[cctbxbb] Bug in structure.expand_to_p1?

[Ralf Grosse-Kunstleve]

Hi Jan,

ref_structure = quartz_structure.expand_to_p1(
  append_number_to_labels=True).sites_mod_positive()

should do the trick. There is also .sites_mod_short().

Ralf


2011/6/20 Jan Marten Simons <marten at xtal.rwth-aachen.de>:
> Hi,
>
> I'm quite puzzled at the moment.
>
> using this code:
>
> if __name__ == '__main__':
>  quartz_structure = xray.structure(
>    special_position_settings=crystal.special_position_settings(
>      crystal_symmetry=crystal.symmetry(
>        unit_cell=(5.01,5.01,5.47,90,90,120),
>        space_group_symbol="P6222")),
>    scatterers=flex.xray_scatterer([
>      xray.scatterer(
>        label="Si",
>        site=(1/2.,1/2.,1/3.),
>        u=0.2),
>      xray.scatterer(
>        label="O",
>        site=(0.197,-0.197,0.83333),
>        u=0)]))
>
>  ref_structure = quartz_structure.expand_to_p1(
>           append_number_to_labels=True)
>
>  print(ref_structure.as_py_code())
>
>
> I get this result:
>
> xray.structure(
>  crystal_symmetry=crystal.symmetry(
>    unit_cell=(5.01, 5.01, 5.47, 90, 90, 120),
>    space_group_symbol="P 1"),
>  scatterers=flex.xray_scatterer([
>    xray.scatterer( #0
>      label="Si_0",
>      site=(0.500000, 0.500000, 0.333333),
>      u=0.200000),
>    xray.scatterer( #1
>      label="Si_1",
>      site=(0.000000, 0.500000, 0.666667),
>      u=0.200000),
>    xray.scatterer( #2
>      label="Si_2",
>      site=(0.500000, 0.000000, 1.000000),
>      u=0.200000),
>    xray.scatterer( #3
>      label="O_0",
>      site=(0.197000, -0.197000, 0.833333),
>      u=0.000000),
>    xray.scatterer( #4
>      label="O_1",
>      site=(0.394000, 0.197000, 1.166667),
>      u=0.000000),
>    xray.scatterer( #5
>      label="O_2",
>      site=(-0.197000, -0.394000, 1.500000),
>      u=0.000000),
>    xray.scatterer( #6
>      label="O_3",
>      site=(0.197000, 0.394000, 1.500000),
>      u=0.000000),
>    xray.scatterer( #7
>      label="O_4",
>      site=(-0.394000, -0.197000, 1.166667),
>      u=0.000000),
>    xray.scatterer( #8
>      label="O_5",
>      site=(-0.197000, 0.197000, 0.833333),
>      u=0.000000)]))
>
>
> It bothers me that there are x,y,z not in [0, 1[. Shouldn't the newly expanded
> cell only contain atoms within the unit cell? I realize, that the quarz
> structure (from the sample code from the website) also violates this with Oy
> beeing negative, but still I think expand_to_p1 should return a regular
> structure.
>
> Also is there a method already implemented to change a structure from a non-
> conventional description into a conventional one (with all atoms within its
> unit cell)?
>
> With regards,
>
>  Dipl. Phys.
>  Jan M. Simons
>
> Institute of Crystallography
> RWTH Aachen University
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