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/ > leem/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
