Re: [cclib-devel] [cclib-users] orbital occupation numbers

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

Axel,

Thanks! I will include some of these files as regressions tess. However,
the Gaussian and Molpro output files for water do not contain natural
orbitals... or am I missing something?

Karol

On Thu, Nov 6, 2014 at 11:57 PM, Karol Langner <kar...@gm...>
wrote:

> Just forwarding this to cclib-dev...
>
>
> ---------- Forwarded message ----------
> From: Axel Schild <axe...@go...>
> Date: Thu, Nov 6, 2014 at 6:13 AM
> Subject: Re: [cclib-users] orbital occupation numbers
> To: "Karol M. Langner" <kar...@gm...>
>
>
> Hi Karol,
>
> sorry for the delay, I first had to check with the other developers and
> this took some time...
>
> Attached please find the files that you may use, i.e. that we release to
> the Public Domain.
>
> Thanks!
> Axel
>
> On Wed, Oct 29, 2014 at 3:50 PM, Karol M. Langner <kar...@gm...
> > wrote:
>
>> Axel,
>>
>> Thanks for the files. Can I use them in our publicly available test
>> suite? In other
>> words, do you release these files into the Public Domain? Also, if you
>> have the Molpro
>> file with the long list of coefficients, that would be helpful, too.
>>
>> We are about to release cclib v1.3, and this certainly won't make it
>> there. But I have
>> already written some code which will go into the dev version:
>> https://github.com/cclib/cclib/pull/148
>>
>> Thanks,
>> Karol
>>
>> On Oct 27 2014, Axel Schild wrote:
>> > Karol,
>> >
>> > I could give you more Gaussian or GamessUS files, but they don't give
>> > anything new compared to the files in
>> > https://github.com/cclib/cclib/tree/master/data
>> >
>> > Attached please find two Molpro logfiles and a psi3 logfile. We don't
>> have
>> > other file formats because we don't use the respective programs (but we
>> > thought about using cclib to load these file formats for users that do
>> use
>> > them).
>> >
>> > Cheers
>> > Axel
>> >
>> > PS: I removed the long list of CI coefficients of the Molpro output for
>> > CH2O.
>> >
>> > On Fri, Oct 24, 2014 at 3:35 PM, Karol Langner <kar...@gm...
>> >
>> > wrote:
>> >
>> > > Axel,
>> > >
>> > > Would you be wlling to help by providing logfiles for programs that
>> you
>> > > would like parse this for?
>> > >
>> > > Karol
>> > >
>> > > On Fri, Oct 24, 2014 at 2:42 AM, Axel Schild <
>> axe...@go...>
>> > > wrote:
>> > >
>> > >> Hi Karol,
>> > >>
>> > >> thank you! I just compared to my test files and yes, those are the
>> > >> numbers that we want.
>> > >>
>> > >> I will follow the progress on the development version to see when we
>> can
>> > >> use cclib for orbkit.
>> > >>
>> > >> Cheers
>> > >> Axel
>> > >>
>> > >> On Thu, Oct 23, 2014 at 6:38 PM, Karol Langner <
>> kar...@gm...>
>> > >> wrote:
>> > >>
>> > >>> I created an issue for this:
>> > >>> https://github.com/cclib/cclib/issues/143
>> > >>>
>> > >>>
>> > >>> On Thu, Oct 23, 2014 at 12:31 PM, Karol Langner <
>> kar...@gm...
>> > >>> > wrote:
>> > >>>
>> > >>>> Axel,
>> > >>>>
>> > >>>> The terminology seems to be a little tricky. To be specific, the NO
>> > >>>> coefficients that we currently parse (for Gaussian) are those that
>> define
>> > >>>> the natural orbital as an eigenvector of the diagonalized density
>> matrix.
>> > >>>>
>> > >>>> Here is an example of the output from out unit tests:
>> > >>>>
>> > >>>>
>> https://github.com/cclib/cclib/blob/master/data/Gaussian/basicGaussian09/water_cis.log#L578
>> > >>>>
>> > >>>> The eigenvalues printed there, I think, are the occupoation
>> numbers you
>> > >>>> need (the population in each orbital), although in that particular
>> case
>> > >>>> some are negative (maybe because the basis set is so small?).
>> Anyway, we
>> > >>>> don't parse them, but we could of course, if that will be useful
>> for you.
>> > >>>>
>> > >>>> Cheers,
>> > >>>> Karol
>> > >>>>
>> > >>>> P.S. A new release of cclib (1.3) is coming out soon. Which
>> version are
>> > >>>> you using? In any case, this will not make it into 1.3, so you
>> will need to
>> > >>>> use the dev version from github.
>> > >>>>
>> > >>>>
>> > >>>> On Thu, Oct 23, 2014 at 12:07 PM, Axel Schild <
>> > >>>> axe...@go...> wrote:
>> > >>>>
>> > >>>>> Hi Karol,
>> > >>>>>
>> > >>>>> I suppose that NO coefficients and orbital occupation numbers are
>> the
>> > >>>>> same, i.e. they should be the diagonals of the diagonalized
>> density
>> > >>>>> matrix.For single-determinant methods they are 2 (or 1) and for
>> > >>>>> multi-determinant methods they have some value between 0 and 2
>> (or 1).
>> > >>>>>
>> > >>>>> At least I cannot think of any other meaning of "NO
>> coefficients", but
>> > >>>>> I never heard that term so far.
>> > >>>>>
>> > >>>>> Thanks, I hope that this feature is available soon as it would be
>> > >>>>> pretty nice to use cclib!
>> > >>>>>
>> > >>>>> Cheers
>> > >>>>> Axel
>> > >>>>>
>> > >>>>> On Thu, Oct 23, 2014 at 2:18 PM, Karol Langner <
>> > >>>>> kar...@gm...> wrote:
>> > >>>>>
>> > >>>>>> Hi Axel,
>> > >>>>>>
>> > >>>>>> The attribute nocoeffs parses NO coefficients, and only for
>> Gaussian
>> > >>>>>> at the moment, I believe. It could be easily extended to other
>> programs,
>> > >>>>>> assuming our test logfiles contain the data.
>> > >>>>>>
>> > >>>>>> If I understand correctly, occupation numbers can be calculated
>> from
>> > >>>>>> the NO coefficients. Is that correct?
>> > >>>>>>
>> > >>>>>> Cheers,
>> > >>>>>> Karol
>> > >>>>>>
>> > >>>>>>
>> > >>>>>> On Thu, Oct 23, 2014 at 3:40 AM, Axel Schild <
>> > >>>>>> axe...@go...> wrote:
>> > >>>>>>
>> > >>>>>>> Hi,
>> > >>>>>>>
>> > >>>>>>> I'm one of the developers of orbkit (
>> > >>>>>>> http://sourceforge.net/projects/orbkit). So far, we are using
>> our
>> > >>>>>>> own Molden, GAMESS US, Gaussian log-file/fchk-file, and
>> WFN-file parser,
>> > >>>>>>> but we thought about (also) using cclib to be able to read all
>> the file
>> > >>>>>>> formats that you support.
>> > >>>>>>>
>> > >>>>>>> However, we need orbital occupation numbers (like those of MCSCF
>> > >>>>>>> orbitals or of natural orbitals).
>> > >>>>>>>
>> > >>>>>>> Is this the data that is stored in the variable <nocoeffs> in
>> the
>> > >>>>>>> development version? If so, will it be available for any other
>> than the
>> > >>>>>>> GAMESS and Gaussian parsers anytime soon? If not, is this
>> feature planned
>> > >>>>>>> to be included?
>> > >>>>>>>
>> > >>>>>>> Cheers
>> > >>>>>>> Axel
>> > >>>>>>>
>> > >>>>>>>
>> > >>>>>>>
>> ------------------------------------------------------------------------------
>> > >>>>>>>
>> > >>>>>>> _______________________________________________
>> > >>>>>>> cclib-users mailing list
>> > >>>>>>> ccl...@li...
>> > >>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>> > >>>>>>>
>> > >>>>>>>
>> > >>>>>>
>> > >>>>>
>> > >>>>
>> > >>>
>> > >>
>> > >
>>
>> --
>> written by Karol M. Langner
>> Wed Oct 29 10:46:23 EDT 2014
>>
>
>
>