[ase-users] problem with the definition of space group 86 in ase.spacegroup.crystal function

[Ask Hjorth Larsen]

2017-04-20 10:48 GMT+02:00 Jens Jørgen Mortensen <jensj at fysik.dtu.dk>:
> On 04/07/2017 06:44 PM, Ask Hjorth Larsen via ase-users wrote:
>>
>> Hi Jesper
>>
>> Would you be able to have a look at this question?
>
>
> I've opened an issue:
>
>     https://gitlab.com/ase/ase/issues/115
>
> Jens Jørgen

I believe Jesper's recent MR solved this.  Thank you variously for
reporting and fixing the issue.

Best regards
Ask

>
>
>> Best regards
>> Ask
>>
>> 2017-03-23 15:57 GMT+01:00 Musil Félix via ase-users
>> <ase-users at listserv.fysik.dtu.dk>:
>>>
>>> Dear all,
>>>
>>>
>>> I am generating an Atoms structure using the ase.spacegroup.crystal
>>> function for space group 86 and it seems that this particular space group
>>> does not follow the definition given by the international table of
>>> crystallography (see example code below and the definition of the general
>>> site of  space group 86).
>>>
>>> I am solving this problem by manually correction the bug in the atom
>>> positions. Would it be easy to fix this issue within the ase package ?
>>>
>>> Thanks in advance,
>>>
>>>
>>> Felix Musil
>>>
>>>
>>> Félix Musil
>>> Doctoral Assistant - Ph.D Student
>>>
>>> EPFL STI IMX COSMO
>>> LABORATORY OF COMPUTATIONAL SCIENCE AND MODELLING
>>> Institute of Materials Science and Engineering
>>> MXG 315
>>> Station 12
>>> CH-1015 Lausanne
>>> Switzerland
>>>
>>> E-mail: felix.musil at epfl.ch
>>> http://cosmo.epfl.ch/
>>>
>>>
>>>
>>>
>>>
>>> A small python code example:
>>>
>>>
>>> from ase.spacegroup import crystal
>>> import ase
>>> from ase.visualize import view
>>> import spglib as spg
>>>
>>> print ase.__version__
>>>
>>>
>>> cc = crystal([14],[  7.5e-01,   4.9e-01,
>>> 5.6e-01],spacegroup=86,cellpar=[  4.8,   4.8,   9.9,  90. ,90. ,  90. ])
>>>
>>> print spg.get_spacegroup(cc)
>>> print cc.get_scaled_positions()
>>>
>>>
>>> cc.arrays['positions'][3][2] = cc.arrays['positions'][2][2]
>>>
>>>
>>> print spg.get_spacegroup(cc)
>>> print cc.get_scaled_positions()
>>>
>>>
>>>
>>> and what it outputs:
>>>
>>>
>>> 3.13.0
>>> P1 (1)
>>> [[ 0.75  0.49  0.56]
>>>   [ 0.25  0.51  0.56]
>>>   [ 0.01  0.25  0.06]
>>>   [ 0.99  0.75  0.94]
>>>   [ 0.75  0.01  0.94]
>>>   [ 0.25  0.99  0.94]
>>>   [ 0.49  0.25  0.44]
>>>   [ 0.51  0.75  0.44]]
>>> P4_2/n (86)
>>> [[ 0.75  0.49  0.56]
>>>   [ 0.25  0.51  0.56]
>>>   [ 0.01  0.25  0.06]
>>>   [ 0.99  0.75  0.06]
>>>   [ 0.75  0.01  0.94]
>>>   [ 0.25  0.99  0.94]
>>>   [ 0.49  0.25  0.44]
>>>   [ 0.51  0.75  0.44]]
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Wyckoff Positions of Group 86 (P42/n) [origin choice 2]
>>>
>>> Multiplicity Wyckoff
>>> letter Site
>>> symmetry Coordinates8g1
>>> (x,y,z) (-x+1/2,-y+1/2,z) (-y,x+1/2,z+1/2) (y+1/2,-x,z+1/2)
>>> (-x,-y,-z) (x+1/2,y+1/2,-z) (y,-x+1/2,-z+1/2) (-y+1/2,x,-z+1/2)
>>>
>>> _______________________________________________
>>> ase-users mailing list
>>> ase-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>
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