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

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I looked at the atomcharges code, and fixed the GAMESS-US parser a bit.

One more thing, though. Our current Jaguar and Molpro log files for unit testing do not contain any partial charges, so there is nothing to test at this point. I could update the Molpro files, but does anyone have access to Jaguar now?

- Karol

On Sep 18 2013, Karol M. Langner 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

-- 
written by Karol M. Langner
Thu Sep 19 00:14:43 EDT 2013