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
