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] 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
Re: [SIESTA-L] lattice constant problem
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
Re: [SIESTA-L] lattice constant problem
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*
Re: [SIESTA-L] lattice constant problem
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
Re: [SIESTA-L] lattice constant problem
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*
[SIESTA-L] lattice constant problem
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* germanene.fdf Description: Binary data
