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

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

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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