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

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

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