[gpaw-users] Ghost atoms in fd mode?

[Marcin Dulak]

On 07/10/12 11:12, Kristen Kaasbjerg wrote:
> Thanks for you help Ask, I think I have the information I was looking for now.
> Another thing, would it be fair to request that ghost atoms should be marked by
> e.g. an asterisk in the printed atom list in the output file?
or rather with BQ prefix (or suffix) that seem to be a dominant standard 
in chemistry codes:
http://www.nwchem-sw.org/index.php/Development:Density_Functional_Theory_for_Molecules#BSSE_--_Basis_Set_Superposition_Error
http://www.gaussian.com/g_tech/g_ur/m_molspec.htm
http://www.spec.org/hpc96/docs/RelatedPublications/gamess/input.html

Marcin
>
> Kristen
>
> ________________________________________
> From: Ask Hjorth Larsen [asklarsen at gmail.com]
> Sent: Tuesday, July 10, 2012 1:28 AM
> To: Kristen Kaasbjerg
> Cc: gpaw-users
> Subject: Re: [gpaw-users] Ghost atoms in fd mode?
>
> Hi
>
> 2012/7/8 Kristen Kaasbjerg<kkaa at fysik.dtu.dk>:
>> Hi again
>>
>>>> 2012/7/8 Kristen Kaasbjerg<kkaa at fysik.dtu.dk>:
>>>> Hi GPAW'ers,
>>>>
>>>> I am interested in calculating the difference in the PAW Hamiltonian including projector
>>>> terms etc between two calculations differing by one removed atom in one of them. That
>>>> would be relatively straight forward if I could replace the atom I would like to remove
>>>> with a ghost atoms, however, since I am using fd mode that does not seem to be possible.
>>>>
>>>> Is the correct and in case yes, any suggestions for how to do this in a simple way?
>>>>
>>>> Thanks
>>>> Kristen
>>> Do you get an error when you try to specify a ghost atom?  It doesn't
>>> seem to me that there should be any fundamental problem with this.
>> As far as I could tell from the wiki the ghost option is only mentioned in the context of
>> LCAO calcuation so I haven't tried it yet. But if you are telling me that chances are that
>> it should work, I will give it a shot.
>>
>>> (A ghost atom does not contribute to the Hamiltonian except if you
>>> represent it in an atomic basis set.  Therefore I do not quite
>>> understand what the purpose of this substitution is.  Do you just want
>>> the Atoms objects to have the same number of atoms?)
>> Since I am going to substract the full PAW hamiltonians from two calculations differing
>> by one removed atom, my experience so far with the projector terms which have sums
>> over atoms tells me that this will be straight forward if both Atoms objects contain the
>> same atoms and associated setups. So this leads me to my next questions: do ghost
>> atoms have the same projectors etc as the elements of the ghost atoms otherwise would
>> have had?
>>
>> Kristen
> How to subtract two "Hamiltonians" depends completely and entirely on
> how the Hamiltonian is represented.  I will not be able to understand
> the operation you are performing without knowing exactly the
> representation in which you work.
>
> Effectively, a ghost atom is a set of basis functions without a setup.
>   Projectors are part of a setup and are thus not found on ghost atoms.
>   (In practice they have, for technical reasons, one projector which
> doesn't affect the calculation because its coefficient is zero)
>
> Regards
> Ask
>
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-- 
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Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk

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