[ase-users] Bug in spacegroup 154

[Jesper Friis]

I have not checked it up, but guess that it is a bug that should be fixed.

Regards
/Jesper

From: Jens Jørgen Mortensen [mailto:jensj at fysik.dtu.dk]
Sent: Friday, February 19, 2016 12:52
To: Jesper Friis <jesper.friis at sintef.no>; Maxime van den Bossche <maxime.vandenbossche at chalmers.se>; ase-users at listserv.fysik.dtu.dk
Subject: Re: [ase-users] Bug in spacegroup 154

On 02/19/2016 12:04 PM, Jesper Friis wrote:

The crystallographic information in this file comes from the spgra.dat file distributed with VESTA - a close source software. To avoid copyright issues, I invented my own little more human readable format when creating spacegroup.dat. I think this should be ok, since the crystallographic data is commonly knowledge and published in International Tables.

That's all fine :-)  But what do you think about the bug in spacegroup 154?

Jens Jørgen


Regards
/Jesper


From: Jens Jørgen Mortensen [mailto:jensj at fysik.dtu.dk]
Sent: Friday, February 19, 2016 10:16
To: Maxime van den Bossche <maxime.vandenbossche at chalmers.se><mailto:maxime.vandenbossche at chalmers.se>; ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>; Jesper Friis <jesper.friis at sintef.no><mailto:jesper.friis at sintef.no>
Subject: Re: [ase-users] Bug in spacegroup 154

On 02/18/2016 10:53 AM, Maxime van den Bossche wrote:


Hello!

I came across a bug when trying to read in the following
quartz SiO2 structure (in CIF format), which belongs
to the P 32 2 1 spacegroup (number 154).

http://rruff.geo.arizona.edu/AMS/CIF_text_files/00859_cif.txt

The number of atoms, as well as atomic positions in the resulting
Atoms object are incorrect, and it seems to be due to errors in
the way the spacegroup's symmetry operations are defined.

The last three lines in the "symmetry operations" block
of the entry 154 in /ase/lattice/spacegroup/spacegroup.dat
are as follows:

    0  1  0     1  0  0     0  0 -1    0.0000000000  0.0000000000  0.0000000000
    1 -1  0     0 -1  0     0  0 -1    0.0000000000  0.0000000000  0.3333333333
   -1  0  0    -1  1  0     0  0 -1    0.0000000000  0.0000000000  0.6666666667

but the symmetry translations should be corrected to:

    0  1  0     1  0  0     0  0 -1    0.0000000000  0.0000000000  0.6666666667
    1 -1  0     0 -1  0     0  0 -1    0.0000000000  0.0000000000  0.0000000000
   -1  0  0    -1  1  0     0  0 -1    0.0000000000  0.0000000000  0.3333333333

After this fix, I got the quartz structure I expected.

Thanks!  Anyone know where the spacegroup.dat file in ASE comes from?

Jens Jørgen



Regards,
Maxime





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