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

[Karol M. L. <kar...@gm...>]

Well, anything >=7.0 would be OK, I guess. If it's newer than 7.0, it would be best to rerun our whole test suite and update the files.

The main thing would be to add population analysis (at least Mulliken), which the Manual says can be chosen in the Method section.

- Karol

On Sep 27 2013, Adam Tenderholt wrote:
> Turns out my former lab does actually have access to Jaguar. I don't know
> which version though. Are there any specific calculations I should try to
> have run?
> 
> 
> 
> On Mon, Sep 23, 2013 at 4:01 PM, Adam Tenderholt <ate...@gm...>wrote:
> 
> > 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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-- 
written by Karol M. Langner
Mon Oct  7 07:47:56 EDT 2013