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: Arijit S. <ari...@gm...> - 2020-12-10 11:12:56
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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 SinhaJunior Research FellowJNCASR (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 SinhaJunior Research FellowJNCASR (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 >> > |
