first of all you relaxed your whole structure by siesta not transiesta .after relaxation you choose first z component of your structure positrons as a left electrode in electrode fdf file and do electrode calculation by transiesta to generated "electrode name.TSHS file.if both left and right electrode is the same one calculation in enough but if both of them are different you have do another transiesta calculation for right lead or electrode to generate another "electrode name.TSHS" file for right one. The electrode must be oriented along the z-axis and the unit cell along the z-direction must be large enough so that orbitals within the unit cell only interact with a single nearest neighbor cell (the size of the unit cell can thus be derived from the range of support for the orbital basis functions).after electrode calculation you put electrode name.TSHS file to SR directory and define all position in fdf file for SR region and do another transiesta run to generate scattering region.TSHS file.after that you put both of TSHS file (generated by electrode and scattering region calculation ) in TBtrance directory and do final calculation by tbtrans not transiesta to earn current.
On Tue, Apr 8, 2014 at 5:54 PM, Chengbo Zhu <cz...@uowmail.edu.au> wrote: > > Dear SIESTA users, > > I am a little confused using TranSIESTA. > > It is advised that the geometry of scattering region(SR) should be > optimised in SIESTA before calculating its transmission in TranSIESTA. > > My questions are: > > 1. if the SR is relaxed in SIESTA, is it necessary to relax it again in > TranSIESTA when calculating the transmission. (I ran several testing model, > the SR is optimized again in TranSIESTA) > > 2. can I relax the SR in TranSIESTA directly. (if MD.NumCGsteps is set to > a non-zero number in Transiesta) > > 3. what is the difference between 1 and 2. In a TranSIESTA run, the > Hamiltonian matrix of SR (and atomic force) is calculated first using > SIESTA, then TranSIESTA begins by reading two TSHS files. So what is the > point to run optimization of SR in SIESTA separately from TranSIESTA. > > Any thoughts would be appreciated. > Thank you in advanced. > > Regards, > Chengbo
