Thank you very much Nick. I changed the positions of the carboxyl atoms, below the first 24 atoms (corresponding to the electrodes) and the calculation runs without errors.
[]'s, Camps On Mon, Oct 24, 2016 at 4:59 AM, Nick Papior <[email protected]> wrote: > The short answer is that transiesta requires a strict input sequence of > atoms. In pre-4.1 versions transiesta requires the first atoms to be > left-buffer+left-electrodes, and the last atoms to be > right-electrode+right-buffer atoms. > > In 4.1 and beyond, this restriction has been lifted while it still > requires that electrode atoms are "blocked" together. > > If you endeavour into transiesta calculations I would highly suggest you > to read the manual and the corresponding articles concerning the > implementation. > > transiesta pre 4.1 > DOI: 10.1103/PhysRevB.65.165401 > transiesta post 4.1 > DOI: 10.1016/j.cpc.2016.09.022 > > 2016-10-22 18:06 GMT+02:00 I. Camps <[email protected]>: > >> Hello SIESTers, >> >> I begin playing with TranSIESTA. To do that I began with some tutorials >> from the SIESTA site. Specifically with one from the link bellow: >> >> Link: http://departments.icmab.es/leem/siesta/tlv14/index.html >> >> From the example "11. Quantum electronic transport: TranSiesta basic, we >> got an script that directly run the combination SIESTA/TranSIESTA/TBTrans >> to obtain the IV curve (http://departments.icmab.es/l >> eem/siesta/tlv14/Exercises/TS.tar.gz) (folder "09. IV"). >> >> I run the example without any problem (in the attachment, the file called >> pristine.zip). >> >> Then, I modified the scattering region binding a carboxil group to the >> surface of the nanotube at its center position (in the attachment, the file >> called functionalized.zip). >> >> Now, when running the functionalized setup I got an error with the >> electrodes: >> "The electrodes are not situated in the same coordinates. Please correct." >> >> I am not understanding the origin of this error, once I didn't modified >> the corresponding electrodes file, neither modified the Z periodicity of >> the scattering region. >> >> Could any one help me with this issue? >> >> Many thanks in advance. >> >> PS: the scattering region is not optimized, it is just with the carboxil >> added to its surface. >> >> []'s, >> >> Camps >> > > > > -- > Kind regards Nick >
