Re: [cclib-devel] [cclib-users] Extract Mulliken atomic charges and spin densities

[Adam T. <ate...@gm...>]

Hi Karol,

Thanks for working on these attributes. Looks like you covered the big five
(Gaussian, ADF, ORCA, GAMESS, and GAMESS-UK). I think there's an iop for
Gaussian that causes Lowdin charges to be printed. Want me to try this?

Adam


On Sat, Oct 6, 2012 at 11:33 AM, Karol M. Langner
<kar...@gm...>wrote:

> On Oct 06 2012, Karol M. Langner wrote:
> > On Oct 05 2012, Noel O'Boyle wrote:
> > > On 5 October 2012 18:53, Adam Tenderholt <ate...@gm...>
> wrote:
> > > > Copying to cclib-dev instead of cclib-users...
> > > >
> > > >> So, Noel, Adam... what do you think? We can't have na attribute for
> > > >> every type of population analysis parsed. I see two options:
> > > >> 1) use a dictionary, with keys like 'Mulliken', 'Loewdin'
> > > >> 2) use a list of tuples consisting of a string and an array of
> charges
> > > >
> > > >
> > > > I agree that it's bad form to have to deal with all permutations of
> > > > attributes like mulliken_charges, loewdin_charges, etc, so it's best
> to have
> > > > just have charges and densities attributes.
> > > >
> > > > I think dictionaries are more elegant than a list of tuples. For
> example,
> > > > getting the Mulliken charges is simply charges["Mulliken"] instead
> of having
> > > > to iterate over the elements in a charges list looking for
> "Mulliken" in
> > > > tuple[0].
> > >
> > > +1
> >
> > I just implemented this in recent commits, for several parsers and
> > Mulliken/Lowdin charges where they are printed. In some cases (Molpro
> > and Jaguar) I could not find them and I think some flag in the input
> > would need to be turned on in order to print them. I don't think I will
> > update the data files and parsers for that unless somebody asks, though.
> >
> > The attribute is called atomcharges and I added unit tests for their
> > length (should equal natom) and sum (should be zero for the unit tests).
> >
> > As far as spin densities are concerned, this is also easily done --
> > should we call the corresponding attribute atomspins?
>
> I went ahead and implemented this for ORCA, too. If you guys think a
> different attribute name will better, jsut change it. Implementing this
> for other parsers will require updating output files to have spin
> densities. I might do that for GAMESS and one more sometime in the
> future, but I suppose the rest will be upon request.
>
> - Karol
>
> --
> written by Karol M. Langner
> Sat Oct  6 20:32:38 CEST 2012
>