As the manual said, the length of electrode unit cell L should satisfy 2*Rmax < L, where Rmax is maximum cutoff radius of atoms. But how can I know cutoff radius for atoms?
best wishes, Yun-Peng > Date: Thu, 5 Jan 2012 20:43:20 +0100 > From: [email protected] > To: [email protected] > Subject: Re: [SIESTA-L] Transiesta: length of electrode unit cell > > Dear David, > > ----- Original Message ----- > okay that was what I've been thinking too. I am calculating a molecular > junction with Au(111) electrodes, the size of the electrode is of course > crucial for the computing time. > > However, if I look through the output of different Transiesta examples¹ > I find that third number to be 3, or even 4.² > Reading the manual and searching the internet I realized that in > Transiesta this means that some part of the Hamiltonian is cut away. The > consequences of this might be negligible, but strictly speaking the > results are wrong in the sense that they contradict the manual. > This surprised me and I was not so sure anymore if that auxiliary > supercell is the right thing to look at or if I've understood the manual > correctly (i.e. that the third number should be 2). > > > > As far as I've understood if you have 2 you are sure things are ok, but > having 3 does not mean things are wrong. I think (again, as far as I've > understood) that if you have 2 the matrix is strictly tridiagonal and certain > numerical routine can be used to do the "Green functions stuff". If you have > 3 the matrix is strictly not tridiagonal, but this could simply mean that you > have a few 0.000001 where you are supposed to have 0.0000. If you manage to > converge numercially your results this should been that the tridiagonal > routines could do their job is spite of the few 0.00001. > In other words, 2 is a recomendation, not a strcit requirement. Now, 4 seems > a bit too much...:) > > Riccardo > > > Best wishes, > David > > ¹ e.g. http://wiki.tstutorial.dreamhosters.com/wiki/Au-BDT (there is a > link to download the output files of that example) > ² in this great example (mehmet_reference/step-1-electrodes/OUTPUT.fdf): > http://unam.bilkent.edu.tr/mt2/transiesta/ >
