Re: [Phonopy-users] P1 symmetry but symmetry operations found
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Re: [Phonopy-users] P1 symmetry but symmetry operations found
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From: Antonio C. <cam...@fe...> - 2024-09-15 09:44:37
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Hi, what I described happens at a constant tolerance value, I was not comparing two structures obtained at different tolerances. Thanks for you answer, I guess what you find goes with the next explanation in the mailing list. Best Antonio Il 14. 09. 24 19:33, MUKESH SINGH ha scritto: > Hi, > > While using phonopy to get unit-cell, it uses some threshold. > Considering some small threshold, I think, there is a possibility of > reduction of unit-cell. Taking inspiration from phonopy generated > structure, I have created (using rotation & translation of cell) a > smaller unit cell with ase and attached and its steps and > reduced_POSCAR_unit, which matches with PPOSCAR file. I hope this > might help. > > > Thanks and regards > Mukesh Singh > Department of Physics, > IIT Bombay, India > > On Sat, Sep 14, 2024 at 10:26 PM MUKESH SINGH > <gkp...@gm...> wrote: > > Hi, > > While using phonopy to get unit-cell, it uses some threshold. > Considering some small threshold, I think, there is a possibility > of reduction of unit-cell. Taking inspiration from phonopy > generated structure, I have created (using rotation & translation > of cell) a smaller unit cell with ase and attached and its steps > and reduced_POSCAR_unit, which matches with PPOSCAR file. I hope > this might help. > > > Thanks and regards > Mukesh Singh > Department of Physics, > IIT Bombay, India > > On Sat, Sep 14, 2024 at 6:47 PM Antonio Cammarata via > Phonopy-users <pho...@li...> wrote: > > Thanks for the answer. It is not still clear to me why there > are equivalent atoms which can be mapped by symmetry > operations if the only symmetry operation is the identity. > From my understanding, if P1 is the space group of the unit > cell provided as input, then every atom in the unit cell > should be unique, then the unit cell is primitive and no > further reduction is possible. > > Antonio > > Il 14. 09. 24 15:00, Atsushi Togo ha scritto: >> Hi, >> >> It is not a bug. >> >> P1 corresponds to a space group type. >> >> Space group S is expanded by cosets, >> S = \sum_i (R_i, t_i) T >> where T is the translation group and (R_i, t_i) are the coset >> representatives (the space group operations). In this way, >> supercell can not be represented in this way. >> >> The symmetry operations returned in your case are the coset >> representatives * translations in supercell. However P1 is >> determined from the primitive cell. >> >> Togo >> >> On Sat, Sep 14, 2024 at 8:29 PM Antonio Cammarata via >> Phonopy-users <pho...@li...> wrote: >> >> Dear all >> >> I am using phonopy 2.28.0 with python 3.9.13 and spglib >> 2.3.1. I have a >> unit cell which phonopy recognises to have space group >> P1, that is, with >> just the identity as symmetry operation. However, when I >> call phonopy, >> for example, to calculate the band structure, it finds >> space group P1 >> but 3 symmetry operations in the supercell. In fact, if I >> issue the command >> >> phonopy --symmetry -c POSCAR_unit_cell >> >> I get a primitive unit cell PPOSCAR which is smaller than >> the provided >> unit cell, and the map of the unique atoms is provided. >> However, all the >> symmetry operations associated to the atoms are >> represented by the >> identity matrix. Accordingly, I expected that the >> primitive unit cell is >> identical to the provided unit cell, as the recognised >> symmetry is P1 >> and the only symmetry operation is the identity. Please, >> let me know if >> I am missing something here. >> >> Please, here attached you find the unit cell to reproduce >> the output. >> >> Thanks a lot in advance for your help! >> >> All the best >> >> Antonio >> >> -- >> _______________________________________________ >> doc. Antonio Cammarata, PhD in Physics >> Associate Professor in Applied Physics >> Advanced Materials Group >> Department of Control Engineering - KN:G-204 >> Faculty of Electrical Engineering >> Czech Technical University in Prague >> Karlovo Náměstí, 13 >> 121 35, Prague 2, Czech Republic >> Phone: +420 224 35 5713 >> Fax: +420 224 91 8646 >> ORCID: orcid.org/0000-0002-5691-0682 >> <http://orcid.org/0000-0002-5691-0682> >> ResercherID: A-4883-2014 >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users >> >> >> >> -- >> Atsushi Togo >> >> >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users > > -- > _______________________________________________ > doc. Antonio Cammarata, PhD in Physics > Associate Professor in Applied Physics > Advanced Materials Group > Department of Control Engineering - KN:G-204 > Faculty of Electrical Engineering > Czech Technical University in Prague > Karlovo Náměstí, 13 > 121 35, Prague 2, Czech Republic > Phone: +420 224 35 5713 > Fax: +420 224 91 8646 > ORCID:orcid.org/0000-0002-5691-0682 <http://orcid.org/0000-0002-5691-0682> > ResercherID: A-4883-2014 > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > -- > Thanks and regards > Mukesh Singh > Research Scholar > Department of Physics, > IIT BOMBAY(400076), India. > Website: Google Sites > <https://sites.google.com/view/mukeshphy/home?authuser=0> > Publications link: Google Scholar > <https://scholar.google.co.in/citations?user=Lfi6CDsAAAAJ&hl=en> > > > > -- > Thanks and regards > Mukesh Singh > Research Scholar > Department of Physics, > IIT BOMBAY(400076), India. > Website: Google Sites > <https://sites.google.com/view/mukeshphy/home?authuser=0> > Publications link: Google Scholar > <https://scholar.google.co.in/citations?user=Lfi6CDsAAAAJ&hl=en> -- _______________________________________________ doc. Antonio Cammarata, PhD in Physics Associate Professor in Applied Physics Advanced Materials Group Department of Control Engineering - KN:G-204 Faculty of Electrical Engineering Czech Technical University in Prague Karlovo Náměstí, 13 121 35, Prague 2, Czech Republic Phone: +420 224 35 5713 Fax: +420 224 91 8646 ORCID: orcid.org/0000-0002-5691-0682 ResercherID: A-4883-2014 |
