[Molecuilder-devel] [SCM] MoleCuilder branch Fix_ConvexizeNonconexEnvelope created. v1.4.8-30-gab72314

Fri Sep 26 17:39:25 CEST 2014

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The branch, Fix_ConvexizeNonconexEnvelope has been created
        at  ab72314934e071f1c33d4d2875f9d27458fb67da (commit)

- Log -----------------------------------------------------------------
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.

commit 78c9509cba8ec6569d3fee2987607785743b7e09
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 71350daef4a36bbd039aa43a5712363fddfc5a00
Merge: 14bede3 c7fe90c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:13:05 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 14bede3ba3e8e2630b00858a76285e0e0439b26a
Merge: 5340768 46ce1c8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:11:02 2014 +0200

    Merge branch 'DynamicMolecules' into Candidate_v1.4.9

commit 5340768e903e79d978c07f327466f51ba993a139
Merge: 2ed3bf3 9d1320c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:10:10 2014 +0200

    Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9

commit 2ed3bf3dd38da578e40e717928f565e66746d252
Merge: 7acbfc4 bbf6dcd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:10:04 2014 +0200

    Merge branch 'MirrorAtoms' into Candidate_v1.4.9

commit 7acbfc4fee584acd54942911e6d4b9c73149b2c7
Merge: 9bce964 054d47f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:09:53 2014 +0200

    Merge branch 'ActionFixes' into Candidate_v1.4.9

commit bbf6dcd010a0439f2e1a441678550e5a56e1cf30
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 10 01:55:39 2014 +0200

    Added AtomMirrorAction.

    - also added regression tests.

commit 9d1320cc5a22b299fc35b50bb519d8bd8b13bc21
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 5c6b432e38763ef95f591b8dae5078375f60c46c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 12 09:39:58 2014 +0200

    Extracted ParsePotentialsAction from FitCompoundPotentialAction.

commit 21c1c5cb23b27248af841d0fb4f026616b41b8c5
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.

commit 46ce1c8a9f9a6af80b7fcf736dcf57f11b47f8b7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 17 20:30:46 2014 +0200

    FIX: World::setTime() now first copies Bondgraph and then sets the time.

    - thus we do not cause GUI updates with each addBond().

commit 8cc22fe4af9577450a3d00a92ea000018b14b366
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 17 00:56:59 2014 +0200

    Changed how trajectories are stored, not as vecor but as map.

    - AtomInfo and atom_bondedparticleinfo now store map<unsigned int, ...> instead
      of vector<...>.
    - UpdateSteps() -> UpdateStep(unsigned int), same with RemoveSteps() and
      AppendTrajectorySteps() and RemoveTrajectorySteps().
    - made changes necessary to UndoRedoHelpers and two Actions.
    - TESTFIX: AtomObserverUnitTest failed as we longer "notify" in case already
      set element is set again. We now check that setType() sets to different
      element.

commit c7fe90cd467a73a0ef32b5c631534b2928c0b926
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Aug 14 22:03:53 2014 +0200

    Added TranslateToOriginAction.

    - also added regression test.

commit f4b626a1fbf68b80e642bace1770e5577aeed6d8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 10:48:59 2014 +0200

    Added AverageMoleculeForceAction for measuring average force acting on a molecule.

commit 7a7b3408459dae333637248d2b3e0bebed301975
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 17 12:10:08 2014 +0200

    FIX: atom's copy cstor does not need to copy positions, ... again.

commit 054d47f3558f3549e6480280882111c4df74ad9f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 11 09:31:52 2014 +0200

    FIX: (Not)AtomByIdAction would fail with assert if not atoms are present.

    - none are selected, we just fail the Action but removed assert.

commit 9bce96471db8bac23510c29ddaa7dbcabf15d765
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 21:26:46 2014 +0200

    DOCU: Fixed all missing links in userguide.

    - each section now has a linkname.

commit f73e0644af36b981af22685b57300f77cb7b0937
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 20:25:06 2014 +0200

    DOCU: Added all missing Actions to userguide.

    - removed XFAIL from associated CodeChecks test.

commit c62e275561001d2ecd22b8489ac47810fd64e5ce
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 18:23:41 2014 +0200

    Added CodeChecks test that every action appears in the userguide.

    - test is marked as XFAIL for the moment.

commit 2a6d8c7977c1f749091ead256bcca349538a8b59
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 20:24:38 2014 +0200

    DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer.

commit ced7f04bae3c2939e0888dfb7559e4b0f342a808
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 20:24:23 2014 +0200

    VersionAction also prints to log, not only to status.

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