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: Atsushi T. <atz...@gm...> - 2024-09-15 01:10:57
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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
>>>> ResercherID: A-4883-2014
>>>> _______________________________________________
>>>> Phonopy-users mailing list
>>>> Pho...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users
>>>>
>>>
>>>
>>> --
>>> Atsushi Togo
>>>
>>>
>>> _______________________________________________
>>> Phonopy-users mailing lis...@li...://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
>>>
>>> _______________________________________________
>>> 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
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