Electron Localization Function analysis via Topmod

Amalda · 2021-10-10 10:38:37

Hello, I hope you are doing well.

I am a complete beginner in electron location function (ELF) analysis. I need to learn how to do the calculation using topmod.
I only have the wfn files of the studied molecules generated by Gaussian09. I don't know how to do the other steps: grid90, bas90... Can you please help me ?

sobereva · 2021-10-10 18:35:57

Using Multiwfn to analyze ELF is *significantly* easier and faster than using Topmod, and Multiwfn provides much more related functions and features (including direct visualization of result). Multiwfn can do all kinds of analysis for ELF, such as plotting curve/plane/isosurface map (main function 3,4,5, respectively), basin analysis (main function 17), topology analysis (main function 2), domain analysis (subfunction 14 of main function 200), high ELF localization domain population and volume (HELP and HELV), CVB index and so on, rich examples can be found in Multiwfn manual.

I don't find any reason to use other codes than Multiwfn for ELF analysis because Multiwfn is capable of doing everything with minimal steps and very fast in ELF analysis, and Multiwfn can do anything that Topmod can do. If you can describe purpose of your study more detailedly, I will be able to provide you more help and guidance of analyzing ELF in Multiwfn.

Amalda · 2021-10-11 10:01:53

Thank you

p.mcardle001@gmail.com · 2022-09-17 16:07:01

In a paper in Inorganic Chemistry (doi:10.1021/ic011003v) Bernard Silvi gives TOPMOD valence electon counts on P in PCl5 and PMe5 of 7.13 and 9.12 respectively. Using MultiWFN I get values that hardly differ
for PCl5
Total localization index (atom index):
1: 10.96822 2: 16.66868 3: 16.66544 4: 16.71506 5: 16.66478
6: 16.71438
for PMe5
Total localization index (atom index):
1: 10.55497 2: 4.49187 3: 4.55057 4: 4.47007 5: 4.55241
6: 4.55770 7: 0.47068 8: 0.47492 9: 0.47038 10: 0.43251
11: 0.43330 12: 0.42961 13: 0.43732 14: 0.42985 15: 0.43172
16: 0.47378 17: 0.47449 18: 0.47112 19: 0.43297 20: 0.43119
21: 0.43452

The lower index is on the more covalent PMe5 which is the opposite of what Silvi reported.
I used I used 17 1 1 3 4 2 y
I think that I must be making an error.

sobereva · 2022-09-17 19:47:20

p.mcardle001@gmail.com wrote:

In a paper in Inorganic Chemistry (doi:10.1021/ic011003v) Bernard Silvi gives TOPMOD valence electon counts on P in PCl5 and PMe5 of 7.13 and 9.12 respectively. Using MultiWFN I get values that hardly differ
for PCl5

You only show localization indices of atoms here, which are quite different to "valence electon counts". If what you really need is "valence electon counts" of P, you should perform basin integration for electron density in every valence basin of P and then manually sum them up. Please refer to "Part 3: Estimate basin properties" in Section 4.17.2 of latest version of Multiwfn manual.

p.mcardle001@gmail.com · 2022-09-18 13:42:10

Many thanks for your prompt help. The valence electron counts I get agree with Silvi's and Many thanks for your xlnt MultiWFN program
Of historical interest and probably well known is that I found no option 12 Assign ELF basin labels in 3.8 (dev) 2020 Sep 22 but option 12 is present in 3.8(dev) 2022 Sep 12.

sobereva · 2022-09-18 16:18:14

"12 Assign ELF basin labels" is only available in relative new version of Multiwfn. Please check "Update History" page on Multiwfn website.

p.mcardle001@gmail.com · 2022-09-18 17:50:48

Thankyou

p.mcardle001@gmail.com · 2022-09-26 14:17:34

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?

sobereva · 2022-09-27 02:16:52

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

p.mcardle001@gmail.com · 2022-09-27 13:50:24

sobereva · 2022-09-27 14:53:22

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.

p.mcardle001@gmail.com · 2022-09-28 14:19:41

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

sobereva · 2022-09-28 16:16:01

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

p.mcardle001@gmail.com · 2022-09-28 17:54:21

Many Thanks for your kind reply

Yes this changes the color

sobereva · 2022-09-28 19:08:35

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.

p.mcardle001@gmail.com · 2022-10-04 13:54:49

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?

sobereva · 2022-10-06 11:50:01

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
http://www.shanxitv.org/multiwfn/forum_attach/568.mp4

p.mcardle001@gmail.com · 2022-10-06 13:48:34

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 =============

sobereva · 2022-10-07 01:55:38

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)

p.mcardle001@gmail.com · 2022-10-07 13:32:24

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

sobereva · 2022-10-07 14:18:24

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

p.mcardle001@gmail.com · 2022-10-08 16:49:51

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

Multiwfn forum

#1 2021-10-10 10:38:37

Electron Localization Function analysis via Topmod

#2 2021-10-10 18:35:57

Re: Electron Localization Function analysis via Topmod

#3 2021-10-11 10:01:53

Re: Electron Localization Function analysis via Topmod

#4 2022-09-17 16:07:01

Re: Electron Localization Function analysis via Topmod

#5 2022-09-17 19:47:20

Re: Electron Localization Function analysis via Topmod

#6 2022-09-18 13:42:10

Re: Electron Localization Function analysis via Topmod

#7 2022-09-18 16:18:14

Re: Electron Localization Function analysis via Topmod

#8 2022-09-18 17:50:48

Re: Electron Localization Function analysis via Topmod

#9 2022-09-26 14:17:34

Re: Electron Localization Function analysis via Topmod

#10 2022-09-27 02:16:52

Re: Electron Localization Function analysis via Topmod

#11 2022-09-27 13:50:24

Re: Electron Localization Function analysis via Topmod

#12 2022-09-27 14:53:22

Re: Electron Localization Function analysis via Topmod

#13 2022-09-28 14:19:41

Re: Electron Localization Function analysis via Topmod

#14 2022-09-28 16:16:01

Re: Electron Localization Function analysis via Topmod

#15 2022-09-28 17:54:21

Re: Electron Localization Function analysis via Topmod

#16 2022-09-28 19:08:35

Re: Electron Localization Function analysis via Topmod

#17 2022-10-04 13:54:49

Re: Electron Localization Function analysis via Topmod

#18 2022-10-06 11:50:01

Re: Electron Localization Function analysis via Topmod

#19 2022-10-06 13:48:34

Re: Electron Localization Function analysis via Topmod

#20 2022-10-07 01:55:38

Re: Electron Localization Function analysis via Topmod

#21 2022-10-07 13:32:24

Re: Electron Localization Function analysis via Topmod

#22 2022-10-07 14:18:24

Re: Electron Localization Function analysis via Topmod

#23 2022-10-08 16:49:51

Re: Electron Localization Function analysis via Topmod

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