Thank you very much for the reply. I still would like more information by asking a couple of questions: 1-What is the definition of short? How long should the electrode be or what is the minimum length of the electrode to be acceptable? 2- From the error file what use does it give me when it says this atom is connected to that atom? 3- Could you elaborate more on your comment? what does 3 5 3 mean i have 3 gold sheets in electrode (left 3 and right 3), in the system i have another 3 sheets left and 3 right + molecule) can you explain how did you deduct that 3 means short? In your electrode calculation, look for: superc: Internal auxiliary supercell: 3 x 5 x 3 = 45
This should have a 3 along the semi-infinite direction. Your electrode in your attached output does seem too short. Thank you and looking forward to your reply. EL_abed El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group | School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 ________________________________ From: [email protected] <[email protected]> on behalf of Nick Papior <[email protected]> Sent: Wednesday, 11 December 2019 8:14 AM To: siesta-l <[email protected]> Subject: Re: [SIESTA-L] Electrode connectivity is not perfect, refer to the manual for achieving a perfect electrode PROBLEM! In your electrode calculation, look for: superc: Internal auxiliary supercell: 3 x 5 x 3 = 45 This should have a 3 along the semi-infinite direction. Your electrode in your attached output does seem too short. Den tir. 10. dec. 2019 kl. 22.03 skrev El-abed Haidar <[email protected]<mailto:[email protected]>>: Good afternoon I really was hoping for someone to explain to me what the error means: Left principal cell is extending out with 480 elements: Atom 19 connects with atom 91 I started off with only 3 sheets of gold but that did not work. I added one sheet for each electrode and still did not work. I added another 2 sheets to expand each electrodes further but still not working out. Please note that the unit cell lattice vectors will only change towards the c direction which i recalculated. Could the mistake because I have x and negative coordinates? Could it be the unit cell vectors are not true. I just was hoping for more explanation than : Electrode connectivity is not perfect, refer to the manual for achieving a perfect electrode. Any thoughts would be highly 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 -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- Kind regards Nick
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
