Re: [SIESTA-L] A draft of small personal tutorial
Thanks for the helpful tutorial. But where is this Siesta pseudopotential database you mention on it? Regards, Eric 2009/6/4 Zhong-Li Liu zl.liu.c...@gmail.com Dear Andrei, Thank you for your kind reply, and I shall have some tests according your suggestion. Best regards, Zhongli On 04/06/2009, apost...@uni-osnabrueck.de apost...@uni-osnabrueck.de wrote: Dear Andrei, You said in your SIESTA-tuto that the frozen phonon calculations usually proceed after CG relaxation. Dear Zhongli, this is not obligatory, techniclly speaking, but any book on phonons tells you how they are introduced from Taylor expansion arond the equilibrium. So, this equilibrium first has to be found. If your system does not have internal coordiates you don't have to worry (say, for pure NaCl you can calculate phonons right away for any lattice constant without a need to relax), but if the internal cordinates are present (as say in wurtzite or rutile) - yes, the relaxation in principle should be done first. Oterwise, you have a chance to get imaginary modes with eigenector pointing towards the relaxed geometry, where the system would be able to lower its energy. Is that means we should first set MD.TypeOfRun CG to relax yes and then change it to MD.TypeOfRun FC with UseSaveData T yes and MD. UseSaveXV T to calculate the force constants? No, in fact I suggested to copy the relaxed coordinates into the .fdf file and then proceed phonons with MD. UseSaveXV F But it is just a suggestion. Best regards Andrei -- PhD. student of IAMP, Sichuan University, China E-mail: zl.liu.c...@gmail.com -- == Eric Perim Martins Universidade Estadual de Campinas - UNICAMP Instituto de Física Gleb Wataghin - IFGW Grupo de Sólidos Orgânicos e Novos Materiais - GSONM Departamento de Física Aplicada (DFA) - Sala 19 Campinas - São Paulo - Brasil CEP 13083-970 Telefone: (19)3521-0289 - Ramal 10289 MSN: pe...@nextwave.com.br ==
Re: [SIESTA-L] A draft of small personal tutorial
Dear Andrei, You said in your SIESTA-tuto that the frozen phonon calculations usually proceed after CG relaxation. Dear Zhongli, this is not obligatory, techniclly speaking, but any book on phonons tells you how they are introduced from Taylor expansion arond the equilibrium. So, this equilibrium first has to be found. If your system does not have internal coordiates you don't have to worry (say, for pure NaCl you can calculate phonons right away for any lattice constant without a need to relax), but if the internal cordinates are present (as say in wurtzite or rutile) - yes, the relaxation in principle should be done first. Oterwise, you have a chance to get imaginary modes with eigenector pointing towards the relaxed geometry, where the system would be able to lower its energy. Is that means we should first set MD.TypeOfRun CG to relax yes and then change it to MD.TypeOfRun FC with UseSaveData T yes and MD. UseSaveXV T to calculate the force constants? No, in fact I suggested to copy the relaxed coordinates into the .fdf file and then proceed phonons with MD. UseSaveXV F But it is just a suggestion. Best regards Andrei
Re: [SIESTA-L] A draft of small personal tutorial
Dear Andrei, Thank you for your kind reply, and I shall have some tests according your suggestion. Best regards, Zhongli On 04/06/2009, apost...@uni-osnabrueck.de apost...@uni-osnabrueck.de wrote: Dear Andrei, You said in your SIESTA-tuto that the frozen phonon calculations usually proceed after CG relaxation. Dear Zhongli, this is not obligatory, techniclly speaking, but any book on phonons tells you how they are introduced from Taylor expansion arond the equilibrium. So, this equilibrium first has to be found. If your system does not have internal coordiates you don't have to worry (say, for pure NaCl you can calculate phonons right away for any lattice constant without a need to relax), but if the internal cordinates are present (as say in wurtzite or rutile) - yes, the relaxation in principle should be done first. Oterwise, you have a chance to get imaginary modes with eigenector pointing towards the relaxed geometry, where the system would be able to lower its energy. Is that means we should first set MD.TypeOfRun CG to relax yes and then change it to MD.TypeOfRun FC with UseSaveData T yes and MD. UseSaveXV T to calculate the force constants? No, in fact I suggested to copy the relaxed coordinates into the .fdf file and then proceed phonons with MD. UseSaveXV F But it is just a suggestion. Best regards Andrei -- PhD. student of IAMP, Sichuan University, China E-mail: zl.liu.c...@gmail.com
Re: [SIESTA-L] A draft of small personal tutorial
Dear Andrei, Thank you for the nice presentation! Nguyen, Ngoc Ha Hanoi National University of Education Faculty of Chemistry Department of Physical Chemistry Tel: Office: 04/8330842 Home: 04/7891674 Mobile: 0989133436
Re: [SIESTA-L] A draft of small personal tutorial
Dear Andrei: Thank you very much for such a good introduction to SIESTA. As usual, your contributions are of a great help. Thanks on behalf of all the team... Yours, The SIESTA Team -- Jose A. Torres, Ph.D. Manager of the SIESTA Software Dear Siesta community, a small document composed by me with the primary aim of giving to students a broader introduction to the concepts of Siesta, is accessible at http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf It is more than one month old, in which time I hoped to update it, and also or to get a chance to see if some of the raised issues disappear in the version 3.0, but none of these opportunities has materialized. So the document is open to all your criticisms and suggestions, which are highly welcome. If whoever would need a source in order to develop it inso something bigger or better, please contact me Best regards --- Andrei Postnikov --- Paul Verlaine University - Institute de Chimie, Physique et Mat'eriaux, Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France -- -- Mensaje enviado mediante una herramienta Webmail integrada en *El Rincon*: - https://rincon.uam.es --
Re: [SIESTA-L] A draft of small personal tutorial
Hello, Thanks for your article. It is very informative but could you give some additional information on how to choose the k-point mesh? --- On Wed, 6/3/09, apost...@uni-osnabrueck.de apost...@uni-osnabrueck.de wrote: From: apost...@uni-osnabrueck.de apost...@uni-osnabrueck.de Subject: [SIESTA-L] A draft of small personal tutorial To: SIESTA-L@listserv.uam.es Date: Wednesday, June 3, 2009, 7:38 AM Dear Siesta community, a small document composed by me with the primary aim of giving to students a broader introduction to the concepts of Siesta, is accessible at http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf It is more than one month old, in which time I hoped to update it, and also or to get a chance to see if some of the raised issues disappear in the version 3.0, but none of these opportunities has materialized. So the document is open to all your criticisms and suggestions, which are highly welcome. If whoever would need a source in order to develop it inso something bigger or better, please contact me Best regards --- Andrei Postnikov --- Paul Verlaine University - Institute de Chimie, Physique et Mat'eriaux, Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France --
Re: [SIESTA-L] A draft of small personal tutorial
http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf Dear Andrei, You said in your SIESTA-tuto that the frozen phonon calculations usually proceed after CG relaxation. Is that means we should first set MD.TypeOfRun CG to relax and then change it to MD.TypeOfRun FC with UseSaveData T and MD. UseSaveXV T to calculate the force constants? Thank you very much! Best wishes, Zhongli -- PhD. student of IAMP, Sichuan University, China E-mail: zl.liu.c...@gmail.com
