OK. I will try to prepare a detailed SIESTA-PHON tutorial at this weekend.
2010/7/28 Marcos Veríssimo Alves <marcos.verissimo.al...@gmail.com> > Mehmet, > > Please do share the knowledge. It is alwayfs useful, especislly because the > calculation of phonons is always of interest. I for one would be very much > interested in knowing how to use Dario's code in conjunction with Siesta. > > Cheers, > > Marcos > > On Wed, Jul 28, 2010 at 1:43 PM, Mehmet Topsakal < > topsa...@unam.bilkent.edu.tr> wrote: > >> Dear Jusar, >> >> I have obtained the attached phonon spectrum in 2 hours by using >> 8-cpu-core. The supercell is 5x5x1 and the MeshCutoff is 300 Ry. I have used >> Dario Alfè's phon program. Because I'm not familiar with siesta utilities >> such as FCBUILD and VIBRA. Phon only needs forces which can be calculated by >> other programs such as VASP and PWSCF. >> >> I can prepare a nice and detaied phon tutorial where the forces are >> calculated by SIESTA if you (or others) want. >> >> Mehmet. >> >> >> >> On Wed, Jul 28, 2010 at 11:46 AM, Juzar Thingna <juza...@gmail.com>wrote: >> >>> Thank you Prof. Postnikov and Mehmet for your quick responses. Here are a >>> few observations. >>> >>> After Mehmets comment on increasing the Mesh cut-off I set it to 800 Ry I >>> still observed negative part but the magnitude has reduced. Sorry I didn't >>> know one had to go to such high cut-offs to observe a change, earlier I was >>> trying cut-offs from 200-500 and there were no changes (or maybe changes >>> that were not very distinguishable). >>> >>> I'm currently trying Prof. Postnikov solution of increasing the >>> super-cell size. Now I have set SuperCell_1 = 5; SuperCell_1 = 5; >>> SuperCell_1 = 1. Increasing the supercell size has drastically increased the >>> computation time (as expected) so I guess it will take a long time to get >>> over. >>> >>> Is there a way to increase the SuperCell size but not affect the >>> computation time drastically? >>> >>> >>> Regards, >>> >>> Juzar Thingna >>> Department of Physics, >>> Center for Computation Science and Engineering, >>> National University of Singapore. >>> >>> >>> On Tue, Jul 27, 2010 at 5:42 PM, <apost...@uni-osnabrueck.de> wrote: >>> >>>> > Hi, >>>> > Thank you Prof. Postnikov and Mehmet for your quick replies. >>>> > >>>> > I do get 3 acoustic modes and 3 optical modes as I should since I just >>>> > have >>>> > a 2 point basis. >>>> > The problem is that one of the acoustic mode starts from zero and goes >>>> > negative immediately (Graph attached). I have tried increasing the >>>> mesh >>>> > cut-off as well as optimized the structure using CG. But still I get >>>> the >>>> > same behavior. >>>> >>>> Dear Juzar, >>>> then it is clear. (You should have described your problem >>>> more precisely in the first place, to save some guess work). >>>> The trouble is due to >>>> insufficient supercell size in your VIBRA calculation. >>>> In other words, the force constants >>>> are not sufficiently converged in real space. You need to construct >>>> a larger supercell, using FCBUILD, then rerun VIBRA. >>>> >>>> > @ Prof. Postnikov: Sir you mentioned "Go search for a better >>>> equilibrium. >>>> > Use eigenvectors of instable modes as a guide." Please could you >>>> elaborate >>>> > on how to use the eigen vectors of the instable mode as a guide? >>>> >>>> Seemingly, this is not your problem here. >>>> However, you may have a look in the following talk >>>> >>>> http://www.home.uni-osnabrueck.de/apostnik/Lectures/APostnikov-Phonons.pdf >>>> - your problem is addressed in pp.18-20. >>>> >>>> Good luck >>>> >>>> Andrei Postnikov >>>> >>>> >>>> >>> >> >> >> -- >> >> Mehmet Topsakal (Ph.D. Student) >> UNAM-Institute of Materials Science and Nanotechnology. >> Bilkent University. 06800 Bilkent, Ankara/Türkiye >> Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 >> UNAM-web : www.nano.org.tr >> >> > -- Mehmet Topsakal (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/Türkiye Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 UNAM-web : www.nano.org.tr
