Thank you gentlemen very very much! That was exactly what I was looking for. I tried using python to rotate and translate my desired molecule to be between gold electrodes (Herbert we sandwich the molecule between gold electrodes and thus the verb sandwiched). Avogadro worked for me since I am using an xyz file. I would love to try GDIS but i could not download it from the website for some reason. I found it on github afterwards but I really am not sure how to properly down load it. For now Avogadro is the trick. Thank you again gentlemen and any further comments or feedback is appreciated. El-Abed
El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group | School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 ________________________________ From: siesta-l-requ...@uam.es <siesta-l-requ...@uam.es> on behalf of Herbert Fruchtl <herbert.fruc...@st-andrews.ac.uk> Sent: Wednesday, 1 May 2019 8:01 AM To: siesta-l@uam.es Subject: Re: [SIESTA-L] How to rotate translate or move molecule from one position to another? Dear El-Habed, I am not quite sure what you mean with "sandwiched" and what plane you want the molecule to lie in, but one tool you might want to look at is gdis. It's a viewer that can read and write fdf files. You can select your molecule in the gap and rotate (ctrl-right-mousebutton) or translate (ctrl-middle-mousebutton). For more precise transformations you can create rotation matrices and translation vectors in the (Tools -> Building -> Editing menu (Transformations tab). On Ubuntu-based Linuxes you can just install it with apt-get from the usual repositories. Good luck, Herbert On 30/04/2019 09:31, El-abed Haidar 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 >
