Re: [cclib-devel] [cclib-users] FMO properties

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My thoughts on the attribute name:

1) It should be plural since it contains more than one value. This matches
the rest of cclib (e.g. aonames, atomnos, atomcoords, etc.)
2) Since it's atomic-orbital level, it should probably contain ao to
distinguish it from atom populations, which are also (sometimes) available
to parse if we decide to support that in the future.
3) We already sometimes abbreviate attributes (e.g. vibsyms, vibfreqs,
mocoeffs), so there's precedent.

Based on these, my vote would be aopops.

Adam

On Wed, Sep 18, 2013 at 7:30 PM, Karol M. Langner
<kar...@gm...>wrote:

> Yeah, forwarding to the dev list.
>
> So... any thoughts for/against these candidates:
> 1. aopop
> 2. aopops
> 3. aopopulation
> 4. aopopulations
> 5. populations
>
> I think I prefer the first one, for its brevity.
>
> Cheers,
> Karol
>
> On Sep 18 2013, Adam Tenderholt wrote:
> > Hi Karol,
> >
> > Thanks for taking care of this. I forgot that an atomcharges attribute
> was
> > added. As far as aopop or aopopuations, perhaps that discussion should be
> > moved to cclib-devel?
> >
> > Adam
> >
> >
> >
> > On Wed, Sep 18, 2013 at 3:24 PM, Karol M. Langner
> > <kar...@gm...>wrote:
> >
> > > Hi,
> > >
> > > Some time ago we actually created the 'atomcharges' attribute:
> > > http://cclib.sourceforge.net/wiki/index.php/Atomcharges
> > > (see that page for the data description)
> > >
> > > So I went ahead and extended that to NPA charges and just commited
> > > code that parses them for Gaussian09. And the newest trunk code
> > > should parse the output file you sent, Fedor.
> > >
> > > We don't have atomcharges coded yet for Turbomole or Jaguar, but it
> > > should not be hard and this would be a good time to do it.
> > >
> > > As far as populations go, I believe we would need to create a new
> attribute
> > > for that, since it doesn't fit anywhere else. It should probably also
> > > be a dictionary.
> > >
> > > To keep with our current naming scheme, how about 'aopop' or
> > > 'aopopulation'?
> > >
> > > Cheers,
> > > Karol
> > >
> > > On Sep 13 2013, Fedor Zhuravlev wrote:
> > > > Hi Adam and Karol,
> > > >
> > > > Frontier Molecular Orbitals: This is exactly what I was looking for
> > > folks,  thanks!
> > > >
> > > > For the NPA analysis:  I have included 3 log files from g09, Jaguar 7
> > > and Turbomole 6.1, all containing the output from the NPA calculations
> (at
> > > the end of the file, they look very similar). The values of interest
> could
> > > be the Natural Charge and Natural Electron Population. Those would be
> nice
> > > to extract.
> > > >
> > > > Fedor
> > > >
> > > > From: Adam Tenderholt [mailto:ate...@gm...]
> > > > Sent: 12 September 2013 18:08
> > > > To: Fedor Zhuravlev
> > > > Cc: Karol M. Langner; ccl...@li...
> > > > Subject: Re: [cclib-users] FMO properties
> > > >
> > > > Hi Fedor,
> > > >
> > > > Getting the energies of the HOMO and LUMO is pretty straight-forward:
> > > >
> > > > from cclib.parser import ccopen
> > > >
> > > > parser = ccopen(logfile)
> > > > data = parser.parser()
> > > > homo = data.homos[0] # assuming spin-restricted
> > > > lumo = homo + 1
> > > >
> > > > homo_energy = data.moenergies[0][homo]
> > > > lumo_energy = data.moenergies[0][lumo]
> > > >
> > > > As far as parsing population analyses, Noel, Karol, and I will have
> to
> > > discuss the potential implementation details. Do you have a favorite QM
> > > package?
> > > >
> > > > Adam
> > > >
> > > >
> > > > On Thu, Sep 12, 2013 at 12:45 AM, Fedor Zhuravlev <fe...@dt...
> <mailto:
> > > fe...@dt...>> wrote:
> > > > Hi Karol and Adam,
> > > >
> > > > Thanks much for the prompt reply. I was looking for the energies of
> HOMO
> > > and LUMO. From there, using the Koopman's theorem one gets the
> ionization
> > > energy (HOMO=IE). (HOMO + LUMO)/2 is chemical potential (CP);
> LUMO-HOMO is
> > > chemical hardness (H), while CP^2/2H is Parr's electrophilicity (JACS,
> > > 1999, 121, 1922).  4 very useful, easily chemically interpretable
> chemical
> > > descriptors for the price of two frontier MO!  Would be very nice to
> have!
> > > >
> > > > As for the natural population analysis the QM code would normally do
> it
> > > itself (at least Gaussian, Turbomole, and Jaguar), so it is just the
> > > question of proper parsing the data.  Most people would normally be
> > > interested in the natural charge and natural population.
> > > >
> > > > That was my wish list for Christmas :)
> > > >
> > > > Fedor Zhuravlev
> > > > Senior Researcher
> > > > DTU Nutech
> > > > Technical University of Denmark
> > > > Center for Nuclear Technologies
> > > > Hevesy Laboratory
> > > > DTU Risø Campus
> > > >
> > > > Frederiksborgvej 399 Building 202
> > > > Building 202
> > > > 4000 Roskilde
> > > > fe...@dt...<mailto:fe...@dt...>
> > > > www.nutech.dtu.dk<http://www.nutech.dtu.dk>
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Karol M. Langner [mailto:kar...@gm...<mailto:
> > > kar...@gm...>]
> > > > Sent: 12 September 2013 00:31
> > > > To: Adam Tenderholt
> > > > Cc: Fedor Zhuravlev; ccl...@li...<mailto:
> > > ccl...@li...>
> > > > Subject: Re: [cclib-users] FMO properties
> > > >
> > > > I assumed fragment energies in the fragment molecular orbital method
> in
> > > GAMESS-US...
> > > >
> > > > On Sep 11 2013, Adam Tenderholt wrote:
> > > > > Hi Fedor,
> > > > >
> > > > > I wanted to follow up on Karol's email. I'm not familiar with the
> > > > > details of NPA, and I briefly looked up the Reed/Weinstock/Weinhold
> > > > > paper. Adding it as a method in cclib is likely possible, but it
> would
> > > > > probably take several hours to fully understand the algorithm, and
> > > > > then implement and test it. This does interest me, although I'm not
> > > > > sure when I could get around to it.
> > > > >
> > > > > Also, what exactly do you mean by FMO energies? To me, FMO could
> stand
> > > > > for either fragment molecular orbitals or frontier molecular
> orbitals.
> > > > > Do you have a concrete example?
> > > > >
> > > > > Adam
> > > > >
> > > > >
> > > > >
> > > > > On Wed, Sep 11, 2013 at 8:01 AM, Karol M. Langner
> > > > > <kar...@gm...<mailto:kar...@gm...>>wrote:
> > > > >
> > > > > > On Sep 11 2013, Fedor Zhuravlev wrote:
> > > > > > > Dear cclib development team,
> > > > > > >
> > > > > > > Just had a first look at cclib and here's my questions:
> > > > > > >
> > > > > > >
> > > > > > > 1.       Is there a single-liner to get FMO energies only?
> > > > > > >
> > > > > > > 2.       What about natural population analysis?
> > > > > > >
> > > > > > > Thanks much,
> > > > > > >
> > > > > > > Fedor
> > > > > >
> > > > > > Hi Fedor,
> > > > > >
> > > > > > Nice to hear from you. I've used cclib to parse FMO output from
> > > > > > GAMESS-US in the past, but it involved a quick custom hack,
> which I
> > > > > > still may have somewhere I guess (I did this outside of version
> > > > > > control). However, this was some years ago, and I think the
> format
> > > > > > has changed significantly since then.
> > > > > >
> > > > > > As far as population analyses are concerned, we do not parse
> them,
> > > > > > although there was a discussion about that in the past. We have
> > > > > > implemented several population analysis algorithms alongside
> cclib,
> > > though:
> > > > > > http://cclib.sourceforge.net/wiki/index.php/Calculation_methods
> > > > > > ... although NAO is not among them. If you're thinking about the
> > > > > > original approach published by Reed/Weinstock/Weinhold, I think
> it's
> > > > > > a modification of Lowdin's orthoganolization, which we do. So you
> > > > > > could try to extend it to get what you want. Maybe Noel or Adam
> has
> > > more thoughts about this?
> > > > > >
> > > > > > If you want something specific parsed, you will generally need to
> > > > > > provide us with an example output file that we can use for
> testing.
> > > > > >
> > > > > > Cheers,
> > > > > > Karol
> > > > > >
> > > > > > --
> > > > > > written by Karol M. Langner
> > > > > > Wed Sep 11 10:51:11 EDT 2013
> > > > > >
> > > > > >
> > > > > >
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> > > >
> > > > --
> > > > written by Karol M. Langner
> > > > Wed Sep 11 18:30:58 EDT 2013
> > > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > written by Karol M. Langner
> > > Wed Sep 18 18:11:05 EDT 2013
> > >
>
> --
> written by Karol M. Langner
> Wed Sep 18 22:29:09 EDT 2013
>