This is a typical problem when one tries to relax a molecular transistor. I suggest that you do the following steps: 1- relax electrodes and molecule separately 2- Build the sandwich device 3- relax the device with geometry constraints( rigid the electrodes and molecule but no constraints on the electrode extension ) Please note that just for the new version of SIESTA the *rigid *command in geometry constraints works(I am using 4-1-b3 version). Good Luck
On Wed, May 1, 2019, 00:30 El-abed Haidar <ehai2...@uni.sydney.edu.au> wrote: > Good afternoon all, > I am trying to use a new molecule below: > > and I would like sandwich it between the gold electrodes i have used in > before. Relaxing the whole structure together after long time did not work. > I have taken the alternative of relaxing the structure on its own. Then > sandwich it directly onto the gold electrodes. > My Problem is the molecule does not belong to the plane where it is > suppose to be sandwiched: > > Both are in complete different positions. Does anyone know what one can do > in this case? > Any advice would be appreciated. > Thank you! > EL-Abed > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group > | School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > >
