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November 2005

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Re: [cctbxbb] Problems with conversion from conventional to primitive cell
by Jörg-Rüdiger Hill 25 Nov '05

25 Nov '05

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 <Joerg-Ruediger.Hill(a)scienomics.com> 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() -- ------------------------------------------------------------------------------- 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: Joerg-Ruediger.Hill(a)scienomics.com 75009 Paris, France Web: http://www.scienomics.com/ -------------------------------------------------------------------------------

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Problems with conversion from conventional to primitive cell
by Jörg-Rüdiger Hill 24 Nov '05

24 Nov '05

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: Joerg-Ruediger.Hill(a)scienomics.com 75009 Paris, France Web: http://www.scienomics.com/ -------------------------------------------------------------------------------

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