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Because pseudopotential is used for Pt in the HF-3c method, you need to properly modify the [Atoms] section of the molden file produced by orca_2mkl, so that Multiwfn can recognize the actual effective nuclear charge of Pt. Please check "Molden input file" paragraph in Section 2.5 of Multiwfn manual, and http://sobereva.com/wfnbbs/viewtopic.php?pid=721
Alternatively, you can simply use ORCA 6.0 or later, then you do not need to manually modify the molden file.
If you double-click Multiwfn.exe, settings.ini in the same folder will be loaded when boots up Multiwfn.
There is no existing function for this purpose. Manually calculating it is easy: Using Multiwfn to simulate spectrum, export the two curves as text files, import them into e.g. Origin, define a new column as their overlap, then perform numerical integration.
If you are using Linux version, it is strongly suggested to set "Multiwfnpath" environmental variable, so that Multiwfn is always able to find settings.ini. See Section 2.1.2 of Multiwfn manual for detail.
If Multiwfn is unable to find settings.ini when boots up, there will be a warning on screen, please take care of it.
I prefer to display all surface extrema, but only manually label some of them, namely the relative important ones (i.e. the ones with relative large magnitude of ESP)
1 sobEDA.sh script only supports Gaussian. Perhaps there are some ways to realize sobEDA in the framework of ORCA, but there is no script available currently.
2 "sum of pair energies" fully corresponds to orbital interaction energy, while Coulomb, exchange, dispersion effects are irrelevant to it.
Dear Alessio,
"(full,mbs,hirshfeld" in fact is redundant.
Multiwfn is unable to print bond order in the exactly same way as NBO, but you can use Multiwfn to calculate Mayer bond order, which is very close to the bond order given by NBO when diffuse functions are not employed. When diffuse functions are needed, you can use Multiwfn to calculate fuzzy bond order, which is quite insensitive to basis set and the result is also quite close to the bond order given by NBO. Introduction to Mayer and fuzzy bond orders can be found in Section 3.11 of Multiwfn manual, and relevant examples are given in Section 4.9.1 of Multiwfn manual.
Best,
Tian
The labels in Fig. 1 are added manually using post-processing tool, such as Photoshop and powerpoint. I always add labels in this way.
In principle, the larger the ngen, the higher the proability to find the most stable configuration, but evidently, the higher the computational cost, which is linearly proportional to ngen.
If you do now know how to set the thresholds, simply using the default value. If you found the number of resulting clusters is too high, you can double the threshold. The meaning is described in http://bbs.keinsci.com/thread-577-1-1.html. Briefly speaking, in isostat, if the energy deviation and geometric deviation between two structures are less than the thresholds, the two structures will be considered to be the same and one of them will be removed, or in other words, they will be classified into one cluster.
The meaning of isuffle is described in http://bbs.keinsci.com/thread-2369-1-1.html. =1 means disrupting the order of adding monomers, =0 means do not do this. If you don't have special reasons to disrupt the order, just use the default one (=0).
Please upload figure(s) to describe the issues you encounted. You raised many questions, but without figures, I can hardly understand your problems and difficulties.
BTW: In the recent Multiwfn introduction paper J. Chem. Phys., 161, 082503 (2024) DOI: 10.1063/5.0216272, Fig. 14 is a very representative ESP colored vdW surface map, I think the graphical effect is good enough.
Dear Saeed,
Your change is correct.
Tian
Dear Saeed,
Yes, it can be easily realized via Molclus. Generally, using genmer (a tool in molclus package) to generate a batch of initial guessing complex structures, and then use molclus to invoke quantum chemistry codes to automatically calculate them (geometry optimization + high-level single point calculation) and then sort the resulting energies via isostat. Examples are given in http://bbs.keinsci.com/thread-2369-1-1.html
Best regards,
Tian
If a valence basin directly contacts core basin of A, core basin of B, core basin of C... then this valence basin will be assigned as V(A,B,C...). I think this assignment is reasonable, at least there is no evidently better way.
The situation you noted is common. For example, for NaCl, there is a ELF basin assigned by Multiwfn as V(Na,Cl), which contains all valence electrons of Cl-. But it is indeed a disynatpic basin, because it contacts both core basins of Na and Cl.
V(A,B,C...) doesn't necessarily imply that the electrons in this valence basin must contribute to covalent bond between A, B, C...
If you believe the automatically assigned labels are not expected, you can manually assign the labels by visualizing the basins or isosurfaces.
New update on 2025-Jun-3:
The aforementioned improvement has also been available for Linux version! Note that for Linux version, before dragging the system to change viewpoint, one should click drawing region once to make icon become a hand.
Multiwfn is not able to calculate dexter eet, but you can use Multiwfn to evaluate product of MO overlaps.
Please check Section 4.100.15 of Multiwfn manual on how to calculate intermolecular orbital overlap.
Around nuclear positions of very heavy atoms, the fluctuation range of Laplacian of rho is extremely large, so the automatically determined Y-axis range is also extremely wide. In order to clearly view the function variation in the bonding region, you should properly adjust range of Y-axis. For example, -100 to 100 a.u.
When loading your .molden file, Multiwfn gives a warning:
!! Warning! Warning! Warning! Warning! Warning! Warning! Warning! Warning !!
The net charge of this system is quite large ( 56)! Probably ECP is employed while you forgot to modify the atomic indices in [atoms] field of the .molden file to actual nuclear charges, in this case some analysis results will be problematic! Please check "Molden" part of Section 2.5 of Multiwfn manual to understand why and how to modify the file
That is, you didn't properly modify the [atoms] field. You should open the .molden file via text editor, replacing these two lines
Sn 3 50 24.1987164196 18.4577165819 26.4652207565
Sn 16 50 24.0385940782 25.8077025181 26.1277229017
with the following lines:
Sn 3 22 24.1987164196 18.4577165819 26.4652207565
Sn 16 22 24.0385940782 25.8077025181 26.1277229017
Then Multiwfn will be able to provide correct EDF information to represent core electrons during loading this file, hence all nuclear CPs can be found, and all bond paths can be generated.
Please send me your input file of quantum chemistry program and wavefunction file to my E-mail, I will try to reproduce your result.
I don't know what are the atoms on both side of CP333, which elements are them and which basis sets were used for them?
Please upload a screenshot of option 0 of topology analysis module, to graphically show current CPs and bond paths. If CP index is correct and corresponding bond paths have already been generated by Multiwfn, there is no reason the curve map cannot be plotted. Section "4.2.3 Plot real space function along bond path" of Multiwfn manual has described full steps of generating this kind of map.
Please enter option 0 and carefully check CP index. Two paths must already be generated from CP314, otherwise you cannot choose this CP index.
In the topology analysis module of Multiwfn, after entering option "-5 Modify or print detail or export paths, or plot property along a path" and then "7 Calculate and plot specific real space function along a path", you will find the following prompt:
Input index of a path, e.g. 3 Input "q" can return
Hint: If input index of two paths (e.g. 6,7) emitted from the same (3,-1) CP, then the real space function along the combined paths will be outputted
Hint: If you input e.g. c6 and meantime the CP6 is BCP, then the two bond paths emitted from it will be chosen
As indicated by the prompt, to plot a complete bond path (linking two atoms and passing through a BCP), it is suggested to input e.g. c6, where 6 is an index of BCP, you will obtain the complete path passing through BCP 6.
Dear Saeed,
There is no unique way. Several methods:
(1) Using orbital localization, see Section 4.19.4 of Multiwfn manual for example
(2) Calculate dipole moment of the ELF basin corresponding to the bond of interest
(3) Decompose dipole moment in Hibert space, and check two-center contributions, see Section 3.200.2 of Multiwfn manual.
Best
Tian
You just need one wavefunction file. After loading it into Multiwfn, you can easily use main function 3 to plot ESP along a specific line. See Section 4.3 of Multiwfn manual for examples of using main function 3.
It doesn't matter, no extra computational cost.
To delete it in Multiwfn, in the topology analysis interface, choose " -5 Modify or print detail or export paths, or plot property along a path", and then "3 Delete some paths", then follow the prompts to input.
You can also choose to show/hidden some topology paths in VMD. In the paths.pdb exported by Multiwfn, you can find different paths correpond to different residue index. So, in VMD, you can enter "Graphics" - "Representation", and in "Selected Molecule" select the ID used to showing paths, then if you input e.g. "not resid 3" in the "Selected Atoms" box, then the 3rd path will be invisible.
Deleting H-H bond path is often acceptable, as it usually only implies an extremely weak interaction (except for case of dihydrogen bond, which is a relatively prominent interaction and the strength is often comparable to H-bond).
Please check Section 5.3 of Multiwfn manual, where I described how to use Multiwfn in batch mode by writting Linux shell script
Dear Tian,
But I need the frequency values and the thermodynamic quantities G and H, although they are not displayed in the output.
They are irrelevant to the warning.
Without full output file, I cannot answer the actual reason.
By the way, using Shermo to calculate thermodynamic quantities based on Gaussian output file of "freq" task is more recommended, see http://sobereva.com/soft/shermo
You don't need to worry about that, it is commonly not harmful.