[Molecuilder-devel] [SCM] MoleCuilder annotated tag v1.4.9 created. v1.4.9

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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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