From git at ins.uni-bonn.de  Fri Oct  3 19:24:25 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri,  3 Oct 2014 19:24:25 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconexEnvelope updated. v1.4.8-40-g572bcde
Message-ID: <20141003172426.3CEFF10000FA@jupiter.ins.uni-bonn.de>

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       via  a28d9dda88e83aa29a4befa44682863f6140e762 (commit)
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- Log -----------------------------------------------------------------
commit 572bcde90dcbf97523476b140d8fae6cafd42d8f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 19:19:38 2014 +0200

    FIX: PickFarthestofTwoBaselines() additionally checks whether baselines "overlap".
    
    - we do not check whether the polygon consisting of the four points defined by
      the two baslines is actually "convex": Convex is not such a good criterion as
      the two triangles (with respect to the baseline) may form a bent structure
      such that the flattended representation of th polygon is not convex while
      the actual angles are all less than pi. Hence, we check whether the closest
      point with respect to one base line on the other is actually still between
      the two endpoints of the baseline. If not, we must not flip the baseline, as
      we then invalidate the tesselation.

commit a28d9dda88e83aa29a4befa44682863f6140e762
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 12:29:08 2014 +0200

    tempcommit: Merge with 39268ec

commit 0b5b00d8330e6747fd1aa47a34e3fa195d11909b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 12:27:57 2014 +0200

    FIX: Filling of non-convex polygon with only minimal angles did not work.
    
    - when removing points from non-convex boundary and we encounter non-convex
      polygons, we must pick smallest angles but close to the non-convex site!

commit e12e836bd699a85e0608283fc6e5577ca1d321f4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:43:03 2014 +0200

    FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly.
    
    - FIX: Very last node was removed twice due to StartNode = EndNode setting.

commit 39268ec511e8f9825248457988fea5b54642f081
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:42:18 2014 +0200

    tempcommit: fixed assert in RemovePointFromTesselatedSurface(). Merge with ...

commit a66f0844410a4b403830a4d74ff5e673a38e9044
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:40:06 2014 +0200

    FIX: Last line in RemovePointFromTesselatedSurface() added falsely.
    
    - AddTesselationLine() now returns whether new or present line was used.
    - FIX: Last inner line in closed polygon has been added by one but last
      triangle already, we added it twice.

commit 1c9d0fab2f0004443f9ff5022852da75abfd7fa6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:39:34 2014 +0200

    tempcommit: Further reduced verbosity noise in tesselation.

commit fb4449480aeaa9e8fe00df8d49cac94aba8332bc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:38:16 2014 +0200

    tempcommit: Reduced verbosity noise from Line::getIntersection().

commit 4fe57a515a5f9818403c090a625a103fca41799b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:40:10 2014 +0200

    MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d.

commit 6c7ec20731376548eb4a33bbfc9da8bc7b31eed3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:35:04 2014 +0200

    FIX: Added Boost::MultiIndexContainer check for MemDebug.
    
    - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation
      with Ubuntu 14.04.

-----------------------------------------------------------------------

Summary of changes:
 LinearAlgebra/src/LinearAlgebra/Line.cpp           |   22 +++----
 configure.ac                                       |    1 +
 m4/boost.m4                                        |    6 ++
 src/Potentials/Specifics/ConstantPotential.cpp     |    2 +-
 .../Specifics/FourBodyPotential_Improper.cpp       |    2 +-
 .../Specifics/FourBodyPotential_Torsion.cpp        |    2 +-
 .../Specifics/ManyBodyPotential_Tersoff.cpp        |    2 +-
 .../Specifics/PairPotential_Harmonic.cpp           |    2 +-
 .../Specifics/PairPotential_LennardJones.cpp       |    2 +-
 src/Potentials/Specifics/PairPotential_Morse.cpp   |    2 +-
 .../Specifics/ThreeBodyPotential_Angle.cpp         |    2 +-
 src/Tesselation/BoundaryLineSet.cpp                |    3 +-
 src/Tesselation/BoundaryPointSet.cpp               |    2 +-
 src/Tesselation/BoundaryTriangleSet.cpp            |    4 +-
 src/Tesselation/tesselation.cpp                    |   69 +++++++++++++++----
 src/Tesselation/tesselation.hpp                    |    2 +-
 src/Tesselation/tesselationhelpers.cpp             |    4 +-
 17 files changed, 87 insertions(+), 42 deletions(-)


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From git at ins.uni-bonn.de  Fri Oct  3 22:09:46 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri,  3 Oct 2014 22:09:46 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconexEnvelope updated. v1.4.8-41-g93201c4
Message-ID: <20141003200946.81B2610000FA@jupiter.ins.uni-bonn.de>

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, Fix_ConvexizeNonconexEnvelope has been updated
       via  93201c49bbfdae2c16403db0fc28d540c671e2d2 (commit)
      from  572bcde90dcbf97523476b140d8fae6cafd42d8f (commit)

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- Log -----------------------------------------------------------------
commit 93201c49bbfdae2c16403db0fc28d540c671e2d2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 22:09:03 2014 +0200

    tempcommit: Fixing regression test for new sphere param. Merge with ...

-----------------------------------------------------------------------

Summary of changes:
 .../testsuite-tesselation-convex-envelope.at       |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)


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From git at ins.uni-bonn.de  Thu Oct  9 20:35:41 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu,  9 Oct 2014 20:35:41 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconexEnvelope deleted. v1.4.8-41-g93201c4
Message-ID: <20141009183541.1D86810000FA@jupiter.ins.uni-bonn.de>

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The branch, Fix_ConvexizeNonconexEnvelope has been deleted
       was  93201c49bbfdae2c16403db0fc28d540c671e2d2

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93201c49bbfdae2c16403db0fc28d540c671e2d2 tempcommit: Fixing regression test for new sphere param. Merge with ...
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From git at ins.uni-bonn.de  Thu Oct  9 20:36:06 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu,  9 Oct 2014 20:36:06 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconvexEnvelope created. v1.4.8-72-g8e74197
Message-ID: <20141009183606.3511910000FA@jupiter.ins.uni-bonn.de>

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, Fix_ConvexizeNonconvexEnvelope has been created
        at  8e74197f1d553ae70622aa7e43efb475e1184738 (commit)

- Log -----------------------------------------------------------------
commit 8e74197f1d553ae70622aa7e43efb475e1184738
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:00:11 2014 +0200

    TESTS: Extended Tesselations tests to convex case.
    
    - moved all present tests to NonConvex folder, added same set but including
      amylose in Convex folder.

commit a7fae96d75cd79c83b97785ed7821b2b69a561f1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:45:56 2014 +0200

    TESTFIX: Regression test Tesselation/BigConvex is now working.

commit 34b691d3b3f0482da15ed9e20312f1f6007422fb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:47:03 2014 +0200

    Convex-envelope has debug parameter DoOutputEveryStep.
    
    - this writes for each convexization step a distinct tesselation file.
    - added parameter to ConvexizeNonconvexEnvelope().

commit de289e773811c03b0c6a61bf90fb689c2c4e6600
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:31:18 2014 +0200

    FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop.
    
    - even if a triangle pair is not removed, it must still be removed from the
      degenerated list or we run into infinite loops.

commit 5047e5d52c54b426be18f9b9cd4c347cc4c63be4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:34:55 2014 +0200

    Added tcl scripts for viewing and debugging convexized surfaces.

commit 44c2ecc19d1ecb36bd9c6c70777229036b43b742
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:34:24 2014 +0200

    tempcommit: Reduced final verbosity for convexization to manageable niveau at level 1.

commit 2973e489b56c03d8c8e7798e99d0888639ced433
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:56:24 2014 +0200

    FIX: Raster3D needs header.r3d, which had been missing so far.

commit 62196cb464d5ee8f4aa632fc527018e9c293e580
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:55:44 2014 +0200

    DOCU: Added extensive explanation how convexization works.
    
    - updated userguide for convex-envelope.

commit a470656afbe5cbda1699c759e035e1981d80c7ed
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:27:36 2014 +0200

    ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface().
    
    - with this convexization of a nonconvex tesselated surface seems to be
      robustly working as we can now deal also with points with degeneracies.

commit b4c673f37d089bb07d6233a3a62e06101a7f50e6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:27:19 2014 +0200

    tempcommit: Merge with f1a7d2f144

commit 37028ce4c639cc80a1c3451414efde550532e3ad
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 09:37:06 2014 +0200

    Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface()
    
    - also added new functions
      Tesselation::RemoveFullConcavePointFromTesselatedSurface() and
      Tesselation::CheckAllConcaveInPolygon().

commit 69ef32536f0d25375af69c9b51d8f2b07dec9661
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 18:14:39 2014 +0200

    FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization.

commit f1a7d2f144b03242611c0e0916fcca57bc718315
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 15:08:11 2014 +0200

    FIX: GainMap is used to store the concavity angle, we flip most concave first.
    
    - this overrules prior flipping those that gives greatest gain in volume.

commit af8892464a53265846abe8a6e324904c954600c8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 14:46:36 2014 +0200

    FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector.
    
    - with the point to be removed we have a very good measure for a vector
      pointing inside. Before we used the average of all normal vectors.

commit 12d31c1d21fe533b7b0c6c1a33919c33c17d35ca
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:57:42 2014 +0200

    tempcommit: Smaller fixes to ConvexizeNonconvexEnvelope().
    
    - just verbosity and little stuff that does not change functionality.

commit bb9499687f8a75bb22a1be2fe45ca98517df99af
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:55:26 2014 +0200

    FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong.
    
    - replaced code by using present function for tetrahedron calculation with
      center of gravity as fourth point when going over all boundary triangles.

commit 779b8ef52c1f0f07f71790fccc8de2636efe8d1a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:38:17 2014 +0200

    tempcommit: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface().

commit a30c74cd5f81bb12d6a38a8bbafda1bf73e734b3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:28:44 2014 +0200

    DOCUFIX: Corrected formuma for general tetrahedron in docu.
    
    - also code now matches with formula to avoid further confusion, although
      the result does not change by that.

commit 6fc7b1a5ac66a0125889161df71e3df59a724f2c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:04:54 2014 +0200

    tempcommit: ConvexizeNonconvexEnvelope() rewritten.
    
    - now works for some sphere radii on amylose (e.g. 40 and 50).
    - before we calculated the average number of concave lines for the four points
      of the tetraeder and picked the minimum as flipping candidate (doing
      nothing, if its baseline was present). Also, we removed points when all
      possible triangles had the point under its plane.
      Now, we always flip the baseline (i.e. add a general tetraeder to the
      non-convex volume) for concave lines when the tetraeder does not intersect
      with present triangles. Also, the point removal if inside of surrounding
      polygon is removed.

commit 31de80f22402fe9f2c8dde82ace46d74276dc209
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 08:57:30 2014 +0200

    FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong.
    
    - before we just took the average of the normal vector of both present
      triangles as guide. Now, we check the intersection of the fourth endpoint
      on the plane of the first triangle and decide by on which side of the
      three boundary lines the intersection lies whether to flip the normal
      vectors sign for the associated (new) triangle or not.

commit d919f2562ba6866bbd4cba4319340f851f91f342
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 5 18:56:03 2014 +0200

    tempcommit: IsPointBelowSurroundingPolygon() creates all triangles as planes and checks whether point is below.

commit 3878ea9e78d59ac40c2e718906eac490fbfdd82c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 5 18:55:31 2014 +0200

    tempcommit: Just writing a single file with incrementing suffix for ConvexEnvelope.

commit 36aad107af42cfc84cfbd14510c05ecebd42a35b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 5 14:21:14 2014 +0200

    tempcommit: Further changes to onvexizeNonconvexEnvelope().
    
    - first full-concave point removal, then baseline flipping with local concavity
      constraint and no present other tetraeder sides (and full-concave priority),
      at last removal of points that are below their surrounding polygon.
    - added Tesselation::IsPointBelowSurroundingPolygon()

commit 9af4c3de2a037e9bd4ad7345b1180bd3e5e16238
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 5 14:20:00 2014 +0200

    tempcommit: Added Tesselation::isConvex(). Merge with 675ad817

commit 50483c4cd544dc029ed78f01991e2ebaf6f58406
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 5 14:19:15 2014 +0200

    tempcommit: Further verbosity reductions to BoundaryTriangleSet.

commit 675ad817bef03c062b24452a9dc3cc7e390689f7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 5 14:18:20 2014 +0200

    tempcommit: ConvexEnvelopeAction checks for convex surface in debug.

commit 69fa6c049528a4cf0d886702243f1675e7f14503
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 16:47:11 2014 +0200

    Revert "FIX: PickFarthestofTwoBaselines() additionally checks whether baselines "overlap"."
    
    This reverts commit 572bcde90dcbf97523476b140d8fae6cafd42d8f.

commit 9a9416cccdb11a9a3da43519bd40f03d04cdf4bd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 16:35:50 2014 +0200

    Reduced verbosity noise in TriangleIntersectionList.

commit 74844de90016057541c79e302dabbbcd7f46f4a2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 16:34:41 2014 +0200

    tempcommit: Rewrote ConvexizeNonconvexEnvelope
    
    - we flip all lines that are concave if they maximize local concavity for a
      single point - that we subseqeuently hope to remove.
    - we just remove at most one point and then start the whole loop again.

commit f8fd4a188c60cb600f54098d5f178a16221e0f8b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 16:33:47 2014 +0200

    tempcommit: LCList did not use SphereRadius. Merge with ...

commit c05c249562ece151dd0ac7042e7ee332c04263dc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 10:44:54 2014 +0200

    Added check whether all points remain inside surface to ConvexEnvelopeAction.

commit 81f5873ea1548ab8a7c8a018a40f470e55d27e89
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 22:09:03 2014 +0200

    tempcommit: Fixing regression test for new sphere param. Merge with ...

commit 572bcde90dcbf97523476b140d8fae6cafd42d8f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 19:19:38 2014 +0200

    FIX: PickFarthestofTwoBaselines() additionally checks whether baselines "overlap".
    
    - we do not check whether the polygon consisting of the four points defined by
      the two baslines is actually "convex": Convex is not such a good criterion as
      the two triangles (with respect to the baseline) may form a bent structure
      such that the flattended representation of th polygon is not convex while
      the actual angles are all less than pi. Hence, we check whether the closest
      point with respect to one base line on the other is actually still between
      the two endpoints of the baseline. If not, we must not flip the baseline, as
      we then invalidate the tesselation.

commit a28d9dda88e83aa29a4befa44682863f6140e762
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 12:29:08 2014 +0200

    tempcommit: Merge with 39268ec

commit 0b5b00d8330e6747fd1aa47a34e3fa195d11909b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 12:27:57 2014 +0200

    FIX: Filling of non-convex polygon with only minimal angles did not work.
    
    - when removing points from non-convex boundary and we encounter non-convex
      polygons, we must pick smallest angles but close to the non-convex site!

commit e12e836bd699a85e0608283fc6e5577ca1d321f4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:43:03 2014 +0200

    FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly.
    
    - FIX: Very last node was removed twice due to StartNode = EndNode setting.

commit 39268ec511e8f9825248457988fea5b54642f081
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:42:18 2014 +0200

    tempcommit: fixed assert in RemovePointFromTesselatedSurface(). Merge with ...

commit a66f0844410a4b403830a4d74ff5e673a38e9044
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:40:06 2014 +0200

    FIX: Last line in RemovePointFromTesselatedSurface() added falsely.
    
    - AddTesselationLine() now returns whether new or present line was used.
    - FIX: Last inner line in closed polygon has been added by one but last
      triangle already, we added it twice.

commit 1c9d0fab2f0004443f9ff5022852da75abfd7fa6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:39:34 2014 +0200

    tempcommit: Further reduced verbosity noise in tesselation.

commit fb4449480aeaa9e8fe00df8d49cac94aba8332bc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:38:16 2014 +0200

    tempcommit: Reduced verbosity noise from Line::getIntersection().

commit 4fe57a515a5f9818403c090a625a103fca41799b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:40:10 2014 +0200

    MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d.

commit 6c7ec20731376548eb4a33bbfc9da8bc7b31eed3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:35:04 2014 +0200

    FIX: Added Boost::MultiIndexContainer check for MemDebug.
    
    - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation
      with Ubuntu 14.04.

commit ab72314934e071f1c33d4d2875f9d27458fb67da
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 21:13:43 2014 +0200

    Changed verbosities in tesselation a lot to make readable.

commit 743052c22b9d7f7591cac44bd5eb2e484a5c3e42
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:20 2014 +0200

    FIX: Changed all performCriticalExit() into ASSERT() in tesselation.

commit d4f9bb3aba23969df122e85d3f5307a0398e5c3f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:03 2014 +0200

    Changed some verbosities in Tesselation code.

commit a07e7053630cf9faa4f5fc18481901cc4f79ab96
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:24:52 2014 +0200

    FIX: RemoveTesselationLine() needs to erase line from OpenLines if present.

commit 8e3d9d4f8f83fa748239e028a866abd8ab8c70d0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:23:50 2014 +0200

    FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex.

commit 10a01718c3a6190cfc9de345527be832011b1f87
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:25:23 2014 +0200

    FIX: AddTesselationLine() would onl work in initial tesselation phase.
    
    - the CandidateForTesselation instance is NULL when we convexize and this
      was not correctly processed by AddTesselationLine().

commit e13991dce439602624fbb51421d9bf3c0a816396
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:24:30 2014 +0200

    Added SphereRadius parameter to ConvexEnvelopeAction.

commit 128616612a611878bc0a942bbc2f1eecab5d0c9a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 23 18:14:18 2014 +0200

    FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.
    
    - causes segfault when notification informs about change and _lastchangeaction
      is still NULL (as the very first Action failed).
    - we now only notify when action succeeded.

commit 56eee6e652088e82274fd47b6fd2b3b70e898feb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 22 22:10:11 2014 +0200

    FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Thu Oct 16 16:44:29 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 16 Oct 2014 16:44:29 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconvexEnvelope deleted. v1.4.8-72-g8e74197
Message-ID: <20141016144429.E34DB10000FA@jupiter.ins.uni-bonn.de>

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The branch, Fix_ConvexizeNonconvexEnvelope has been deleted
       was  8e74197f1d553ae70622aa7e43efb475e1184738

-----------------------------------------------------------------------
8e74197f1d553ae70622aa7e43efb475e1184738 TESTS: Extended Tesselations tests to convex case.
-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Thu Oct 16 16:44:33 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 16 Oct 2014 16:44:33 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconvexEnvelope created. v1.4.8-53-g5cfdcf7
Message-ID: <20141016144433.77FC210000FA@jupiter.ins.uni-bonn.de>

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, Fix_ConvexizeNonconvexEnvelope has been created
        at  5cfdcf70299145cf832d0ed47f1308237b9e42d6 (commit)

- Log -----------------------------------------------------------------
commit 5cfdcf70299145cf832d0ed47f1308237b9e42d6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:00:11 2014 +0200

    TESTS: Extended Tesselations tests to convex case.
    
    - moved all present tests to NonConvex folder, added same set but including
      amylose in Convex folder.

commit d31cae77953f6678555ca8b2d0cb60b57041ba7e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 16 16:34:13 2014 +0200

    TESTFIX: Regression test Tesselation/BigConvex is now working.

commit f1a18e2659c017087b33aed876cdb5203495e0ea
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:47:03 2014 +0200

    Convex-envelope has debug parameter DoOutputEveryStep.
    
    - this writes for each convexization step a distinct tesselation file.
    - added parameter to ConvexizeNonconvexEnvelope().

commit 606c3ea8ad09230c97cbe3f8a4a8e94094d14427
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:24:30 2014 +0200

    Added SphereRadius parameter to ConvexEnvelopeAction.

commit 565ae0a560723f992a92b32ce0ff794b1207a009
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:34:55 2014 +0200

    Added tcl scripts for viewing and debugging convexized surfaces.

commit 70fbbf5b5f4e695fb5e9b24e83507fb0927bec70
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:55:44 2014 +0200

    DOCU: Added extensive explanation how convexization works.
    
    - updated userguide for convex-envelope.

commit 0e75b00e5e0ad230f928dcf40a31545a477d5bbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 10:44:54 2014 +0200

    Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction.

commit 14fafa978ad8f073e3f6bfc71896bed224bc275c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:27:36 2014 +0200

    ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface().
    
    - with this convexization of a nonconvex tesselated surface seems to be
      robustly working as we can now deal also with points with degeneracies.

commit 20c18051dace481e30b64e5ba906d722ba28b834
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 18:14:39 2014 +0200

    FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization.

commit 6f7356114f3d1165f43fd8cc7d1f5a5635ae4ce1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 15:08:11 2014 +0200

    FIX: GainMap is used to store the concavity angle, we flip now always most concave.
    
    - this overrules prior flipping those that gives greatest gain in volume.

commit 4b54f73aba95c7e3039546e82c9a1df393327308
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 16:34:41 2014 +0200

    Rewrote ConvexizeNonconvexEnvelope().
    
    - now works for some sphere radii on amylose (e.g. 40 and 50).
    - we first remove all points that are only attached to concave lines.
    - also, we always flip the baseline (i.e. add a general tetraeder to the
      non-convex volume) for concave lines when the tetraeder does not intersect
      with present triangles.

commit 8d778fa588719f6983eed36294b74582c67f6184
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:31:18 2014 +0200

    FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop.
    
    - even if a triangle pair is not removed, it must still be removed from the
      degenerated list or we run into infinite loops.

commit 3c6b9d0e0d1f7572ed80073caafed6d5eeedf2e6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 09:37:06 2014 +0200

    Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface()
    
    - also added new functions
      Tesselation::RemoveFullConcavePointFromTesselatedSurface() and
      Tesselation::CheckAllConcaveInPolygon().

commit 633576c77a8f88ab8b74845376e2ab706fdea53a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:38:17 2014 +0200

    FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface().

commit ee886b36fc89715a5380053cc9ef0ec633424871
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 14:46:36 2014 +0200

    FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector.
    
    - with the point to be removed we have a very good measure for a vector
      pointing inside. Before we used the average of all normal vectors.

commit c1c8bc20ece846bb15d0be96187f99a80646eafb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:55:26 2014 +0200

    FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong.
    
    - replaced code by using present function for tetrahedron calculation with
      center of gravity as fourth point when going over all boundary triangles.
    - TESTFIX: volume change in convex regression test.

commit e6b793d18f5032e7033b3bf8de0eef2da63cb33c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 08:57:30 2014 +0200

    FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong.
    
    - before we just took the average of the normal vector of both present
      triangles as guide. Now, we check the intersection of the fourth endpoint
      on the plane of the first triangle and decide by on which side of the
      three boundary lines the intersection lies whether to flip the normal
      vectors sign for the associated (new) triangle or not.

commit 97d98600955169f39319e9ee925d91b2bf88c7d5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 14 18:37:03 2014 +0200

    Added Tesselation::IsPointBelowSurroundingPolygon().
    
    - IsPointBelowSurroundingPolygon() creates all triangles as planes and checks
      whether point is below.

commit 5a4d8f9201f96f0199f6c5855c9cf149b1ef97cd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 12:27:57 2014 +0200

    FIX: Filling of non-convex polygon with only minimal angles did not work.
    
    - when removing points from non-convex boundary and we encounter non-convex
      polygons, we must pick smallest angles but close to the non-convex site!

commit aad7aa64cf795a5b4af656e636efc9d343590816
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:43:03 2014 +0200

    FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly.
    
    - FIX: Very last node was removed twice due to StartNode = EndNode setting.

commit 3c460f1ba60995d3104ee413bf980ed1dc7a1ad9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:38:16 2014 +0200

    FIX: Reduced verbosity noise from Line::getIntersection().
    
    - removed use of info and toned down verbosity levels (which are so low
      because of now missing info).

commit df82bca737770e1707f61dfafdd306da22481bcf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:03 2014 +0200

    Changed some verbosities in Tesselation code.
    
    - modifications in BoundaryPointSet, BoundaryLineSet, BoundaryTriangleSet.
    - also to CandidateForTesselation, TriangleIntersectionList, tesselation,
      tesselation helpers and boundary code.

commit 921e9bcac84adb5c685919dd87089396207a8f67
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:28:44 2014 +0200

    DOCUFIX: Corrected formula for general tetrahedron in docu.
    
    - also code now matches with formula to avoid further confusion, although
      the result does not change by that.

commit 307d7bb6db49ea9b0aeb0342f3714194a2a539a4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:23:50 2014 +0200

    FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex.
    
    - AddTesselationLine() now returns whether new or present line was used.
    - FIX: Last inner line in closed polygon has been added by one but last
      triangle already, we added it twice.

commit d8632f2bc865ecf3f0bdcd26294ad717d79617b9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:24:52 2014 +0200

    FIX: RemoveTesselationLine() needs to erase line from OpenLines if present.

commit 85e1ef4c292dfea8eacd77e1b1607d2c8bd13d65
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:25:23 2014 +0200

    FIX: AddTesselationLine() would only work in initial tesselation phase.
    
    - the CandidateForTesselation instance is NULL when we convexize and this
      was not correctly processed by AddTesselationLine().

commit 4136c923ec473144f05170e1b8b9d4fe976b1c81
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:20 2014 +0200

    FIX: Changed all performCriticalExit() into ASSERT() in tesselation.

commit 1f176d5e27f7338dc5acf15caae1fb5580036cbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:56:24 2014 +0200

    FIX: Raster3D needs header.r3d, which had been missing so far.

commit 9265d6e802e9e84c5414209cf2ec20c38f7f3843
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 23 18:14:18 2014 +0200

    FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.
    
    - causes segfault when notification informs about change and _lastchangeaction
      is still NULL (as the very first Action failed).
    - we now only notify when action succeeded.

commit 543ab66a5e35f55a7501e3650ece13ab6a61d92d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 22 22:10:11 2014 +0200

    FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized.

commit 52e33b90484b6053378ed709009faea5b574a77a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:40:10 2014 +0200

    MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d.

commit 1fd8c58c1cfe63dcdc56d6a60a7f5d2f5d28b462
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:35:04 2014 +0200

    FIX: Added Boost::MultiIndexContainer check for MemDebug.
    
    - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation
      with Ubuntu 14.04.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Fri Oct 17 15:54:41 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri, 17 Oct 2014 15:54:41 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconvexEnvelope deleted. v1.4.8-53-g5cfdcf7
Message-ID: <20141017135442.0BDE710000FA@jupiter.ins.uni-bonn.de>

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, Fix_ConvexizeNonconvexEnvelope has been deleted
       was  5cfdcf70299145cf832d0ed47f1308237b9e42d6

-----------------------------------------------------------------------
5cfdcf70299145cf832d0ed47f1308237b9e42d6 TESTS: Extended Tesselations tests to convex case.
-----------------------------------------------------------------------


hooks/post-receive
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From git at ins.uni-bonn.de  Fri Oct 17 15:54:46 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri, 17 Oct 2014 15:54:46 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconvexEnvelope created. v1.4.8-53-ga87919a
Message-ID: <20141017135446.9BCBD10000FA@jupiter.ins.uni-bonn.de>

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, Fix_ConvexizeNonconvexEnvelope has been created
        at  a87919ab9cbb43b7e4b635445eed99502f832efe (commit)

- Log -----------------------------------------------------------------
commit a87919ab9cbb43b7e4b635445eed99502f832efe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:00:11 2014 +0200

    TESTS: Extended Tesselations tests to convex case.
    
    - moved all present tests to NonConvex folder, added same set but including
      amylose in Convex folder.

commit 39fa01a02f0ec194ce6058e65b277536d9a1fe22
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 16 16:34:13 2014 +0200

    TESTFIX: Regression test Tesselation/BigConvex is now working.

commit 9155d6ea8290bd7d8d19341219a4e1a486f14e4b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:47:03 2014 +0200

    Convex-envelope has debug parameter DoOutputEveryStep.
    
    - this writes for each convexization step a distinct tesselation file.
    - added parameter to ConvexizeNonconvexEnvelope().

commit 649aa9249b6121a2a1190dad8781b8358595257c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:24:30 2014 +0200

    Added SphereRadius parameter to ConvexEnvelopeAction.

commit ef479b42bd736ec67e8e4b56c777e0a28da02395
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:34:55 2014 +0200

    Added tcl scripts for viewing and debugging convexized surfaces.

commit 6290d24872224cd9c67492f61112826d620702e1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:55:44 2014 +0200

    DOCU: Added extensive explanation how convexization works.
    
    - updated userguide for convex-envelope.

commit aa2e20d92facf7716a4ff5c79760b2b63f38ef04
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 10:44:54 2014 +0200

    Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction.

commit 14fafa978ad8f073e3f6bfc71896bed224bc275c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:27:36 2014 +0200

    ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface().
    
    - with this convexization of a nonconvex tesselated surface seems to be
      robustly working as we can now deal also with points with degeneracies.

commit 20c18051dace481e30b64e5ba906d722ba28b834
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 18:14:39 2014 +0200

    FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization.

commit 6f7356114f3d1165f43fd8cc7d1f5a5635ae4ce1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 15:08:11 2014 +0200

    FIX: GainMap is used to store the concavity angle, we flip now always most concave.
    
    - this overrules prior flipping those that gives greatest gain in volume.

commit 4b54f73aba95c7e3039546e82c9a1df393327308
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 16:34:41 2014 +0200

    Rewrote ConvexizeNonconvexEnvelope().
    
    - now works for some sphere radii on amylose (e.g. 40 and 50).
    - we first remove all points that are only attached to concave lines.
    - also, we always flip the baseline (i.e. add a general tetraeder to the
      non-convex volume) for concave lines when the tetraeder does not intersect
      with present triangles.

commit 8d778fa588719f6983eed36294b74582c67f6184
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:31:18 2014 +0200

    FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop.
    
    - even if a triangle pair is not removed, it must still be removed from the
      degenerated list or we run into infinite loops.

commit 3c6b9d0e0d1f7572ed80073caafed6d5eeedf2e6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 09:37:06 2014 +0200

    Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface()
    
    - also added new functions
      Tesselation::RemoveFullConcavePointFromTesselatedSurface() and
      Tesselation::CheckAllConcaveInPolygon().

commit 633576c77a8f88ab8b74845376e2ab706fdea53a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:38:17 2014 +0200

    FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface().

commit ee886b36fc89715a5380053cc9ef0ec633424871
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 14:46:36 2014 +0200

    FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector.
    
    - with the point to be removed we have a very good measure for a vector
      pointing inside. Before we used the average of all normal vectors.

commit c1c8bc20ece846bb15d0be96187f99a80646eafb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:55:26 2014 +0200

    FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong.
    
    - replaced code by using present function for tetrahedron calculation with
      center of gravity as fourth point when going over all boundary triangles.
    - TESTFIX: volume change in convex regression test.

commit e6b793d18f5032e7033b3bf8de0eef2da63cb33c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 08:57:30 2014 +0200

    FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong.
    
    - before we just took the average of the normal vector of both present
      triangles as guide. Now, we check the intersection of the fourth endpoint
      on the plane of the first triangle and decide by on which side of the
      three boundary lines the intersection lies whether to flip the normal
      vectors sign for the associated (new) triangle or not.

commit 97d98600955169f39319e9ee925d91b2bf88c7d5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 14 18:37:03 2014 +0200

    Added Tesselation::IsPointBelowSurroundingPolygon().
    
    - IsPointBelowSurroundingPolygon() creates all triangles as planes and checks
      whether point is below.

commit 5a4d8f9201f96f0199f6c5855c9cf149b1ef97cd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 12:27:57 2014 +0200

    FIX: Filling of non-convex polygon with only minimal angles did not work.
    
    - when removing points from non-convex boundary and we encounter non-convex
      polygons, we must pick smallest angles but close to the non-convex site!

commit aad7aa64cf795a5b4af656e636efc9d343590816
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:43:03 2014 +0200

    FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly.
    
    - FIX: Very last node was removed twice due to StartNode = EndNode setting.

commit 3c460f1ba60995d3104ee413bf980ed1dc7a1ad9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:38:16 2014 +0200

    FIX: Reduced verbosity noise from Line::getIntersection().
    
    - removed use of info and toned down verbosity levels (which are so low
      because of now missing info).

commit df82bca737770e1707f61dfafdd306da22481bcf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:03 2014 +0200

    Changed some verbosities in Tesselation code.
    
    - modifications in BoundaryPointSet, BoundaryLineSet, BoundaryTriangleSet.
    - also to CandidateForTesselation, TriangleIntersectionList, tesselation,
      tesselation helpers and boundary code.

commit 921e9bcac84adb5c685919dd87089396207a8f67
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:28:44 2014 +0200

    DOCUFIX: Corrected formula for general tetrahedron in docu.
    
    - also code now matches with formula to avoid further confusion, although
      the result does not change by that.

commit 307d7bb6db49ea9b0aeb0342f3714194a2a539a4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:23:50 2014 +0200

    FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex.
    
    - AddTesselationLine() now returns whether new or present line was used.
    - FIX: Last inner line in closed polygon has been added by one but last
      triangle already, we added it twice.

commit d8632f2bc865ecf3f0bdcd26294ad717d79617b9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:24:52 2014 +0200

    FIX: RemoveTesselationLine() needs to erase line from OpenLines if present.

commit 85e1ef4c292dfea8eacd77e1b1607d2c8bd13d65
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:25:23 2014 +0200

    FIX: AddTesselationLine() would only work in initial tesselation phase.
    
    - the CandidateForTesselation instance is NULL when we convexize and this
      was not correctly processed by AddTesselationLine().

commit 4136c923ec473144f05170e1b8b9d4fe976b1c81
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:20 2014 +0200

    FIX: Changed all performCriticalExit() into ASSERT() in tesselation.

commit 1f176d5e27f7338dc5acf15caae1fb5580036cbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:56:24 2014 +0200

    FIX: Raster3D needs header.r3d, which had been missing so far.

commit 9265d6e802e9e84c5414209cf2ec20c38f7f3843
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 23 18:14:18 2014 +0200

    FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.
    
    - causes segfault when notification informs about change and _lastchangeaction
      is still NULL (as the very first Action failed).
    - we now only notify when action succeeded.

commit 543ab66a5e35f55a7501e3650ece13ab6a61d92d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 22 22:10:11 2014 +0200

    FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized.

commit 52e33b90484b6053378ed709009faea5b574a77a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:40:10 2014 +0200

    MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d.

commit 1fd8c58c1cfe63dcdc56d6a60a7f5d2f5d28b462
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:35:04 2014 +0200

    FIX: Added Boost::MultiIndexContainer check for MemDebug.
    
    - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation
      with Ubuntu 14.04.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Fri Oct 17 17:11:19 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri, 17 Oct 2014 17:11:19 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconvexEnvelope deleted. v1.4.8-53-ga87919a
Message-ID: <20141017151119.8ABA410000FA@jupiter.ins.uni-bonn.de>

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The branch, Fix_ConvexizeNonconvexEnvelope has been deleted
       was  a87919ab9cbb43b7e4b635445eed99502f832efe

-----------------------------------------------------------------------
a87919ab9cbb43b7e4b635445eed99502f832efe TESTS: Extended Tesselations tests to convex case.
-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Fri Oct 17 17:11:29 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri, 17 Oct 2014 17:11:29 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconvexEnvelope created. v1.4.8-53-gf40d8dd
Message-ID: <20141017151129.3C48110000FA@jupiter.ins.uni-bonn.de>

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, Fix_ConvexizeNonconvexEnvelope has been created
        at  f40d8dd765907294031f269bb2aee70f44522f5f (commit)

- Log -----------------------------------------------------------------
commit f40d8dd765907294031f269bb2aee70f44522f5f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:00:11 2014 +0200

    TESTS: Extended Tesselations tests to convex case.
    
    - moved all present tests to NonConvex folder, added same set but including
      amylose in Convex folder.

commit 5dcf7f15dc3a3f0a8e49f6cb75fac6944dff7a1b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 16 16:34:13 2014 +0200

    TESTFIX: Regression test Tesselation/BigConvex is now working.

commit fe2aa94863b0c598bfc0fe9a836c274cad414aba
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:47:03 2014 +0200

    Convex-envelope has debug parameter DoOutputEveryStep.
    
    - this writes for each convexization step a distinct tesselation file.
    - added parameter to ConvexizeNonconvexEnvelope().

commit caf1c49fd6d0d3ea742cfcd9465a27bb2586e1bd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:24:30 2014 +0200

    Added SphereRadius parameter to ConvexEnvelopeAction.

commit 424aa9f2367194493c6a2dfd66eef6addc0f8bcd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:34:55 2014 +0200

    Added tcl scripts for viewing and debugging convexized surfaces.

commit 81c536e142093bc4778cdced24084570dad28dc0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:55:44 2014 +0200

    DOCU: Added extensive explanation how convexization works.
    
    - updated userguide for convex-envelope.

commit 5c69254ae69e4c974ce0f37d9f92e7af7e38400a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 10:44:54 2014 +0200

    Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction.

commit 14fafa978ad8f073e3f6bfc71896bed224bc275c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:27:36 2014 +0200

    ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface().
    
    - with this convexization of a nonconvex tesselated surface seems to be
      robustly working as we can now deal also with points with degeneracies.

commit 20c18051dace481e30b64e5ba906d722ba28b834
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 18:14:39 2014 +0200

    FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization.

commit 6f7356114f3d1165f43fd8cc7d1f5a5635ae4ce1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 15:08:11 2014 +0200

    FIX: GainMap is used to store the concavity angle, we flip now always most concave.
    
    - this overrules prior flipping those that gives greatest gain in volume.

commit 4b54f73aba95c7e3039546e82c9a1df393327308
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 16:34:41 2014 +0200

    Rewrote ConvexizeNonconvexEnvelope().
    
    - now works for some sphere radii on amylose (e.g. 40 and 50).
    - we first remove all points that are only attached to concave lines.
    - also, we always flip the baseline (i.e. add a general tetraeder to the
      non-convex volume) for concave lines when the tetraeder does not intersect
      with present triangles.

commit 8d778fa588719f6983eed36294b74582c67f6184
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:31:18 2014 +0200

    FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop.
    
    - even if a triangle pair is not removed, it must still be removed from the
      degenerated list or we run into infinite loops.

commit 3c6b9d0e0d1f7572ed80073caafed6d5eeedf2e6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 09:37:06 2014 +0200

    Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface()
    
    - also added new functions
      Tesselation::RemoveFullConcavePointFromTesselatedSurface() and
      Tesselation::CheckAllConcaveInPolygon().

commit 633576c77a8f88ab8b74845376e2ab706fdea53a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:38:17 2014 +0200

    FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface().

commit ee886b36fc89715a5380053cc9ef0ec633424871
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 14:46:36 2014 +0200

    FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector.
    
    - with the point to be removed we have a very good measure for a vector
      pointing inside. Before we used the average of all normal vectors.

commit c1c8bc20ece846bb15d0be96187f99a80646eafb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:55:26 2014 +0200

    FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong.
    
    - replaced code by using present function for tetrahedron calculation with
      center of gravity as fourth point when going over all boundary triangles.
    - TESTFIX: volume change in convex regression test.

commit e6b793d18f5032e7033b3bf8de0eef2da63cb33c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 08:57:30 2014 +0200

    FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong.
    
    - before we just took the average of the normal vector of both present
      triangles as guide. Now, we check the intersection of the fourth endpoint
      on the plane of the first triangle and decide by on which side of the
      three boundary lines the intersection lies whether to flip the normal
      vectors sign for the associated (new) triangle or not.

commit 97d98600955169f39319e9ee925d91b2bf88c7d5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 14 18:37:03 2014 +0200

    Added Tesselation::IsPointBelowSurroundingPolygon().
    
    - IsPointBelowSurroundingPolygon() creates all triangles as planes and checks
      whether point is below.

commit 5a4d8f9201f96f0199f6c5855c9cf149b1ef97cd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 12:27:57 2014 +0200

    FIX: Filling of non-convex polygon with only minimal angles did not work.
    
    - when removing points from non-convex boundary and we encounter non-convex
      polygons, we must pick smallest angles but close to the non-convex site!

commit aad7aa64cf795a5b4af656e636efc9d343590816
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:43:03 2014 +0200

    FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly.
    
    - FIX: Very last node was removed twice due to StartNode = EndNode setting.

commit 3c460f1ba60995d3104ee413bf980ed1dc7a1ad9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:38:16 2014 +0200

    FIX: Reduced verbosity noise from Line::getIntersection().
    
    - removed use of info and toned down verbosity levels (which are so low
      because of now missing info).

commit df82bca737770e1707f61dfafdd306da22481bcf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:03 2014 +0200

    Changed some verbosities in Tesselation code.
    
    - modifications in BoundaryPointSet, BoundaryLineSet, BoundaryTriangleSet.
    - also to CandidateForTesselation, TriangleIntersectionList, tesselation,
      tesselation helpers and boundary code.

commit 921e9bcac84adb5c685919dd87089396207a8f67
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:28:44 2014 +0200

    DOCUFIX: Corrected formula for general tetrahedron in docu.
    
    - also code now matches with formula to avoid further confusion, although
      the result does not change by that.

commit 307d7bb6db49ea9b0aeb0342f3714194a2a539a4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:23:50 2014 +0200

    FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex.
    
    - AddTesselationLine() now returns whether new or present line was used.
    - FIX: Last inner line in closed polygon has been added by one but last
      triangle already, we added it twice.

commit d8632f2bc865ecf3f0bdcd26294ad717d79617b9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:24:52 2014 +0200

    FIX: RemoveTesselationLine() needs to erase line from OpenLines if present.

commit 85e1ef4c292dfea8eacd77e1b1607d2c8bd13d65
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:25:23 2014 +0200

    FIX: AddTesselationLine() would only work in initial tesselation phase.
    
    - the CandidateForTesselation instance is NULL when we convexize and this
      was not correctly processed by AddTesselationLine().

commit 4136c923ec473144f05170e1b8b9d4fe976b1c81
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:20 2014 +0200

    FIX: Changed all performCriticalExit() into ASSERT() in tesselation.

commit 1f176d5e27f7338dc5acf15caae1fb5580036cbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:56:24 2014 +0200

    FIX: Raster3D needs header.r3d, which had been missing so far.

commit 9265d6e802e9e84c5414209cf2ec20c38f7f3843
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 23 18:14:18 2014 +0200

    FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.
    
    - causes segfault when notification informs about change and _lastchangeaction
      is still NULL (as the very first Action failed).
    - we now only notify when action succeeded.

commit 543ab66a5e35f55a7501e3650ece13ab6a61d92d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 22 22:10:11 2014 +0200

    FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized.

commit 52e33b90484b6053378ed709009faea5b574a77a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:40:10 2014 +0200

    MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d.

commit 1fd8c58c1cfe63dcdc56d6a60a7f5d2f5d28b462
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:35:04 2014 +0200

    FIX: Added Boost::MultiIndexContainer check for MemDebug.
    
    - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation
      with Ubuntu 14.04.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Mon Oct 20 09:52:41 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 20 Oct 2014 09:52:41 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.9
	deleted. v1.4.8-21-g78c9509
Message-ID: <20141020075241.B868510000FA@jupiter.ins.uni-bonn.de>

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, Candidate_v1.4.9 has been deleted
       was  78c9509cba8ec6569d3fee2987607785743b7e09

-----------------------------------------------------------------------
78c9509cba8ec6569d3fee2987607785743b7e09 FIX: QtHomologyList's plot widget was too high (and fixed).
-----------------------------------------------------------------------


hooks/post-receive
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From git at ins.uni-bonn.de  Mon Oct 20 09:52:57 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 20 Oct 2014 09:52:57 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.9
	created. v1.4.8-54-g0516fd9
Message-ID: <20141020075257.AE4CD10000FA@jupiter.ins.uni-bonn.de>

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, Candidate_v1.4.9 has been created
        at  0516fd9f440d63cdfbb63b946c9933f28f304b68 (commit)

- Log -----------------------------------------------------------------
commit 0516fd9f440d63cdfbb63b946c9933f28f304b68
Merge: 3b17982 33ee996
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 19 19:13:32 2014 +0200

    Merge branch 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9

commit 33ee9960e3c188eaa1d7490c6b14994fbd779863
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:00:11 2014 +0200

    TESTS: Extended Tesselations tests to convex case.
    
    - moved all present tests to NonConvex folder, added same set but including
      amylose in Convex folder.

commit 565695bc8823d4df417f859cee34ed9b17e3b0b8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 16 16:34:13 2014 +0200

    TESTFIX: Regression test Tesselation/BigConvex is now working.

commit 5f7b95f1f29d4009517dae2f5ef5ae993e846ce8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:47:03 2014 +0200

    Convex-envelope has debug parameter DoOutputEveryStep.
    
    - this writes for each convexization step a distinct tesselation file.
    - added parameter to ConvexizeNonconvexEnvelope().

commit bcb83114d92eb11cccb67975f4967b7fb251de3d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:24:30 2014 +0200

    Added SphereRadius parameter to ConvexEnvelopeAction.

commit 991c35d557cd7eb1196fd569a74860662f03eeb6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:34:55 2014 +0200

    Added tcl scripts for viewing and debugging convexized surfaces.

commit 8544b32bd227c145f76c3bf5a30ca16c01e9a7d9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:55:44 2014 +0200

    DOCU: Added extensive explanation how convexization works.
    
    - updated userguide for convex-envelope.

commit e2396e6d7030fd404f25afa9b5e8d1e1bc72bdb8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 10:44:54 2014 +0200

    Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction.

commit aac19f2bb7cdef195d60c2e090de27fd193f1ee9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:27:36 2014 +0200

    ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface().
    
    - with this convexization of a nonconvex tesselated surface seems to be
      robustly working as we can now deal also with points with degeneracies.

commit 2ef2cc3b3e76c8ecb94ddaddfb1203081ea07eb0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 18:14:39 2014 +0200

    FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization.

commit 81ffd87c0c1926d2a925cdbb620380e16e421cbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 15:08:11 2014 +0200

    FIX: GainMap is used to store the concavity angle, we flip now always most concave.
    
    - this overrules prior flipping those that gives greatest gain in volume.

commit d289c64b86bc28a435d03cdf4f3ece926c6debf6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 16:34:41 2014 +0200

    Rewrote ConvexizeNonconvexEnvelope().
    
    - now works for some sphere radii on amylose (e.g. 40 and 50).
    - we first remove all points that are only attached to concave lines.
    - also, we always flip the baseline (i.e. add a general tetraeder to the
      non-convex volume) for concave lines when the tetraeder does not intersect
      with present triangles.

commit 6da9e995abeca059d65efd473cd2ac3eacf8279d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:31:18 2014 +0200

    FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop.
    
    - even if a triangle pair is not removed, it must still be removed from the
      degenerated list or we run into infinite loops.

commit 30ce7d21a0bc0d344058826d689837a313b01efd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 09:37:06 2014 +0200

    Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface()
    
    - also added new functions
      Tesselation::RemoveFullConcavePointFromTesselatedSurface() and
      Tesselation::CheckAllConcaveInPolygon().

commit 77eec57c5ebcc041fb7d83112c887c95824f977d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:38:17 2014 +0200

    FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface().

commit e26c3533deedb0298b184037987b587e4d718562
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 14:46:36 2014 +0200

    FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector.
    
    - with the point to be removed we have a very good measure for a vector
      pointing inside. Before we used the average of all normal vectors.

commit d45a5bfcf5b03614dc189256f1861f31e819f103
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:55:26 2014 +0200

    FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong.
    
    - replaced code by using present function for tetrahedron calculation with
      center of gravity as fourth point when going over all boundary triangles.
    - TESTFIX: volume change in convex regression test.

commit 32d7e4e99ad240050c6936e8be2d5450c409f996
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 08:57:30 2014 +0200

    FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong.
    
    - before we just took the average of the normal vector of both present
      triangles as guide. Now, we check the intersection of the fourth endpoint
      on the plane of the first triangle and decide by on which side of the
      three boundary lines the intersection lies whether to flip the normal
      vectors sign for the associated (new) triangle or not.

commit d33bb8a2c2523a42b0a9e36768e551c57c340cbc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 14 18:37:03 2014 +0200

    Added Tesselation::IsPointBelowSurroundingPolygon().
    
    - IsPointBelowSurroundingPolygon() creates all triangles as planes and checks
      whether point is below.

commit f1ae15bf748d2c4746bb9ed901593b75d8a44b1f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 12:27:57 2014 +0200

    FIX: Filling of non-convex polygon with only minimal angles did not work.
    
    - when removing points from non-convex boundary and we encounter non-convex
      polygons, we must pick smallest angles but close to the non-convex site!

commit c2c786e40198b3b955ca9b66593dd013bd531b2e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:43:03 2014 +0200

    FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly.
    
    - FIX: Very last node was removed twice due to StartNode = EndNode setting.

commit 6d52807f7b413a18b8d814ac5501fdce735fcdea
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:38:16 2014 +0200

    FIX: Reduced verbosity noise from Line::getIntersection().
    
    - removed use of info and toned down verbosity levels (which are so low
      because of now missing info).

commit b8d21539ab1899769efb705f4de59ef647f234b1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:03 2014 +0200

    Changed some verbosities in Tesselation code.
    
    - modifications in BoundaryPointSet, BoundaryLineSet, BoundaryTriangleSet.
    - also to CandidateForTesselation, TriangleIntersectionList, tesselation,
      tesselation helpers and boundary code.

commit dfe0549d4ce8433fde1acf2f7886d20fc1f0174a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:28:44 2014 +0200

    DOCUFIX: Corrected formula for general tetrahedron in docu.
    
    - also code now matches with formula to avoid further confusion, although
      the result does not change by that.

commit 75d42ad5b96258a67afde9aa02cf39b04a4f6059
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:23:50 2014 +0200

    FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex.
    
    - AddTesselationLine() now returns whether new or present line was used.
    - FIX: Last inner line in closed polygon has been added by one but last
      triangle already, we added it twice.

commit c2f30642d960bd67dc5b7bca66d267525a8f58ab
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:24:52 2014 +0200

    FIX: RemoveTesselationLine() needs to erase line from OpenLines if present.

commit bb86bd850f990066e79d37a776337c627624df65
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:25:23 2014 +0200

    FIX: AddTesselationLine() would only work in initial tesselation phase.
    
    - the CandidateForTesselation instance is NULL when we convexize and this
      was not correctly processed by AddTesselationLine().

commit 613790861011df25a40877f5c6bfb2156def7a8c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:20 2014 +0200

    FIX: Changed all performCriticalExit() into ASSERT() in tesselation.

commit cead3fe0679f2e6b3b53a7300f42efde4b3cc552
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:56:24 2014 +0200

    FIX: Raster3D needs header.r3d, which had been missing so far.

commit cfb9c59bbf7a92a53173e5044b42303e74361093
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 23 18:14:18 2014 +0200

    FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.
    
    - causes segfault when notification informs about change and _lastchangeaction
      is still NULL (as the very first Action failed).
    - we now only notify when action succeeded.

commit 1b6cec8a7217342cc34f00da7084bcec75e948a3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 22 22:10:11 2014 +0200

    FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized.

commit 7d320c29fb3cf5f18317f1e2370bbf89802448e4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:40:10 2014 +0200

    MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d.

commit 4da4defddffa2503040fe329681f55b1f6f8c856
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:35:04 2014 +0200

    FIX: Added Boost::MultiIndexContainer check for MemDebug.
    
    - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation
      with Ubuntu 14.04.

commit 3b179825d4e6f17bd22fbd7f880f59cc7fd8924e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 13:19:18 2014 +0200

    FIX: QtHomologyList's plot widget was too high (and fixed).
    
    - also the sizes of splitter's children in QtHomologyList are now stored to
      settings (as QsizePolicy does not have an effect on a splitter).

commit 5c8807e908af52740778a67bac4173280b6d141b
Merge: b119a09 c7fe90c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 19 19:12:11 2014 +0200

    Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9
    
    Conflicts:
    	doc/userguide/userguide.xml
    	tests/regression/Atoms/testsuite-atoms.at
    
    - mirror-atoms and translate-to-origins occupied the same places.

commit b119a092aa1848936f8c80974f857ded3c098885
Merge: 9e1bfbc 46ce1c8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 19 19:10:16 2014 +0200

    Merge branch 'DynamicMolecules' into Candidate_v1.4.9

commit 9e1bfbc27ee42cdb562491c7e51fdb9da26faaf0
Merge: 2ed3bf3 0ea063b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 19 19:09:30 2014 +0200

    Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9

commit 0ea063beb1f1de6945df69f74ce759aab7643539
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 12 09:54:12 2014 +0200

    Extracted SavePotentialsAction.
    
    - PotentialTrainer::StorePotentials removed.
    - Fit...Actions do not store anymore.
    - TESTFIX: potential regression tests now use save-potentials and compare
      against stored file.

commit f1eabd03d00ab44fb84ebc758d0ebfc85d6dee6d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 12 09:39:58 2014 +0200

    Extracted ParsePotentialsAction from FitCompoundPotentialAction.

commit 98d166e8fbc83bccb5843ecc5d4296f2c25488c0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 11 22:38:05 2014 +0200

    Split FitPotentialAction into two actions.
    
    - FitPotentialAction fits just a single potential.
    - new FitCompoundPotentialAction fits via a potential file.
    - PotentialTrainer contains all helper functions and common code and is only
      compiled when CONDLEVMAR.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Thu Oct 23 00:04:23 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 23 Oct 2014 00:04:23 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder annotated tag v1.4.9 created.
	v1.4.9
Message-ID: <20141022220423.2981C10000FA@jupiter.ins.uni-bonn.de>

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 annotated tag, v1.4.9 has been created
        at  ed071df08976dd4a9e83a9dcd39827e1d10dc656 (tag)
   tagging  42344903478721db21dff3e7385e7c5f037aff66 (commit)
  replaces  v1.4.8
 tagged by  Frederik Heber
        on  Wed Oct 22 23:40:06 2014 +0200

- Log -----------------------------------------------------------------
Convex envelopes and thereby volume measurments are fully working.
Trajectories no longer need to be consecutive (we store time step and position)
Some new actions and small fixes.
Userguide now contains explanation of every present Action.

This version contains the following branches:
33ee996	Fix_ConvexizeNonconvexEnvelope (volumes can now sensibly be measured)
78c9509	GUI_Enhancements (fixed appearance of QtHomologyList widget)
c7fe90c	Experiment_AmyloseWater (new TranslateToOriginAction eases rotations)
46ce1c8	Dynamic_Molecules (trajectories stored as map, not vector)
9d1320c Refactoring_PotentialActions (split FitPotentialAction, extracted save
	and load potentials)
bbf6dcd	MirrorAtoms (new MirrorAtoms action)
054d47f	ActionFixes (fixing AtomByIdAction)
9bce964	CodeCheck_ActionInUserguide (check that every Action appears in user
	guide)

Frederik Heber (56):
      VersionAction also prints to log, not only to status.
      DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer.
      Added CodeChecks test that every action appears in the userguide.
      DOCU: Added all missing Actions to userguide.
      DOCU: Fixed all missing links in userguide.
      FIX: (Not)AtomByIdAction would fail with assert if not atoms are present.
      FIX: atom's copy cstor does not need to copy positions, ... again.
      Added AverageMoleculeForceAction for measuring average force acting on a molecule.
      Added TranslateToOriginAction.
      Changed how trajectories are stored, not as vecor but as map.
      FIX: World::setTime() now first copies Bondgraph and then sets the time.
      Added AtomMirrorAction.
      Merge branch 'ActionFixes' into Candidate_v1.4.9
      Merge branch 'MirrorAtoms' into Candidate_v1.4.9
      Split FitPotentialAction into two actions.
      Extracted ParsePotentialsAction from FitCompoundPotentialAction.
      Extracted SavePotentialsAction.
      Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9
      Merge branch 'DynamicMolecules' into Candidate_v1.4.9
      Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9
      FIX: QtHomologyList's plot widget was too high (and fixed).
      FIX: Added Boost::MultiIndexContainer check for MemDebug.
      MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d.
      FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized.
      FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.
      FIX: Raster3D needs header.r3d, which had been missing so far.
      FIX: Changed all performCriticalExit() into ASSERT() in tesselation.
      FIX: AddTesselationLine() would only work in initial tesselation phase.
      FIX: RemoveTesselationLine() needs to erase line from OpenLines if present.
      FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex.
      DOCUFIX: Corrected formula for general tetrahedron in docu.
      Changed some verbosities in Tesselation code.
      FIX: Reduced verbosity noise from Line::getIntersection().
      FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly.
      FIX: Filling of non-convex polygon with only minimal angles did not work.
      Added Tesselation::IsPointBelowSurroundingPolygon().
      FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong.
      FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong.
      FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector.
      FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface().
      Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface()
      FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop.
      Rewrote ConvexizeNonconvexEnvelope().
      FIX: GainMap is used to store the concavity angle, we flip now always most concave.
      FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization.
      ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface().
      Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction.
      DOCU: Added extensive explanation how convexization works.
      Added tcl scripts for viewing and debugging convexized surfaces.
      Added SphereRadius parameter to ConvexEnvelopeAction.
      Convex-envelope has debug parameter DoOutputEveryStep.
      TESTFIX: Regression test Tesselation/BigConvex is now working.
      TESTS: Extended Tesselations tests to convex case.
      Merge branch 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9
      MEMFIX: PotentialTrainer::getFirstGraphwithSpecifiedElements() used olditer pointing nowhere.
      DISTFIX: POTENTIALSOURCES was overwritten, not added to.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Thu Oct 23 00:05:03 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 23 Oct 2014 00:05:03 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconvexEnvelope deleted. v1.4.8-53-gf40d8dd
Message-ID: <20141022220503.5CBC710000FA@jupiter.ins.uni-bonn.de>

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, Fix_ConvexizeNonconvexEnvelope has been deleted
       was  f40d8dd765907294031f269bb2aee70f44522f5f

-----------------------------------------------------------------------
f40d8dd765907294031f269bb2aee70f44522f5f TESTS: Extended Tesselations tests to convex case.
-----------------------------------------------------------------------


hooks/post-receive
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From git at ins.uni-bonn.de  Thu Oct 23 00:06:07 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 23 Oct 2014 00:06:07 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.9
	deleted. v1.4.8-54-g0516fd9
Message-ID: <20141022220607.9577E10000FA@jupiter.ins.uni-bonn.de>

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
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The branch, Candidate_v1.4.9 has been deleted
       was  0516fd9f440d63cdfbb63b946c9933f28f304b68

-----------------------------------------------------------------------
0516fd9f440d63cdfbb63b946c9933f28f304b68 Merge branch 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Thu Oct 23 00:21:10 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 23 Oct 2014 00:21:10 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder annotated tag v1.4.9 deleted.
	v1.4.8-56-g4234490
Message-ID: <20141022222110.6F61A10000FA@jupiter.ins.uni-bonn.de>

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 annotated tag, v1.4.9 has been deleted
       was  ed071df08976dd4a9e83a9dcd39827e1d10dc656

-----------------------------------------------------------------------
tag v1.4.9

Convex envelopes and thereby volume measurments are fully working.
Trajectories no longer need to be consecutive (we store time step and position)
Some new actions and small fixes.
Userguide now contains explanation of every present Action.

This version contains the following branches:
33ee996	Fix_ConvexizeNonconvexEnvelope (volumes can now sensibly be measured)
78c9509	GUI_Enhancements (fixed appearance of QtHomologyList widget)
c7fe90c	Experiment_AmyloseWater (new TranslateToOriginAction eases rotations)
46ce1c8	Dynamic_Molecules (trajectories stored as map, not vector)
9d1320c Refactoring_PotentialActions (split FitPotentialAction, extracted save
	and load potentials)
bbf6dcd	MirrorAtoms (new MirrorAtoms action)
054d47f	ActionFixes (fixing AtomByIdAction)
9bce964	CodeCheck_ActionInUserguide (check that every Action appears in user
	guide)
42344903478721db21dff3e7385e7c5f037aff66 DISTFIX: POTENTIALSOURCES was overwritten, not added to.
-----------------------------------------------------------------------


hooks/post-receive
-- 
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From git at ins.uni-bonn.de  Thu Oct 23 00:22:14 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 23 Oct 2014 00:22:14 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder annotated tag v1.4.9 created.
	v1.4.9
Message-ID: <20141022222214.34D2C10000FA@jupiter.ins.uni-bonn.de>

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 annotated tag, v1.4.9 has been created
        at  ac3336b2fd7cdc1a9122e0a901e3b2e4b22a3406 (tag)
   tagging  7b38d3ce5a4b0f857769b4fa0009f95a8f574d78 (commit)
  replaces  v1.4.8
 tagged by  Frederik Heber
        on  Thu Oct 23 00:21:22 2014 +0200

- Log -----------------------------------------------------------------
Convex envelopes and thereby volume measurments are fully working.
Trajectories no longer need to be consecutive (we store time step and position)
Some new actions and small fixes.
Userguide now contains explanation of every present Action.

This version contains the following branches:
4234490	Candidate_v1.4.9 (version setting and mem and distcheck fixes)
33ee996	Fix_ConvexizeNonconvexEnvelope (volumes can now sensibly be measured)
78c9509	GUI_Enhancements (fixed appearance of QtHomologyList widget)
c7fe90c	Experiment_AmyloseWater (new TranslateToOriginAction eases rotations)
46ce1c8	Dynamic_Molecules (trajectories stored as map, not vector)
0ea063b Refactoring_PotentialActions (split FitPotentialAction, extracted save
	and load potentials)
bbf6dcd	MirrorAtoms (new MirrorAtoms action)
054d47f	ActionFixes (fixing AtomByIdAction)
9bce964	CodeCheck_ActionInUserguide (check that every Action appears in user
	guide)

Frederik Heber (57):
      VersionAction also prints to log, not only to status.
      DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer.
      Added CodeChecks test that every action appears in the userguide.
      DOCU: Added all missing Actions to userguide.
      DOCU: Fixed all missing links in userguide.
      FIX: (Not)AtomByIdAction would fail with assert if not atoms are present.
      FIX: atom's copy cstor does not need to copy positions, ... again.
      Added AverageMoleculeForceAction for measuring average force acting on a molecule.
      Added TranslateToOriginAction.
      Changed how trajectories are stored, not as vecor but as map.
      FIX: World::setTime() now first copies Bondgraph and then sets the time.
      Added AtomMirrorAction.
      Merge branch 'ActionFixes' into Candidate_v1.4.9
      Merge branch 'MirrorAtoms' into Candidate_v1.4.9
      Split FitPotentialAction into two actions.
      Extracted ParsePotentialsAction from FitCompoundPotentialAction.
      Extracted SavePotentialsAction.
      Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9
      Merge branch 'DynamicMolecules' into Candidate_v1.4.9
      Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9
      FIX: QtHomologyList's plot widget was too high (and fixed).
      FIX: Added Boost::MultiIndexContainer check for MemDebug.
      MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d.
      FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized.
      FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.
      FIX: Raster3D needs header.r3d, which had been missing so far.
      FIX: Changed all performCriticalExit() into ASSERT() in tesselation.
      FIX: AddTesselationLine() would only work in initial tesselation phase.
      FIX: RemoveTesselationLine() needs to erase line from OpenLines if present.
      FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex.
      DOCUFIX: Corrected formula for general tetrahedron in docu.
      Changed some verbosities in Tesselation code.
      FIX: Reduced verbosity noise from Line::getIntersection().
      FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly.
      FIX: Filling of non-convex polygon with only minimal angles did not work.
      Added Tesselation::IsPointBelowSurroundingPolygon().
      FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong.
      FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong.
      FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector.
      FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface().
      Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface()
      FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop.
      Rewrote ConvexizeNonconvexEnvelope().
      FIX: GainMap is used to store the concavity angle, we flip now always most concave.
      FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization.
      ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface().
      Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction.
      DOCU: Added extensive explanation how convexization works.
      Added tcl scripts for viewing and debugging convexized surfaces.
      Added SphereRadius parameter to ConvexEnvelopeAction.
      Convex-envelope has debug parameter DoOutputEveryStep.
      TESTFIX: Regression test Tesselation/BigConvex is now working.
      TESTS: Extended Tesselations tests to convex case.
      Merge branch 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9
      MEMFIX: PotentialTrainer::getFirstGraphwithSpecifiedElements() used olditer pointing nowhere.
      DISTFIX: POTENTIALSOURCES was overwritten, not added to.
      Set version to 1.4.9.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Thu Oct 23 00:22:20 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 23 Oct 2014 00:22:20 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch stable updated. v1.4.9
Message-ID: <20141022222220.32C7810000FA@jupiter.ins.uni-bonn.de>

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, stable has been updated
       via  7b38d3ce5a4b0f857769b4fa0009f95a8f574d78 (commit)
      from  42344903478721db21dff3e7385e7c5f037aff66 (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.

- Log -----------------------------------------------------------------
commit 7b38d3ce5a4b0f857769b4fa0009f95a8f574d78
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 23 00:19:36 2014 +0200

    Set version to 1.4.9.
    
    - MoleCuilder library is now 14:2:0.
    - Codename "Squares" (1,2, and 3 squared)

-----------------------------------------------------------------------

Summary of changes:
 configure.ac |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)


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From git at ins.uni-bonn.de  Thu Oct 23 00:04:17 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 23 Oct 2014 00:04:17 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch stable updated.
	v1.4.8-56-g4234490
Message-ID: <20141022220417.4649A10000FA@jupiter.ins.uni-bonn.de>

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The branch, stable has been updated
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- Log -----------------------------------------------------------------
commit 42344903478721db21dff3e7385e7c5f037aff66
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 22 20:07:11 2014 +0200

    DISTFIX: POTENTIALSOURCES was overwritten, not added to.

commit e63edb93a800204ca8a32bfc45eed103c7679210
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 22 20:05:30 2014 +0200

    MEMFIX: PotentialTrainer::getFirstGraphwithSpecifiedElements() used olditer pointing nowhere.
    
    - check for not checking the same key again was broken, causing the invalid
      read error. This is fixed by correcting the check.
    - also fixed occurence in FitParticleChargesAction.

-----------------------------------------------------------------------

Summary of changes:
 LinearAlgebra/src/LinearAlgebra/Line.cpp           |   22 +-
 configure.ac                                       |    1 +
 doc/userguide/userguide.xml                        | 1582 ++++++++++++++++----
 m4/boost.m4                                        |    6 +
 src/Actions/ActionQueue.cpp                        |   13 +-
 .../AnalysisAction/AverageMoleculeForceAction.cpp  |   95 ++
 .../AnalysisAction/AverageMoleculeForceAction.def  |   29 +
 .../AnalysisAction/AverageMoleculeForceAction.hpp  |   21 +
 src/Actions/AtomAction/MirrorAction.cpp            |  117 ++
 src/Actions/AtomAction/MirrorAction.def            |   40 +
 src/Actions/AtomAction/MirrorAction.hpp            |   22 +
 src/Actions/AtomAction/TranslateToOriginAction.cpp |  108 ++
 src/Actions/AtomAction/TranslateToOriginAction.def |   34 +
 src/Actions/AtomAction/TranslateToOriginAction.hpp |   22 +
 src/Actions/CommandAction/VersionAction.cpp        |    1 +
 src/Actions/GlobalListOfActions.hpp                |   12 +-
 src/Actions/Makefile.am                            |   30 +-
 .../MoleculeAction/ForceAnnealingAction.cpp        |    1 -
 .../MoleculeAction/VerletIntegrationAction.cpp     |   12 +-
 .../PotentialAction/FitCompoundPotentialAction.cpp |  123 ++
 .../PotentialAction/FitCompoundPotentialAction.def |   49 +
 .../PotentialAction/FitCompoundPotentialAction.hpp |   22 +
 .../PotentialAction/FitParticleChargesAction.cpp   |    7 +-
 src/Actions/PotentialAction/FitPotentialAction.cpp |  275 +---
 src/Actions/PotentialAction/FitPotentialAction.def |   15 +-
 .../PotentialAction/ParsePotentialsAction.cpp      |  114 ++
 .../PotentialAction/ParsePotentialsAction.def      |   37 +
 .../PotentialAction/ParsePotentialsAction.hpp      |   22 +
 .../PotentialAction/SavePotentialsAction.cpp       |  100 ++
 .../PotentialAction/SavePotentialsAction.def       |   36 +
 .../PotentialAction/SavePotentialsAction.hpp       |   22 +
 .../SelectionAction/Atoms/AtomByIdAction.cpp       |    2 +-
 .../SelectionAction/Atoms/NotAtomByIdAction.cpp    |    2 +-
 .../TesselationAction/ConvexEnvelopeAction.cpp     |   32 +-
 .../TesselationAction/ConvexEnvelopeAction.def     |   16 +-
 src/Actions/UndoRedoHelpers.cpp                    |   12 +-
 src/Actions/UndoRedoHelpers.hpp                    |    9 +-
 src/Atom/TesselPoint.cpp                           |   12 +-
 src/Atom/TesselPoint.hpp                           |    4 +-
 src/Atom/atom.cpp                                  |   23 +-
 src/Atom/atom.hpp                                  |    4 +-
 src/Atom/atom_atominfo.cpp                         |  499 +++----
 src/Atom/atom_atominfo.hpp                         |   18 +-
 src/Atom/atom_bondedparticle.cpp                   |   80 +-
 src/Atom/atom_bondedparticleinfo.cpp               |   52 +-
 src/Atom/atom_bondedparticleinfo.hpp               |   17 +-
 src/Atom/unittests/AtomObserverUnitTest.cpp        |    3 +-
 src/Fragmentation/Exporters/HydrogenPool.cpp       |    2 +-
 .../Exporters/SaturationDistanceMaximizer.hpp      |    4 +-
 src/LinkedCell/unittests/stubs/TesselPointStub.cpp |    4 +-
 src/Potentials/Makefile.am                         |    7 +
 src/Potentials/PotentialTrainer.cpp                |  217 +++
 src/Potentials/PotentialTrainer.hpp                |   52 +
 src/Potentials/Specifics/ConstantPotential.cpp     |    2 +-
 .../Specifics/FourBodyPotential_Improper.cpp       |    2 +-
 .../Specifics/FourBodyPotential_Torsion.cpp        |    2 +-
 .../Specifics/ManyBodyPotential_Tersoff.cpp        |    2 +-
 .../Specifics/PairPotential_Harmonic.cpp           |    2 +-
 .../Specifics/PairPotential_LennardJones.cpp       |    2 +-
 src/Potentials/Specifics/PairPotential_Morse.cpp   |    2 +-
 .../Specifics/ThreeBodyPotential_Angle.cpp         |    2 +-
 src/Tesselation/BoundaryLineSet.cpp                |    3 +-
 src/Tesselation/BoundaryPointSet.cpp               |    2 +-
 src/Tesselation/BoundaryTriangleSet.cpp            |   27 +-
 src/Tesselation/CandidateForTesselation.cpp        |   16 +-
 src/Tesselation/boundary.cpp                       |  233 +++-
 src/Tesselation/boundary.hpp                       |    2 +-
 src/Tesselation/tesselation.cpp                    | 1355 ++++++++++-------
 src/Tesselation/tesselation.hpp                    |   14 +-
 src/Tesselation/tesselationhelpers.cpp             |   26 +-
 src/Tesselation/triangleintersectionlist.cpp       |   18 +-
 .../Views/Qt4/Plotting/QSeisPlotPage.cpp           |   43 +-
 .../Views/Qt4/Plotting/QSeisPlotPage.hpp           |    6 +
 src/UIElements/Views/Qt4/QtHomologyList.cpp        |   20 +-
 src/World.cpp                                      |   21 +-
 src/documentation/constructs/tesselation.dox       |   66 +-
 src/molecule_geometry.cpp                          |   19 +-
 tests/CodeChecks/Makefile.am                       |    1 +
 .../testsuite-action_present_in_userguide.at       |   42 +
 tests/CodeChecks/testsuite.at                      |    4 +-
 tests/Python/AllActions/options.dat                |    6 +
 .../testsuite-1_2-dimethoxyethane.at               |   40 -
 .../testsuite-1_2-dimethylbenzene.at               |   40 -
 .../testsuite-2-methylcyclohexanone.at             |   40 -
 .../pre/1_2-dimethoxyethane.xyz                    |    0
 .../testsuite-1_2-dimethoxyethane.at               |   40 +
 .../pre/1_2-dimethylbenzene.xyz                    |    0
 .../testsuite-1_2-dimethylbenzene.at               |   42 +
 .../pre/2-methylcyclohexanone.xyz                  |    0
 .../testsuite-2-methylcyclohexanone.at             |   40 +
 .../pre/N_N-dimethylacetamide.xyz                  |    0
 .../testsuite-N_N-dimethylacetamide.at             |   40 +
 tests/Tesselations/Convex/amylose/pre/amylose.pdb  |  470 ++++++
 .../Convex/amylose/testsuite-amylose.at            |   40 +
 .../{ => Convex}/benzene/pre/benzene.xyz           |    0
 .../Convex/benzene/testsuite-benzene.at            |   42 +
 .../{ => Convex}/cholesterol/pre/cholesterol.xyz   |    0
 .../Convex/cholesterol/testsuite-cholesterol.at    |   40 +
 .../{ => Convex}/cycloheptane/pre/cycloheptane.xyz |    0
 .../Convex/cycloheptane/testsuite-cycloheptane.at  |   40 +
 .../pre/dimethyl_bromomalonate.xyz                 |    0
 .../testsuite-dimethyl_bromomalonate.at            |   40 +
 .../{ => Convex}/glucose/pre/glucose.xyz           |    0
 .../Convex/glucose/testsuite-glucose.at            |   40 +
 .../{ => Convex}/heptan/pre/heptan.xyz             |    0
 .../Tesselations/Convex/heptan/testsuite-heptan.at |   40 +
 .../{ => Convex}/isoleucine/pre/isoleucine.xyz     |    0
 .../Convex/isoleucine/testsuite-isoleucine.at      |   40 +
 .../{ => Convex}/neohexane/pre/neohexane.xyz       |    0
 .../Convex/neohexane/testsuite-neohexane.at        |   40 +
 .../{ => Convex}/proline/pre/proline.xyz           |    0
 .../Convex/proline/testsuite-proline.at            |   40 +
 .../{ => Convex}/putrescine/pre/putrescine.xyz     |    0
 .../Convex/putrescine/testsuite-putrescine.at      |   40 +
 .../tartaric_acid/pre/tartaric_acid.xyz            |    0
 .../tartaric_acid/testsuite-tartaric_acid.at       |   42 +
 tests/Tesselations/Makefile.am                     |   90 +-
 .../testsuite-N_N-dimethylacetamide.at             |   40 -
 .../NonConvexEnvelope-1_2-dimethoxyethane-1.5.dat  |    0
 .../NonConvexEnvelope-1_2-dimethoxyethane-2.5.dat  |    0
 .../NonConvexEnvelope-1_2-dimethoxyethane-2.dat    |    0
 .../NonConvexEnvelope-1_2-dimethoxyethane-25.dat   |    0
 .../NonConvexEnvelope-1_2-dimethoxyethane-3.5.dat  |    0
 .../NonConvexEnvelope-1_2-dimethoxyethane-3.dat    |    0
 .../NonConvexEnvelope-1_2-dimethoxyethane-4.dat    |    0
 .../pre/1_2-dimethoxyethane.xyz                    |    0
 .../testsuite-1_2-dimethoxyethane.at               |   40 +
 .../NonConvexEnvelope-1_2-dimethylbenzene-1.5.dat  |    0
 .../NonConvexEnvelope-1_2-dimethylbenzene-2.5.dat  |    0
 .../NonConvexEnvelope-1_2-dimethylbenzene-2.dat    |    0
 .../NonConvexEnvelope-1_2-dimethylbenzene-25.dat   |    0
 .../NonConvexEnvelope-1_2-dimethylbenzene-3.5.dat  |    0
 .../NonConvexEnvelope-1_2-dimethylbenzene-3.dat    |    0
 .../NonConvexEnvelope-1_2-dimethylbenzene-4.dat    |    0
 .../pre/1_2-dimethylbenzene.xyz                    |    0
 .../testsuite-1_2-dimethylbenzene.at               |   40 +
 ...NonConvexEnvelope-2-methylcyclohexanone-1.5.dat |    0
 ...NonConvexEnvelope-2-methylcyclohexanone-2.5.dat |    0
 .../NonConvexEnvelope-2-methylcyclohexanone-2.dat  |    0
 .../NonConvexEnvelope-2-methylcyclohexanone-25.dat |    0
 ...NonConvexEnvelope-2-methylcyclohexanone-3.5.dat |    0
 .../NonConvexEnvelope-2-methylcyclohexanone-3.dat  |    0
 .../NonConvexEnvelope-2-methylcyclohexanone-4.dat  |    0
 .../pre/2-methylcyclohexanone.xyz                  |    0
 .../testsuite-2-methylcyclohexanone.at             |   40 +
 ...NonConvexEnvelope-N_N-dimethylacetamide-1.5.dat |    0
 ...NonConvexEnvelope-N_N-dimethylacetamide-2.5.dat |    0
 .../NonConvexEnvelope-N_N-dimethylacetamide-2.dat  |    0
 .../NonConvexEnvelope-N_N-dimethylacetamide-25.dat |    0
 ...NonConvexEnvelope-N_N-dimethylacetamide-3.5.dat |    0
 .../NonConvexEnvelope-N_N-dimethylacetamide-3.dat  |    0
 .../NonConvexEnvelope-N_N-dimethylacetamide-4.dat  |    0
 .../pre/N_N-dimethylacetamide.xyz                  |    0
 .../testsuite-N_N-dimethylacetamide.at             |   40 +
 .../benzene/post/NonConvexEnvelope-benzene-1.5.dat |    0
 .../benzene/post/NonConvexEnvelope-benzene-2.5.dat |    0
 .../benzene/post/NonConvexEnvelope-benzene-2.dat   |    0
 .../benzene/post/NonConvexEnvelope-benzene-25.dat  |    0
 .../benzene/post/NonConvexEnvelope-benzene-3.5.dat |    0
 .../benzene/post/NonConvexEnvelope-benzene-3.dat   |    0
 .../benzene/post/NonConvexEnvelope-benzene-4.dat   |    0
 .../NonConvex}/benzene/pre/benzene.xyz             |    0
 .../NonConvex/benzene/testsuite-benzene.at         |   40 +
 .../post/NonConvexEnvelope-cholesterol-1.5.dat     |    0
 .../post/NonConvexEnvelope-cholesterol-2.5.dat     |    0
 .../post/NonConvexEnvelope-cholesterol-2.dat       |    0
 .../post/NonConvexEnvelope-cholesterol-25.dat      |    0
 .../post/NonConvexEnvelope-cholesterol-3.5.dat     |    0
 .../post/NonConvexEnvelope-cholesterol-3.dat       |    0
 .../post/NonConvexEnvelope-cholesterol-4.dat       |    0
 .../NonConvex}/cholesterol/pre/cholesterol.xyz     |    0
 .../NonConvex/cholesterol/testsuite-cholesterol.at |   40 +
 .../post/NonConvexEnvelope-cycloheptane-1.5.dat    |    0
 .../post/NonConvexEnvelope-cycloheptane-2.5.dat    |    0
 .../post/NonConvexEnvelope-cycloheptane-2.dat      |    0
 .../post/NonConvexEnvelope-cycloheptane-25.dat     |    0
 .../post/NonConvexEnvelope-cycloheptane-3.5.dat    |    0
 .../post/NonConvexEnvelope-cycloheptane-3.dat      |    0
 .../post/NonConvexEnvelope-cycloheptane-4.dat      |    0
 .../NonConvex}/cycloheptane/pre/cycloheptane.xyz   |    0
 .../cycloheptane/testsuite-cycloheptane.at         |   40 +
 ...onConvexEnvelope-dimethyl_bromomalonate-1.5.dat |    0
 ...onConvexEnvelope-dimethyl_bromomalonate-2.5.dat |    0
 .../NonConvexEnvelope-dimethyl_bromomalonate-2.dat |    0
 ...NonConvexEnvelope-dimethyl_bromomalonate-25.dat |    0
 ...onConvexEnvelope-dimethyl_bromomalonate-3.5.dat |    0
 .../NonConvexEnvelope-dimethyl_bromomalonate-3.dat |    0
 .../NonConvexEnvelope-dimethyl_bromomalonate-4.dat |    0
 .../pre/dimethyl_bromomalonate.xyz                 |    0
 .../testsuite-dimethyl_bromomalonate.at            |   40 +
 .../glucose/post/NonConvexEnvelope-glucose-1.5.dat |    0
 .../glucose/post/NonConvexEnvelope-glucose-2.5.dat |    0
 .../glucose/post/NonConvexEnvelope-glucose-2.dat   |    0
 .../glucose/post/NonConvexEnvelope-glucose-25.dat  |    0
 .../glucose/post/NonConvexEnvelope-glucose-3.5.dat |    0
 .../glucose/post/NonConvexEnvelope-glucose-3.dat   |    0
 .../glucose/post/NonConvexEnvelope-glucose-4.dat   |    0
 .../NonConvex}/glucose/pre/glucose.xyz             |    0
 .../NonConvex/glucose/testsuite-glucose.at         |   40 +
 .../heptan/post/NonConvexEnvelope-heptan-1.5.dat   |    0
 .../heptan/post/NonConvexEnvelope-heptan-2.5.dat   |    0
 .../heptan/post/NonConvexEnvelope-heptan-2.dat     |    0
 .../heptan/post/NonConvexEnvelope-heptan-25.dat    |    0
 .../heptan/post/NonConvexEnvelope-heptan-3.5.dat   |    0
 .../heptan/post/NonConvexEnvelope-heptan-3.dat     |    0
 .../heptan/post/NonConvexEnvelope-heptan-4.dat     |    0
 .../NonConvex}/heptan/pre/heptan.xyz               |    0
 .../NonConvex/heptan/testsuite-heptan.at           |   40 +
 .../post/NonConvexEnvelope-isoleucine-1.5.dat      |    0
 .../post/NonConvexEnvelope-isoleucine-2.5.dat      |    0
 .../post/NonConvexEnvelope-isoleucine-2.dat        |    0
 .../post/NonConvexEnvelope-isoleucine-25.dat       |    0
 .../post/NonConvexEnvelope-isoleucine-3.5.dat      |    0
 .../post/NonConvexEnvelope-isoleucine-3.dat        |    0
 .../post/NonConvexEnvelope-isoleucine-4.dat        |    0
 .../NonConvex}/isoleucine/pre/isoleucine.xyz       |    0
 .../NonConvex/isoleucine/testsuite-isoleucine.at   |   40 +
 .../post/NonConvexEnvelope-neohexane-1.5.dat       |    0
 .../post/NonConvexEnvelope-neohexane-2.5.dat       |    0
 .../post/NonConvexEnvelope-neohexane-2.dat         |    0
 .../post/NonConvexEnvelope-neohexane-25.dat        |    0
 .../post/NonConvexEnvelope-neohexane-3.5.dat       |    0
 .../post/NonConvexEnvelope-neohexane-3.dat         |    0
 .../post/NonConvexEnvelope-neohexane-4.dat         |    0
 .../NonConvex}/neohexane/pre/neohexane.xyz         |    0
 .../NonConvex/neohexane/testsuite-neohexane.at     |   40 +
 .../proline/post/NonConvexEnvelope-proline-1.5.dat |    0
 .../proline/post/NonConvexEnvelope-proline-2.5.dat |    0
 .../proline/post/NonConvexEnvelope-proline-2.dat   |    0
 .../proline/post/NonConvexEnvelope-proline-25.dat  |    0
 .../proline/post/NonConvexEnvelope-proline-3.5.dat |    0
 .../proline/post/NonConvexEnvelope-proline-3.dat   |    0
 .../proline/post/NonConvexEnvelope-proline-4.dat   |    0
 .../NonConvex}/proline/pre/proline.xyz             |    0
 .../NonConvex/proline/testsuite-proline.at         |   40 +
 .../post/NonConvexEnvelope-putrescine-1.5.dat      |    0
 .../post/NonConvexEnvelope-putrescine-2.5.dat      |    0
 .../post/NonConvexEnvelope-putrescine-2.dat        |    0
 .../post/NonConvexEnvelope-putrescine-25.dat       |    0
 .../post/NonConvexEnvelope-putrescine-3.5.dat      |    0
 .../post/NonConvexEnvelope-putrescine-3.dat        |    0
 .../post/NonConvexEnvelope-putrescine-4.dat        |    0
 .../NonConvex}/putrescine/pre/putrescine.xyz       |    0
 .../NonConvex/putrescine/testsuite-putrescine.at   |   40 +
 .../post/NonConvexEnvelope-tartaric_acid-1.5.dat   |    0
 .../post/NonConvexEnvelope-tartaric_acid-2.5.dat   |    0
 .../post/NonConvexEnvelope-tartaric_acid-2.dat     |    0
 .../post/NonConvexEnvelope-tartaric_acid-25.dat    |    0
 .../post/NonConvexEnvelope-tartaric_acid-3.5.dat   |    0
 .../post/NonConvexEnvelope-tartaric_acid-3.dat     |    0
 .../post/NonConvexEnvelope-tartaric_acid-4.dat     |    0
 .../NonConvex}/tartaric_acid/pre/tartaric_acid.xyz |    0
 .../tartaric_acid/testsuite-tartaric_acid.at       |   40 +
 tests/Tesselations/benzene/testsuite-benzene.at    |   40 -
 .../cholesterol/testsuite-cholesterol.at           |   40 -
 .../cycloheptane/testsuite-cycloheptane.at         |   40 -
 .../testsuite-dimethyl_bromomalonate.at            |   40 -
 tests/Tesselations/glucose/testsuite-glucose.at    |   40 -
 tests/Tesselations/heptan/testsuite-heptan.at      |   40 -
 .../isoleucine/testsuite-isoleucine.at             |   40 -
 .../Tesselations/neohexane/testsuite-neohexane.at  |   40 -
 tests/Tesselations/proline/testsuite-proline.at    |   40 -
 .../putrescine/testsuite-putrescine.at             |   40 -
 .../tartaric_acid/testsuite-tartaric_acid.at       |   40 -
 tests/Tesselations/testsuite.at                    |   82 +-
 .../regression/Atoms/Mirror/post/test-mirrored.xyz |    5 +
 tests/regression/Atoms/Mirror/post/test.xyz        |    5 +
 tests/regression/Atoms/Mirror/pre/test.xyz         |    5 +
 .../Atoms/Mirror/testsuite-atoms-mirror.at         |   53 +
 .../post/test-shifted-weighted.xyz                 |    5 +
 .../TranslationToOrigin/post/test-shifted.xyz      |    5 +
 .../Atoms/TranslationToOrigin/post/test.xyz        |    5 +
 .../Atoms/TranslationToOrigin/pre/test.xyz         |    5 +
 .../testsuite-atoms-translation-to-origin.at       |   65 +
 tests/regression/Atoms/testsuite-atoms.at          |    6 +
 tests/regression/Makefile.am                       |    2 +
 .../testsuite-potential-fit-potential.at           |   96 +-
 .../Tesselation/BigConvex/post/ConvexEnvelope.dat  |   90 ++
 .../Tesselation/BigConvex/post/ConvexEnvelope.r3d  |  277 ++++
 .../BigConvex/post/NonConvexEnvelope.dat           |  123 --
 .../BigConvex/post/NonConvexEnvelope.r3d           |  321 ----
 .../Tesselation/BigConvex/post/test.conf           |  147 --
 .../testsuite-tesselation-big-convex-envelope.at   |    7 +-
 .../testsuite-tesselation-convex-envelope.at       |    4 +-
 utils/developer/raster3d/header.r3d                |   20 +
 utils/developer/tcl/analyseconvexizing.tcl         |  161 ++
 utils/developer/tcl/convexizing.tcl                |   79 +
 287 files changed, 7014 insertions(+), 2961 deletions(-)
 create mode 100644 src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp
 create mode 100644 src/Actions/AnalysisAction/AverageMoleculeForceAction.def
 create mode 100644 src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp
 create mode 100644 src/Actions/AtomAction/MirrorAction.cpp
 create mode 100644 src/Actions/AtomAction/MirrorAction.def
 create mode 100644 src/Actions/AtomAction/MirrorAction.hpp
 create mode 100644 src/Actions/AtomAction/TranslateToOriginAction.cpp
 create mode 100644 src/Actions/AtomAction/TranslateToOriginAction.def
 create mode 100644 src/Actions/AtomAction/TranslateToOriginAction.hpp
 create mode 100644 src/Actions/PotentialAction/FitCompoundPotentialAction.cpp
 create mode 100644 src/Actions/PotentialAction/FitCompoundPotentialAction.def
 create mode 100644 src/Actions/PotentialAction/FitCompoundPotentialAction.hpp
 create mode 100644 src/Actions/PotentialAction/ParsePotentialsAction.cpp
 create mode 100644 src/Actions/PotentialAction/ParsePotentialsAction.def
 create mode 100644 src/Actions/PotentialAction/ParsePotentialsAction.hpp
 create mode 100644 src/Actions/PotentialAction/SavePotentialsAction.cpp
 create mode 100644 src/Actions/PotentialAction/SavePotentialsAction.def
 create mode 100644 src/Actions/PotentialAction/SavePotentialsAction.hpp
 create mode 100644 src/Potentials/PotentialTrainer.cpp
 create mode 100644 src/Potentials/PotentialTrainer.hpp
 create mode 100644 tests/CodeChecks/testsuite-action_present_in_userguide.at
 delete mode 100644 tests/Tesselations/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at
 delete mode 100644 tests/Tesselations/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at
 delete mode 100644 tests/Tesselations/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at
 rename tests/Tesselations/{ => Convex}/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at
 rename tests/Tesselations/{ => Convex}/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at
 rename tests/Tesselations/{ => Convex}/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at
 rename tests/Tesselations/{ => Convex}/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at
 create mode 100644 tests/Tesselations/Convex/amylose/pre/amylose.pdb
 create mode 100644 tests/Tesselations/Convex/amylose/testsuite-amylose.at
 rename tests/Tesselations/{ => Convex}/benzene/pre/benzene.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/benzene/testsuite-benzene.at
 rename tests/Tesselations/{ => Convex}/cholesterol/pre/cholesterol.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/cholesterol/testsuite-cholesterol.at
 rename tests/Tesselations/{ => Convex}/cycloheptane/pre/cycloheptane.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/cycloheptane/testsuite-cycloheptane.at
 rename tests/Tesselations/{ => Convex}/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at
 rename tests/Tesselations/{ => Convex}/glucose/pre/glucose.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/glucose/testsuite-glucose.at
 rename tests/Tesselations/{ => Convex}/heptan/pre/heptan.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/heptan/testsuite-heptan.at
 rename tests/Tesselations/{ => Convex}/isoleucine/pre/isoleucine.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/isoleucine/testsuite-isoleucine.at
 rename tests/Tesselations/{ => Convex}/neohexane/pre/neohexane.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/neohexane/testsuite-neohexane.at
 rename tests/Tesselations/{ => Convex}/proline/pre/proline.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/proline/testsuite-proline.at
 rename tests/Tesselations/{ => Convex}/putrescine/pre/putrescine.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/putrescine/testsuite-putrescine.at
 rename tests/Tesselations/{ => Convex}/tartaric_acid/pre/tartaric_acid.xyz (100%)
 create mode 100644 tests/Tesselations/Convex/tartaric_acid/testsuite-tartaric_acid.at
 delete mode 100644 tests/Tesselations/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at
 rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at
 rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at
 rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/benzene/post/NonConvexEnvelope-benzene-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/benzene/pre/benzene.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/benzene/testsuite-benzene.at
 rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cholesterol/post/NonConvexEnvelope-cholesterol-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/cholesterol/pre/cholesterol.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/cholesterol/testsuite-cholesterol.at
 rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/cycloheptane/post/NonConvexEnvelope-cycloheptane-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/cycloheptane/pre/cycloheptane.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/cycloheptane/testsuite-cycloheptane.at
 rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at
 rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/glucose/post/NonConvexEnvelope-glucose-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/glucose/pre/glucose.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/glucose/testsuite-glucose.at
 rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/heptan/post/NonConvexEnvelope-heptan-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/heptan/pre/heptan.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/heptan/testsuite-heptan.at
 rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/isoleucine/post/NonConvexEnvelope-isoleucine-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/isoleucine/pre/isoleucine.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/isoleucine/testsuite-isoleucine.at
 rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/neohexane/post/NonConvexEnvelope-neohexane-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/neohexane/pre/neohexane.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/neohexane/testsuite-neohexane.at
 rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/proline/post/NonConvexEnvelope-proline-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/proline/pre/proline.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/proline/testsuite-proline.at
 rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/putrescine/post/NonConvexEnvelope-putrescine-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/putrescine/pre/putrescine.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/putrescine/testsuite-putrescine.at
 rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-1.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-2.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-2.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-25.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-3.5.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-3.dat (100%)
 rename tests/Tesselations/{ => NonConvex}/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-4.dat (100%)
 copy tests/{Fragmentations/Fragmenting => Tesselations/NonConvex}/tartaric_acid/pre/tartaric_acid.xyz (100%)
 create mode 100644 tests/Tesselations/NonConvex/tartaric_acid/testsuite-tartaric_acid.at
 delete mode 100644 tests/Tesselations/benzene/testsuite-benzene.at
 delete mode 100644 tests/Tesselations/cholesterol/testsuite-cholesterol.at
 delete mode 100644 tests/Tesselations/cycloheptane/testsuite-cycloheptane.at
 delete mode 100644 tests/Tesselations/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at
 delete mode 100644 tests/Tesselations/glucose/testsuite-glucose.at
 delete mode 100644 tests/Tesselations/heptan/testsuite-heptan.at
 delete mode 100644 tests/Tesselations/isoleucine/testsuite-isoleucine.at
 delete mode 100644 tests/Tesselations/neohexane/testsuite-neohexane.at
 delete mode 100644 tests/Tesselations/proline/testsuite-proline.at
 delete mode 100644 tests/Tesselations/putrescine/testsuite-putrescine.at
 delete mode 100644 tests/Tesselations/tartaric_acid/testsuite-tartaric_acid.at
 create mode 100644 tests/regression/Atoms/Mirror/post/test-mirrored.xyz
 create mode 100644 tests/regression/Atoms/Mirror/post/test.xyz
 create mode 100644 tests/regression/Atoms/Mirror/pre/test.xyz
 create mode 100644 tests/regression/Atoms/Mirror/testsuite-atoms-mirror.at
 create mode 100644 tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz
 create mode 100644 tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz
 create mode 100644 tests/regression/Atoms/TranslationToOrigin/post/test.xyz
 create mode 100644 tests/regression/Atoms/TranslationToOrigin/pre/test.xyz
 create mode 100644 tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at
 create mode 100644 tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.dat
 create mode 100644 tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.r3d
 delete mode 100644 tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.dat
 delete mode 100644 tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.r3d
 delete mode 100644 tests/regression/Tesselation/BigConvex/post/test.conf
 create mode 100644 utils/developer/raster3d/header.r3d
 create mode 100644 utils/developer/tcl/analyseconvexizing.tcl
 create mode 100644 utils/developer/tcl/convexizing.tcl


hooks/post-receive
-- 
MoleCuilder


From git at ins.uni-bonn.de  Fri Oct 24 19:49:32 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri, 24 Oct 2014 19:49:32 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Fix_VMGForces created.
	v1.4.9-8-g307f15a
Message-ID: <20141024174933.00FDE10000F9@jupiter.ins.uni-bonn.de>

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, Fix_VMGForces has been created
        at  307f15aa52220dace3dc7f00c0ad7699e70cd2c2 (commit)

- Log -----------------------------------------------------------------
commit 307f15aa52220dace3dc7f00c0ad7699e70cd2c2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:49:08 2014 +0200

    tempcommit: Fixes to InterfaceVMGJob.

commit 48efe779baefa7303b2d6478f91585da471e2b2e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:37:21 2014 +0200

    Added new SetValues FragmentForces.

commit d16a3ccd3112252652ee21663b63528d5c216823
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:36:38 2014 +0200

    tempcommit: Merge with 940da75c

commit e28a70c22648ae28dce0acbf4b507bbb99b7bba9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:34:31 2014 +0200

    tempcommit: Merge with d302c57b

commit 7ba727725051002d1b7602f8fdc9f567f13c4a4d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 23 19:09:06 2014 +0200

    tempcommit: Fix. Merge with d302c57b

commit 6e0506ff9f4acaada53ea1a545ee688456c4be4b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 17 19:29:19 2014 +0200

    FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob.
    
    - note that so far domains needs to be cubic.

commit d302c57b6c1c3d75803d9a2b0ad332dd5c11a911
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 20 18:31:42 2014 +0100

    Added particle_forces entity to VMGData.
    
    - needs to get filled yet.

commit 940da75c02ac96c8907eed986c8467a38fccea32
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 20 18:30:19 2014 +0100

    Added extraction of long-range forces from VMGData's array f.

-----------------------------------------------------------------------


hooks/post-receive
-- 
MoleCuilder


From git at ins.uni-bonn.de  Sat Oct 25 13:06:27 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Sat, 25 Oct 2014 13:06:27 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Fix_VMGForces updated.
	v1.4.9-11-g2c2d023
Message-ID: <20141025110628.46B0D10000F9@jupiter.ins.uni-bonn.de>

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, Fix_VMGForces has been updated
       via  2c2d0231a7e6dfbdddb7194afd82d5edfb85e7c9 (commit)
       via  72c797595c5e794f89a48a37bca44c1f7834f850 (commit)
       via  1d9591267e76f1e0ced09ce7f8c309c384007294 (commit)
      from  307f15aa52220dace3dc7f00c0ad7699e70cd2c2 (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.

- Log -----------------------------------------------------------------
commit 2c2d0231a7e6dfbdddb7194afd82d5edfb85e7c9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 12:49:02 2014 +0200

    Split off sampled_potential im VMGDataMap_t into separate fusion container.
    
    - this should correct the output in ..._VMGEnergy.dat

commit 72c797595c5e794f89a48a37bca44c1f7834f850
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 09:56:46 2014 +0200

    tempcommit: FragmentForces was missing in some parts.

commit 1d9591267e76f1e0ced09ce7f8c309c384007294
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 09:54:37 2014 +0200

    FIX: Shared libraries's Makefile.am rules are now consistent.
    
    - pkgconfig is just given once (in src/Makefile.am).
    - all have version information, including now pyMoleCuilder.so.

-----------------------------------------------------------------------

Summary of changes:
 .../AnalyseFragmentationResultsAction.cpp          |   12 +++--
 .../FragmentationAutomationAction.cpp              |    1 +
 src/Fragmentation/Makefile.am                      |    7 ---
 .../Containers/FragmentationLongRangeResults.cpp   |    9 +++-
 .../Containers/FragmentationLongRangeResults.hpp   |    4 ++
 src/Fragmentation/Summation/Containers/VMGData.cpp |    1 +
 src/Fragmentation/Summation/Containers/VMGData.hpp |    2 +-
 .../Summation/Containers/VMGDataMap.hpp            |   14 +++++--
 .../Summation/Converter/DataConverter.hpp          |   21 +++++++++-
 src/Fragmentation/Summation/Makefile.am            |    7 ---
 .../Summation/SetValues/FragmentForces.cpp         |    8 ++++
 .../Summation/SetValues/FragmentForces.hpp         |    2 +-
 src/Jobs/Makefile.am                               |    7 ---
 src/Makefile.am                                    |    2 +-
 src/UIElements/Makefile.am                         |   42 ++++++++++++++-----
 src/UIElements/Views/Qt4/Plotting/Makefile.am      |   30 +++++++++++++-
 16 files changed, 118 insertions(+), 51 deletions(-)


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From git at ins.uni-bonn.de  Sun Oct 26 00:02:26 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Sun, 26 Oct 2014 00:02:26 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Fix_VMGForces deleted.
	v1.4.9-11-g2c2d023
Message-ID: <20141025220226.A5F4710000F9@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Fix_VMGForces has been deleted
       was  2c2d0231a7e6dfbdddb7194afd82d5edfb85e7c9

-----------------------------------------------------------------------
2c2d0231a7e6dfbdddb7194afd82d5edfb85e7c9 Split off sampled_potential im VMGDataMap_t into separate fusion container.
-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Sun Oct 26 00:02:31 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Sun, 26 Oct 2014 00:02:31 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Fix_VMGForces created.
	v1.4.9-15-g080a424
Message-ID: <20141025220231.4A7AF10000F9@jupiter.ins.uni-bonn.de>

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, Fix_VMGForces has been created
        at  080a424203e0ebca556daa66aeee341639f7c857 (commit)

- Log -----------------------------------------------------------------
commit 080a424203e0ebca556daa66aeee341639f7c857
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 26 00:01:51 2014 +0200

    tempcommit: Some changes to InterfaceVMGJob on force summation.
    
    - added some debug output.

commit a9b2563e739c20b2dbe939a7c5246a57b7fa06e2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 26 00:00:30 2014 +0200

    MPQCData now also uses FragmentForces (instead of typedef forcevector).
    
    - required small changes to MPQCCommandJob due to changed typedef.

commit e99b6854ddb97a11c933537772a31331beb695d5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 26 00:00:05 2014 +0200

    tempcommit: Removed += and -= operators again from FragmentForces.

commit 7b1bee90e5dc6cbda55f0799628df9f04a0a25e3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 23:56:32 2014 +0200

    Again changes to obtain correct longrange forces.
    
    - renamed particle_forces -> forces to make it consistent with MPQCData_Fused.
    - MPQCData_Fused and VMGData_Fused are structs and no longer namespace as the
      latter cannot serve as template arguments.
    - split off forces in VMGData into VMGDataForceMap_t and VMGDataForceVector_t.
    - changed ConvertMPQCDataToForceMap() into template function
      ConvertDataToForceMap(), working also on VMGDataForceMap_t.
    - this required changes in FragmentationShortRangeResults.
    - FragmentationLongRangeResults now also converts the longrange forces
      correctly.
    - AnalyseFragmentResults now prints also a ..VMGForces.dat file.

commit 001ff0e359be41e9130809c0b1b3acb4483165df
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 12:49:02 2014 +0200

    Split off sampled_potential im VMGDataMap_t into separate fusion container.
    
    - this should correct the output in ..._VMGEnergy.dat

commit 72c797595c5e794f89a48a37bca44c1f7834f850
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 09:56:46 2014 +0200

    tempcommit: FragmentForces was missing in some parts.

commit 1d9591267e76f1e0ced09ce7f8c309c384007294
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 09:54:37 2014 +0200

    FIX: Shared libraries's Makefile.am rules are now consistent.
    
    - pkgconfig is just given once (in src/Makefile.am).
    - all have version information, including now pyMoleCuilder.so.

commit 307f15aa52220dace3dc7f00c0ad7699e70cd2c2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:49:08 2014 +0200

    tempcommit: Fixes to InterfaceVMGJob.

commit 48efe779baefa7303b2d6478f91585da471e2b2e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:37:21 2014 +0200

    Added new SetValues FragmentForces.

commit d16a3ccd3112252652ee21663b63528d5c216823
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:36:38 2014 +0200

    tempcommit: Merge with 940da75c

commit e28a70c22648ae28dce0acbf4b507bbb99b7bba9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:34:31 2014 +0200

    tempcommit: Merge with d302c57b

commit 7ba727725051002d1b7602f8fdc9f567f13c4a4d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 23 19:09:06 2014 +0200

    tempcommit: Fix. Merge with d302c57b

commit 6e0506ff9f4acaada53ea1a545ee688456c4be4b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 17 19:29:19 2014 +0200

    FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob.
    
    - note that so far domains needs to be cubic.

commit d302c57b6c1c3d75803d9a2b0ad332dd5c11a911
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 20 18:31:42 2014 +0100

    Added particle_forces entity to VMGData.
    
    - needs to get filled yet.

commit 940da75c02ac96c8907eed986c8467a38fccea32
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 20 18:30:19 2014 +0100

    Added extraction of long-range forces from VMGData's array f.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Sun Oct 26 00:02:48 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Sun, 26 Oct 2014 00:02:48 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch GUI_smallchanges
	created. v1.4.9-2-g7305d52
Message-ID: <20141025220248.B2E8410000F9@jupiter.ins.uni-bonn.de>

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, GUI_smallchanges has been created
        at  7305d5268402221ff02978b5f2ec39cb12bbd238 (commit)

- Log -----------------------------------------------------------------
commit 7305d5268402221ff02978b5f2ec39cb12bbd238
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 17 18:04:58 2014 +0200

    Removed extra option actionname from HelpAction.
    
    - this shortens the way to getting help a lot.
    - TESTFIX: regression potentials fixed due to removed actionname.

commit fe02bf3a9081343f5898f5348bfea7aa2dd6e3de
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 17 18:50:10 2014 +0200

    CommandLineParser adds Action's default values as implicit.
    
    - this allows to have action's token as option with both empty (then default is
      used) and some given argument.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Sun Oct 26 00:02:56 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Sun, 26 Oct 2014 00:02:56 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch ThreadFixes deleted.
	v1.4.7-20-gca890d1
Message-ID: <20141025220256.233B110000F9@jupiter.ins.uni-bonn.de>

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, ThreadFixes has been deleted
       was  ca890d10159865475183bd08e46c1d304c75cc3f

-----------------------------------------------------------------------
ca890d10159865475183bd08e46c1d304c75cc3f Cleaned up use of mutexes in ActionQueue.
-----------------------------------------------------------------------


hooks/post-receive
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From git at ins.uni-bonn.de  Sun Oct 26 00:02:58 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Sun, 26 Oct 2014 00:02:58 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch ThreadFixes created.
	v1.4.9-3-gfff8fcb
Message-ID: <20141025220258.6997810000F9@jupiter.ins.uni-bonn.de>

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, ThreadFixes has been created
        at  fff8fcbd58abd7059236c3fbddafc1000d300ae9 (commit)

- Log -----------------------------------------------------------------
commit fff8fcbd58abd7059236c3fbddafc1000d300ae9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 21:26:17 2014 +0200

    Cleaned up use of mutexes in ActionQueue.
    
    - tempqueue now has its own mutex.
    - more often using lock_guard.
    - run_thread_isIdle has own mutex.

commit 9a4949ffbc4c1ce8a083f8878c8ff61e484e6e79
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 19:21:08 2014 +0200

    Added extra flag run_thread_running to ActionQueue.
    
    - helgrind admonished race conditions when thread is joined. This did not fix
      them but should be safer as we cannot know whether the other thread has
      already been started when suddenly shutting down molecuilder due to an
      exception.

commit 23b6cf7ccc51b9a98424d0793c25f776ae063e5f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 29 11:46:02 2014 +0200

    THREADFIX: Fixed ActionQueue with respect to mutex and threads.
    
    - run_thread is now last member variable, hence started after all other
      variables are initialized.
    - separated accesses to queues and to run_thread_isIdle flag. Also renamed
      its mutex for easier association with it.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Sun Oct 26 00:04:00 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Sun, 26 Oct 2014 00:04:00 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch GUI_smallerchanges
	created. v1.4.8-22-g107bfd9
Message-ID: <20141025220400.CE9ED10000F9@jupiter.ins.uni-bonn.de>

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, GUI_smallerchanges has been created
        at  107bfd9a3f982894a7922552138617bab4d117b7 (commit)

- Log -----------------------------------------------------------------
commit 107bfd9a3f982894a7922552138617bab4d117b7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 17 15:41:21 2014 +0200

    Increased timer interval in QtStatusBar to 4secs.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Tue Oct 28 00:20:55 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Tue, 28 Oct 2014 00:20:55 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Fix_VMGForces deleted.
	v1.4.9-15-g080a424
Message-ID: <20141027232057.4AF1010000F9@jupiter.ins.uni-bonn.de>

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, Fix_VMGForces has been deleted
       was  080a424203e0ebca556daa66aeee341639f7c857

-----------------------------------------------------------------------
080a424203e0ebca556daa66aeee341639f7c857 tempcommit: Some changes to InterfaceVMGJob on force summation.
-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Tue Oct 28 00:21:06 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Tue, 28 Oct 2014 00:21:06 +0100 (CET)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Fix_VMGForces created.
	v1.4.9-15-g30bff67
Message-ID: <20141027232108.8EB1810000F9@jupiter.ins.uni-bonn.de>

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, Fix_VMGForces has been created
        at  30bff67aa3428b5502ae8a9a116a176be12a5572 (commit)

- Log -----------------------------------------------------------------
commit 30bff67aa3428b5502ae8a9a116a176be12a5572
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 26 00:01:51 2014 +0200

    tempcommit: Some changes to InterfaceVMGJob on force summation.
    
    - added some debug output.

commit 354da21f4a522a1ae6d997961f3a85fafbd7b5d3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 26 00:00:30 2014 +0200

    MPQCData now also uses FragmentForces (instead of typedef forcevector).
    
    - required small changes to MPQCCommandJob due to changed typedef.

commit aa6e95a3c0d7f5e1411fd1763fcdd29df7f5e95d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Oct 26 00:00:05 2014 +0200

    tempcommit: Removed += and -= operators again from FragmentForces.

commit 8b4b9679e5f127dfb10da1f1bfde79e89f877c68
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 23:56:32 2014 +0200

    Again changes to obtain correct longrange forces.
    
    - renamed particle_forces -> forces to make it consistent with MPQCData_Fused.
    - MPQCData_Fused and VMGData_Fused are structs and no longer namespace as the
      latter cannot serve as template arguments.
    - split off forces in VMGData into VMGDataForceMap_t and VMGDataForceVector_t.
    - changed ConvertMPQCDataToForceMap() into template function
      ConvertDataToForceMap(), working also on VMGDataForceMap_t.
    - this required changes in FragmentationShortRangeResults.
    - FragmentationLongRangeResults now also converts the longrange forces
      correctly.
    - AnalyseFragmentResults now prints also a ..VMGForces.dat file.

commit 001ff0e359be41e9130809c0b1b3acb4483165df
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 12:49:02 2014 +0200

    Split off sampled_potential im VMGDataMap_t into separate fusion container.
    
    - this should correct the output in ..._VMGEnergy.dat

commit 72c797595c5e794f89a48a37bca44c1f7834f850
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 09:56:46 2014 +0200

    tempcommit: FragmentForces was missing in some parts.

commit 1d9591267e76f1e0ced09ce7f8c309c384007294
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 25 09:54:37 2014 +0200

    FIX: Shared libraries's Makefile.am rules are now consistent.
    
    - pkgconfig is just given once (in src/Makefile.am).
    - all have version information, including now pyMoleCuilder.so.

commit 307f15aa52220dace3dc7f00c0ad7699e70cd2c2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:49:08 2014 +0200

    tempcommit: Fixes to InterfaceVMGJob.

commit 48efe779baefa7303b2d6478f91585da471e2b2e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:37:21 2014 +0200

    Added new SetValues FragmentForces.

commit d16a3ccd3112252652ee21663b63528d5c216823
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:36:38 2014 +0200

    tempcommit: Merge with 940da75c

commit e28a70c22648ae28dce0acbf4b507bbb99b7bba9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 24 19:34:31 2014 +0200

    tempcommit: Merge with d302c57b

commit 7ba727725051002d1b7602f8fdc9f567f13c4a4d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 23 19:09:06 2014 +0200

    tempcommit: Fix. Merge with d302c57b

commit 6e0506ff9f4acaada53ea1a545ee688456c4be4b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 17 19:29:19 2014 +0200

    FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob.
    
    - note that so far domains needs to be cubic.

commit d302c57b6c1c3d75803d9a2b0ad332dd5c11a911
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 20 18:31:42 2014 +0100

    Added particle_forces entity to VMGData.
    
    - needs to get filled yet.

commit 940da75c02ac96c8907eed986c8467a38fccea32
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Mar 20 18:30:19 2014 +0100

    Added extraction of long-range forces from VMGData's array f.

-----------------------------------------------------------------------


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