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

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

I've added a regression test for Gaussian 09 Lowdin charges (dvb_lowdin).
The logfile should be wget-able, and the regression file currently fails
because it can't find lowdin in atomcharges (but can find mulliken).

On Mon, Oct 8, 2012 at 9:14 AM, Karol M. Langner <kar...@gm...>wrote:

> 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
>