Re: [Phonopy-users] Post processing error
Brought to you by:
atztogo
Menu
▾
▴
Re: [Phonopy-users] Post processing error
|
From: Nenian C. <nc...@dr...> - 2013-05-09 14:04:09
|
Hi Togo, Yes, I am interested in trying. I have a number of calculations like this so it would be great if I could find a solution. NC On 05/09/13, Atsushi Togo <atz...@gm...> wrote: > Hello Sooran, > > It may be OK If the symmetry operations found in phonopy for the unit > cell is same as those found in VASP (with spin polarization). SOC may > break some symmetry, too. If I understand it correctly, time reversal > symmetry is broken, so if your crystal structure is > non-centrosymmetric, then thermal properties may be wrongly calculated > in phonopy because time reversal symmetry is always considered for > searching symmetry in reciprocal space. > > Togo > > > On Thu, May 9, 2013 at 11:36 AM, 김수란 <lor...@gm...> wrote: > > Hello > > > > During reading your dialog, I have a question about the phonopy with > > anti-ferromagnetic(AFM) system and spin-orbit coupling(SOC) system. > > > > You wrote that "currently phonopy doesn't support magnetic moments > > that breaks the crystal symmetry" > > > > I think that AFM and SOC system can breaks the crystal symmetry with > > magnetic moments. > > I calculated both systems (AFM and SOC) but I did not get any error or > > stopping. > > > > Therefore, now I confused. Can phonopy calculate AFM or SOC system? > > If I did not get any error or warning, can I believe my calculations? > > > > Best regards > > Sooran Kim > > > > > > 2013/5/9 Atsushi Togo <atz...@gm...> > >> > >> Hello, > >> > >> The symmetry of forces is broken. It seems you did spin polarized > >> calculation. But currently phonopy doesn't support magnetic moments > >> that breaks the crystal symmetry. I don't support it yet, but I have > >> implemented symmetry handling with co-linear magnetic moments before. > >> So if you are interested in it, I will help you though I don't > >> guarantee the calculation goes well. > >> > >> Togo > >> > >> On Wed, May 8, 2013 at 10:36 AM, Atsushi Togo <atz...@gm...> wrote: > >> > Hello, > >> > > >> > As the other possibility, sometimes vasprun</x>.xml can be written as > >> > broken xml even if vasp finishes correctly. > >> > Could you send vasprun</x>.xml's to me directly? I don't know how much the > >> > size is, but it would be OK if they are compressed. > >> > > >> > Togo > >> > > >> > On Wed, May 8, 2013 at 12:39 AM, Nenian Charles <nc...@dr...> > >> > wrote: > >> >> Hello, > >> >> > >> >> Thanks for the reply. Yes they are consistent this was the first thing > >> >> that > >> >> I checked. > >> >> > >> >> I would include the relevant files in this email however my vasprun</x>.xml > >> >> files are too large. > >> >> > >> >> Thanks, > >> >> > >> >> Charles > >> >> > >> >> > >> >> > >> >> -------------------------------------------------------------------------------------- > >> >> > >> >> Hi, > >> >> > >> >> I guess the number of vasprun</x></x>.xml's is not consistent with the > >> >> number > >> >> of displacements written in disp.yaml. Can you check it? > >> >> > >> >> Togo > >> >> > >> >> On Tue, May 7, 2013 at 12:34 AM, Nenian Charles <nc...@dr...> > >> >> wrote: > >> >> > >> >> Hello, > >> >> > >> >> I preformed a frozen phonon calculation in vasp using phonopy inputs > >> >> for a > >> >> 2x1x1 supercell. The VASP scf calculations converged normally, and > >> >> phonpy > >> >> creates the FORCE_SETS file, however when I try to construct the bands > >> >> I get > >> >> the following error. > >> >> > >> >> Band structure mode > >> >> Settings: > >> >> Force constants: write > >> >> Force constants symmetrization: 30 times > >> >> Supercell: [2 1 1] > >> >> Spacegroup: Fm-3m (225) > >> >> Calculating force constants... > >> >> Input forces are not enough to calculate force constants, > >> >> or something wrong (e.g. crystal structure does not match). > >> >> Traceback (most recent call last): > >> >> File "/home/nenian/software/phonopy-1.6.4/scripts/phonopy", line 728, > >> >> in > >> >> <module> > >> >> dynamical_matrix_decimals=settings.get_dm_decimals()) > >> >> File > >> >> "/home/nenian/software/phonopy-1.6.4/lib/python/phonopy/__init__.py", > >> >> line 262, in set_post_process > >> >> force_constants_decimals=force_constants_decimals) > >> >> File > >> >> "/home/nenian/software/phonopy-1.6.4/lib/python/phonopy/__init__.py", > >> >> line 314, in set_force_constants_from_forces > >> >> decimals=force_constants_decimals) > >> >> File > >> >> > >> >> "/home/nenian/software/phonopy-1.6.4/lib/python/phonopy/harmonic/force_constants.py", > >> >> line 51, in get_force_constants > >> >> range(supercell.get_number_of_atoms())) > >> >> File > >> >> > >> >> "/home/nenian/software/phonopy-1.6.4/lib/python/phonopy/harmonic/force_constants.py", > >> >> line 132, in run_force_constants > >> >> symmetry) > >> >> File > >> >> > >> >> "/home/nenian/software/phonopy-1.6.4/lib/python/phonopy/harmonic/force_constants.py", > >> >> line 180, in distribute_force_constants > >> >> symprec) > >> >> File > >> >> > >> >> "/home/nenian/software/phonopy-1.6.4/lib/python/phonopy/harmonic/force_constants.py", > >> >> line 257, in get_atom_mapping_by_symmetry > >> >> raise ValueError > >> >> ValueError > >> >> > >> >> Can you please help. > >> >> > >> >> Thanks > >> >> > >> >> > >> >> ------------------------------------------------------------------------------ > >> >> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET > >> >> Get 100% visibility into your production application - at no cost. > >> >> Code-level diagnostics for performance bottlenecks with <2% overhead > >> >> Download for free and get started troubleshooting in minutes. > >> >> https://lists.sourceforge.net/lists/listinfo/phonopy-users(http://p.sf.net/sfu/appdyn" target="l">http://p.sf.net/sfu/appdyn</x></x>_d2d_ap1 > >> >> _______________________________________________ > >> >> Phonopy-users mailing list > >> >> Pho...@li... > >> >> <a href=) > >> >> > >> >> -- > >> >> Atsushi Togo > >> >> http://atztogo.github.com/ > >> >> atz...@gm... > >> > > >> > > >> > > >> > -- > >> > Atsushi Togo > >> > http://atztogo.github.com/ > >> > atz...@gm... > >> > >> > >> > >> -- > >> Atsushi Togo > >> http://atztogo.github.com/ > >> atz...@gm... > >> > >> > >> ------------------------------------------------------------------------------ > >> Learn Graph Databases - Download FREE O'Reilly Book > >> "Graph Databases" is the definitive new guide to graph databases and > >> their applications. This 200-page book is written by three acclaimed > >> leaders in the field. The early access version is available now. > >> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > >> > >> _______________________________________________ > >> Phonopy-users mailing list > >> Pho...@li... > >> https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > > > > > -- > Atsushi Togo > http://atztogo.github.com/ > atz...@gm... > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and > their applications. This 200-page book is written by three acclaimed > leaders in the field. The early access version is available now. > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > > |