Dear avogadro developers, I noticed that some symmetry code in the crystallography extension relies on spglib and some relies on openbabel. This is problematic because it turns out that openbabel fails to honor the spacegroup setting.
The material I work with has spacegroup 148 and rhombohedral cell. When I use the Perceive Spacegroup action which uses spglib, it is perceived correctly. However, the Fill Unit Cell action which uses openbabel to generate symmetry operations gets it wrong. It generates 18 operations, which, if I'm reading the tables correctly, corresponds to the hexagonal setting of spacegroup 148, whereas the rhombohedral setting has 6 operations. I wrote a short python script using pyspglib and it seems to work. I propose to move more code in the cyrstallography extension to spglib. I'm willing to do the work (at least some of it), starting with the Fill Unit Cell action. My question is, how to go about this, gerrit-wise? This is the first time I'm dealing with gerrit. There seem to be changes to AvoSpg yet to be merged, e.g. in the QuantumEspressoInput branch. Should my branch depend on that one or should I base it on master? Also, I had to add an include path for Eigen to fix building, do I have to make a separate branch for that single commit? Is there an easy way to check if an unmerged branch fixes the same problem? Best regards Jure Varlec ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk _______________________________________________ Avogadro-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-devel
