Thank you Assa very much. I got you, I just did not know that I could generate an output file for tbtrans. I thought it generates only .AVTRANS, .TRANS, TEIG, LDOS, RDOS files.
Best regards, Artem On Thu, Jun 21, 2012 at 11:49 PM, Asa Aravindh <mails2...@gmail.com> wrote: > Hi, > I would like to answer your last question. > If you specify "TS.Voltage" parameter in the input file with some value, > say 0.1 eV, and carry out transiesta and subsequently tbtrans, in your > output file, the current will be written at the end, along with the input > voltage. > > Best, > Assa > > > On Fri, Jun 22, 2012 at 4:21 AM, Artem Baskin <abas...@gmail.com> wrote: > >> Dear SIESTA/TRANSIESTA users, >> >> I have recently read the paper (PRB 81, 205437) and found it very >> interesting and enlightening. Since I want to reproduce these results, >> >> I faced with some questions that I want to address here, some of them are >> technical >> >> whereas others are conceptual. From hereon I will refer to the mentioned >> above paper and the >> materials that I found >> http://unam.bilkent.edu.tr/mt2/transiesta/agnr8-transiesta/README.txt >> >> >> 1) What is (are) the particular reason(-s) to choose 8AGNR as >> an electrode? In this case, the scattering region is defined in a dummy >> way since the only difference between scattering and electrode regions is >> >> >> for which area the charge neutrality is preserved and how many atoms are >> treated out of equilibrium. Am I right? >> >> 2) In the example >> (http://unam.bilkent.edu.tr/mt2/transiesta/agnr8-transiesta/README.txt) I >> >> >> found >> TS.NumUsedAtomsLeft/Right 16 >> TS.BufferAtomsLeft/Right 16 >> >> Is there any reason why to use these values? >> >> 3) Did anyone try to evaluate the Fermi wavelength for such a system as >> compared to the width of the ribbon to make sure that we deal with a >> >> >> truly 1D system? >> >> 4) Due to the specific choice of the electrode for the set up (the middle >> part coincides with the leads) one may interpret the transmission spectra >> using the band structure of the electrode region only. From that >> >> >> perspective it is unclear for me how one would explain the conductance >> profile for the non zero bias. Moreover, what if the electrodes were of >> the different material, say, gold or nikel? >> >> 5) Another technical issue arises when I try to apply this "approach" to >> >> >> the case when the electrode are made of different material as compared to >> the scattering region. The Siesta Manual says: "it is also crucial that >> the atomic positions specified at the left (right) EL calculation must be >> >> >> equivalent to the left (right) electrode part of the SR set up. Here, >> equivalent means that they can be made equal by a simple translation in >> space." In the examples provided in Siesta and in the case of paper the EL >> and SR >> >> >> are the same, that is why it is easy to provide the equivalence of the >> atoms of the electrodes and those of the SR just multiplying the first two >> lattice vectors for the EL by integer number(s). But what if the lattice >> >> >> constants for EL and SR are not commensurable, how can I get the >> equivalence of the atomic positions for EL and SR? What is the "electrode >> part of the SR"? >> >> 5) By definition, the whole set up in reality should not have the >> >> >> translation symmetry, the scattering region does not have translational >> invariance. Yet, in TRANSIESTA set up we have to apply the periodic >> boundary conditions in the xy-directions, moreover, we need to apply the >> >> >> periodic boundary conditions along the current direction (z). Can anyone >> comment on this? Why do we need them? If I want to analyse (and visualise) >> the wave functions of the scattering region then I have a problem to >> >> >> decide for which k-point in 3D Brillouin-zone I need to construct the wf >> of a given eigenvalue. It is very counter-intuitive to consider the >> scattering region as a chain (or even bulk) rather than a "super-molecule" >> >> >> with molecular orbitals as it is should be. >> >> 6) Could you generally comment the meaning of >> TS.NumUsedAtomsLeft/Right >> TS.BufferAtomsLeft/Right >> TS.ReplicateA1(A2)Left/Right >> >> parameters in terms of their physical meaning and geometry of the set up? >> >> >> >> 7) It is known that <SystemLabel>.TSDE contains the info about the >> non-equilibrium density matrix. Manual says that .TSDE file can be used to >> analyse the non equilibrium charge density with the aid of DENCHAR. >> >> >> However, Denchar needs .DM file but not .TSDE. I renamed .TSDE file by .DM >> file to see the difference but I did not see any difference between >> equilibrium and non equilibrium charge density even when I applied bias of 2 >> or >> >> >> more Volts. Have you tried to do this, if so, please, share with me what >> you got and what we should get. >> >> 8) According to the Manual, TBTrans Utility can be used to calculate >> transmission spectrum and the electronic current. However, neither in the >> >> >> Utility/TBTrans directory nor in files (see above link) I did not find the >> code or >> something which calculates the current. What I should indicate in the >> TRANSIESTA input file to have the I(V) characteristic done? Should I >> >> >> integrate the Tr(E;V) by hand on my own to get I(V)? >> >> I would be very much obliged if someboby could comment these questions (at >> least some of them) and I hope other users will find your answers very >> useful. >> >> >> Sincerely, >> >> >> >> Artem Baskin >> >> PhD candidate, >> Department of Chemistry, >> University of Illinois at Chicago >> >> > > > -- > Assa Aravindh.S > Research Scholar > IGCAR,India > >
