Re: [Spglib-users] Spglib and Octopus

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> 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...