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

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

I also don't have access to Jaguar, and my former lab no longer licenses
it. So I guess we have a few options: don't provide support, ask
Schroedinger for a complimentary license, or seek out potential
collaborators (i.e. ccl.net). Thoughts?


On Mon, Sep 23, 2013 at 8:51 AM, Noel O'Boyle <bao...@gm...> wrote:

> I no longer have access to any of these I'm afraid...
>
> On 19 September 2013 05:18, Karol M. Langner <kar...@gm...>
> wrote:
> > 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
> >
> >
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