On Wednesday 12 of February 2014 17:43:25 Atsushi Togo wrote: > Yes. I think there is no ambiguity. But we have to be careful about > that it's still arbitrary with respect to lattice translation. So for > this, we employ some convention, e.g., translation part (t) of a > symmetry operation is restricted 0 <= t < 1. > The decoding of Hall symbol is not difficult. You can do it following > http://cci.lbl.gov/sginfo/hall_symbols.html . > > I still have not yet understood what you want to do. But there may be > other ambiguities, or say conventions. For example, there are reverse > and observe settings of hexagonal rhombohedral (hR), which gives 60 > degrees difference along c-axis, but gives, I guess, the same set of > symmetry operations for a space group type. So spg_refine_cell always > returns primitive rhombohedral (pR). > > Togo
Thanks for clarification. I want to do two things. First, learn more about this topic, and I am very grateful for all your comments. Second, consider that Avogadro uses spglib to do spacegroup perception, cell refinement and similar. But it uses OpenBabel to do other things like filling the unit cell. Spglib cannot be used for this simply because it cannot work with an incomplete unit cell. Also, OpenBabel's spacegroup and unit cell functionality is accessible from anywhere in Avogadro because the data is stored in the OpenBabel's molecule structure. Therefore, it would be convenient if spglib and OpenBabel used compatible conventions. To clarify further, I will summarize the problem. I assumed (correctly, as you stated) that spg_refine_cell puts the cell into spglib's "native" setting. I then compared the symmetry operations in the spglib database to those in OpenBabel's database. I found that they were the same in almost all cases, except for groups indexed by Hall symbols B -2bc, R 3 -2", F 4d 2 3 and P 4 2 3 -1n". Which means that for these four groups, when we use spg_refine_cell, we obtain a cell which is not compatible with OpenBabel. What is worse, I tried taking a cubic cell, choosing F 4d 2 3, placing a single atom and calling Fill Unit Cell, which uses OpenBabel. After that, Perceive Spacegroup, which uses Spglib, detected F -4c 2 3. When I repeated this procedure later, it detected -F 4c 2 3. This kind of thing did not happen with -P 3*. I am not sure what to do about this. Do spglib or OpenBabel have incorrect data? Is it simply a different convention, and if so, what to do about it? Should we try to use only one of these libraries? Regards Jure ------------------------------------------------------------------------------ Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk _______________________________________________ Avogadro-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-devel
