Dear Yunpeng, As your qestions about how to find these cutoffs. I guess you usually use PAO.BasisSize DZP or so to define the basis. Even if this, you can get all the cutoffs in your output file. You can locate it by find the keywords "%block PAO.Basis". But care should be taken, the cutoffs are in unit of Bohr. The criterion 2*Rmax < Lz is a sufficient criterion for including all possible interactions. But it worth noting that the Lz is basis dependent because Rmax for the same atom species depend on the options which denfine it, such as "PAO.EnergyShift", "PAO.BasisSize" and "BasisPressure" and so on.
For Au(111), and an ABC unitcell in the z direction usually satisfies your criterion for PAO.EnergyShift= 100 meV and PAO.BasisSize=SZP. I think no one would like to set DZP for Au especially he has a great compuation power. Please point out if I am wrong. Guangping 2012-01-08 Guangping Zhang 发件人：Yunpeng Wang 发送时间：2012-01-06 10:54 主题：RE: [SIESTA-L] Transiesta: length of electrode unit cell 收件人：siesta-l 抄送： 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/ >
