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

[Musil Félix]

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)<http://www.cryst.ehu.es/cgi-bin/cryst/programs/find_comp_op?ita=86&xc=x&yc=y&zc=z&orgpos=x,y,z&standard=1>      (-x+1/2,-y+1/2,z)<http://www.cryst.ehu.es/cgi-bin/cryst/programs/find_comp_op?ita=86&xc=-xpp1/2&yc=-ypp1/2&zc=z&orgpos=-xpp1/2,-ypp1/2,z&standard=1>    (-y,x+1/2,z+1/2)<http://www.cryst.ehu.es/cgi-bin/cryst/programs/find_comp_op?ita=86&xc=-y&yc=xpp1/2&zc=zpp1/2&orgpos=-y,xpp1/2,zpp1/2&standard=1>       (y+1/2,-x,z+1/2)<http://www.cryst.ehu.es/cgi-bin/cryst/programs/find_comp_op?ita=86&xc=ypp1/2&yc=-x&zc=zpp1/2&orgpos=ypp1/2,-x,zpp1/2&standard=1>
(-x,-y,-z)<http://www.cryst.ehu.es/cgi-bin/cryst/programs/find_comp_op?ita=86&xc=-x&yc=-y&zc=-z&orgpos=-x,-y,-z&standard=1>     (x+1/2,y+1/2,-z)<http://www.cryst.ehu.es/cgi-bin/cryst/programs/find_comp_op?ita=86&xc=xpp1/2&yc=ypp1/2&zc=-z&orgpos=xpp1/2,ypp1/2,-z&standard=1>       (y,-x+1/2,-z+1/2)<http://www.cryst.ehu.es/cgi-bin/cryst/programs/find_comp_op?ita=86&xc=y&yc=-xpp1/2&zc=-zpp1/2&orgpos=y,-xpp1/2,-zpp1/2&standard=1>    (-y+1/2,x,-z+1/2)<http://www.cryst.ehu.es/cgi-bin/cryst/programs/find_comp_op?ita=86&xc=-ypp1/2&yc=x&zc=-zpp1/2&orgpos=-ypp1/2,x,-zpp1/2&standard=1>
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