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Re: Electron Localization Function analysis via Topmod

dummy@example.com (p.mcardle001@gmail.com) — Sat, 08 Oct 2022 16:49:51 +0000

Many many thanks for your kind help and your excellent program.

Re: Electron Localization Function analysis via Topmod

dummy@example.com (sobereva) — Fri, 07 Oct 2022 14:18:24 +0000

If there is only one type of basins, then there is no reason to use b.

Re: Electron Localization Function analysis via Topmod

dummy@example.com (p.mcardle001@gmail.com) — Fri, 07 Oct 2022 13:32:24 +0000

Sorry for not being clear. Does the b option require two basin types or can just one be used.

Re: Electron Localization Function analysis via Topmod

dummy@example.com (sobereva) — Fri, 07 Oct 2022 01:55:38 +0000

I don't understand your meaning. As can be seen from the list, ClF5 have two types of basins, namely C (Core) and 1-synaptic V (Valence)

Re: Electron Localization Function analysis via Topmod

dummy@example.com (p.mcardle001@gmail.com) — Thu, 06 Oct 2022 13:48:34 +0000

Many thanks for the video. I have got it to work. I have used cd in the vmd window to go to the current working directory using cd c:/folder etc.

What is the correct answer to the b command when there is only one type of basin (no 2-synaptic basins) as in ClF5?

Sorting basins according to labels...
The following information is printed according to order of basin labels
Basin indices, populations (e), volumes (Angstrom^3) and assigned labels
# 1 Basin 15 Pop.: 2.2556 Vol.: 0.003 Label: C(Cl1)
# 2 Basin 19 Pop.: 2.1474 Vol.: 0.026 Label: C(F4)
# 3 Basin 17 Pop.: 2.2113 Vol.: 0.026 Label: C(F3)
# 4 Basin 14 Pop.: 7.7482 Vol.: 0.346 Label: C(Cl1)
# 5 Basin 6 Pop.: 2.1938 Vol.: 0.026 Label: C(F2)
# 6 Basin 13 Pop.: 2.1186 Vol.: 0.025 Label: C(F5)
# 7 Basin 12 Pop.: 2.2079 Vol.: 0.025 Label: C(F6)
# 8 Basin 8 Pop.: 0.4998 Vol.: 0.538 Label: V(Cl1)
# 9 Basin 9 Pop.: 0.4945 Vol.: 0.528 Label: V(Cl1)
# 10 Basin 10 Pop.: 0.5004 Vol.: 0.539 Label: V(Cl1)
# 11 Basin 7 Pop.: 0.8436 Vol.: 0.931 Label: V(Cl1)
# 12 Basin 18 Pop.: 7.1988 Vol.: 83.540 Label: V(F4)
# 13 Basin 16 Pop.: 0.4949 Vol.: 0.526 Label: V(Cl1)
# 14 Basin 5 Pop.: 2.4478 Vol.: 46.739 Label: V(Cl1)
# 15 Basin 4 Pop.: 7.2012 Vol.: 82.722 Label: V(F3)
# 16 Basin 3 Pop.: 7.2085 Vol.: 77.508 Label: V(F2)
# 17 Basin 2 Pop.: 7.2123 Vol.: 83.916 Label: V(F5)
# 18 Basin 11 Pop.: 0.1322 Vol.: 0.070 Label: V(F6)
# 19 Basin 1 Pop.: 6.9126 Vol.: 69.651 Label: V(F6)

Number of core basins is 7, their indices:
6,12-15,17,19
Number of 1-synaptic basins is 12, their indices:
1-5,7-11,16,18

============= Basin analysis =============

Re: Electron Localization Function analysis via Topmod

dummy@example.com (sobereva) — Thu, 06 Oct 2022 11:50:01 +0000

p.mcardle001@gmail.com wrote:

I have tried many times with different compounds but I always get the same result. I don't know what I am doing wrong. I am sorry to be looking for so much help. Are cub and vmd files available for an example which I could try to emulate?

Please check this video illustration, hope this could clarify enough. I am using VMD 1.9.3 and Multiwfn 3.8(dev) updated on 2022-Oct-4
//www.umsyar.com/multiwfn/forum_attach/568.mp4

Re: Electron Localization Function analysis via Topmod

dummy@example.com (p.mcardle001@gmail.com) — Tue, 04 Oct 2022 13:54:49 +0000

I have tried many times with different compounds but I always get the same result. I don't know what I am doing wrong. I am sorry to be looking for so much help. Are cub and vmd files available for an example which I could try to emulate?

Re: Electron Localization Function analysis via Topmod

dummy@example.com (sobereva) — Wed, 28 Sep 2022 19:08:35 +0000

Perhaps the grid data was not properly generated. Please double check steps described in Section 4.17.10 of Multiwfn manual, and use latest version of Multiwfn, and make sure that VMD is 1.9.3 32bit version.

Re: Electron Localization Function analysis via Topmod

dummy@example.com (p.mcardle001@gmail.com) — Wed, 28 Sep 2022 17:54:21 +0000

Many Thanks for your kind reply

Yes this changes the color

Re: Electron Localization Function analysis via Topmod

dummy@example.com (sobereva) — Wed, 28 Sep 2022 16:16:01 +0000

In Graphics - Representation, you can set coloring method to ColorID and then specify a color, does this manner properly change color on your computer?

Re: Electron Localization Function analysis via Topmod

dummy@example.com (p.mcardle001@gmail.com) — Wed, 28 Sep 2022 14:19:41 +0000

I have tried three different PCs with updated graphics drivers and I get the same result.
I have tried setting the environment variable "VMDSIMPLEGRAPHICS" to "1" and the result is that the black is changed to light grey.
I will try more PCs.

Thanks

Re: Electron Localization Function analysis via Topmod

dummy@example.com (sobereva) — Tue, 27 Sep 2022 14:53:22 +0000

Often, this problems comes from incompatibility between VMD and running environment or graphical card, please use another computer or upgrade graphical card driver and retry.

Re: Electron Localization Function analysis via Topmod

dummy@example.com (p.mcardle001@gmail.com) — Tue, 27 Sep 2022 13:50:24 +0000

Re: Electron Localization Function analysis via Topmod

dummy@example.com (sobereva) — Tue, 27 Sep 2022 02:16:52 +0000

p.mcardle001@gmail.com wrote:

I have a problem getting VMD to display ELF analysis in color. I have followed the oxirane example in the manual. The picture I get in VMD is exactly as the manual however the only color for the surfaces is black. The "atoms" are colored correctly i.e. O is red. I have tried several other examples and the I only get black surfaces. The cub and VMD files are all in the same folder. Is it correct to use VMD command "Load visualization state" to load the VMD file?

Please upload a screenshot

Re: Electron Localization Function analysis via Topmod

dummy@example.com (p.mcardle001@gmail.com) — Mon, 26 Sep 2022 14:17:34 +0000

I have a problem getting VMD to display ELF analysis in color. I have followed the oxirane example in the manual. The picture I get in VMD is exactly as the manual however the only color for the surfaces is black. The "atoms" are colored correctly i.e. O is red. I have tried several other examples and the I only get black surfaces. The cub and VMD files are all in the same folder. Is it correct to use VMD command "Load visualization state" to load the VMD file?