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#1 Multiwfn and wavefunction analysis » Warning that charge is high in Molden input file » 2022-11-29 15:54:13
- p.mcardle001@gmail.com
- Replies: 1
Orca input file
# shrock
! MP2 RHF def2-TZVP FrozenCore TightSCF
! Pmodel AIM
%maxcore 16128
%PAL NPROC 3
end
* xyz 0 1
atom coordinates
Compound formula
Mo(CH2)(OtBu)2(NC8H10)
I get the message "Orca terminated normally" and the total charge was zero in the Orca listing file
When I try to use MultiWFN to do a LOBA calculation I get
!! Warning! Warning! Warning! Warning! Warning! Warning! Warning! Warning !!
The net charge of this system is quite large ( 28)! 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
The command I use to generate the Molden input file is
c:\ORCA\ORCA_2MKL jobname -molden
I had a look at the molden input file but am unable to follow the advics on modifying the atomic indices.
#2 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 2022-10-08 16:49:51
Many many thanks for your kind help and your excellent program.
#3 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 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.
#4 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 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 =============
#5 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 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?
#6 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 2022-09-28 17:54:21
Many Thanks for your kind reply
Yes this changes the color
#7 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 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
#8 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 2022-09-27 13:50:24
#9 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 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?
#10 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 2022-09-18 17:50:48
Thankyou
#11 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 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.
#12 Re: Multiwfn and wavefunction analysis » Electron Localization Function analysis via Topmod » 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.
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