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

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

Hi Axel,

I see... I thought you might have attached the wrong file :)

Anyway, I don't think it is a good idea to parse the occuptation of
canonical MOs from RHF as nooccnos, because these are not calculated but
simply defined as occupied or not. I would reserve the natural orbital
attributes to things that are not equivalent to the mo* attributes. In any
case, we don't parse the occuptaion of canonical MOs, simply because they
are trivial and can be deduced from the HOMO.

IMO, a better way to convey more information downstream is to parse some
metadata about the calculation, namely if it's RHF/CASSCF/CI, whatever.
There are also other reasons to do that, so this is a general thing that I
think will be added at some point (although we have resisted it so far).
Would it be useful for your purposes?

Best,
Karol


On Fri, Nov 7, 2014 at 5:41 AM, Axel Schild <axe...@go...>
wrote:

> 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
>>>>
>>>
>>>
>>>
>>
>