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

[Axel S. <axe...@go...>]

Hi Karol,

in water_molpro.out and water_gaussian.inp.log we have a Hartree-Fock
calculation, for which the natural orbitals are the same as the canonical
orbitals (in the Molpro output they are just called "ELECTRON ORBITALS" but
in the Gaussian output they are given below "Natural Orbital Coefficients"
).

For a Hartree-Fock calculation they are trivial, but it would nevertheless
be useful to have nooccnos return these values so that we need not to
distinguish between different types of calculations.

Cheers
Axel

On Fri, Nov 7, 2014 at 6:08 AM, Karol Langner <kar...@gm...>
wrote:

> 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
>>>
>>
>>
>>
>