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[Jmol-developers] [ jmol-Bugs-3134903 ] Vibrations display with unit cell broken in 12.x series
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From: SourceForge.net <no...@so...> - 2010-12-11 20:35:23
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Bugs item #3134903, was opened at 2010-12-11 04:24 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3134903&group_id=23629 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: Application Group: None Status: Closed Resolution: Fixed Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Bob Hanson (hansonr) Summary: Vibrations display with unit cell broken in 12.x series Initial Comment: The functionality for loading an extended xyz file with vibrational modes with the addition of unit cell parameters used to work well in the 11.x series. In 12.0.24 and 12.1.25 it is broken. How to reproduce: 1. Unpack the attached testcase 2. Load with "jmol -s Si2-k222-ai-300.spt" 3.Click "Right arrow" button or use menu to display any of modes 2-n. Expected result: The atom positions do not change between the different modes Actual result: Atom co-ordinates jump outside unit cell for any but lowest mode ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2010-12-11 14:35 Message: Glad to see this is useful to you. I think it's one of the most interesting capabilities of Jmol -- to load XYZ coordinates with added unit cells and symmetry operators. Thanks for pointing this out. The problem was that after the first model, atom coordinates were not being converted to fractional coordinates for unit-cell processing. Next release of Jmol 12.0 will fix this; 12.1.26 version can be downloaded at http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2010-12-11 14:20 Message: 12.1.26 also 12.0.25 # bug fix: applying unit cell in LOAD command to XYZ file containing multiple models # does not convert later model coordinates to fractional ones. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3134903&group_id=23629 |