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Re: [cclib-users] gbasis with Orca
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From: Felix P. <fel...@un...> - 2016-03-04 17:23:07
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Hi, I double checked this and it looks like gbasis is parsed correctly. If I do the same calculation with Orca and Gaussian, then I get the same results with ccget orca.out gbasis and ccget gaussian.log gbasis So everything looks fine and I get the same canonical result. The thing that confused me initially is that Orca uses a different order for the p-functions - and because of that things looked differently. But this is already parsed correctly by cclib: ccget orca.out aonames [ ..., u'C1_1PZ', u'C1_1PX', u'C1_1PY', ...] And I will just have to reorder the MO-coefficients accordingly for my purposes. As I see it, everything looks fine, and I'll send the pull request. By the way, getting the correct ordering of the basis functions would also be a challenge for the Molden writer. My own little tool cc2molden.py https://sourceforge.net/p/theodore-qc/code/ci/master/tree/bin/cc2molden.py failed because of this ordering. And that is what confused me ... -Felix On 03/04/2016 03:06 PM, Karol Langner wrote: > > I think we want to parse the canonical gbasis before any > normalization, because that's transferable. In any case, we want it to > be the same for all programs. Is there an easy way to unnormalize? > > On Mar 4, 2016 1:49 AM, "Felix Plasser" <fel...@un... > <mailto:fel...@un...>> wrote: > > Hi Karol and Eric, > > I do have the parser now > https://github.com/felixplasser/cclib/commit/0f8e6db49910aedb92a1cad5e0ba384a3fc0efaa?diff=unified > > This parses gbasis as it is printed out in the standard output. > The problem is that internally ORCA changes the normalization > factors, and then this gbasis is no longer consistent with the > MO-coefficients. For example when I run orca_2mkl, it tells me > "The basis set has NOT been un-normalized for printing" > And then I get the un-normalized coefficients that are used > internally and that are consistent with mocoeffs. But they are not > the same coefficients printed in the output file. > > For my specific application gbasis works they way it is parsed > now. But I do not really know what gbasis is supposed to be: the > input coefficients, or the coefficients used internally. > > About Molden format: it would just parse a few attributes, mainly > atmnos, atomcoords, gbasis, and mocoeffs > But the important point here would be that gbasis and mocoeffs are > consistent and well-defined (assuming that the molden file was > created properly) > > Felix > > On 03/03/2016 09:35 PM, Eric Berquist wrote: >> Hi Felix and Karol, >> >> If a pull request is made, I guarantee I'll take a look at it, >> since I'm trying to be more active in the project. >> >> We don't have a Molden parser yet, though I started a Molden >> writer for cclib, and have something standalone that attempts to >> clean up the Molden output produced by a few different programs, >> since Molden itself seemed pretty picky about the section >> ordering: >> https://github.com/berquist/scripts/blob/master/fix_molden.py >> >> Eric >> >> On Thu, Mar 3, 2016 at 3:25 PM, Karol Langner >> <kar...@gm... <mailto:kar...@gm...>> wrote: >> >> Yes, pull requests are definitely the way to go. Turnaround >> time varies with how busy people are. >> >> Parsing molden files is possible, just requires some work. >> However, I'm not sure what kind of coverage of cclib >> attribute one could get from those files. Are they text >> format or binary? >> >> On Thu, Mar 3, 2016 at 3:01 AM, Felix Plasser >> <fel...@un... >> <mailto:fel...@un...>> wrote: >> >> Ok, sounds good. I will try to set it up. And then I'll >> send a pull-request via github, if that's the way to do >> it ... >> >> By the way, another thing I am thinking about is that >> cclib would be able to parse files in Molden format. That >> would be a nice way to get: atmonos, atomcoords, gbasis, >> and mocoeffs in a standardized way. >> >> Cheers, >> Felix >> >> On 03/03/2016 06:54 AM, Karol Langner wrote: >>> Hi Felix, >>> >>> If you look at the table showing coverage of attributes >>> (http://cclib.github.io/data.html#details-of-current-implementation) >>> you'll see there's a T/D for gbasis/ORCA. That's >>> automatically generated from the code, and as you've >>> observed there is no parsing code for that yet :) >>> apparently I put that note there to not forget. >>> >>> If you implement this, please do contribute it to cclib. >>> I probably won't get around to it anytime soon. >>> >>> Cheers, >>> Karol >>> >>> >>> On Wed, Mar 2, 2016 at 7:05 AM, Karol Langner >>> <kar...@gm... >>> <mailto:kar...@gm...>> wrote: >>> >>> Hi Felix, >>> >>> It might be lingering in a branch or pull request. >>> Let me check and get back to you. >>> >>> Karol >>> >>> On Mar 2, 2016 6:57 AM, "Felix Plasser" >>> <fel...@un... >>> <mailto:fel...@un...>> wrote: >>> >>> Hi, I am just testing cclib for a new project of >>> ours. >>> >>> What I was wondering is: Is it possible to get >>> the gbasis attribute from Orca? In the "parsed >>> data notes" it says the it should work if I >>> include the line >>> Print[ P_Basis ] 2 in the output block >>> >>> Indeed, that will print out the basis >>> coefficients and exponents (see the attached >>> orca.out file), but the gbasis attribute is not >>> parsed. I checked the newest source from github >>> and it looks like the file orcaparser.py does >>> not contain the word gbasis anywhere. So I >>> assume this is not parsed? >>> >>> I guess it will not be too much trouble for me >>> to add the functionality. I just wanted to check >>> if this is already there before I would try to >>> implement it myself. >>> >>> Thank you, >>> Felix >>> >>> -- >>> Felix Plasser >>> Institute for Theoretical Chemistry >>> University of Vienna >>> Währingerstr. 17/404 >>> 1090 Wien >>> fel...@un... >>> <mailto:fel...@un...> >>> http://homepage.univie.ac.at/felix.plasser/ >>> Tel.: +43-1-4277-52757 <tel:%2B43-1-4277-52757> >>> >>> >>> ------------------------------------------------------------------------------ >>> Site24x7 APM Insight: Get Deep Visibility into >>> Application Performance >>> APM + Mobile APM + RUM: Monitor 3 App instances >>> at just $35/Month >>> Monitor end-to-end web transactions and take >>> corrective actions now >>> Troubleshoot faster and improve end-user >>> experience. Signup Now! >>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>> _______________________________________________ >>> cclib-users mailing list >>> ccl...@li... >>> <mailto:ccl...@li...> >>> https://lists.sourceforge.net/lists/listinfo/cclib-users >>> >>> >> >> -- >> Felix Plasser >> Institute for Theoretical Chemistry >> University of Vienna >> Währingerstr. 17/404 >> 1090 Wien >> fel...@un... <mailto:fel...@un...> >> http://homepage.univie.ac.at/felix.plasser/ >> Tel.: +43-1-4277-52757 >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into >> Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just >> $35/Month >> Monitor end-to-end web transactions and take corrective >> actions now >> Troubleshoot faster and improve end-user experience. >> Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >> _______________________________________________ >> cclib-users mailing list >> ccl...@li... >> <mailto:ccl...@li...> >> https://lists.sourceforge.net/lists/listinfo/cclib-users >> >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application >> Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective >> actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >> _______________________________________________ >> cclib-users mailing list >> ccl...@li... >> <mailto:ccl...@li...> >> https://lists.sourceforge.net/lists/listinfo/cclib-users >> >> > > -- > Felix Plasser > Institute for Theoretical Chemistry > University of Vienna > Währingerstr. 17/404 > 1090 Wien > fel...@un... <mailto:fel...@un...> > http://homepage.univie.ac.at/felix.plasser/ > Tel.: +43-1-4277-52757 > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > cclib-users mailing list > ccl...@li... > <mailto:ccl...@li...> > https://lists.sourceforge.net/lists/listinfo/cclib-users > -- Felix Plasser Institute for Theoretical Chemistry University of Vienna Währingerstr. 17/404 1090 Wien fel...@un... http://homepage.univie.ac.at/felix.plasser/ Tel.: +43-1-4277-52757 |
