This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Cleanup_old_code has been created at 5a9f4c1e1caa72f88ad756fdaa11851f54a9426b (commit) - Log ----------------------------------------------------------------- commit 5a9f4c1e1caa72f88ad756fdaa11851f54a9426b Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Sep 7 20:27:04 2014 +0200 Removed lots of commented-out code from GLWorldView. commit 2b7375290eb8729da103864ee7aab10467ed3346 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Sep 7 18:50:10 2014 +0200 Removed PrepareClustersInWater(). commit aa55d00dbcc8c34ecf6c22c2d29232d84d0cc262 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Sep 5 20:31:09 2014 +0200 Moved and renamed SuspendInWaterAction from Molecule.. to FillAction/SuspendInMoleculeAction. - copied code from PrepareClustersInWater() and FillRegularGridAction as a start, not working yet. - TESTFIX: Removed -u from regression tests InvalidCommands as new SuspendInMoleculeAction no longer has any values without default values. commit 2528d8462c54c9cdfb2d41b92bd6e34d9fd0c364 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Sep 1 17:57:23 2014 +0200 Removed FillBoxWithMolecule(), FillVoidWithMolecule, and helper functions. - these are no longer needed as Actions have been removed. commit 16c7dd3fc6c66022b4b13c912de169a1f812196c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Sep 1 17:54:30 2014 +0200 Removed FillVoidWithMolecule and FillWithMolecule actions. - these can be replaced by FillRegularGrid/FillVolume and FillSurface. - TESTFIX: DipoleCorrelation used fill-void, replaced by fill-regular-grid. commit df9f200764a5636d8eb51224f34c27dbd7463b9a Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Sep 3 21:11:14 2014 +0200 Refactored FillSurfaceAction to also use FillerPreparators. - added ShapeSurfaceFillerPreparator for preparing the filler. - added new SurfaceRandomInserter for randomly translating filled-in molecule on shape's surface (no rotational randomness as RandomInserter cannot be forced to the alignment axis). - TESTFIX: renamed Filling regression folder SphericalSurface -> FillSurface. - TESTS: added FillSurface filling regression tests for every present shape, we let everywhere and nowhere fail hard in performCall(), as this works also with disable-debug. commit 6801f4f3b7ed127fa9a9c8afe64f82d34df963d2 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Sep 3 20:00:26 2014 +0200 Added FillVolumeAction for filling a Shape's volume. - added ShapeFillerPreparator for preparing the volume filler. - FIX: MeshAdaptor should include Mesh.hpp. - added regression tests for FillVolume for all present shapes. - all but cylinder fail because of missing implementation, are marked as XFAIL for the moment, except everywhere and nowhere of FillVolume which say they fail explicitly. (this is not an implementation problem, for these shapes filling makes no sense.) We explicitly check for the currently failing shape types and let the Action fail (cause this works also in disable-debug). commit 36f45c7566bcbd1eab7647b44689588ab0fb839c Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Thu Sep 4 17:30:59 2014 +0200 FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in Filling/. commit cae61447a8c102b09ec82b970c3991c54f311fb5 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Tue Sep 2 17:06:31 2014 +0200 Extracted filler preparing functionality from FillRegularGridAction. - initialization functions placed into BaseFillerPreparator and derived BoxFillerPreparator. - slimmed down FillRegularGridAction. - DOCU: Extended documentation on new FillerPreparators. commit a090e3bbbb29271069f6efbe5ae41f0b9d0dcd57 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Fri Aug 15 14:46:54 2014 +0200 FIX: FillRegularGridAction requires filler molecule at origin. - FillRegularGridAction uses CenterEdge as does FillRegularSurface. - TESTFIX: coordinates shifted by z=0.504 because filler water molecule was not centered at origin before (and not fully inside positive octant either). commit 833b155e089160225200039831a7742be7bb1a16 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Mon Sep 1 17:54:02 2014 +0200 FIX: Changes to function signatures in molecule_geometry. - no more returning allocated pointer (Vector *) - no more Pointers as parameters. - removed functions that are only convenience and have nothing to do with the molecule. - changes elsewhere due to signature changes. commit 2d701e7056fe4b1af51c7f20e51cc77ee82ff91b Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Wed Aug 20 14:36:11 2014 +0200 FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), CenterPeriodic(), and CenterAtVector(). commit 40bb9e2215e41bb1d3b215cb9b5ae55b04153352 Author: Frederik Heber <heber@ins.uni-bonn.de> Date: Sun Aug 17 12:10:53 2014 +0200 FIX: molecule::Translate() uses AtomSet directly. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder