[Pw_forum] Help in cif file atomic positions

[Michael Mehl]

Since C and N are neighbors in the periodic table, you could put a
"virtual" atom at the site, with charge Z = 6.5.  That would at least give
you the right electron count for the system and preserve the system
symmetry.  The downside is that a pseudopotential for "Cargen" or
"Nitrobon" probably doesn't exist, so you'd have to generate it yourself.
I think VASP is able to handle this somehow, but I've never tried it.

Another alternative is to generate a supercell, randomly populate that site
with C and N atoms, and average over configurations.  Look up various
articles by Alex Zunger et al. (
http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.65.353, to
start) on Special Quasirandom Structures for some hints on how to do this
efficiently.  The downside of this is that you'll need a fair number of
structures, and you'll lose the hexagonal symmetry in the individual
calculations.

AFAIK, there aren't any really good solutions for this problem with the
current generation of DFT codes.  At one time there was some work with the
Coherent Potential Approximation and KKR (see
http://journals.aps.org/prb/pdf/10.1103/PhysRevB.67.115109, e.g.), but I
don't think any modern KKR codes are easily available, much less KKR+CPA.

On Fri, Oct 7, 2016 at 7:50 AM, Krishnaiah Kallamadi <
krishnsustain at gmail.com> wrote:

> As per my knowledge,
> espresso can't deal with above cif file. Please help me and correct if I
> am wrong.
>
> On Fri, Oct 7, 2016 at 11:33 AM, Andrius Merkys <andrius.merkys at gmail.com>
> wrote:
>
>> [image: Boxbe] <https://www.boxbe.com/overview> This message is eligible
>> for Automatic Cleanup! (andrius.merkys at gmail.com) Add cleanup rule
>> <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3DXwuYbtQTWmfZGZsFKbO6InxZfjQtGSxrL%252FwuVJ%252FUXAE%253D%26token%3DJUW0Wts7GmUB4X1qCEMY8jvGAd0zfkPK1lTr9NzQRQI0yaxZFlH1MMfBGJfWwNxAn9vrVh0QLSJUWizBuQx1RH1a7mw3Iol2zUDxjiWVehZ%252Bx2PzIhsM%252FIEhy78t1KraT3iv3nEj9prEPJ0yaqyzmA%253D%253D&tc_serial=27072627350&tc_rand=1012971690&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
>> | More info
>> <http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=27072627350&tc_rand=1012971690&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
>>
>> Dear Krishna,
>>
>> On 07/10/16 08:30, Krishnaiah Kallamadi wrote:
>>
>> In a *cif* file attached below, two different atoms have same atomic
>> positions with occupancy of 0.5. Due to this i am not able to generate *scf.in
>> <http://scf.in>* file from cif2cell program. Please help me.
>>
>>
>> you have to account for a joint 0.5N+0.5C site at this position. I am not
>> sure if/how such thing is possible at QE input, but AFAIK, people are
>> dealing with such models.
>>
>> HTH,
>> Andrius
>>
>> --
>> Andrius Merkys
>> PhD student at Vilnius University Institute of Biotechnology, SaulÄ—tekio al. 7
>> LT-10223 Vilnius, Lithuania
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> Thanks and Regards,
>
> K.Krishna
> JRF, AcSIR-RE
> CSIR-SERC
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 

[image: USNA_Gold_Seal.png]

Michael J. Mehl, Ph.D.

Kinnear Chair in Physics

The United States Naval Academy

Mail Stop 9C

572 Holloway Road

Chauvenet Hall 257

Annapolis MD 21402

(410)293-6685

mmehl at usna.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20161007/f1521a57/attachment.html>