Re: [Spglib-users] get_symmetry basis

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

Hi,

Spglib doesn't support Atoms object fully.

structure.pbc = (1, 1, 0)

This doesn't work.

Togo

On Wed, Oct 11, 2017 at 3:42 PM, Anders Christian Riis-Jensen
<ac...@fy...> wrote:
> Here is my code:
>
>
> import sys
> import spglib
> import numpy as np
> from numpy import pi, sin, cos, arccos, sqrt, dot
> from ase import Atoms
>
> # Input: Structure
> a = 2.46
> cell = np.array([[a, 0, 0,], [-a/2, a*sin(60*pi/180), 0], [0, 0, 5*a]])
>
> structure = Atoms('C2', cell=cell,
>              scaled_positions=np.array([[0, 0, 0],
>                         [2./3, 1./3, 0]]),
>              )
>
> structure.pbc = (1, 1, 0)
>
> cell = structure.get_cell()
>
> #Define rotation matrix:
> rot60 = np.array([[1/2, -sqrt(3)/2, 0], [sqrt(3)/2, 1/2, 0], [0, 0, 1]])
>
> # Get all symmetry operations
> symop = spglib.get_symmetry(structure, symprec=1e-5)
> rotaa = symop['rotations']
> trlaa = symop['translations']
>
> rotxy = []
> trlxy = []
>
> #Transform matrices to cartesian coordinates:
> for j in range(len(rotaa)):
>     rot_t = np.dot(np.linalg.inv(cell), np.dot(rotaa[j], cell))
>     trl_t = np.dot(np.dot(np.linalg.inv(cell), trlaa[j]), cell)
>     rotxy.append(rot_t)
>     trlxy.append(trl_t)
>
>
>
>
> Anders
>
> ________________________________
> Fra: Atsushi Togo <atz...@gm...>
> Sendt: 11. oktober 2017 02:14:17
> Til: Anders Christian Riis-Jensen
> Cc: spg...@li...
> Emne: Re: [Spglib-users] get_symmetry basis
>
> Hi,
>
> Could you give your script?
>
> Togo
>
> On Tue, Oct 10, 2017 at 7:18 PM, Anders Christian Riis-Jensen
> <ac...@fy...> wrote:
>> I am using the built-in function get_symmetry from spglib, and I seem to
>> have some issues with this. In this context I have a question.
>> I will here give an example showing my problem:
>>
>> If I define the unit cell for graphene:
>> cell = np.array([[a, 0, 0,], [-a/2, a*sin(60*pi/180), 0], [0, 0, 5*a]])
>> and put the carbon atoms in the (scaled) positions [0,0,0] and [0, 2/3,
>> 1/3]
>> I then run spglib.get_symmetry on the system (with the default tolerance).
>> I
>> get a set of symmetry transformations (I understand each transformation is
>> a
>> combination of a matrix multiplication and a translation). I want to have
>> the symmetry matrices (M) in cartesian coordinates and therefore make the
>> following basis transformation:
>> inverse(cell).M.cell
>> And here I would for example expect to find the standard 60 degrees
>> rotation
>> matrix, however this I dot not get. I therefore realize that the original
>> symmetry matrices might not be written in the lattice basis as I expected.
>>
>> Which basis is used and what is the proper transformation to get to
>> cartesian coordinates?
>>
>> Any answer will be greatly appreciated.
>>
>> Best regards
>> Anders Riis-Jensen
>>
>>
>>
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>
>
>
> --
> 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...