Re: [SIESTA-L] why the result (lattice constant...etc.) of Siesta and Vasp can't compare?
Because they use different algorithm, different potential and different basis set. On Fri, Aug 22, 2014 at 11:15 AM, joyce79928cc . joyce79...@gmail.com wrote: Dear: I have asked this similar question before. why the result (lattice constant...etc.) of Siesta and Vasp can't compare? because I have use this two software to calculate the example provided by Siesta and also create the input file for Vasp. Though I have tried my best to set the same flag. but the results are just very different. why the result (lattice constant...etc.) of Siesta and Vasp can't compare? Thank you! the file attached is my input for vasp and siesta -- Best Regards 邱芳瑜 Chiu Fang Yu 國立成功大學 材料科學與工程學系碩一 MOBILE：0930287221(中華) GMAIL：joyce79...@gmail.com wisdom4...@gmail.com -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232*
[SIESTA-L] Forceful termination of the program
Dear user, I have a question. Suppose I have made MD.UseSaveXV, MD.UseSaveCG and DM.UseSaveDM flags true and run a simulation. Then suppose I have to stopped the program forcefully before its completion.Then I will again run the unfinished program. My question is will the program start from where I have stopped it forcefully before the completion. -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232*
Re: [SIESTA-L] why the result (lattice constant...etc.) of Siesta and Vasp can't compare?
What is very different? 1-2% in the lattice constant are to be expected in a first attempt with different programs, pseudopotentials and basis sets, as somebody already mentioned. Looking at your FDF file, the K-points seem to be specified for a band structure calculation. For a bulk optimisation, you need a Monkhorst-Pack grid (and a fairly dense one, since it's a metal using the primitive cell). I don't know what K-points you used for VASP, since they are not in INCAR. Herbert On 22/08/14 06:45, joyce79928cc . wrote: Dear: I have asked this similar question before. why the result (lattice constant...etc.) of Siesta and Vasp can't compare? because I have use this two software to calculate the example provided by Siesta and also create the input file for Vasp. Though I have tried my best to set the same flag. but the results are just very different. why the result (lattice constant...etc.) of Siesta and Vasp can't compare? Thank you! the file attached is my input for vasp and siesta -- Best Regards 邱芳瑜 Chiu Fang Yu 國立成功大學 材料科學與工程學系碩一 MOBILE：0930287221(中華) GMAIL：joyce79...@gmail.com mailto:wisdom4...@gmail.com -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532
[SIESTA-L] vibrational frequencies
Dear Siesta users, I am calculating vibrational frequencies with the vibrator package. The system consists of a titanium oxide surface adsorbing an acid. I first did geometry optimization with slabdipolecorrection and a certain k-grid. Then I want to calculate the vibrational frequencies of the acid: a) When applying the fcbuilld, I noticed that both slabdipolecorrection and k-grid is not taken into account. Is it necessary to add both parameters to calculate the vibrational frequencies or is a calculation considering only the gamma point sufficient? b) I am mostly interested in the vibrational frequencies of the acid on the surface. Is it possible to calculate only the vibrational frequencies of the acid? Kind regards, Davy Geldof Structural Chemistry Group, Department of Chemistry University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium davy.gel...@uantwerpen.be
Re: [SIESTA-L] lattice constant problem
I believe cartesian coordinate is orthogonal http://en.wikipedia.org/wiki/Cartesian_coordinate_system It is better to use reduced? 2014-08-22 7:23 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com: Yes I have corrected entered the coordinated, because when the make the supercell I am getting the structure which I want but with zero z coordinate and with much much longer lattice constant. Cartesian coordinate can be of any system not necessarily of orthogonal system. On Fri, Aug 22, 2014 at 1:28 AM, Максим Арсентьев ars21031...@gmail.com wrote: PLs give us the link of the literature. K point grid should be more dense. Did you properly entered coordinates (cartesian are for ortogonal system)? 2014-08-21 21:04 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com: But after optimization the 2D sheet no longer remains 2D. It must have some non -zero buckling. On Thu, Aug 21, 2014 at 9:54 PM, Sergio Ferrari lic.sergio.ferr...@gmail.com wrote: I simply notice that you said that you want to optimize a two dimensional sheet of germanium, so all atoms should be put in a plane (of your choice), of course 2 atoms are allways in a plane but I wonder if for simplicity it is preferable to write the coordinates of the atoms in the x-y plane. Also in your kgrid_Monkhorst_Pack your k points are equal en all directions, that is clearly wrong if you want to simulate a 2D sheet. 2014-08-15 5:27 GMT-03:00 Suman Chowdhury sumanchowdhur...@gmail.com: Dear siesta user, I am trying to optimize the two dimensional sheet of germanium. I am using the pp given in the siesta website. The lattice constant given in the literature is within 3.97 to 4.01 A with buckling 0.6 to 0.7 A. But each time I run the siesta program I am getting the lattice constant just the double of this and with almost zero buckling. I started with lattice constant 3.97 and buckling 0.7 A. Can anyone help to solve the problem. I am attaching the .fdf file. -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Dr. Sergio Ferrari Depto. de Física-Fac. de Ingeniería INTECIN (UBA-CONICET) Av. Paseo Colón 850 C1063ACV-Ciudad de Buenos Aires ARGENTINA Tel: +54 (11) 4342-1396 (Directo) 4342-9184/4343-0891/4343-2775 (Int. 1021) http://intecin.fi.uba.ar -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS
Re: [SIESTA-L] lattice constant problem
No I don't think so.. On Fri, Aug 22, 2014 at 4:38 PM, Максим Арсентьев ars21031...@gmail.com wrote: I believe cartesian coordinate is orthogonal http://en.wikipedia.org/wiki/Cartesian_coordinate_system It is better to use reduced? 2014-08-22 7:23 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com: Yes I have corrected entered the coordinated, because when the make the supercell I am getting the structure which I want but with zero z coordinate and with much much longer lattice constant. Cartesian coordinate can be of any system not necessarily of orthogonal system. On Fri, Aug 22, 2014 at 1:28 AM, Максим Арсентьев ars21031...@gmail.com wrote: PLs give us the link of the literature. K point grid should be more dense. Did you properly entered coordinates (cartesian are for ortogonal system)? 2014-08-21 21:04 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com: But after optimization the 2D sheet no longer remains 2D. It must have some non -zero buckling. On Thu, Aug 21, 2014 at 9:54 PM, Sergio Ferrari lic.sergio.ferr...@gmail.com wrote: I simply notice that you said that you want to optimize a two dimensional sheet of germanium, so all atoms should be put in a plane (of your choice), of course 2 atoms are allways in a plane but I wonder if for simplicity it is preferable to write the coordinates of the atoms in the x-y plane. Also in your kgrid_Monkhorst_Pack your k points are equal en all directions, that is clearly wrong if you want to simulate a 2D sheet. 2014-08-15 5:27 GMT-03:00 Suman Chowdhury sumanchowdhur...@gmail.com : Dear siesta user, I am trying to optimize the two dimensional sheet of germanium. I am using the pp given in the siesta website. The lattice constant given in the literature is within 3.97 to 4.01 A with buckling 0.6 to 0.7 A. But each time I run the siesta program I am getting the lattice constant just the double of this and with almost zero buckling. I started with lattice constant 3.97 and buckling 0.7 A. Can anyone help to solve the problem. I am attaching the .fdf file. -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Dr. Sergio Ferrari Depto. de Física-Fac. de Ingeniería INTECIN (UBA-CONICET) Av. Paseo Colón 850 C1063ACV-Ciudad de Buenos Aires ARGENTINA Tel: +54 (11) 4342-1396 (Directo) 4342-9184/4343-0891/4343-2775 (Int. 1021) http://intecin.fi.uba.ar -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232*
Re: [SIESTA-L] vibrational frequencies
Hi, fcbuild just sets up the crystallography for latter use by vibra. What are the correct parameters for running siesta, such as to get the force constants matrix, is still your responsibily. Thus, a) add the slabdipolecorrection and the k-point grid you already used. b) not sure you can do that easily; you might try to perform the siesta run with constraints, namely, fix every coordinate but those of the acid. This will produce a reduced force constants matrix (*.FC file) to feed vibra ... and hopefuly ... Regards, Roberto On 08/22/2014 06:47 AM, Geldof Davy wrote: Dear Siesta users, I am calculating vibrational frequencies with the vibrator package. The system consists of a titanium oxide surface adsorbing an acid. I first did geometry optimization with slabdipolecorrection and a certain k-grid. Then I want to calculate the vibrational frequencies of the acid: a) When applying the fcbuilld, I noticed that both slabdipolecorrection and k-grid is not taken into account. Is it necessary to add both parameters to calculate the vibrational frequencies or is a calculation considering only the gamma point sufficient? b) I am mostly interested in the vibrational frequencies of the acid on the surface. Is it possible to calculate only the vibrational frequencies of the acid? Kind regards, Davy Geldof Structural Chemistry Group, Department of Chemistry University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium davy.gel...@uantwerpen.be
Re: [SIESTA-L] lattice constant problem
To either use Cartesian or reduced is at choice, but you have to be carefull in writing the proper numbers respecting your choice. Please notice that other users of Siesta coincide in the same critic about the k-grid of points that it should be more dense in the plane of study (x-y or whatever) and reduced to only 1 k-point in the orthogonal direction of your plane of study. 2014-08-22 8:53 GMT-03:00 Suman Chowdhury sumanchowdhur...@gmail.com: No I don't think so.. On Fri, Aug 22, 2014 at 4:38 PM, Максим Арсентьев ars21031...@gmail.com wrote: I believe cartesian coordinate is orthogonal http://en.wikipedia.org/wiki/Cartesian_coordinate_system It is better to use reduced? 2014-08-22 7:23 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com: Yes I have corrected entered the coordinated, because when the make the supercell I am getting the structure which I want but with zero z coordinate and with much much longer lattice constant. Cartesian coordinate can be of any system not necessarily of orthogonal system. On Fri, Aug 22, 2014 at 1:28 AM, Максим Арсентьев ars21031...@gmail.com wrote: PLs give us the link of the literature. K point grid should be more dense. Did you properly entered coordinates (cartesian are for ortogonal system)? 2014-08-21 21:04 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com : But after optimization the 2D sheet no longer remains 2D. It must have some non -zero buckling. On Thu, Aug 21, 2014 at 9:54 PM, Sergio Ferrari lic.sergio.ferr...@gmail.com wrote: I simply notice that you said that you want to optimize a two dimensional sheet of germanium, so all atoms should be put in a plane (of your choice), of course 2 atoms are allways in a plane but I wonder if for simplicity it is preferable to write the coordinates of the atoms in the x-y plane. Also in your kgrid_Monkhorst_Pack your k points are equal en all directions, that is clearly wrong if you want to simulate a 2D sheet. 2014-08-15 5:27 GMT-03:00 Suman Chowdhury sumanchowdhur...@gmail.com : Dear siesta user, I am trying to optimize the two dimensional sheet of germanium. I am using the pp given in the siesta website. The lattice constant given in the literature is within 3.97 to 4.01 A with buckling 0.6 to 0.7 A. But each time I run the siesta program I am getting the lattice constant just the double of this and with almost zero buckling. I started with lattice constant 3.97 and buckling 0.7 A. Can anyone help to solve the problem. I am attaching the .fdf file. -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Dr. Sergio Ferrari Depto. de Física-Fac. de Ingeniería INTECIN (UBA-CONICET) Av. Paseo Colón 850 C1063ACV-Ciudad de Buenos Aires ARGENTINA Tel: +54 (11) 4342-1396 (Directo) 4342-9184/4343-0891/4343-2775 (Int. 1021) http://intecin.fi.uba.ar -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Best wishes, Maxim Arsent'ev, D.Sc.(Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS -- *Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India.* * Ph no-+91-9830512232* -- Dr. Sergio Ferrari Depto. de Física-Fac. de Ingeniería INTECIN (UBA-CONICET) Av. Paseo Colón 850 C1063ACV-Ciudad de Buenos Aires ARGENTINA Tel: +54 (11) 4342-1396 (Directo) 4342-9184/4343-0891/4343-2775 (Int. 1021) http://intecin.fi.uba.ar
