Find critical points along atomic interaction lines

Louischarlc0 · 2020-12-02 11:02:36

Hi there

I'm trying to label specific critical points along certain atomic interaction lines, but when a enter the command labc all into VMD then it just label all the critical points. How can I remove the ones that I do not need and only label certain ones?

Thanks in advance

Regards
Louis-Charl

sobereva · 2020-12-02 13:39:29

Dear Louis-Charl,

I just updated Multiwfn 3.8(dev) on Multiwfn website, the AIM.vmd has been updated, a new command "labcpidx" has been introduced. You can use for example "labcpidx 5" to only label CP 5.

Best Regards,

Tian

Louischarlc0 · 2020-12-02 15:05:53

Thank you so much

Regards
Louis-Charl

Louischarlc0 · 2020-12-02 15:10:14

However, I've entered that command but it says invalid command

Regards
Louis-Charl

sobereva · 2020-12-02 15:48:20

Please make sure that in the examples\scripts\AIM.vmd, you can find the following information, and this file has been moved to VMD folder

proc labcpidx {cpidx {labsize 1.8} {offsetx -0.1} {offsety 0.0}} {
label delete Atoms all
color Labels Atoms blue
label textthickness 2.000000
label textsize $labsize
set sel [atomselect 0 "serial $cpidx"]
set k 0
foreach i [$sel list] {
label add Atoms 0/$i
label textformat Atoms $k { %1i }
label textoffset Atoms $k "$offsetx $offsety"
incr k
}
$sel delete
}

Louischarlc0 · 2020-12-04 08:20:22

Everything is cluttered. Is it possible to find only the CPs that lies on the AILs and eliminate the others?

Thanks in advance

Regards
Louis-Charl

sobereva · 2020-12-04 10:12:31

What does "AILs" mean?

Louischarlc0 · 2020-12-04 10:19:07

Atomic interaction lines

Regards
Louis-Charl

Louischarlc0 · 2020-12-04 10:20:19

Or paths

regards
Louis-Charl

sobereva · 2020-12-04 15:08:59

Assume that you only need BCP and corresponding bond paths between atom 4 and atom 8, you should first locate BCP and then generate bond paths as usual, then choose
-5 // Modify or print detail or export paths, or plot property along a path
8 // Only retain bond paths (and corresponding CPs) connecting two specific molecular fragments while remove all other bond paths and BCPs
4
8
y // Also delete BCPs
Then you will find only the BCP and bond path connecting atoms 4 and 8 are retained, all others have been deleted.

Section 4.2.6 of Multiwfn manual also illustrated this point.

Louischarlc0 · 2020-12-04 16:06:35

Thank you for your response but how will I know the label of the atoms?

Regards
Louis-Charl

Louischarlc0 · 2020-12-04 16:08:48

Or how will I be able to locate the BCP between the atoms that I want?

Regards
Louis-Charl

Louischarlc0 · 2020-12-04 17:41:13

I see the method on page 374 in the new manual. However, when I try it then it eliminates the paths. i want to retain all the paths. Its the BCP that does not lie on these paths that I want to eliminate. How can I do that?

Thanks in advance

regards
Louis-Charl

sobereva · 2020-12-05 11:08:27

Louischarlc0 wrote:

Thank you for your response but how will I know the label of the atoms?

Regards
Louis-Charl

You can visualize atomic labels in main function 0 of Multiwfn, or visualize the system by third-part softwares such as GaussView, Chem3D, Avogadro and so on, all of them are able to show atomic indices. In addition, in VMD program you can press button 0 on your keyboard to enter query mode, then click the center of an atom, the index of the atom will be shown in console window of VMD, the "index" value plus 1 is the actual atomic index.

sobereva · 2020-12-05 11:12:51

Louischarlc0 wrote:

I see the method on page 374 in the new manual. However, when I try it then it eliminates the paths. i want to retain all the paths. Its the BCP that does not lie on these paths that I want to eliminate. How can I do that?

Thanks in advance

regards
Louis-Charl

I don't fully understand your meaning. If you simply want to delete specific CPs, you can enter "-4 Modify or export CPs" and then choose "2 Delete some CPs", there are different options used to delete unwanted CPs.

Louischarlc0 · 2020-12-05 11:54:37

I see in section 4.2.6 that you should boot up multiwfn and input GCGC.wfn as an input file. I did it as a practice run and it went fine. However, for my own compounds should I also generate similar .wfn files and if so should I use a different gaupath as in the previous version? Will it also generate a CPprop file that gives the exact RDG values for BCPs along the paths?

Thanks in advance

Regards
Louis-Charl

sobereva · 2020-12-05 21:31:43

The "gaupath" in settings.ini file is completely irrelevant to the topology analysis.

You can use any file containing GTF information as input file for AIM topology analysis, including .wfn/.wfx/.fch/.mwfn/.molden/.gms format, see Section 2.5 for introduction of these files and beginning of Chapter 4 of Multiwfn manual on how to generate them.

Multiwfn forum

#12020-12-02 11:02:36

Find critical points along atomic interaction lines

#22020-12-02 13:39:29

Re: Find critical points along atomic interaction lines

#32020-12-02 15:05:53

Re: Find critical points along atomic interaction lines

#42020-12-02 15:10:14

Re: Find critical points along atomic interaction lines

#52020-12-02 15:48:20

Re: Find critical points along atomic interaction lines

#62020-12-04 08:20:22

Re: Find critical points along atomic interaction lines

#72020-12-04 10:12:31

Re: Find critical points along atomic interaction lines

#82020-12-04 10:19:07

Re: Find critical points along atomic interaction lines

#92020-12-04 10:20:19

Re: Find critical points along atomic interaction lines

#102020-12-04 15:08:59

Re: Find critical points along atomic interaction lines

#112020-12-04 16:06:35

Re: Find critical points along atomic interaction lines

#122020-12-04 16:08:48

Re: Find critical points along atomic interaction lines

#132020-12-04 17:41:13

Re: Find critical points along atomic interaction lines

#142020-12-05 11:08:27

Re: Find critical points along atomic interaction lines

#152020-12-05 11:12:51

Re: Find critical points along atomic interaction lines

#162020-12-05 11:54:37

Re: Find critical points along atomic interaction lines

#172020-12-05 21:31:43

Re: Find critical points along atomic interaction lines

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