[DFTB-Plus-User] overlap between two MD frames

[Sharma SRK Chaitanya Yamijala]

Dear Ben,

Thanks a lot for your reply and for offering me a helping hand.

Currently, I am taking the average between overlaps calculated at two
geometries (rather than calculating overlap of the intermediate geometry).
I will also consider your suggestions and get back to you.

Thanking you again for your time and help,
Sincerely,
Sharma.





--------------------------------------------------------------------
Sharma
http://www.chem.rochester.edu/groups/huo/people/


On Thu, Oct 6, 2016 at 1:04 PM, Ben Hourahine <
benjamin.hourahine at strath.ac.uk> wrote:

> Hello Sharma,
>
> the nearest thing to a quick hack would be to calculate the overlap for
> a geometry mid-way between the two cases. If the two geometries are
> sufficiently close together, then this should be the leading term in the
> series expansion of the overlap. The code can write out the overlap
> matrix to disc for a specified geometry (WriteHS keyword).
>
> If you need to actually calculating the overlap, there may be a problem
> if the atomic displacements are small. Many of the SK files only contain
> overlap data beyond a short distance out from the nucleus, so cannot be
> used to calculate overlaps between orbitals for less than this distance
> (usually several rows of value 0 appear at the start of the SK file in
> this case). This would stop you from being able to calculate the overlap
> between orbitals on the same atom.
>
> To actually calculate the overlaps, assuming the displacements are large
> enough, an external hack would be to
> 1) construct a geometry with both the atoms at the original and
> displaced geometries together
> 2) Call the code with WriteHS, and take the block of the overlap matrix
> associated with overlaps between the two sets of atoms
>
> You might have to remove the tests for atoms being on top of each other
> in this case. In principle this could be done inside of the code, but as
> you've notice this involves calling several routines, if you do want to
> do this I can offer some guidance.
>
> Regards
>
> Ben
>
>
> On 04/10/16 15:29, Sharma SRK Chaitanya Yamijala wrote:
>
> Dear Ben,
>
> Thank you for your quick response. I am interested in calculating the
> overlap between atomic orbitals of one frame with the atomic orbitals of
> the other.
> Sij = < Xi | Xj >,
> Xi = 1st frame atomic orbitals
> Xj = 2nd frame atomic orbitals
>
> Thanking you again for your quick response,
> Sincerely,
> Sharma.
>
>
>
>
>
> --------------------------------------------------------------------
> Sharma
> http://www.chem.rochester.edu/groups/huo/people/
>
>
> On Tue, Oct 4, 2016 at 10:24 AM, Ben Hourahine <
> benjamin.hourahine at strath.ac.uk> wrote:
>
>> Hello Sharma,
>> what sort of overlap are you trying to calculate, positional similarity,
>> wavefunction overlap or something else?
>>
>> Regards
>>
>> Ben
>>
>>
>> On 04/10/16 15:12, Sharma SRK Chaitanya Yamijala wrote:
>>
>> Dear all,
>>
>> Is there any simple hack to calculate the overlap between two frames
>> using DFTB+. I have gone through the source code and I found that it is
>> dependent on many modules in lib_dftb like non-scc.f90, sk.f90,
>> slako_cont.f90 ... and also on the lib_math modules like sort.f90,
>> bisection.f90 (while calculating neighbor lists) etc. Any suggestion,
>> please?
>>
>> Thank you for your help,
>> Sincerely,
>> Sharma.
>>
>>
>>
>>
>> --------------------------------------------------------------------
>> Sharma
>> http://www.chem.rochester.edu/groups/huo/people/
>>
>>
>>
>> _______________________________________________
>> DFTB-Plus-User mailing listDFTB-Plus-User at mailman.zfn.uni-bremen.dehttps://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>>
>> --
>>       Dr. B. Hourahine, SUPA, Department of Physics,
>>     University of Strathclyde, John Anderson Building,
>>             107 Rottenrow, Glasgow G4 0NG, UK.
>>     +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>>
>> 2013/4 THE Awards Entrepreneurial University of the Year
>>       2012/13 THE Awards UK University of the Year
>>
>>    The University of Strathclyde is a charitable body,
>>         registered in Scotland, number SC015263
>>
>> _______________________________________________ DFTB-Plus-User mailing
>> list DFTB-Plus-User at mailman.zfn.uni-bremen.de
>> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
> _______________________________________________
> DFTB-Plus-User mailing listDFTB-Plus-User at mailman.zfn.uni-bremen.dehttps://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
> --
>       Dr. B. Hourahine, SUPA, Department of Physics,
>     University of Strathclyde, John Anderson Building,
>             107 Rottenrow, Glasgow G4 0NG, UK.
>     +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>
> 2013/4 THE Awards Entrepreneurial University of the Year
>       2012/13 THE Awards UK University of the Year
>
>    The University of Strathclyde is a charitable body,
>         registered in Scotland, number SC015263
>
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20161006/a70061b0/attachment-0001.html>