Re: [cclib-users] FMO properties

[Adam T. <ate...@gm...>]

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...> 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...
> www.nutech.dtu.dk
>
>
>
>
>
>
> -----Original Message-----
> From: Karol M. Langner [mailto:kar...@gm...]
> Sent: 12 September 2013 00:31
> To: Adam Tenderholt
> Cc: Fedor Zhuravlev; 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...>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
>