[Wien] 'x symmetry' issue

[Gavin Abo]

Seems like it could be related to numerical precision.  Taking the 
test2.struct that you sent, I also see the "2 missing" with WIEN2k 24.1 
for Y=0.66666666 for ATOM 74 and 98, but it seems to go away 
if Y=0.66666667 is used:

username at computername:~/wiendata/test2$ grep "ATOM  74" test2.struct
ATOM  74: X=0.33333333 Y=0.66666666 Z=0.70000000
username at computername:~/wiendata/test2$ grep "ATOM  98" test2.struct
ATOM  98: X=0.33333333 Y=0.66666666 Z=0.50000000
username at computername:~/wiendata/test2$ x symmetry
  SPACE GROUP DOES NOT CONTAIN INVERSION
STOP 2 missing
0.141u 0.011s 0:00.15 100.0%    0+0k 0+664io 0pf+0w

username at computername:~/wiendata/test2$ gedit test2.struct
username at computername:~/wiendata/test2$ grep "ATOM  74" test2.struct
ATOM  74: X=0.33333333 Y=0.66666667 Z=0.70000000
username at computername:~/wiendata/test2$ grep "ATOM  98" test2.struct
ATOM  98: X=0.33333333 Y=0.66666667 Z=0.50000000
username at computername:~/wiendata/test2$ x symmetry
  SPACE GROUP DOES NOT CONTAIN INVERSION
0.190u 0.010s 0:00.20 100.0%    0+0k 0+728io 0pf+0w

Kind Regards,

Gavin
WIEN2k user

On 5/29/2026 2:57 AM, Stefaan Cottenier via Wien wrote:
>
> (I'm re-sending this message, as the attached struct file in my 
> previous post was too large. Now it's gzipped and smaller)
>
>
> Dear WIEN2k developers,
>
> I ran into an issue that is probably a communication problem between 
> sgroup and symmetry. The attached struct file is a large supercell (Ag 
> substitutional impurity in hcp-Zn), that has been created by sgroup as 
> space group P-6 with 102 inequivalent positions.
>
> When running 'x symmetry' in a folder that contains only this struct 
> file, it fails for the 18^th  inequivalent position (Zn17):
>
> ATOM  18: X=0.33333333 Y=0.66666666 Z=0.10000000
>           MULT= 2          ISPLIT= 8
>       18: X=0.33333333 Y=0.66666666 Z=0.90000000
> Zn17       NPT=  781  R0=0.00005000 RMT=    2.3700   Z: 30.0
> LOCAL ROT MATRIX:    1.0000000 0.0000000 0.0000000
>                      0.0000000 1.0000000 0.0000000
>                      0.0000000 0.0000000 1.0000000
>
> The last lines of case.outputs read:
>
>  ATOM:          18
> Zn17       operation #  1     1
> Zn17       operation # 22     3 || -z
>   pointgroup is 2 (neg. iatnr!!)
>   axes should be: 2 || z
>
> Both case.struct_st and case.in2_sy (that are produced by 'x 
> symmetry') are truncated after the 17^th  inequivalent position. The 
> screen output is:
>
>  SPACE GROUP DOES NOT CONTAIN INVERSION
> 2 missing
> 0.010u 0.003s 0:00.01 100.0%    0+0k 0+0io 0pf+0w
>
> It looks like symmetry finds a point group "2", and does not recognize 
> that one.
>
> Not sure whether the problem is in sgroup, in symmetry, or in the way 
> how they communicate to each other.
>
> This was done with version 24.1. Any suggestion how to fix this?
>
> Best regards,
> Stefaan
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