Current date: 2025-09-01  Time: 10:25:19 )

 Both following papers ***MUST BE CITED IN MAIN TEXT*** if Multiwfn is used:
  Tian Lu, Feiwu Chen, J. Comput. Chem., 33, 580 (2012) DOI: 10.1002/jcc.22885
  Tian Lu, J. Chem. Phys., 161, 082503 (2024) DOI: 10.1063/5.0216272
 See "How to cite Multiwfn.pdf" in Multiwfn binary package for more information

 Now input file path, for example, E:\Shakugan_no_Shana\Shana.mwfn
 (.wfn/wfn/wfx/fch/molden/pdb/xyz/mol2/cif/cub... see Section 2.5 of manual)
 Hint: Pressing ENTER button directly can select a file in a GUI window. To reload the past file, inputting "o". Input such as ?miku.fch can open the miku.fch in the same folder as the past file
C:\Users\sober\Desktop\a.out
 Please wait...
 Trying to load geometry from this file...
 Geometry (final, input orientation) has been loaded from this file
 Number of alpha/beta/total electrons:     181     181     362

 Loaded C:\Users\sober\Desktop\a.out successfully!

 Formula: Bq200 B1 C20 O20 Mn5      Total atoms:     246
 Molecule weight:       845.70406 Da

 "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, PDOS, OPDOS, local DOS, COHP 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
 26 Structure and geometry related analyses
 100 Other functions (Part 1)            200 Other functions (Part 2)
 300 Other functions (Part 3)
25

    ================ Delocalization and aromaticity analyses ===============
  0 Return to main menu
  1 Multicenter bond order
 -1 Multicenter bond order in NAO basis
  2 AV1245 index
  3 Iso-chemical shielding surface (ICSS)
  4 NICS_ZZ for non-planar or tilted system
  5 ELF-sigma/pi and LOL-sigma/pi
  6 Harmonic oscillator measure of aromaticity (HOMA) and Bird indices
  6a HOMAc (reparameterized HOMA)   6b HOMER (HOMA for excited states)
  7 Shannon aromaticity index
  8 Para-delocalization index (PDI)
  9 Aromatic fluctuation index (FLU) and FLU-pi
 10 Para linear response index (PLR)
 11 Information-theoretic (ITA) aromaticity index
 12 Properties of ring critical point
 13 NICS-1D scan curve map, integral NICS (INICS) and FiPC-NICS
 14 NICS-2D scan plane map
13

                ---------- NICS-1D scan and integral ----------
 0 Return
 Choose the way of defining the two end points of the line for scanning
 1 Directly input Cartesian coordinates of two end points
 2 The two end points are above and below the center of a plane fitted for specific atoms, and the line perpendicularly passes through their center
1
 Input X,Y,Z of the first end point in Angstrom, e.g. 3.2,0.1,-9.5
-0.799429    0.96579        0.115633
 Input X,Y,Z of the second end point in Angstrom, e.g. 3.2,0.1,-9.5
-0.799429    0.96579    -9.776147

 How many points evenly distributing in the scanning line? e.g. 50
 If press ENTER button directly,    99 points will be used, which is fine enough
200

 0 Exit
 1 Generate Gaussian input file for NICS-1D scanning
 2 Load Gaussian output file of NICS-1D scanning
2
 Input path of Gaussian output file of NICS-1D scanning task
 e.g. D:\Aqours\Mari\shiny.out
C:\Users\sober\Desktop\a.out
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                   ---------- Post-processing menu ----------
 -3 Invert direction of X-axis
 -2 Multiply NICS data by a factor
 -1 Select component of NICS, current: Along the scanning line
 0 Exit to main menu
 1 Plot NICS curve along the line
 2 Save image file of NICS curve along the line
 3 Export NICS curve data along the line
 4 Calculate integral of NICS along the line
 5 Find minima and maxima along NICS curve
 6 Calculate FiPC-NICS
1
 Integral of NICS component:    -76.59 ppm*Angstrom

                   ---------- Post-processing menu ----------
 -3 Invert direction of X-axis
 -2 Multiply NICS data by a factor
 -1 Select component of NICS, current: Along the scanning line
 0 Exit to main menu
 1 Plot NICS curve along the line
 2 Save image file of NICS curve along the line
 3 Export NICS curve data along the line
 4 Calculate integral of NICS along the line
 5 Find minima and maxima along NICS curve
 6 Calculate FiPC-NICS
6
 The scanning direction is found to be Z

 FiPC-NICS.txt has been generated in current folder, meaning of each column:
 Column 1: Point index
 Column 2: Scanning distance in Angstrom
 Column 3: In-plane component of NICS
 Column 4: Out-of-plane component of NICS

 FiPC-NICS is   -1.116487 ppm, at   4.182 Angstrom

Perhaps the commands you inputted in Multiwfn were incorrect.

sobereva · Quantum Chemistry

In TDDFT calculation, M06-2X represents triplet excited state better than most other functionals, you can have a try.

In addition, I strongly suggest using UKS instead of TDDFT to optimize T1, the former is not only significantly faster, but also the result is more robust.

sobereva · Multiwfn and wavefunction analysis

Hello,

I have no experience in using the EFP feature in GAMESS. I suggest:
(1) Check if the wavefunction generated with EFP can be properly loaded into Multiwfn. Please check section "6.5 Check sanity of wavefunction" of Multiwfn manual.
(2) Plot electron density difference (EDD) between the wavefunction with and without the presence of EFP, and check if the EDD makes sense (i.e. properly reflecting the polarization effect caused by EFP). Please check Section 5.5 of Multiwfn manual on how to plot isosurface map of EDD.

If the above tests can be successfully passed, then you can normally perform other analyses on the wavefunction generated with EFP, including calculating electronic spatial extent.

sobereva · Multiwfn and wavefunction analysis

Increasing number of grid point will not evidently affect the observed result.

Please take care of the calculation equation of Pauli potential used in Multiwfn (part 60 of Section 2.7 of Multiwfn manual). As you can see there are three component terms in the case of ispecial=0, you can individually plot them via Multiwfn to understand the detail. In which, Weizsacker potential (Vw) corresponds to iuserfunc=4, exchange-correlation potential (V_XC) corresponds to iuserfunc=1100.
BTW: Note that the position of nucleus is a singular point of the nuclear attractive potential in ESP, Multiwfn arbitrarily sets nuclear contribution to ESP at this point to 1000 a.u.

Because of approximations, such as approximated V_XC and finite-sized basis set, the resulting curve may not be well consistent with analyical solution.

sobereva · Multiwfn and wavefunction analysis

This map is plotted for Ar calculated at B3LYP/6-31G* level using latest version of Multiwfn with iuserfunc=60, iDFTxcsel=84 and ispecial=0, the basic character is more close to your first image.

sobereva · Multiwfn and wavefunction analysis

In this case, your steps are correct.

sobereva · Multiwfn and wavefunction analysis

In this way it is impossible to check if the Pauli potential is actually spherically symmetric. You should view isosurface map (via main function 5. Using isovalue of e.g. 0.7). You will find the isosurface is perfectly spherical.

sobereva · Multiwfn and wavefunction analysis

Using iuserfunc=60 is correct. But as I mentioned, I cannot reproduce your observation, at least for Ar atom... More detailed information, such as input file, all commands you inputted in Multiwfn, the result, should be given.

sobereva · Multiwfn and wavefunction analysis

Without description of your calculation steps in Multiwfn, it is difficult for me to make comment. I just tried, using Pauli potential (iuserfunc=53 with ispecial=0 or 1), to calculate grid data for Ar atom, the isosurface of Pauli potential is indeed fully spherically symmetric.

sobereva · Multiwfn and wavefunction analysis

Hello,

You can use .molden.input files exported by orca_2mkl instead of the .fch files in this post.
.fch and .molden files provide essentially the same information for Multiwfn, see Section 2.5 of Multiwfn manual for more information.

sobereva · Quantum Chemistry

There is no necessary contradiction. For example, MOLOPT basis set in CP2K is fully generally contracted, while it is used in combination with GTH pseudopotential. I suggest checking original paper of MOLOPT: THE JOURNAL OF CHEMICAL PHYSICS, 127, 114105 (2007).

sobereva · Quantum Chemistry

I suggest changing to def2 basis set using "Extrapolate(3/4,def2) def2-QZVPP/C", the ECP should be automatically assigned for Rh.

sobereva · Multiwfn and wavefunction analysis

Multiwfn doesn't directly support .dat file. For GAMESS-US users, one can obtain .wfn file from .dat file and then use it as Multiwfn input file, please check beginning part of Chapter 4 of Multiwfn manual on how to do.

After that, you can use Multiwfn to perform a wide variety of analyses, including calculating grid data of electron density around the interested region using main function 5, please check Section 4.5 of manual for examples. The region to be calculated can be flexibly defined, see Section 3.6 of manual about the different modes for setting up grids.

sobereva · Multiwfn and wavefunction analysis

If your purpose is generating path from BCP, you should select option "8 Generating the paths connecting (3,-3) and (3,-1) CPs" rather than "9 Generating the paths connecting (3,+1) and (3,+3) CPs", the former doesn't need (3,+3).

sobereva · Quantum Chemistry

It is not possible to use wB97X-D3(BJ) in G16, but ORCA supports it.

sobereva · Multiwfn and wavefunction analysis

Hello,

This is no corresponding option, however, you can delete other type of CPs (option "-4 Modify or export CPs" and then "2 Delete some CPs") before printing out properties of BCP.
Also, note that in option -3 of topology analysis module there are suboptions "4 Save CPs to CPs.txt in current folder" and "5 Load CPs from a file", via them you can restore all CPs after deleting some of them.

Best regards,

Tian

sobereva · Multiwfn and wavefunction analysis

As I noted earlier, this depends on how the surface is defined. If it is defined as isosurface of electron density, then "a" will be a constant for all atoms and all molecules, making the discussion completely meaningless.

sobereva · Multiwfn and wavefunction analysis

Detailed description about these modes can be found in Section 3.6 of Multiwfn manual. The most convenient way is using option 10, by which you can visually setting up the box.

sobereva · Multiwfn and wavefunction analysis

HELP and HELV, in their original paper, were used to characterize lone pair, it seems that you hope to use them to study bonding ELF basin, this might also make sense but I am not fully sure.

You may visualize other basins surrounding the An to try to identify their meaning, I think they should not be significant and thus can be ignored if your purpose is simply studying bonding.

By the way, to greatly save computational cost of basin analysis of ELF for large systems like this, you can properly define the box when setting up grid so that the box only cover the An atom and coordination atoms around it.

Multiwfn forum

#1 Re: Multiwfn and wavefunction analysis » Plot electron density along a line with fixed atom positions » Today 10:26:56

#2 Re: Multiwfn and wavefunction analysis » Help: how to define a color scale transition method? » 2025-09-14 09:41:46

#3 Re: Multiwfn and wavefunction analysis » Problem in MCI calculation with NAO basis » 2025-09-11 15:03:39

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#7 Re: Multiwfn and wavefunction analysis » dipole moments » 2025-09-06 08:47:18

#8 Re: Multiwfn and wavefunction analysis » Using ORCA to speed up ESP calculations like with Gaussian » 2025-09-05 10:18:50

#9 Re: Multiwfn and wavefunction analysis » Nucleophilic idenx calculation in Multiwfn » 2025-09-04 10:01:29

#10 Re: Multiwfn and wavefunction analysis » Problem in MCI calculation with NAO basis » 2025-09-04 09:53:19

#11 Multiwfn and wavefunction analysis » The way of generating excited state wavefunction file for ORCA » 2025-09-02 10:26:23

#12 Re: Multiwfn and wavefunction analysis » Problem in FiPC NICS calculations » 2025-09-01 02:30:57

#13 Re: Quantum Chemistry » T1 state optimization problem » 2025-09-01 00:13:08

#14 Re: Multiwfn and wavefunction analysis » Electronic spatial extent with GAMESS EFP model » 2025-08-30 00:52:40

#15 Re: Multiwfn and wavefunction analysis » Calculation of Pauli potential using multiwfn » 2025-08-27 20:53:16

#16 Re: Multiwfn and wavefunction analysis » Calculation of Pauli potential using multiwfn » 2025-08-27 09:49:43

#17 Re: Multiwfn and wavefunction analysis » Calculation of Pauli potential using multiwfn » 2025-08-27 08:04:02

#18 Re: Multiwfn and wavefunction analysis » Calculation of Pauli potential using multiwfn » 2025-08-26 04:18:10

#19 Re: Multiwfn and wavefunction analysis » Calculation of Pauli potential using multiwfn » 2025-08-21 18:20:42

#20 Re: Multiwfn and wavefunction analysis » Calculation of Pauli potential using multiwfn » 2025-08-20 18:37:35

#21 Re: Multiwfn and wavefunction analysis » Intermolecular orbital overlap integral from Orca output » 2025-08-15 18:41:25

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#24 Re: Multiwfn and wavefunction analysis » Comparing Cube Files from Different Sized Grids » 2025-08-12 00:11:06

#25 Re: Multiwfn and wavefunction analysis » Failer to generate the BCP path » 2025-08-11 15:22:49

#26 Re: Quantum Chemistry » How to add GD3(BJ) to wb97X functional? » 2025-08-08 20:04:16

#27 Re: Multiwfn and wavefunction analysis » List of BCP (3, -1) only » 2025-08-07 12:46:37

#28 Re: Multiwfn and wavefunction analysis » surface charge density » 2025-08-06 18:45:42

#29 Re: Multiwfn and wavefunction analysis » Electron density integrated into Electron Localization Function basins » 2025-08-06 18:42:49

#30 Re: Multiwfn and wavefunction analysis » Electron density integrated into Electron Localization Function basins » 2025-08-06 15:30:36

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