Re: [Spglib-users] Spglib is not detecting the correct symmetry from POSCAR file
Brought to you by:
atztogo
Menu
▾
▴
Re: [Spglib-users] Spglib is not detecting the correct symmetry from POSCAR file
|
From: Atsushi T. <atz...@gm...> - 2020-12-10 12:32:32
|
Hi, There are many options depending on what you want to do. So please read the documentation to find your answer. Togo On Thu, Dec 10, 2020 at 8:13 PM Arijit Sinha <ari...@gm...> wrote: > > Dear Atsushi, > After going through some materials online, I think I understand the reason for the discrepancy. Actually, there is a standard-setting implemented by spglib according to which it is modifying my input structures and changing lattice parameter orders. Is there any way to turn off the standard-setting and continuing with the input structure only? > -- > Thanking you, > > Arijit Sinha > Junior Research Fellow > JNCASR (Theoretical Sciences Unit), > Jakkur, Bangalore(India). > > > > > On Wed, Dec 9, 2020 at 7:46 PM Arijit Sinha <ari...@gm...> wrote: >> >> Sir, >> As you said I have constructed the structure by hand and try to get the space group but the problem(lattice parameters getting jumbled up) is appearing again I'm sending you the script and the relevant change in the input and the corresponding output. >> ********************************************************************************************************************************************************************************************************************************** >> Input structure: >> TNS = ([(3.416000127800, 0.000000000000, 0.00000000000), >> (0.000000000000, 12.123309135400, 0.00000007500), >> (0.000000000000, -0.000000093700, 15.1484184265)], >> [(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)], >> [73, 73, 73, 73, 73, 73, 73, 73, 28, 28, 28, 28, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16]) >> >> ************************************************************************************************************************************************************* >> Relevant output: >> Input structure >> 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 >> ********************************************************************************************************************************************************************* >> Unable to get >> -- >> Thanking you, >> >> Arijit Sinha >> Junior Research Fellow >> JNCASR (Theoretical Sciences Unit), >> Jakkur, Bangalore(India). >> >> >> >> >> On Wed, Dec 9, 2020 at 6:16 PM Atsushi Togo <atz...@gm...> wrote: >>> >>> 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 >>> >>> >>> _______________________________________________ >>> 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 |
