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

[Jens Jørgen Mortensen]

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

> 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)
>>
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