Dear Aaron and Nick, Thanks a lot to both of you for your kind helpings. I really appreciate it. Good point! I'm not sure about the size of basic sets, I should check it.
I've tried to use the k-point used in a Transiesta example for Au-BDT ( http://dipc.ehu.es/frederiksen/tstutorial/index.php/Au-BDT). However, I found it now that the structure is also periodic in transverse directions. I've already optimized the structure using siesta and I don't think that the geometry be the problem. I'll check it again. I will try to change the convergence parameters as you said and do my calculations again. Thank you both again. Kind wishes, Raha On Mon, May 23, 2016 at 3:04 PM, Nick Papior <[email protected]> wrote: > Let me add that your current simulation does not advocate using k-point > sampling transverse to the transport direction. > > 1. Why do you have no transverse periodicity? > > Also, your converged scattering region is "missing" more than 1 electron. > This tells me that your system is ill-setup, either from a geometrical > point of view, or from a calculation parameter point of view. > > 2. Check your convergence parameters. I would say your lower energy bound > is too high. You should probably go to -30 eV or even lower. > > > > 2016-05-23 12:21 GMT+02:00 Aaron <[email protected]>: > >> Hi Raha, >> >> It can be slightly difficult to compare between methods. Are you ensuring >> that the basis set size is the same between DFTB and DFT methods for >> example? >> >> I can suggest either tightening convergence criteria or else increasing >> number of k points. (In the paper linked they used a 4x4 k point grid >> whereas you use gamma point). Averaging over multiple k points would help >> to smear out the spikes. >> >> Regards, >> Aaron >> >> >> On 22/05/16 13:41, Raha khalili wrote: >> >> >> Dear Nick and Aaron, >> >> Many thanks for your reply. Yes, my calculations has converged as you can >> see in my attached output files. >> >> On Sun, May 22, 2016 at 1:34 AM, Thong, Aaron <[email protected]> >> wrote: >> >>> Hi Raha, >>> >>> How do you define what is correct for your transmission? Are you trying >>> to reproduce a certain literature result? >>> >> >> I am trying to do some calculations on amine-linked single molecular >> junctions with DFTB and I need to compare my results to DFT (the results >> from DFTB are attached). My DFTB transmission is smoother than DFT one and >> I can not compare these two calculations. There also is a DFT calculation >> on a same structure in "PHYSICAL REVIEW B 83, 115108 (2011)" that differs >> from my calculations. >> >> I'm not sure if my Transiesta calculations is correct or not. As first, I >> optimized the attached molecule to electrodes by siesta, then used the >> optimized structure in my Transiesta calculation. >> >> Regards, >> Raha >> >> >>> >>> >>> Spike peaks in transmission is quite common for single molecule >>> junctions since the Dos of these junctions would be spikes. >>> >>> Regards >>> Aaron >>> >>> >>> >>> Sent from my Samsung device >>> >>> >>> -------- Original message -------- >>> From: Raha khalili <[email protected]> >>> Date: 21/05/2016 9:35 pm (GMT+00:00) >>> To: [email protected] >>> Subject: [SIESTA-L] Transmission problem >>> >>> Dear All, >>> >>> I am trying to find the transmission of a single molecule junction by >>> using Transiesta but the final result doesn't seem to be correct with many >>> spike-like peaks. >>> >>> Here are attached my input files and final T results. >>> Any help will be really appreciated. >>> >>> kind regards, >>> Raha >>> >>> >>> -- >>> Khadijeh Khalili >>> Nanotechnology group, Physics department, university of Mazandaran >>> Babolsar, Iran >>> >> >> >> >> -- >> Khadijeh Khalili >> Nanotechnology group, Physics department, university of Mazandaran >> Babolsar, Iran >> >> >> -- >> PhD student >> B321/28 >> Aaron Thong >> >> > > > -- > Kind regards Nick > -- Khadijeh Khalili Nanotechnology group, Physics department, university of Mazandaran Babolsar, Iran
