[Molecuilder-devel] [SCM] MoleCuilder branch Cleanup_old_code created. v1.4.7-13-g5a9f4c1

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The branch, Cleanup_old_code has been created
        at  5a9f4c1e1caa72f88ad756fdaa11851f54a9426b (commit)

- Log -----------------------------------------------------------------
commit 5a9f4c1e1caa72f88ad756fdaa11851f54a9426b
Author: Frederik Heber <heber at 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 at ins.uni-bonn.de>
Date:   Sun Sep 7 18:50:10 2014 +0200

    Removed PrepareClustersInWater().

commit aa55d00dbcc8c34ecf6c22c2d29232d84d0cc262
Author: Frederik Heber <heber at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at ins.uni-bonn.de>
Date:   Sun Aug 17 12:10:53 2014 +0200

    FIX: molecule::Translate() uses AtomSet directly.

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