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

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

Sure, if you can spare the time, add them as a regression or replace the
current unit test.

- Karol

P.S. I also took a stab at updating the wiki for atomcharges/atomspins,
but in the end it would be good to generate some of the wiki (parsed data
tables) automatically.

On Oct 08 2012, Adam Tenderholt wrote:
> 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
> >

-- 
written by Karol M. Langner
Mon Oct  8 18:13:15 CEST 2012