I am thankful indeed.
On 11/18/14, Nick Papior Andersen <[email protected]> wrote: > 2014-11-18 18:05 GMT+00:00 Seyed Mohammad Tabatabaei <[email protected]>: > >> 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? >> > No. Not a short vacuum. Well it could be that it works. But... > >> >> 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? >> > Again, I would encourage you to draw a sketch of what that flag means. > >> >> 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 >> > >> > > > > -- > Kind regards Nick >
