Dear Dr Verma, Thanks for your time and consideration. I am doing that by increasing the length of the third lattice vector which is along the z direction. The original LatticeVectors block is:
%block LatticeVectors +16.5000000000 +0.0000000000 +0.0000000000 +0.0000000000 +8.0000000000 +0.0000000000 +0.0000000000 +0.0000000000 +30.8203000000 %endblock LatticeVectors I change it to this: %block LatticeVectors +16.5000000000 +0.0000000000 +0.0000000000 +0.0000000000 +8.0000000000 +0.0000000000 +0.0000000000 +0.0000000000 +32.8203000000 %endblock LatticeVectors Or this: %block LatticeVectors +16.5000000000 +0.0000000000 +0.0000000000 +0.0000000000 +8.0000000000 +0.0000000000 +0.0000000000 +0.0000000000 +40.8203000000 %endblock LatticeVectors I have attached the files for the calculation for your reference. These files were actually made available on the forum recently from the link below and provided me with an invaluable reference on TranSIESTA. http://unam.bilkent.edu.tr/mt2/transiesta/agnr8-transiesta/README.txt They are useful for learning SIESTA. My final goal is to simulate a system with quite different left and right electrodes. I want to include a vacuum in my scattering calculation cell in the z direction so that the left and right electrodes are sufficiently apart to gaurantee that they would not interact and affect the final results. I have also thought of some buffer electrode unit cells which may help. Any comments on the methodology I should adopt is indeed welcome. Best wishes, Mohammad, University of Tehran, On 11/18/14, Dr. Mohan L. Verma <[email protected]> wrote: > Dear Mohammad > I am not getting how you are increasing the required vector length in z > direction. Go thought the output file keenly, may be some difference (if > any ) will be there. Can you please send me your fdf file for first two > cases. > > Dr Mohan L Verma > Prof & Head > Department of Applied Physics > FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) > INDIA > 490020 > [email protected] > > > On Monday, 17 November 2014 2:03 PM, Seyed Mohammad Tabatabaei > <[email protected]> wrote: > > > 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: > > 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? > > 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. > > 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, > >
input_only.rar
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