Patches item #3452482, was opened at 2011-12-06 07:22 Message generated for change (Tracker Item Submitted) made by coudert You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428742&aid=3452482&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: François-Xavier Coudert (coudert) Assigned to: Nobody/Anonymous (nobody) Summary: Fix fillUC Initial Comment: I created this patch to fix bug id #3452445 (https://sourceforge.net/tracker/?func=detail&aid=3452445&group_id=40728&atid=428740). In fillUC, images of an atom are created by applying symmetry operations, and then checked so that no too images end up too close (otherwise, one of them is a duplicate of the other). Except that when calculating distances, periodic boundary conditions were not taken into account. Thus, a point at coordinates (0,0,0) and a point at coordinates (1,0,0) would both be kept. This was apparently deemed not an issue, because atoms are wrapped inside the unit cell before distance calculation, but this doesn't tolerate rounding errors. We could thus have a point at (0,0,0) and a point at (0.99999, 0, 0), and both would be kept. Tthe patch uses a small areDuplicateAtoms() function which does the job. I also took the liberty of remove the previously used transformedFractionalCoordinate2() function, which had a comment at the top saying to should be replaced by an API call. It seems to me that pUC->WrapFractionalCoordinate() does exactly that, so I used it instead. Thanks for considering the patch! ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428742&aid=3452482&group_id=40728 ------------------------------------------------------------------------------ Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
