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

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

Done.

On 8 October 2012 18:56, Adam Tenderholt <ate...@gm...> wrote:
> 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
>
>
>
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