Re: [Spglib-users] Spglib is not detecting the correct symmetry from POSCAR file
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Re: [Spglib-users] Spglib is not detecting the correct symmetry from POSCAR file
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From: Atsushi T. <atz...@gm...> - 2020-12-09 12:46:02
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Hi, I tested your POSCAR using phonopy (phonopy uses spglib.) I doubt your script. You use ASE. Please write your script without using ASE. See https://spglib.github.io/spglib/python-spglib.html#crystal-structure-cell. Togo On Wed, Dec 9, 2020 at 9:40 PM Arijit Sinha <ari...@gm...> wrote: > > Dear Atsushi, > Thank you for your fast reply I have done that also but nothing changed. I think this is not related to symmetry tolerance because the code is reading the lattice parameters wrong all together it is printing a as c, c as b nd so on. the atomic position order is also jumbled up. I am writing down the input and output for your convenience below > ********************************************************************************************************************************************************************************************************************************* > Input: > XCrySDen XSF file > 1.0 > 3.416000127800 0.000000000000 0.000000000000 > 0.000000000000 12.123309135400 0.000000075000 > 0.000000000000 -0.000000093700 15.148418426500 > Ta Ni S > 8 4 20 > Direct > 0.000000000 0.221787274 0.108938992 > 0.000000000 0.778212726 0.891061008 > 0.000000000 0.778212667 0.608938992 > 0.000000000 0.221787304 0.391061008 > 0.500000000 0.721793473 0.108937271 > 0.500000000 0.278206497 0.891062737 > 0.500000000 0.278206557 0.608937263 > 0.500000000 0.721793473 0.391062707 > 0.000000000 0.699588060 0.250000000 > 0.000000000 0.300411940 0.750000000 > 0.500000000 0.199598417 0.250000000 > 0.500000000 0.800401568 0.750000000 > 0.500000000 0.082921132 0.136132896 > 0.500000000 0.917078853 0.863867104 > 0.500000000 0.917078853 0.636132836 > 0.500000000 0.082921162 0.363867134 > 0.000000000 0.582922995 0.136127144 > 0.000000000 0.417077035 0.863872886 > 0.000000000 0.417077065 0.636127174 > 0.000000000 0.582922935 0.363872826 > 0.000000000 0.147209421 0.950776219 > 0.000000000 0.852790594 0.049223803 > 0.000000000 0.852790534 0.450776190 > 0.000000000 0.147209466 0.549223840 > 0.500000000 0.647215426 0.950776398 > 0.500000000 0.352784544 0.049223613 > 0.500000000 0.352784604 0.450776398 > 0.500000000 0.647215426 0.549223602 > 0.000000000 0.322443128 0.250000000 > 0.000000000 0.677556872 0.750000000 > 0.500000000 0.822440684 0.250000000 > 0.500000000 0.177559301 0.750000000 > **************************************************************************************************************************************************************************** > Output Standardize_cell using , tprimitive=0, no_idealize=0): > Basis vectors: > a 15.14842 0.00000 0.00000 > b 0.00000 3.41600 0.00000 > c 0.00000 0.00000 12.12331 > Atomic points: > 73 0.10894 0.00000 0.22179 > 73 0.89106 0.00000 0.77821 > 73 0.60894 0.00000 0.77821 > 73 0.39106 0.00000 0.22179 > 73 0.10894 0.50000 0.72179 > 73 0.89106 0.50000 0.27821 > 73 0.60894 0.50000 0.27821 > 73 0.39106 0.50000 0.72179 > 28 0.25000 0.00000 0.69959 > 28 0.75000 0.00000 0.30041 > 28 0.25000 0.50000 0.19960 > 28 0.75000 0.50000 0.80040 > 16 0.13613 0.50000 0.08292 > 16 0.86387 0.50000 0.91708 > 16 0.63613 0.50000 0.91708 > 16 0.36387 0.50000 0.08292 > 16 0.13613 0.00000 0.58292 > 16 0.86387 0.00000 0.41708 > 16 0.63613 0.00000 0.41708 > 16 0.36387 0.00000 0.58292 > 16 0.95078 0.00000 0.14721 > 16 0.04922 0.00000 0.85279 > 16 0.45078 0.00000 0.85279 > 16 0.54922 0.00000 0.14721 > 16 0.95078 0.50000 0.64722 > 16 0.04922 0.50000 0.35278 > 16 0.45078 0.50000 0.35278 > 16 0.54922 0.50000 0.64722 > 16 0.25000 0.00000 0.32244 > 16 0.75000 0.00000 0.67756 > 16 0.25000 0.50000 0.82244 > 16 0.75000 0.50000 0.17756 > ************************************************************************************************************************************************************************************** > > Thanking you, > > Arijit Sinha > Junior Research Fellow > JNCASR (Theoretical Sciences Unit), > Jakkur, Bangalore(India). > > > > > On Wed, Dec 9, 2020 at 5:56 PM Atsushi Togo <atz...@gm...> wrote: >> >> Hi, >> >> You can loosen the symmetry search tolerance (e.g. symprec=1e-3). >> >> Togo >> >> On Wed, Dec 9, 2020 at 8:31 PM Arijit Sinha <ari...@gm...> wrote: >> > >> > Dear Users and Experts, >> > I am new in spglib but my material which has a symmetry of Cmcm is not getting captured correctly by spglib in python it is jumbling up the lattice vectors order given in poscar (but FINDSYM showing the correct symmetry) below I am attaching the code as well as the files please tell me if it is my mistake or something else. >> > -- >> > Thanking you, >> > >> > Arijit Sinha >> > Junior Research Fellow >> > JNCASR (Theoretical Sciences Unit), >> > Jakkur, Bangalore(India). >> > >> > >> > _______________________________________________ >> > Spglib-users mailing list >> > Spg...@li... >> > https://lists.sourceforge.net/lists/listinfo/spglib-users >> >> >> >> -- >> Atsushi Togo >> >> >> _______________________________________________ >> Spglib-users mailing list >> Spg...@li... >> https://lists.sourceforge.net/lists/listinfo/spglib-users > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
