Problems with conversion from conventional to primitive cell
Dear All, I am trying to convert from a conventional cell to a primitive cell using cctbx, but I am having some problems. 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. 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 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. 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 ? Best Regards, Jörg-Rüdiger Hill -- ------------------------------------------------------------------------------- Dr. Jörg-Rüdiger Hill Tel.: +33 1 53 43 51 05 Director R & D Tel. (direct): +49 89 613 05 700 Scienomics Fax: +33 1 53 43 92 92 17 Square Edouard VII E-Mail: [email protected] 75009 Paris, France Web: http://www.scienomics.com/ -------------------------------------------------------------------------------
--- Jörg-Rüdiger Hill
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() __________________________________ Yahoo! Music Unlimited Access over 1 million songs. Try it free. http://music.yahoo.com/unlimited/
participants (2)
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Jörg-Rüdiger Hill -
Ralf W. Grosse-Kunstleve