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Question about vector unity cell in Au(1 1 1) surface Date: 2014/04/11 06:15 Name: Leone   <leoqmc@gmail.com> Dear colleagues, I am new User's openmx. Help me please. I am interested in Electron transport properties through benzene molecules disubstituted with π-accepting cyanide and isocyanide anchor groups at their para positions. I'm actually trying to reproduce the results of this work: J. Phys. Chem. C 2012, 116, 20607−20616. In this case the molecule is located between two surfaces of gold (Au (1 1 1)). The work mentioned provides the coordinates of the junction electrode-molecule-electrode. How do I determine the unit cell vectors(<Atoms.UnitVectors ??? Atoms.UnitVectors>) to perform the first step of the calculation of transport in openMX? thanks for any help. Leone

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Re: Question about vector unity cell in Au(1 1 1) surface ( No.1 ) Date: 2014/04/12 01:26 Name: Leone  <leoqmc@gmail.com> Gentlemen, I apologize for the very basic question. The "Automatic determination of the cell size" option solves my problem? Thanks in advance. Re: Question about vector unity cell in Au(1 1 1) surface ( No.2 ) Date: 2014/04/14 16:07 Name: T. Ozaki Hi, > Gentlemen, I apologize for the very basic question. The "Automatic determination of the > cell size" option solves my problem? No, it dose not work. I hope that you carefully read the manual and the corresponding paper which tell you how the structure of model can be prepared. In your case, the central part should include a part of lead as -[Au-B-Au]- Then, you can consider the structure of lead so that the lead can be semi-infinite as ....-Au-Au-Au-[Au-B-Au]-Au-Au-Au-..... Hope this helps you. Regards, TO Re: Question about vector unity cell in Au(1 1 1) surface ( No.3 ) Date: 2014/04/24 00:01 Name: Leone  <leoqmc@gmail.com> Dear T. Ozaki, I really appreciate your help. Congratulations for the excellent work. Regards, Leone Re: Question about vector unity cell in Au(1 1 1) surface ( No.4 ) Date: 2014/05/07 11:54 Name: Umar   <umarfarooqphysics@gmail.com> Dear T. Ozaki, I have a similar question I am working on the two denominational system (layered systems), as i know in the case of SIESTA or others we have to do as you told to Leone. But In the openmx case the central region C0 automatically extends to C taking some part of leads L0 and R0. Is not it enough in layered systems, if we are studying the layered system AA-B-AA to use only B=C0 as central , AA left, or AA right, as i know openmx will make it A-[A-B-A]-A, [A-B-A] will be the extended central regon C, A=L1 and A=R1 ... or layerd system will must be like as u told to Au-[Au-B-Au]-Au Regards Umar Re: Question about vector unity cell in Au(1 1 1) surface ( No.5 ) Date: 2014/05/12 22:17 Name: Artem  <artem.pulkin@epfl.ch> Umar, Technically it is enough to have B as scattering region and A as leads. But usually it is NOT enough for the reason of self-consistency since the charge density may have significant perturbations far from the scattering region. Therefore it is better to have [ABA] or [AABAA] (and so on) for the scattering region. Artem

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