Re: [SIESTA-L] Off-topic: Vesta
Hey all, How did you manage the fact that gdis does not actually differentiate the atoms on display ? Eric. On 04/05/2011 01:46 PM, Marcos Veríssimo Alves wrote: Hi all, This has nothing to do with Siesta, strictly speaking, but it could be of general interest: supercell building. I see many people here use and like GDIS. I have tried to download and compile it once, but it didn't compile. With the executable version of GDIS that came with Ubuntu, I found it rather cryptical to use. I feel more comfortable with Vesta, so I would like to know if there are any people knowledgeable in this software here, willing to share a few tips for my specific case? I'll gladly explain it if someone who knows a bit of Vesta is willing to do so :) Cheers, Marcos -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. Éric 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 /
Re: Re: [SIESTA-L] Off-topic: Vesta
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
Re: [SIESTA-L] Off-topic: Vesta
If you want to build a supercell, you can use the Boundary button to define the extant of the supercell, then use the option Export Data under file menu to save as a .xyz file. It will ask to save hidden atoms too?. Select yes or no, depending on whether you have deleted some of the atoms or not after selecting them. Other options in the export menu only save the unit cell. Regards Sharat Chandra --- On Tue, 5/4/11, Marcos Veríssimo Alves marcos.verissimo.al...@gmail.com wrote: From: Marcos Veríssimo Alves marcos.verissimo.al...@gmail.com Subject: [SIESTA-L] Off-topic: Vesta To: siesta-l@uam.es Date: Tuesday, 5 April, 2011, 11:16 PM Hi all, This has nothing to do with Siesta, strictly speaking, but it could be of general interest: supercell building. I see many people here use and like GDIS. I have tried to download and compile it once, but it didn't compile. With the executable version of GDIS that came with Ubuntu, I found it rather cryptical to use. I feel more comfortable with Vesta, so I would like to know if there are any people knowledgeable in this software here, willing to share a few tips for my specific case? I'll gladly explain it if someone who knows a bit of Vesta is willing to do so :) Cheers, Marcos
Re: [SIESTA-L] Off-topic: Vesta
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
Re: [SIESTA-L] Off-topic: Vesta
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 marcos.verissimo.al...@gmail.co m 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
Re: [SIESTA-L] Off-topic: Vesta
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 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 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 / — Mahatma Gandhi — Dr. Éric 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 /
Re: [SIESTA-L] Off-topic: Vesta
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
