Re: [Spglib-users] Spglib and Octopus

[Atsushi T. <atz...@gm...>]

Hi,

Maybe it is worth to see and try spacegroup utility in Elk package if
you haven't seen it,
http://elk.sourceforge.net/

Togo

On Thu, Aug 17, 2017 at 11:43 PM, Atsushi Togo <atz...@gm...> wrote:
>> Yes but here the lattice is the same in both cell.
>> The atom of one cell are a subset of the atoms of the other cell, which
>> exclude the possible translation.
>
> The following is the result of representations for your two cells. I
> see there is not internal pure translation for both cells. The
> difference of the translation parts comes from the difference of
> location of origin shifts. This is all I know.
>
> {'rotations': array([[[ 1,  0,  0],
>         [ 0,  1,  0],
>         [ 0,  0,  1]],
>
>        [[-1,  0,  0],
>         [ 0, -1,  0],
>         [ 0,  0, -1]],
>
>        [[ 0,  1,  0],
>         [ 1,  0,  0],
>         [ 0,  0, -1]],
>
>        [[ 0, -1,  0],
>         [-1,  0,  0],
>         [ 0,  0,  1]]], dtype=int32), 'translations': array([[ 0.  ,
> 0.  ,  0.  ],
>        [ 0.34,  0.66,  0.72],
>        [ 0.34,  0.66,  0.22],
>        [ 1.  ,  1.  ,  0.5 ]]), 'equivalent_atoms': array([0, 0], dtype=int32)}
>
>
> {'rotations': array([[[ 1,  0,  0],
>         [ 0,  1,  0],
>         [ 0,  0,  1]],
>
>        [[-1,  0,  0],
>         [ 0, -1,  0],
>         [ 0,  0, -1]],
>
>        [[ 0,  1,  0],
>         [ 1,  0,  0],
>         [ 0,  0, -1]],
>
>        [[ 0, -1,  0],
>         [-1,  0,  0],
>         [ 0,  0,  1]]], dtype=int32), 'translations': array([[
> 0.00000000e+00,   0.00000000e+00,   0.00000000e+00],
>        [  0.00000000e+00,   0.00000000e+00,   0.00000000e+00],
>        [  1.38777878e-17,   0.00000000e+00,   5.00000000e-01],
>        [  1.38777878e-17,   0.00000000e+00,   5.00000000e-01]]),
> 'equivalent_atoms': array([0, 0, 0, 0], dtype=int32)}
>
>> This is the full point of what I am trying to understand:
>> How can spglib can find the same spacegroup and at the same time different
>> symmetry operations for the same lattice?
>
> Because the coordinates of atoms. Have you studied crystallography
> before? If not, please find somebody else who knows it around you and
> give the same question. This is not the matter of spglib, but I think
> about the basic knowledge on crystallography.
>
> Togo
>
>
>> This seems to be incompatible to me, but maybe you have a nice explanation
>> for it.
>>
>> Nicolas
>>
>>
>> On 08/17/2017 04:21 PM, Atsushi Togo wrote:
>>>
>>> What I can guess is
>>> 1. lattice translation
>>> 2. choice
>>>
>>> Togo
>>>
>>> On Thu, Aug 17, 2017 at 11:14 PM, Nicolas Tancogne-Dejean
>>> <nic...@mp...> wrote:
>>>>
>>>> The result of the routine spg_get_symmetry
>>>>
>>>> Nicolas
>>>>
>>>>
>>>> On 08/17/2017 04:12 PM, Atsushi Togo wrote:
>>>>
>>>> Can you explain more detail about your definition of the word 'symmetry'?
>>>>
>>>> Togo
>>>>
>>>> On Thu, Aug 17, 2017 at 10:56 PM, Nicolas Tancogne-Dejean
>>>> <nic...@mp...> wrote:
>>>>
>>>> Hi,
>>>>
>>>> But if the spacegroups are the same, why the symmetries returned by
>>>> spglib
>>>> are different?
>>>> Note that I do not use python, but the Fortran interface.
>>>>
>>>> Nicolas
>>>>
>>>>
>>>> On 08/17/2017 10:52 AM, Atsushi Togo wrote:
>>>>
>>>> Hi,
>>>>
>>>> I got 15 for both. I cross-checked using findsym and I got 15 for both.
>>>> I'm glad if you give the test in python script from next time as follows.
>>>>
>>>> import spglib
>>>>
>>>> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
>>>>              [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
>>>>              [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]]
>>>> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01],
>>>>             [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]]
>>>> numbers = [1, 1]
>>>> cell = (lattice, points, numbers)
>>>> print(spglib.get_spacegroup(cell))
>>>>
>>>> lattice = [[ 3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
>>>>              [-3.5000000000E+00, 4.0000000000E+00, 0.0000000000E+00],
>>>>              [ 1.5628335990E+00, 4.5539510139E-16, 8.8632697771E+00]]
>>>> points = [[ 3.2000000000E-01, 9.8000000000E-01, 1.1000000000E-01],
>>>>             [ 9.8000000000E-01, 3.2000000000E-01, 3.9000000000E-01],
>>>>             [ 6.8000000000E-01, 2.0000000000E-02, 8.9000000000E-01],
>>>>             [ 2.0000000000E-02, 6.8000000000E-01, 6.1000000000E-01]]
>>>> numbers = [1, 1, 1, 1]
>>>> cell = (lattice, points, numbers)
>>>> print(spglib.get_spacegroup(cell))
>>>>
>>>> Togo
>>>>
>>>> On Thu, Aug 17, 2017 at 5:42 PM, Nicolas Tancogne-Dejean
>>>> <nic...@mp...> wrote:
>>>>
>>>> Hi,
>>>>
>>>> Lattice vectors are stored in rows.
>>>>
>>>> Nicolas
>>>>
>>>>
>>>>
>>>> On 08/17/2017 10:36 AM, Atsushi Togo wrote:
>>>>
>>>> Lattice vectors are column vectors or row vectors?
>>>>
>>>> Togo
>>>>
>>>> On Thu, Aug 17, 2017 at 5:15 PM, Nicolas Tancogne-Dejean
>>>> <nic...@mp...> wrote:
>>>>
>>>> Hi,
>>>>
>>>> Please find below the definition of two cells, generated by Abinit as
>>>> being
>>>> spacegroup 9 and 15.
>>>> I got from spglib that the spacegroup number in both cases is 15.
>>>>
>>>> The symmetries returns by spglib are however exactly the same as given
>>>> by
>>>> Abinit.
>>>>
>>>> Thanks in advance for your help.
>>>> Nicolas
>>>>
>>>> Cell 1:
>>>>
>>>> %LatticeParameters
>>>>     1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00
>>>> %
>>>> %LatticeVectors
>>>>     3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>>>     -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>>>     1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00
>>>> %
>>>> %ReducedCoordinates
>>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01
>>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01
>>>> %
>>>>
>>>>
>>>> Cell 2:
>>>>
>>>> %LatticeParameters
>>>>     1.0000000000E+00 | 1.0000000000E+00 | 1.0000000000E+00
>>>> %
>>>> %LatticeVectors
>>>>     3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>>>     -3.5000000000E+00 | 4.0000000000E+00 | 0.0000000000E+00
>>>>     1.5628335990E+00 | 4.5539510139E-16 | 8.8632697771E+00
>>>> %
>>>> %ReducedCoordinates
>>>> "H" | 3.2000000000E-01 | 9.8000000000E-01 | 1.1000000000E-01
>>>> "H" | 9.8000000000E-01 | 3.2000000000E-01 | 3.9000000000E-01
>>>> "H" | 6.8000000000E-01 | 2.0000000000E-02 | 8.9000000000E-01
>>>> "H" | 2.0000000000E-02 | 6.8000000000E-01 | 6.1000000000E-01
>>>> %
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>> --
>>>> Nicolas Tancogne-Dejean
>>>>
>>>> Post-doctoral Researcher,
>>>> Theory Department,
>>>> Max Planck Institute for the Structure and Dynamics of Matter
>>>>
>>>> Bldg. 99 (CFEL)
>>>> Luruper Chaussee 149
>>>> 22761 Hamburg
>>>> Phone: + 49 (0) 40 8998-8322
>>>>
>>>>
>>>> --
>>>> Nicolas Tancogne-Dejean
>>>>
>>>> Post-doctoral Researcher,
>>>> Theory Department,
>>>> Max Planck Institute for the Structure and Dynamics of Matter
>>>>
>>>> Bldg. 99 (CFEL)
>>>> Luruper Chaussee 149
>>>> 22761 Hamburg
>>>> Phone: + 49 (0) 40 8998-8322
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Nicolas Tancogne-Dejean
>>>>
>>>> Post-doctoral Researcher,
>>>> Theory Department,
>>>> Max Planck Institute for the Structure and Dynamics of Matter
>>>>
>>>> Bldg. 99 (CFEL)
>>>> Luruper Chaussee 149
>>>> 22761 Hamburg
>>>> Phone: + 49 (0) 40 8998-8322
>>>
>>>
>>>
>>
>> --
>> Nicolas Tancogne-Dejean
>>
>> Post-doctoral Researcher,
>> Theory Department,
>> Max Planck Institute for the Structure and Dynamics of Matter
>>
>> Bldg. 99 (CFEL)
>> Luruper Chaussee 149
>> 22761 Hamburg
>> Phone: + 49 (0) 40 8998-8322
>>
>
>
>
> --
> Atsushi Togo
> Elements Strategy Initiative for Structural Materials, Kyoto university
> E-mail: atz...@gm...



-- 
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...