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

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

I was thinking more of a Python script that infers all of the parsed attributes from the cclib codebase. No need for manual intervention after we get something like that working. It should be possible, since we have unit tests designed explicitely to test the parsed attributes.

- Karol

On Oct 08 2012, Noel O'Boyle wrote:
> I've been thinking that a shared Google spreadsheet would be a good
> way to go. If it's in there, I can write a script to generate the wiki
> text from that.
> 
> - Noel
> 
> On 8 October 2012 17:14, 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
> >
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-- 
written by Karol M. Langner
Mon Oct  8 18:25:25 CEST 2012