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 now on 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) I was trying to reproduce some of the results. I took 17AGNR as an electrode with a standard unit cell (38 atoms). As a scattering region, I choose the same 17AGNR of 4 and 6 unit cells long. I have arranged carefully the atoms in the scattering regions so that first and last 38 atoms correspond to the electrode regions. To my surprise, for the scattering region with 4 unit cells I got a pretty decent resulting transmission spectrum (step like) whereas for the scattering region with 6 unit cells the transmission spectra is just a set of delta-functions. Does anybody have a clue why is it so? Moreover, when transiesta takes over and calculates the Green's functions I see a very strange charge population on atomic orbitals (H atoms at the edges get zero or even negative charge!!!!) How it can be ok for the smaller SR and terribly weird for just a two unit cells bigger SR? Do I need to worry about parameters defining complex contour integration options (I double checked the TS.ComplexContour.Emin to make sure that it is below the min eigenvalue in both cases)? 4) I also played with relaxation of the geometry of the SR. So I used several CG steps to equilibrate the structure. I expected, SIESTA first takes over and does the relaxation and then Transiesta calculates the Gree's functions upon the relaxed geometry. Instead, Transiesta calculates its stuff at each relaxation step. Is it ok? Why is it so? 5) 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? 6) 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? 7) 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"? 8) 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. 9) 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? 10) 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. If anyone could comment on at least one of the issues listed above, I would be very obliged. Best, Artem Baskin
