Re: [cctbxbb] Problems with conversion from conventional to primitive cell

25 Nov 2005


      Thanks for your script. I am doing this in C++. I can't find a xray::structure 
class in the C++ documentation. Does this only exist in Python ?
Nevertheless, I run your script in Python and the result is somewhat different 
from what I get, but I still think it is wrong. If I create and visualize a 
supercell from the coordinates given by the script (e. g., with gdis) I no 
longer see the hexagonal arrangement of the atoms typical for the 
conventional cell. Since the conversion from conventional to primitive cell 
should only redefine the cell but not the atom positions (in Cartesian 
coordinates) I believe the output is incorrect.

Best Regards,
Jörg-Rüdiger Hill
...
--- J?rg-R?diger Hill  wrote:
...
Dear All,
I am trying to convert from a conventional cell to a primitive cell using
cctbx, but I am having some problems.
Are you doing this in C++ or in Python?
...
What I do is the following:
1) I construct a spaceGroup object using the space group symbol
2) I retrieve the change of basis operator using z2p_op() from the space
   group object
3) I apply this operator to the conventional cell
4) I take a list of symmetry unique atoms and apply the operator to their
  fractional coordinates
At this point I have a primitive cell which agrees exactly with what I get
from other codes.
Note that there are ambiguities in the choice of the change-of-basis operator
to the primitive cell. You may get different results from different programs,
which are all correct. It is a coincidence if you get the same result.
...
The problem comes when I am trying to construct all atoms
from the symmetry unique ones. I do this by the following procedure:
5) I take the space group object and call its change_basis() method with
   the z2p_op() operator
6) I loop over all order_z() symmetry operations in the space group
applying the operation to the fractional coordinates making sure that I
don't create two atoms at the same position
You could use the site_symmetry and sym_equiv_sites classes to deal with the
special positions.
...
The whole procedure works well, e. g., for cubic crystals. However, if I
take a hexagonal crystal (e. g., Cr2O3, R -3 c) the crystal build by steps
5 and 6 above is not correct. In this case the conventional cell has a=b !=
c,
alpha=beta=90, and gamma=120, but the primitive cell has a=b=c and
alpha=beta=gamma.
That's what I'd expect.
...
I have tried to add ":R" to the space group symbol and
constructing a new spaceGroup object in step 5 above, but that does not
make any difference. What do I have to do to build the crystal in this case
or what is wrong with my procedure ?
Attached is a copy of the new cctbx/cctbx/examples/cr2o3_primitive_cell.py
script (in the CVS already; will also be in the next set of auto-build
bundles). Could you please compare your results to the output of this script?
The script shows a high-level implementation. I could add a lower-level
equivalent that is more in line with what you'd do in C++. Let me know if
this is what you need.
Cheers,
       Ralf
from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex
def demo():
 """
 Result of ICSD query:
   N * -Cr2O3-[R3-CH] Baster, M.;Bouree, F.;Kowalska, A.;Latacz, Z(2000)
   C 4.961950 4.961950 13.597400 90.000000 90.000000 120.000000
   S GRUP R -3 C
   A Cr1    0.000000 0.000000 0.347570 0.000000
   A O1    0.305830 0.000000 0.250000
 """
 crystal_symmetry = crystal.symmetry(
   unit_cell="4.961950 4.961950 13.597400 90.000000 90.000000 120.000000",
   space_group_symbol="R -3 C")
 scatterers = flex.xray_scatterer()
 scatterers.append(xray.scatterer(
   label="Cr1", site=(0.000000,0.000000,0.347570)))
 scatterers.append(xray.scatterer(
   label="O1", site=(0.305830,0.000000,0.250000)))
 icsd_structure = xray.structure(
   crystal_symmetry=crystal_symmetry,
   scatterers=scatterers)
 icsd_structure.show_summary().show_scatterers()
 print
 icsd_structure.show_distances(distance_cutoff=2.5)
 print
 primitive_structure = icsd_structure.primitive_setting()
 primitive_structure.show_summary().show_scatterers()
 print
 p1_structure = primitive_structure.expand_to_p1()
 p1_structure.show_summary().show_scatterers()
 print
 print "OK"
if (__name__ == "__main__"):
 demo()
-- 
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