[DFTB-Plus-User] R: electron phonon interaction and matrix derivative

Dirk Ziemann dirk.ziemann at physik.hu-berlin.de
Mon Jun 4 10:22:28 CEST 2018 

Dear Alessandro,

thank you for your answer and for the insights. In this case, it was the 
right way to work on an alternative.

best wishes   dirk

On 04/06/18 09:16, Alessandro Pecchia wrote:
>
> Dear Dirk,
>
> I can also add an answer to this question.
>
> At the time when we worked on electron-vibron scattering in molecular 
> junctions we implemented all calculations in a very old version of DFTB.
>
> In the current version of dftb+ all that machinery is still missing. 
> But the approaching strategy should be changed a lot. In that old code 
> I changed the core routines to perform the numerical differences:
>
> [H_ab (dq) – H_ab(0)] / dq   and  overlap.
>
> In practice I ended with an executable that was able to do only this 
> calculation.
>
> In dftb+ the strategy should be quite different and has not been 
> developed yet.
>
> This is not the end of the story, because libNEGF currently has only 
> part of the code needed to compute inelastic scattering. For sure it 
> is not equipped to load and use the gamma^q_ab couplings. [The reason 
> is that in libNEGF we wanted to do something much better and efficient 
> than in the old code but things remained behind].
>
> So I am sorry to say that with the current version of dftb+ it is not 
> possible to do real electron-phonon scattering or IETS through 
> molecular junctions. But there is ongoing work to complete the 
> implementations.
>
> Regards,
>
> Alessandro Pecchia
>
> *Da:*DFTB-Plus-User 
> [mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de] *Per conto 
> di *Gabriele Penazzi
> *Inviato:* venerdì 25 maggio 2018 15:31
> *A:* User list for DFTB+ related questions
> *Oggetto:* Re: [DFTB-Plus-User] electron phonon interaction and matrix 
> derivative
>
> Hi Dirk,
>
> I first calculate all the modes, and then dH/dR_ix, dH/dR_ix where 
> R_ix is the 'x' component of the normale displacement for the mode 
> 'i'. It can surely be done better, but it was good enough for me as I 
> was looking at few modes and performance was a non-issue.
>
> 2018-05-25 14:46 GMT+02:00 Dirk Ziemann 
> <dirk.ziemann at physik.hu-berlin.de 
> <mailto:dirk.ziemann at physik.hu-berlin.de>>:
>
> thank you for the quick and helpful answer.
>
> this goes in the right direction and I will have a deeper look into 
> your program. At a first look, I do not see, how you get the 
> derivative of the overlap S and hamilton matrix H. Is it possible to 
> get it from dftb+ (SCC or non-SCC) or did you calculated it by 
> yourself?  I think this is the most crucial part of the el-ph coupling.
> from the papers on the negf transport calculations , I assume that 
> these matrices are calculated in the dftb+ mpi-negf code and maybe 
> also the el-ph coupling (gamma) on the level of atomic orbitals:
>
> gamma_ab^q   \approx  d H_ab / d_q  -  \sum_mn  d S_am / d_q  S^-1_mn 
> H_nb - ...
> (atomic orbitals a,b; vibration q)
>
> it would be really nice to get these matrices or coupling out of the 
> program.
>
> thank you again and best wishes  dirk
>
>
>
>
> On 25/05/18 13:14, Gabriele Penazzi wrote:
>
>     Hi Dirk,
>
>     I assume you are speaking about the formulation as used for
>     example for IETS spectra in molecular junctions.
>
>     I don't think that is is supported in the current version, even
>     though there may be ongoing work on that.
>
>     Some time ago I wanted to calculate the coupling matrices for some
>     molecules, and I did some scripting to help on that.
>
>     It worked only on molecules (or in Gamma, for bulk), and I would
>     guess it won't run without hassle
>
>     with the new versions of DFTB+ because it has been written 3 or 4
>     years ago and never used again, but maybe
>
>     if that's what you need, you can use it as inspiration. It's
>     public domain: https://bitbucket.org/gpenazzi/dftbtools (lok in
>     elcoupl,py).
>
>     It has also the ASE package (Atomic Simulation Environment) as a
>     requirement.
>
>     2018-05-25 11:27 GMT+02:00 Dirk Ziemann
>     <dirk.ziemann at physik.hu-berlin.de
>     <mailto:dirk.ziemann at physik.hu-berlin.de>>:
>
>     Dear all,
>
>     I am interested in the electron phonon interaction like it is
>     performed
>
>     in the negf version and described in the corresponding papers.
>
>     Is it possible to get the coupling matrix in dependence on the single
>
>     particle states and phonon modes out of the negf version? Or is it
>
>     possible to get the matrix derivative of the overlap/hamiltonian with
>
>     respect to x/y/z direction? or something similar to simply create the
>
>     coupling by "hand"?
>
>     Thank you very much and best wishes
>
>     dirk
>
>
>     p.s. I posted this question some time ago, but it was never
>     answered. because I am still interested in this topic I want to
>     ask this again.
>
>     -- 
>
>     Dirk Ziemann
>
>     Humboldt Universität zu Berlin, Institut für Physik
>
>
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>
>
>
>
>     -- 
>
>     -- 
>
>     Gabriele Penazzi
>
>     mobile: +45 51894907
>
>     skype: gabriele.penazzi
>
>     _______________________________________________
>
>     DFTB-Plus-User mailing list
>
>     DFTB-Plus-User at mailman.zfn.uni-bremen.de
>     <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
>
>     https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
> -- 
> Dirk Ziemann
> Humboldt Universität zu Berlin, Institut für Physik
> AG Photobiophysik
> Newtonstr. 15, D-12489 Berlin
> Room    1'406
> Phone   +49 30 2093 4997
> E-mail ziemann at physik.hu-berlin.de <mailto:ziemann at physik.hu-berlin.de>
>
>
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>
>
>
> -- 
>
> -- 
> Gabriele Penazzi
> mobile: +45 51894907
> skype: gabriele.penazzi
>
>
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-- 
Dirk Ziemann
Humboldt Universität zu Berlin, Institut für Physik
AG Photobiophysik
Newtonstr. 15, D-12489 Berlin
Room	 1'406
Phone	 +49 30 2093 4997
E-mail	 ziemann at physik.hu-berlin.de

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