Partial atomic charges g16

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mosera
Posts: 8
Joined: Tue Aug 03, 2021 11:12 pm
Full Name: Adam Moser
Organization: Loras College

Partial atomic charges g16

Post by mosera »

Moving the topic over here from the features forum. Looks like partial atomic charges aren’t being shown in WebMO output when using g16. Tried a few different molecules with a few different calculation types. Any thoughts or confirmations?

schmidt
Posts: 50
Joined: Sat May 30, 2020 3:00 pm
Full Name: JR Schmidt
Organization: WebMO, LLC

Re: Partial atomic charges g16

Post by schmidt »

Can you clarify which Gaussian version (exactly, including build number) AND WebMO version? This certainly appears to work fine for me on with the latest WebMO versions and several versions of G16. An example output file would also be useful.

mosera
Posts: 8
Joined: Tue Aug 03, 2021 11:12 pm
Full Name: Adam Moser
Organization: Loras College

Re: Partial atomic charges g16

Post by mosera »

G16 c.01. WebMO 20.0.012p

Output of HF geom attached and screenshot of output
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Gaussian output
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mosera
Posts: 8
Joined: Tue Aug 03, 2021 11:12 pm
Full Name: Adam Moser
Organization: Loras College

Re: Partial atomic charges g16

Post by mosera »

Any thoughts or things I can try? I'm a bit stuck and we have assignments they use the partial charge for.

jwk
Posts: 29
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Partial atomic charges g16

Post by jwk »

Hi, Your Mulliken charges are in the output578.txt file at line 550. With g16 and WebMO you will need to search the output.log file for "Mulliken charges" to find that information.
John Keller
University of Alaska Fairbanks

mosera
Posts: 8
Joined: Tue Aug 03, 2021 11:12 pm
Full Name: Adam Moser
Organization: Loras College

Re: Partial atomic charges g16

Post by mosera »

John, Thanks for the reply. It isn't that I can't find it in the raw output; it is that WebMO is either not parsing the gaussian output to find them or it is parsing properly, but not realizing it should put it in the "Calculated Quantities" block below the molecule. It used to do this and does it when I used g09. Since I'm using it with first year students, I really don't want to try to teach them how to open and search the actual gaussian output because I think they would find it overwhelming.

What is odd to me is that g09 and g16 seem to format the partial charge information the same. Also I can't see anything in parse_gaussian.cgi or view_jog.cgi that would stop WebMO from both finding and displaying the charges in the WebMO "Calculated Quantities" section. I'm clearly missing something, but I'm sure the intention is that atomic partial charges are meant to be displayed.

jwk
Posts: 29
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Partial atomic charges g16

Post by jwk »

Hi Adam,
I posted about this problem here last year, but no answer was forthcoming. My solution now is to have a teaching WebMO queue that runs g09, and a research queue that runs g16. The older version is perfectly fine for students. Of course, you would need to have both versions to do this.

jwk
Posts: 29
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Partial atomic charges g16

Post by jwk »

This problem is fixed in WebMO 21. See the Demo site which runs G16.

polik
Posts: 16
Joined: Fri May 29, 2020 6:20 pm
Full Name: Will Polik
Organization: WebMO LLC

Re: Partial atomic charges g16

Post by polik »

While there are many other reasons to upgrade from WebMO 20 to WebMO 21, the fix for this is so straightforward that folks still running WebMO 20 can easily implement it on their implementations.

There was a minor formatting change in the output of g16 from:
Population analysis using the SCF density
to:
Population analysis using the SCF Density

The patch to parse both versions of output is to edit parse_gaussian.cgi and change line 778 from:
local $i = search_from_end("Population analysis using the \\S+ density", \@logfileText);
to
local $i = search_from_end("Population analysis using the \\S+ [Dd]ensity", \@logfileText);
Note that "d" becomes "[Dd]".

This change is implemented in WebMO 21.

jwk
Posts: 29
Joined: Sat Jun 20, 2020 3:37 am
Full Name: John Keller
Organization: University of Alaska Fairbanks
Subdiscipline: Chemistry

Re: Partial atomic charges g16

Post by jwk »

Thanks, Will. This also works in WebMO 19. On line 770 of parse_gaussian.cgi the same change is made.

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