[Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.7 created. v1.4.6-34-g8e20e36

Mon Aug 18 21:20:12 CEST 2014

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The branch, Candidate_v1.4.7 has been created
        at  8e20e36dcc35c56d5a90a9967b3b89ff17846858 (commit)

- Log -----------------------------------------------------------------
commit 8e20e36dcc35c56d5a90a9967b3b89ff17846858
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Aug 14 11:05:32 2014 +0200

    FIX: QtTimeLine::recieveNotification() checked falsely against AtomObserver.

    - publisher is always the atom, not the relay.
    - that's why the time line did not get updated when a molecule with more than
      one timestep was loaded.

commit fb55065f34f19f831cc839df4504c71af959e0ca
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 13 17:08:14 2014 +0200

    MPQCCommandFragmentController supports FragmentationAutomationAction being a Process.

    - i.e. it also calls an update handler when more results have been received.

commit 3df57f2e7d807f5db30f539726be285674ae8227
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 13 15:59:54 2014 +0200

    FIX: PdbParser would write coordinates 4.1000 instead of 5.000.

    - we did round in printCoordinates(), without checking for overflow, resulting
      in 1000 for 999.9 instead of 999.
    - extended ParserPdbUnitTest to test these cases.

commit c7212c1d7bc21c1f8e7249d31eae711aa179115f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Aug 11 19:56:03 2014 +0200

    Giving the maximum components over all force vectors in ForceAnnealing.

commit 24b66db290e0f96f9b9eed3221e779ca570dc9da
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 10 15:17:52 2014 +0200

    FIX: typos in AtomicForceManipulator.hpp.

commit 51cfda11221ab02d7db630f150d0ba120ec6dff3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 10 14:47:43 2014 +0200

    FIX: CheckOrderAtSite() called PrintAtomMask() with wrong AtomCount.

commit 622e44a48d1737a7ede7a36df157afdbef7f88c7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 2 18:22:46 2014 +0200

    Added MakroAction StructureOptimizationAction.

    - performs similarly as MolecularDynamicsAction only using ForceAnnealing.

commit ffa509902bdaef0fce358b99bc31165d858391c7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 16 17:40:44 2014 +0200

    FIX: MolecularDynamicsAction works also without JobMarket.

    - since FragmentationAutomation works without.

commit 75869021a53f72dfd0b76aa0d1d11b0dcae8f5f8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 2 12:05:40 2014 +0200

    Added ForceAnnealingAction.

    - also added regression test.
    - added output-every-step for debugging.

commit c7390ef3bc9bd50283ccac940a2ad75a4d40d33b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 2 12:01:05 2014 +0200

    Added CodeCheck for ensuring testsuite..at's appear in tests/regression/Makefile.am.

    - brought files in tests/regression/Makefile.am in alphabetical order.
    - FIX: testsuite-potential.at was missing.

commit 8a5780b12c77470597a7d4796295943179ed98ee
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 2 11:43:22 2014 +0200

    Extended VerletIntegrationAction wirth Undo/Redo.

    - using new UndoRedoHelpers for this.
    - VerletForceIntegration::operator() does not return bool anymore, check for
      empty atom set is done in Action.
    - TESTFIX: Removed XFAIl from regression tests verlet-integration.

commit 9c308e95470d81793fa114b4a5bee29600e534d8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 2 10:00:14 2014 +0200

    Extended UndoRedoHelpers.

    - added removeLastStep(), addNewStep().
    - FIX: some UndoRedoHelper functions did not have const arguments as they
      should.
    - FIX: AtomicInfo did not set/store force vector of atom.
    - added AtomInfo::removeTrajectoryStep() and BondedParticleInfo::...() to
      allow for removal of a time step in the course of undoing. Enhanced
      AtomInfo, atom, and TesselPoint by removeSteps(), similar to UpdateSteps().

commit ea2b2a3230ff75e1a00a6a3d230028d9c9ef79f7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 2 08:54:30 2014 +0200

    Sorted GlobalListOfActions.

    - note that Redo must remain at the front due to technical reasons.

commit 50f5e97ca0b56ad057decac0decb279efee916bd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 2 07:05:12 2014 +0200

    Added StructuralOptimizationAction.

    - performs a single optimization step.

commit 343c5aa67b8af4355dabe12bc32e94678574ee19
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 2 06:51:13 2014 +0200

    Added CorrectBondDegreeAction and fixed Calculation tests.

    - pdb files do have bond graph but not the right degrees.
    - there also lies some ambiguity in here as double bonds depend on the chosen
      matching.

commit 5d555048c6955ac3bda0b2cb4b3e6b20ab49880e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jul 18 19:45:45 2014 +0200

    FragmentationAction now compiles global saturation positions information.

commit a1d1dd8b043f6987e14d6d37973e71bd8ccad587
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 30 20:50:13 2014 +0200

    Added SaturationDistanceMaximizer to determine best alphas for SaturatedBonds.

    - also added simple unit tests that ascertains that with just degree 1 bonds
      nothing happens.

commit bac32f93be11686cd34925f6b8ddc570e886dce7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 30 20:45:14 2014 +0200

    Added SaturatedBond as container for a "dangling bond" and its saturation hydrogens.

    - most member variables are private, this prints them for debugging.

commit a8f1d258e9e7fda6f62cbc12bf57a09cb5102256
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 23 23:50:08 2014 +0200

    Added new Vector::IsParallelTo().

commit 98a293b9263c73baadd2152296722d9dd0d401e9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jul 18 19:08:09 2014 +0200

    SaturatedFragment can deal with a global saturation position map.

    - so far, we create an empty one in FragmentationAction such that nothing's
      changed for the moment.
    - similarly in StoreSaturatedFragmentAction. However, there this is intended
      as only local information is required (it's only a single fragment).

commit bdd5a84d9caf9791ea18d3a07979dee75f9bc54e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 23 11:26:42 2014 +0200

    FIX: VectorContent::Normalize() had int, not double.

commit 3834b60a172eb5fc5a8f0c36a9bc18ca164bb189
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jul 17 23:52:05 2014 +0200

    TESTFIX: extracheck threshold is _relative_ 1e-5.

commit fec597f5b80c0f86e5d9e73637b0ffff32750b57
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Jul 12 13:56:14 2014 +0200

    Added new convenience library libMolecuilderTesselation.

    - we need this for getting the connection information between the nearest
      neighboring points on the sphere.

commit de2cbfe9e898e38b885f3727e766bc34f57f9c60
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu May 29 12:00:26 2014 +0200

    Added SaturateFragment()::saturateAtom() replacing all cut bonds at once.

    - so far, we have just outsourced the loop over each cut bond into this
      function.

commit 9e3fca9793f8283b21549888452621aad9772a63
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu May 29 12:30:49 2014 +0200

    FIX: BondedParticleInfo::BondList is now a typedef.

    - removed the define.

commit 9d32646c6dd4acfd9baa5f5b17e41207adee8b18
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu May 29 11:55:28 2014 +0200

    Refactored SaturatedFragment::saturate() using list of cut bonds.

    - this is preparatory for replacing AddHydrogenReplacementAtom().

commit 3fbdca6228d7cb54dd1ec647f23636bf048cea6d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Aug 26 21:53:59 2013 +0200

    SaturatedFragment::AddHydrogenReplacementAtom() uses degree 1 if other is missing.

commit 06804b923c9b82a6dd4f7d932a21781d6e4eae6e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Aug 26 21:49:32 2013 +0200

    Removed molecule::AddHydrogenReplacement() and BreadthFirstSearchAdd.

    - this capability has been transfered to SaturatedFragment, and BFSAdd has
      not been used for a long, long time.

commit 9fd44f7f53b271add9c0ff9fe035e67c63361f09
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jul 10 19:06:56 2014 +0200

    Vector::Is...() functions extended for numeric threshold.

    - if none given we use LINALG_MYEPSILON(), otherwise given to function.
    - this allows for rounding-sensible IsEqualTo() checking and more.

commit 74d179f0dff39a6c2ff23bdd8c5bae931bc4bd12
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 30 20:48:11 2014 +0200

    FIX: elements db uses wrong hbondangle for degree 1.

    - angle is cone's opening angle and needs to be zero for degree 1 because the
      cone is just a line.

commit 3567e21ff36698dd519060d6ddaa4ba24e65685f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jul 3 19:13:39 2014 +0200

    FIX: Plane's cstor did not check for linear dependence in a numerical stable way.

    - we check with NormSquared() and we use Projection() instead of Angle() to
      check whether vectors are linear dependent.

commit c77d36e7ff07e14a81c2f181349203f9d7fd8a50
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 13 13:22:14 2014 +0200

    FIX: VectorContent::Normalize() did not check for zero factor.

commit 72eada0a916425172fc2053704f4ca36992494be
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 23 20:00:48 2014 +0200

    FIX: CodePatterns_LIBS was introduced in AM_LDFLAGS and not in LIBS.

    - this might have caused problems with libtool not correctly noting down this
      lib as a dependency.

commit 8e2779350975a8ced8c8e2d73ad3c4b62c79ab34
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jul 30 20:46:56 2014 +0200

    TESTFIX: Regression test series Calculations would not run in parallel.

    - we have to use $(MAKE), otherwise jobobserver cannot deduce whether it calls
      a make and does not pass "-j4" option.
    - regression tests Fragmentations now give status in color.

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