Re: [SIESTA-L] LO phonons with SIESTA
Dear SIESTA Users, I think that the inability of SIESTA to correctly describe LO phonons in polar materials such as AlN at the limit q tend to 0 is porbably due to the fact that this code uses atom-centred basis sets which fail to describe the long wavelengths near gamma well far from the the atomic centers. Karim this might be useful : http://chianti.geol.ucl.ac.uk/~dario/tutorial_phonons.tar.gz On Fri, Apr 15, 2011 at 12:48 PM, karim rezouali rezoual...@yahoo.fr wrote: Dear all, I am currently working on the phonons in the whole Brillouin -zone of bulk wurtzite AlN (VIBRA- supercell of 500 atoms) and I encounter a serious problem with LO phonons in the limit of gamma. I calculated the Born charges and the dielectric tensor (LO-TO spleeting) and the results (attached file: dipersion along gamma point- A point) do not agree with calculations reported in the litterature using other softwares (linear response method). I increased the size of the supercell (700 atoms) but no change in the shape of the LO branch was observed. Is the problem intrinsic to SIESTA because no works are available (to my knowledge) on the whole-Brillouin zone optical phonons using this code in the literature?!. Thanks in advance, Karim -- Mehmet Topsakal (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/Turkey Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 http://www.researcherid.com/rid/A-5015-2010
Re: [SIESTA-L] Please help
Hello Varrun, Your input and output files seem OK, but the optimisation is not yet finished: you can check that the forces are decreasing (but are still large), and energies (E_KS(eV)) are converging, but are still far from being converged. 26 optimisation steps is clearly not enough yet. Few more points: the xyz file has 171 atoms, but NumberOfAtoms is 168, so your calculation runs with only one Ti atom, not 4. Also, I advise to keep the cell volume fixed, to save computational time and not allow the cell to become too small: MD.VariableCell F Best regards, Natalia On 4/16/11, Varrun Ashok varrun.as...@gmail.com wrote: Hi all, I am very new to siesta and DFT calculations. I need your support and help. I am running a fdf file comprising a system consisting of a triglyceride molecule and a 4 atom Ti tetrahedral cluster near a double of the molecule. The aim is to check how strongly the cluster interacts with double bond. The system is not converging. The Max atomic forces values are erratic. I have attached a copy of the fdf file, the .xyz file and the .out file and also a 3D image of the molecule+Ti system. Kindly provide recommendations. Regards, Varrun Ashok
Re: [SIESTA-L] Please help
Hi, THank you very much. I spent 2 days already on this simulation. I will be more careful next time to write the correct number of atoms. REgards, Varrun Ashok On 18 April 2011 16:03, Natalia Martsinovich n.martsinov...@gmail.comwrote: Hello Varrun, Your input and output files seem OK, but the optimisation is not yet finished: you can check that the forces are decreasing (but are still large), and energies (E_KS(eV)) are converging, but are still far from being converged. 26 optimisation steps is clearly not enough yet. Few more points: the xyz file has 171 atoms, but NumberOfAtoms is 168, so your calculation runs with only one Ti atom, not 4. Also, I advise to keep the cell volume fixed, to save computational time and not allow the cell to become too small: MD.VariableCell F Best regards, Natalia On 4/16/11, Varrun Ashok varrun.as...@gmail.com wrote: Hi all, I am very new to siesta and DFT calculations. I need your support and help. I am running a fdf file comprising a system consisting of a triglyceride molecule and a 4 atom Ti tetrahedral cluster near a double of the molecule. The aim is to check how strongly the cluster interacts with double bond. The system is not converging. The Max atomic forces values are erratic. I have attached a copy of the fdf file, the .xyz file and the .out file and also a 3D image of the molecule+Ti system. Kindly provide recommendations. Regards, Varrun Ashok
Re: [SIESTA-L] Tutorial for armchair and zigzag graphene nanoribbons modelling by using tetr, cheers.
Dear Hongzi, Could you please share with me the fdf files? If you think you should not post them here, please email me: hua...@gmail.com. Thank you very much Huan Tran On Mon, Apr 18, 2011 at 4:18 AM, hongyi.z...@gmail.com wrote: Dear All, In order to build the input files for siesta of armchair and zigzag graphene nanoribbons with the advanced tool tetr written by Dr. Lev Kantorovitch, I've asked a few questions for help and Lev has given me some tutorials for this purpose. I hope this tutorial will help the ones who want to do the similar thing. Please find the tutorial from here: www.cmmp.ucl.ac.uk/~lev/codes/lev00http://www.cmmp.ucl.ac.uk/%7Elev/codes/lev00 Lev also give me the corresponding fdf files for these examples and the latest version of tetr. I don't know whether I can post the attachments to this list. So if you want them, please tell me. Regards. -- Hongsheng Zhao hongyi.z...@gmail.com School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China GnuPG DSA: 0xD108493 2011-4-18 -- Regards Huan Tran Department of Physics University of Basel, Switzerland Email: huan.t...@unibas.ch
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 /
