Hello Haidar, Thank you for the kind response. In my case, I am using two similar electrodes at both ends. This is why I defined the electrode.fdf in the following way. 1. Relaxed the structure of the 80 electrode atoms using a SIESTA run. 2. Since the electrode is similar to the scattering region for my case, I used the ASE library to repeat the relaxed structure in the transport direction 9 times. 3. I used the relaxed structure from step 1 for the electrode calculation. 4. In the case of the scattering region, the structure from step 2 was used where the 80 leftmost and rightmost atoms were each specified as the electrodes.
Further, I agree that the 400Ry energy cutoff is massive. I shall decrease this to around 100Ry. Also, the k-points were not the converged case. I wanted to get a working tbtrans run before checking for the convergence of k-points. Should I increase this and check? As mentioned by you, should I change my steps as follows? 1. Relax the structure of the 80 atoms using a SIESTA run. 2. Since the electrode is similar to the scattering region for my case, use the ASE library to repeat the relaxed structure in the transport direction 9 times. 3. Use the first 80 atoms to define the left electrode. 4. Use the last 80 atoms to define the right electrode. In this case, do I leave a vacuum in the left side of the cell? As I am aware, the simulation box in siesta always starts from 0,0,0 coordinates. However since the first 640 atoms should not be included in the electrode calculation, how do I account for periodicity while maintaining the same coordinates as in the scattering.fdf? 4. Use the Left and Right TSHS files to do the scattering region calculation. Thank you On Thu, 16 Dec 2021 at 02:35, El-abed Haidar <ehai2...@uni.sydney.edu.au> wrote: > Hi Pasan, > > From the error and by looking at the electrode.fdf, I would say the right > electrode and electrode.fdf are not the same. > > I would take the longer but safer approach and define left.fdf and > right.fdf with the exact coordinates as the scattering.fdf (which showed > some discrepancies). > > > > So in your case use the first 80 atoms in left.fdf and the last 80 atoms > into a right.fdf file. Then use left.TSHS and right.TSHS in the scattering > region. > > > > Another thing is that you might want to look at your parameters for the > rest of the calculations. For example, I feel the 400 Ry cut off energy is > massive no? Is the number of K pts chosen 1 20 50 the converged case? > > > > Hope that helps. > > > > Cheers, > > EL-Abed > > > > El-Abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group| School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > *From: *Pasan Henadeera <henadeer...@gmail.com> > *Sent: *Wednesday, 15 December 2021 8:06 AM > *To: *email@example.com > *Subject: *[SIESTA-L] Problem with Transiesta > > > > Dear developers and users > > > > I have been trying to learn the Transiesta package to study > current-voltage characteristics of a Si slab. During my scattering region > calculation, the SIESTA run detects the positions of the electrodes and the > scattering region properly as, > > > > transiesta: Regions of atoms: > ## (80): Elec.Left > [ 1 -- 80 ] > ## (80): Elec.Right > [ 641 -- 720 ] > -- (560): Device > [ 81 -- 640 ] > > > > Although so, the SIESTA run does not complete and display the "Job > completed" message, and I have been unable to find an error printed either. > > > > Following this, I attempted to conduct the Tbtrans calculation anyway, and > was surprised to see that the atomic positions are not properly detected at > this stage. > > > > Electrode position does not exist > Stopping Program from Node: 0 > 641 80 > Electrode position does not exist > > > > Does anyone have any advice or experience regarding this? I have attached > my electrode and scattering region calculation files as well. > > > > elec.fdf -> Input file for electrode run (80 atoms) > > scat.fdf -> Input file for scattering region calculation (720 atoms, with > first and last 80 atoms being the electrodes at the two ends of the > structure) > > scat.out -> Output of the scattering region calculation > > > > Thank you > > -- > > Best regards > > Pasan Henadeera > > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Best regards Pasan Henadeera
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)