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 09:47:16
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OK, now it is clear, thanks a lot for the explanation!
All the best
Antonio
Il 15. 09. 24 3:10, Atsushi Togo ha scritto:
> Hi,
>
> space_group_operations:
> - rotation: # 1
> - [ 1, 0 , 0]
> - [ 0, 1 , 0]
> - [ 0, 0 , 1]
> translation: [ 0.00000, 0.00000, 0.00000 ]
> - rotation: # 2
> - [ 1, 0 , 0]
> - [ 0, 1 , 0]
> - [ 0, 0 , 1]
> translation: [ 0.66667, 0.33333, 0.00000 ]
> - rotation: # 3
> - [ 1, 0 , 0]
> - [ 0, 1 , 0]
> - [ 0, 0 , 1]
> translation: [ 0.33333, 0.66667, 0.00000 ]
>
> The first one is what we often call identity, but the following two
> are not because their translation parts are not zero. Your
> POSCAR_unit_cell contains three lattice points, which means it is not
> a primitive cell.
>
> A theoretical crystal is defined by a primitive cell and its lattice.
> The primitive cell is copied on all the lattice points.
>
> S = \sum_i (R_i, t_i) T
>
> Group theoretically, the translation group T represents the lattice
> translations and T is an infinite group. The set of the coset
> representatives {(R_i, t_i)} represents the set of the space group
> operations which is combined (either from left or right) with every
> lattice translation. The set may not form a group, but the collection
> of the rotation parts {R_i} forms a group, which is called the
> crystallographic point group. What may be confusing is that
> "supercell" that we call is not described using this terminology. What
> phonopy returns (in fact spglib) as the space group operations are
> something like coset representatives, but in the case for supercell,
> the lattice translations within supercell are multiplied, which is
> just for convenience for our calculations.
>
> Togo
>
> On Sun, Sep 15, 2024 at 2:33 AM 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 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>
> _______________________________________________
> 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
ResercherID: A-4883-2014
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