Thanks Ricardo! I'll try to do that and I'll let you know the outcome. Cheers,
Marcos On Wed, Apr 6, 2011 at 3:52 PM, Ricardo Faccio <[email protected]> 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 Física > > 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 Veríssimo Alves < > [email protected]> 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 >> >
