I am deeply thankful for your sincere support. Hopefully, my last questions are:
You said: "Yes, the idea as I said is that you want the electrodes to behave "as much as bulk as you can". So I would put in a big vacuum" I think you mean a "big vacuum" full of buffer unit cells at the two ends of the scattering region plus a short vaccum to avoid direct contact between left and right electrodes. Am I right? Also, I am doubtful on what value should be used for TS.UpdateDMCROnly and why? Would you please elaborate this point for me a little bit more? Best regards, Mohammad, On 11/18/14, Nick Papior Andersen <[email protected]> wrote: > 2014-11-18 14:40 GMT+01:00 Seyed Mohammad Tabatabaei <[email protected]>: > >> Dear Nick, >> >> I am very happy that you are here and thank you for your guidance. I >> would be indebted to you if you help me better understand the point. I >> have tried to put my questions in a yes/no format so that it takes you >> a short time to answer them. In case I was wrong or misunderstood, I >> would be thankful if you provide me with brief explanations. >> >> Even if I add buffer unit cells to the left and right electrodes, say >> 4 buffer unit cells on each side, again a VACUUM is required because >> the left and right electrodes are still different and cannot form a >> continuous system. Then, am I getting you right? I mean a short vacuum >> is inevitable in such a system. >> > Yes, the idea as I said is that you want the electrodes to behave "as much > as bulk as you can". > So I would put in a big vacuum. > > >> If the first .DM is only an initial guess for TranSIESTA, then, it >> should not affect the final results. Its function is to help >> TranSIESTA converge more rapidly to the final result. Am I right? I >> mean the .DM would not enter any other calculations except the first >> guess. >> > In principle yes, in reality not so much... Your initial starting guess can > certainly have an impact on your final converged system. You may end up in > a local minima... > > >> I read the SIESTA manual and, as you noted in your response, it says >> it does not include buffer atoms in the TranSIESTA run. I also added >> the entry for TS.UpdateDMCROnly here: >> >> "TS.UpdateDMCROnly (logical): During the TranSiesta (Green’s >> functions) self consistent cycle, it updates only the density matrix >> elements of the contact region, if set to true. The electrodes and >> coupling terms are kept as the ones obtained in a first Siesta run. If >> set as false, the coupling terms are also updated by the Green’s >> functions density matrix. If a larger number of electrode layers >> (metallic systems) are included in the contact region, the coupling >> terms may not need to be updated. If set to false, however, may result >> in larger number of iterations to converge." >> >> I think this flag should be set to "false" to account for the worst >> case. :) I would be really grateful if you further explain it to me. >> Particularly, I can not undestand "If a larger number of electrode >> layers (metallic systems) are included in the contact region, the >> coupling terms may not need to be updated." As far as I can >> understand, the geometry for the scattering region calculation is >> composed of the left electrode + contact region + right electrode. >> Then, no electrode layers would exist in the contact region. Moreover, >> I do not understand why updating the coupling terms is not needed in >> this case. >> > Again, you want the electrodes to behave "as much as bulk as you can". If > they are not, how can you couple a bulk semi infinite region to your device > region. > This is really important! > Try and sketch how siesta perceives things, then how transiesta does, then > overlay those two scenarios. This should make it clear how to engage > calculations you want to perform. > >> >> Finally, I have exprimented one more thing with SIESTA and wanted to >> know your notion about that. Since my first intention was to add a >> vacuum between scattering regions, I tried to do this in a >> continuation-like run scheme. That is, for the system I presented in >> my question, I first run a Transiesta calculation from scratch in the >> case with no vacuum which generated new .DM and .TSDE files. Then I >> copied the electrode .TSHS file along with the .TSDE file to another >> folder and increased the vector in the z direction by 2 Angs. I did >> the same thing five times, that is, I inserted a 10 Angs vacuum in the >> fifth run. Fortunately, all the transiesta calculations converged. Is >> it a correct practice for inserting a vacuum? Whats wrong with it? It >> is important to note that the calculations did not converged in cases >> where I also copied the .DM file maybe because the .DM from the >> previous calculations were a bad guess. >> > It will probably restart from a clean sheet. It will only use the DM > information in cases where the sparsity pattern does not change. > I would definitely advice you NOT to re-use the DM file from another > geometry. Only if you increase the vacuum for non-interacting cells (which > will only happen for large vacuum) is this allowed/sensible. > >> >> Best wishes, >> >> >> >> >> >> >> >> >> >> On 11/18/14, Nick Papior Andersen <[email protected]> wrote: >> > 2014-11-17 8:31 GMT+00:00 Seyed Mohammad Tabatabaei <[email protected]>: >> > >> >> Dear SIESTA Users, >> >> >> >> I have a few conceptual questions about TranSIESTA and would be really >> >> grateful if you help me with them. In fact, the answer to these >> >> questions is quite important for my calculations. I have used >> >> TranSIESTA >> >> to study the current in an 8-AGNR system. My system consists of >> >> 16X7=112 >> >> carbon atoms. 16 atoms make the left electrode, 5X16=80 atoms make the >> >> scattering region, and 16 atoms make the right electrode. As the >> >> transport >> >> direction is along the z direction, my system would look like this >> >> along >> >> the z direction: >> >> >> >> ... + Left 16 atoms + Scat. region 80 atoms + Right 16 atoms + Left 16 >> >> atoms + Scat. region 80 atoms + Right 16 atoms + ... >> >> >> >> I successfully calculated the current in this case for a particular >> bias. >> >> Then, I increased the length of the vector along the z direction by >> about >> >> 3 >> >> Angs and repeated the calculation. Note that I only increased the >> >> length >> >> of >> >> the vector and did not add any atoms. All the other settings in the >> >> .fdf >> >> file was kept intact. In this case, my system looked like the >> >> following: >> >> >> >> ... + Vacuum of about 3 Angs + Left 16 atoms + Scat. region 80 atoms + >> >> Right 16 atoms + Vacuum of about 3 Angs + Left 16 atoms + Scat. region >> >> 80 atoms + Right 16 atoms + ... >> >> >> >> Interestingly, I found almost identical current values as the ones >> >> obtained in the case with no vacuum. Finally, I increased the void to >> >> 10 >> >> Angs without modifying any other settings. In this case, although the >> >> DM >> >> did not converged in 1000 iterations, the code calculated currents >> >> similar >> >> to the ones obtained for no vacuum but with about 40 percent >> >> deviation. >> >> My >> >> questions are the following: >> >> >> > I would not recommend that you _only_ increase the vacuum. Consider >> > that >> > the initial guess for transiesta is that of a SIESTA calculation. When >> you >> > enter transiesta the first iterations "sees" a bulk hamiltonian where >> > the >> > electrodes exists, however the initial guess from SIESTA is that of a >> > vacuum just of the electrode. >> > That is very unphysical to start converging a system with such >> > deviating >> > boundary conditions. >> > >> > The reason that the first one converges may well be that the initial >> guess >> > is closer than the 10 ang case, and hence it will converge to the same >> > Hamiltonian. >> > >> >> >> >> 1- Does the neighboring scattering regions affect each other in the >> >> scattering region calculation? What is the difference between >> >> calculations >> >> which do not include any vacuum with calculations which consider, say >> >> a >> >> 10 >> >> Angs, vacuum? >> >> >> > No. They do not per see effect each other, however the periodicity >> > allows >> > the initial guess to be somewhat close to the open boundary conditions >> > imposed by transiesta. >> > Hence if they do mean something, you have set up your system >> > incorrectly. >> > >> >> >> >> 2- How should I make the code converge when I increase the void to 10 >> >> Angs? How should I modify my .fdf code in the case with vacuum so that >> >> I >> >> can obtain identical currents to the case with no vacuum. >> >> >> > You should add buffer atoms. >> > The reasoning and guidelines for this are quite simple: >> > 1. Your device region electrodes should behave as bulk electrodes. >> > 2. This means that you need enough layers (on BOTH sides of the >> electrode) >> > to satisfy a "bulk"-like Hamiltonian. >> > 3. If you have different types of electrodes, add buffer atoms. >> > 4. Buffer atoms does not cost anything in transiesta (however, they do >> cost >> > something in terms of internal data structures), so you can be generous >> > here if your system is not that big. >> > 5. If you do add buffer atoms you are almost certainly (I would highly >> > recommend that you use it!) required to utilise the flag >> TS.UpdateDMCROnly. >> > Please read about this flag in the manual, with the above information >> > you >> > should be able to understand which value it should be set to, AND why >> > it >> is >> > important. :) >> > >> >> >> >> Sorry for my bother-making. I am trying to simulate a system with >> >> TranSIESTA which contains quite different left and right electrodes >> >> that >> >> cannot come into direct contact without the scattering region in >> between. >> >> The only way for me is to introduce vacuum between neighboring >> scattering >> >> regions. In brief, I would be really grateful if you tell me how can I >> >> determine the size of the sufficient vacuum >> >> between neighboring scattering regions so that my results can be >> >> credible. >> >> >> >> Best wishes, >> >> Mohammad, >> >> >> > >> > >> > >> > -- >> > Kind regards Nick >> > >> > > > > -- > Kind regards Nick >
