Multiwfn forum / Find critical points along atomic interaction lines

Re: Find critical points along atomic interaction lines

dummy@example.com (sobereva) — Sat, 05 Dec 2020 21:31:43 +0000

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.

Re: Find critical points along atomic interaction lines

dummy@example.com (Louischarlc0) — Sat, 05 Dec 2020 11:54:37 +0000

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

Re: Find critical points along atomic interaction lines

dummy@example.com (sobereva) — Sat, 05 Dec 2020 11:12:51 +0000

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.

Re: Find critical points along atomic interaction lines

dummy@example.com (sobereva) — Sat, 05 Dec 2020 11:08:27 +0000

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.

Re: Find critical points along atomic interaction lines

dummy@example.com (Louischarlc0) — Fri, 04 Dec 2020 17:41:13 +0000

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

Re: Find critical points along atomic interaction lines

dummy@example.com (Louischarlc0) — Fri, 04 Dec 2020 16:08:48 +0000

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

Regards
Louis-Charl

Re: Find critical points along atomic interaction lines

dummy@example.com (Louischarlc0) — Fri, 04 Dec 2020 16:06:35 +0000

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

Regards
Louis-Charl

Re: Find critical points along atomic interaction lines

dummy@example.com (sobereva) — Fri, 04 Dec 2020 15:08:59 +0000

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.

Re: Find critical points along atomic interaction lines

dummy@example.com (Louischarlc0) — Fri, 04 Dec 2020 10:20:19 +0000

Or paths

regards
Louis-Charl

Re: Find critical points along atomic interaction lines

dummy@example.com (Louischarlc0) — Fri, 04 Dec 2020 10:19:07 +0000

Atomic interaction lines

Regards
Louis-Charl

Re: Find critical points along atomic interaction lines

dummy@example.com (sobereva) — Fri, 04 Dec 2020 10:12:31 +0000

What does "AILs" mean?

Re: Find critical points along atomic interaction lines

dummy@example.com (Louischarlc0) — Fri, 04 Dec 2020 08:20:22 +0000

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

Re: Find critical points along atomic interaction lines

dummy@example.com (sobereva) — Wed, 02 Dec 2020 15:48:20 +0000

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
}

Re: Find critical points along atomic interaction lines

dummy@example.com (Louischarlc0) — Wed, 02 Dec 2020 15:10:14 +0000

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

Regards
Louis-Charl

Re: Find critical points along atomic interaction lines

dummy@example.com (Louischarlc0) — Wed, 02 Dec 2020 15:05:53 +0000

Thank you so much

Regards
Louis-Charl