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

[Noel O'B. <bao...@gm...>]

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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