Dear Marcos, Can you give me a detail description on how to use a .xyz file (that only contains the number of atoms and their coordinates) to generate a crystal or repeat the it at a certain direcion. I can not find it in the manual, and I find in the cif file it uses fractional coordinates. So directly edit the lattice vector does not work.
Best. Guangping 2011-04-12 Guangping Zhang 发件人: "Ricardo Faccio" <rfac...@fq.edu.uy> 发送时间: 2011-04-07 09:24 主 题: Re: [SIESTA-L] Off-topic: Vesta 收件人: siesta-l@uam.es Hi Eric The process is as following: Edit-> Structure-> Remove Symmetry -> Apply! Remember to save a cif file! Regards Ricardo > Hey Ricardo, > > May I ask you how do you save a structure with the P1 symmetry. > Actually, when I set the symmetry to P1 and save it, it does not seem to > work. > Yours, > > Eric. > > On 04/06/2011 09:52 AM, Ricardo Faccio wrote: >> Hi Marcos >> I think that you procedure is fine. The problem with vesta is that it >> needs yo save changes by step. I mean, first Open your file and remove >> the symmetry, and get a p1 structure. Then save it as a cif file. >> Afyer this read this file and perform the transformation, and save it >> as a different cif file. Finally load it and apply the symmetry, if >> you want, and get another cif file. If you have further problems send >> me your sf and i'll try to check it >> Regards >> Ricardo >> >> -------------------------------------------- >> Dr. Ricardo Faccio >> Prof. Adj. de FÃsica >> >> Av. Gral. Flores 2124. CC 1157. CP 11800. >> Phone: + 598 2 924 9859 >> Fax: + 598 2 924 1906 >> Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm >> --------------------------------------------- >> >> El 06/04/2011, a las 10:27, Marcos VerÃssimo Alves >> <marcos.verissimo.al...@gmail.com> escribió: >> >>> Hi all, >>> >>> So, great to know there are knowledgeable people on Vesta in the >>> mailing list. My question is the following: I have a cubic structure, >>> a perovskite. I have a [sqrt(2) x sqrt(2)] cell of this structure, >>> with relaxed positions with rotated oxygen octahedra in the x-y plane >>> only, out of which I would like to create a [2 x 2] cell. I actually >>> managed to do it (using a xsf file that i created from the xyz >>> output), but in a way which I would not call the most elegant. It is >>> also a way that is more prone to errors, than I wish it were. >>> >>> The problem is, when one loads an xsf file with the coordinates in >>> Vesta, it displays a structure with more atoms than the unit cell >>> actually does, and apparently it is the equivalent of XCrysDen's >>> conventional cell mode. However, one can choose, in XCrysDen, to >>> display only the translational asymmetric unit. This is one thing I >>> don't know how to do in Vesta. For a matter of convenience (laziness, >>> actually :) ), I have set both PRIMVEC and CONVVEC to the cubic >>> lattice vectors, in the xsf file. >>> >>> Although I have managed to create a [2 x 2] cell, starting from the >>> [sqrt(2) x sqrt(2)] using a transformation matrix (easy to deduce), I >>> have to eliminate some atoms by setting boundaries to the fractional >>> coordinates and checking that the number of atoms is actually the >>> expected number. In the case of a [2 x 2] cell, of course, we have 4 >>> times as many atoms as in the [1 x 1] cell. However, I would be more >>> reassured if there were an automatic way to guarantee that the >>> correct number of atoms would be output, instead of having to make >>> somewhat extensive checks to ensure this. >>> >>> Another doubt is about symmetrization of atomic coordinates. If I >>> choose a space group for Vesta to symmetrize the atoms' coordinates, >>> it ends up creating extra atoms which I can't seem to eliminate - at >>> least i don't know the correct way to do it. I have tried the option >>> "remove duplicate atoms", but it didn't work. Has anyone run into >>> such problems? >>> >>> If things are not clear, I'll be glad to provide an xsf file to >>> illustrate the issues. >>> >>> Best regards, >>> >>> Marcos >> > > -- > /Be the change you wish to see in the world > / â Mahatma Gandhi â > > Dr. Ãric Germaneau <mailto:german...@gucas.ac.cn> > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > /Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / > > -- ------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de Física Mail: Cryssmat-Lab., Cátedra de Física, DETEMA Facultad de Química, Universidad de la República Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfac...@fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
