Re: [cclib-users] gbasis with Orca

[Karol L. <kar...@gm...>]

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...> 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...>
> 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...
>> > 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...>
>>> 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...>
>>>> 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...
>>>>> http://homepage.univie.ac.at/felix.plasser/
>>>>> Tel.: +43-1-4277-52757
>>>>>
>>>>>
>>>>>
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>>>
>>> --
>>> Felix Plasser
>>> Institute for Theoretical Chemistry
>>> University of Vienna
>>> Währingerstr. 17/404
>>> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
>>> Tel.: +43-1-4277-52757
>>>
>>>
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>>
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>
> --
> Felix Plasser
> Institute for Theoretical Chemistry
> University of Vienna
> Währingerstr. 17/404
> 1090 Wie...@un...http://homepage.univie.ac.at/felix.plasser/
> Tel.: +43-1-4277-52757
>
>
>
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