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Re: [Jmol-users] Natural Bond Orbital Display Issues
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From: Conor B. <cbr...@ma...> - 2020-10-29 19:43:54
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Hi All, I've attached a .tar file with the archive of an acetone run on my default WebMO settings + calling the PLOT and ARCHIVE commands in the input. Unfortunately, it doesn't look like it outputs a .60 file (though it does output a .36 file). Hopefully there will be a workaround, but if not I'll be chatting with my research advisor about upgrading NBO on Monday, though I'm not sure how that would work as we use consortium machines/software to do computational work. Best, - Conor archive147227.tar <https://drive.google.com/file/d/11Bp9hAiF__XjBz8BDo2kz7-A2mrzXZLo/view?usp=drive_web> On Thu, Oct 29, 2020 at 1:23 PM Robert Hanson via Jmol-users < jmo...@li...> wrote: > ... file 60. Can you send me that? > > John, if Conor renames file 60 to file 36 will we have the right format? > Or are they totally different? > > > Best, though, would be to upgrade NBO. > > On Thu, Oct 29, 2020 at 2:20 PM Robert Hanson <ha...@st...> wrote: > >> Conor, looks like your older version is storing labels in >> >> >> On Thu, Oct 29, 2020 at 1:37 PM Conor Broderick <cbr...@ma...> >> wrote: >> >>> Hi Dr. Keller, >>> >>> I just tried running your input script, and unfortunately it fails when >>> run in my version of webMO. I checked out the default state of the file for >>> me and it is the following: >>> >>> #N B3LYP/6-31G(d) SP GFINPUT POP=(FULL,NBORead) Geom=Connectivity >>> >>> Acetone_NBO_Test >>> >>> 0 1 >>> C >>> C 1 B1 >>> C 2 B2 1 A1 >>> H 3 B3 2 A2 1 D1 >>> H 3 B4 2 A3 1 D2 >>> H 3 B5 2 A4 1 D3 >>> O 2 B6 1 A5 3 D4 >>> H 1 B7 2 A6 3 D5 >>> H 1 B8 2 A7 3 D6 >>> H 1 B9 2 A8 3 D7 >>> >>> B1 1.540000394 >>> B2 1.540000394 >>> B3 1.090000499 >>> B4 1.089999580 >>> B5 1.089999580 >>> B6 1.275000000 >>> B7 1.090000499 >>> B8 1.089999580 >>> B9 1.089999580 >>> A1 119.9999310 >>> A2 109.4712505 >>> A3 109.4712163 >>> A4 109.4712163 >>> A5 120.0000345 >>> A6 109.4712505 >>> A7 109.4712163 >>> A8 109.4712163 >>> D1 180.0000000 >>> D2 -60.00000517 >>> D3 60.00000517 >>> D4 180.0000000 >>> D5 180.0000000 >>> D6 -60.00000517 >>> D7 60.00000517 >>> >>> 1 2 1 8 1 9 1 10 1 >>> 2 1 1 7 2 3 1 >>> 3 2 1 4 1 5 1 6 1 >>> 4 3 1 >>> 5 3 1 >>> 6 3 1 >>> 7 2 2 >>> 8 1 1 >>> 9 1 1 >>> 10 1 1 >>> >>> $NBO FILE=NBODATA >>> AOPNAO=W32 AOPNHO=W34 AOPNBO=W36 >>> DMNAO=W82 DMNHO=W84 DMNBO=W86 >>> FNAO=W92 FNHO=W94 FNBO=W96 ARCHIVE >>> PLOT >>> $END >>> >>> >>> When copying your script and replacing the POP=(FULL, NBO6READ) with >>> POP=(FULL, *NBOREAD*), I was able to get a run to complete, but it >>> again did not generate a .46 file (all other xxx.## files generated fine). >>> At this point I think either I'll need to install a newer version of the >>> NBO software or do the earlier brute forcing attempt, unless there is a >>> command with which I can directly generate the .46 file that is not ARCHIVE >>> or PLOT. >>> >>> best, and thank you for the help >>> >>> - Conor >>> >>> On Wed, Oct 28, 2020 at 11:15 PM John Keller <jwk...@al...> >>> wrote: >>> >>>> Here is what I am doing now. No need to get nbo 7. >>>> >>>> >>>> >>>> ------------- >>>> >>>> #N B3LYP/6-31G(d,p) SP GFINPUT POP=(FULL,NBO6Read) >>>> >>>> >>>> >>>> C3H6O >>>> >>>> >>>> >>>> 0 1 >>>> >>>> C 0.00000000 0.00000000 0.00000000 >>>> >>>> C 0.00000000 -1.33367900 0.77000100 >>>> >>>> C 0.00000000 -2.66735800 0.00000000 >>>> >>>> H 0.00000000 -3.49584500 0.70831500 >>>> >>>> H -0.88998100 -2.72509900 -0.62665700 >>>> >>>> H 0.88998100 -2.72509900 -0.62665700 >>>> >>>> O 0.00000000 -1.33367900 2.04500100 >>>> >>>> H 0.00000000 0.82848700 0.70831500 >>>> >>>> H 0.88998100 0.05774100 -0.62665700 >>>> >>>> H -0.88998100 0.05774100 -0.62665700 >>>> >>>> >>>> >>>> $NBO FILE=NBODATA PLOT ARCHIVE $END >>>> >>>> ------------- >>>> >>>> >>>> >>>> In WebMO Job Manager, Select the job, Download the Job Archive. Expand >>>> the archive on your local machine, then in Jmol: >>>> >>>> >>>> >>>> $ cd <folder containing the job files> >>>> >>>> $ load nbodata.31 >>>> >>>> $ nbo type nbo >>>> >>>> $ nbo 10 >>>> >>>> >>>> >>>> I assume it’s possible to modify the appearance of these surfaces, and >>>> hopefully plot more than one simultaneously. >>>> >>>> John K. >>>> >>>> >>>> >>>> >>>> >>>> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for >>>> Windows 10 >>>> >>>> >>>> >>>> *From: *Conor Broderick <cbr...@ma...> >>>> *Sent: *Wednesday, October 28, 2020 7:42 PM >>>> *To: *Robert Hanson <ha...@st...> >>>> *Cc: *jmo...@li... >>>> *Subject: *Re: [Jmol-users] Natural Bond Orbital Display Issues >>>> >>>> >>>> >>>> Amazing! Thanks for the update. Hopefully this will be the last >>>> question on my end, but do you happen to know the Gaussian command (I am >>>> using Gaussian 16) to output the .46 file? It doesn't seem to generate with >>>> "plot" and "archive," and I tried adding "label" but those runs seemed to >>>> fail immediately. I'm concerned that this may have run up against the >>>> limits of what I can do without getting NBO7. >>>> >>>> >>>> >>>> best, >>>> >>>> >>>> >>>> - COnor >>>> >>>> >>>> >>>> On Wed, Oct 28, 2020 at 9:09 PM Robert Hanson <ha...@st...> >>>> wrote: >>>> >>>> (actually, it accesses those files immediately upon loading. >>>> >>>> >>>> >>>> On Wed, Oct 28, 2020 at 10:08 PM Robert Hanson <ha...@st...> >>>> wrote: >>>> >>>> Meaning, what we need are these: >>>> >>>> >>>> >>>> >>>> >>>> >>>> * // .31 AO basis // .46 (labels)* >>>> >>>> >>>> >>>> What you do is load one of these: >>>> >>>> >>>> >>>> // .32 PNAO no beta coef >>>> // .33 NAO no beta coef ; adds orbital types >>>> // .34 PNHO alpha+beta >>>> // .35 NHO alpha+beta >>>> // .36 PNBO alpha+beta >>>> // .37 NBO alpha+extra+beta+extra >>>> // .38 PNLMO alpha+beta >>>> // .39 NLMO alpha+extra+beta+extra >>>> // .40 MO alpha+beta >>>> // .41 NO alpha+beta >>>> // .44 PRNBO alpha+beta >>>> // .45 RNBO alpha+beta >>>> >>>> >>>> >>>> And it will automatically access the .31 and .46 files when you then >>>> issue the NBO command. Or you can load the .31 file and then use >>>> >>>> >>>> >>>> NBO TYPE NLMO >>>> >>>> >>>> >>>> or similar command, then >>>> >>>> >>>> >>>> NBO 10 >>>> >>>> >>>> >>>> Bob >>>> >>>> >>>> >>>> -- >>>> >>>> Robert M. Hanson >>>> Professor of Chemistry >>>> St. Olaf College >>>> Northfield, MN >>>> http://www.stolaf.edu/people/hansonr >>>> >>>> >>>> If nature does not answer first what we want, >>>> it is better to take what answer we get. >>>> >>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>>> >>>> >>>> >>>> *We stand on the homelands of the Wahpekute Band of the Dakota Nation. >>>> We honor with gratitude the people who have stewarded the land throughout >>>> the generations and their ongoing contributions to this region. We >>>> acknowledge the ongoing injustices that we have committed against the >>>> Dakota Nation, and we wish to interrupt this legacy, beginning with acts of >>>> healing and honest storytelling about this place.* >>>> >>>> >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We >> honor with gratitude the people who have stewarded the land throughout the >> generations and their ongoing contributions to this region. We acknowledge >> the ongoing injustices that we have committed against the Dakota Nation, >> and we wish to interrupt this legacy, beginning with acts of healing and >> honest storytelling about this place.* >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We > honor with gratitude the people who have stewarded the land throughout the > generations and their ongoing contributions to this region. We acknowledge > the ongoing injustices that we have committed against the Dakota Nation, > and we wish to interrupt this legacy, beginning with acts of healing and > honest storytelling about this place.* > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
