[Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.7 created. v1.4.6-50-g29b35ef

22 Aug 2014


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The branch, Candidate_v1.4.7 has been created
        at  29b35efc972c36f104ccae2ad8b50ce095b475e8 (commit)

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commit 29b35efc972c36f104ccae2ad8b50ce095b475e8
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Aug 20 15:23:07 2014 +0200

    Set version to 1.4.7.
    
    - MoleCuilder library is now 14:0:0.
    - Codename "Capitalism" (According to a 2011 research article on system theory,
      147 companies control the major part of global capitalism)

commit a91710c7feb7eb12c5521615d53366bd9ac68106
Merge: 4c9101d 0c72e21
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Aug 21 08:59:33 2014 +0200

    Merge branch 'Fixes_Ubuntu14_04' into stable

commit 0c72e21652645146e2cbb1f6242fc50afb6067c9
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Aug 21 08:59:06 2014 +0200

    DOCU: Updated documentation on Ubuntu 14.04.

commit 07ecc54679bad772b20fd501b5a70c8bbc1d1a43
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Aug 19 15:05:10 2014 +0200

    FIX: FragmentationAutomationAction did not fail correctly with JobMarket in debug mode.
    
    - an assert fails in JobMarket when ids are requested after conneciton to
      Server was refused and received illegalids are used in jobs and added.
    - this did not occur so far, as we test only against release JobMarket in
      version checks.

commit 748fc7c0d1024191307cd0382559ca5a2f64eacb
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Aug 19 13:17:27 2014 +0200

    libMolecuilder is now a shared library.
    
    - linking error Vector::IsZero(double) with molecuilder(gui), related to
      libMolecuilderShapes was the root cause for this change. Again, it was not
      deducible why this error occured:
    - probably (me tired of these obfuscated linker errors ...) faulted because
      libMolecuilder is convenience lib while libMolecuilderUI and ..QtUI are
      shared and deps did not get passed along properly (by libtool) (e.g. ldd
      showed libMolecuilderShapes prior to libLinearAlgebra, containing said
      function Vector::IsZero(double), but I cannot influence this ordering and it
      should not even matter (dynamic linking).)
    - some cleanup in builder_init.cpp (no more loading of BondGraph from file
      named "\n".
    - TESTFIX: libMolecuilder.so added to all unittests, required for e.g.
      World::purgeInstance() ... and sometimes added libMolecuilderUI.so because
      libMolecuilder pulled them in due to static entities ... sigh.
    - removed all src object files from unittest .._SOURCES. This caused distclean
      faults "thanks" to new subdir-objects (automake).

commit 4c9101d28554cfb93912863dd0480b0c485d2c41
Merge: fc3aff4 2cb77c2
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Aug 20 15:10:38 2014 +0200

    Merge branch 'VariousFixes' into stable

commit fc3aff49ca5c026f908b539cde856e13e75c55ba
Merge: ee4f2da 3a33e3e
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Aug 20 15:10:07 2014 +0200

    Merge branch 'StructuralOptimization' into stable

commit ee4f2da6990041aedcb8b339896459f5b4e9b05b
Merge: 2a03b00 343c5aa
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Aug 20 15:09:40 2014 +0200

    Merge branch 'EnhancingHydrogenSaturation' into stable

commit 2cb77c2ea89ddde7cf8251e67ae8abf0a42baa4c
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Aug 20 14:01:24 2014 +0200

    FIX: Fragmentations tests used -I and not --correct-bonddegree in case of pdb files.
    
    - this bond graph was always recalculated and not taken from the parsed file.

commit 83cc3e89cbdfa13ae454644478d1b5f9ab0a75cb
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Aug 20 13:47:12 2014 +0200

    FIX: CyclicStructureAnalysis did not robustly detect all cycles.
    
    - it depended on the sequence of the back edges. In Coronene most back edges
      lead to two cycles but at least one back edge is attached to only one cycle.
    - The change is that we now continue after having found a cycle - regardless
      of whether it is already present or not. This ensures that we find all
      cycles present.
    - finding a cycle sets however the size of the BFS horizon (we just look for
      the minimal cycles). This prevents the BFS from stepping through the whole
      graph.
    - rename CycleBFStoRoot() -> findAllCyclesforBackEdge(), calls
      RetrieveCycleMembers() on each found cycle (not in operator() anymore).
    - Modified RetrieveCycleMembers() to check whether cycle is present, using
      IsCyclic checking as a faster mean.
    - operator() dropped NumCycles, is redundantly contained in allcycles.size().

commit 4d6d6a41aa48054402d4325bc285f9594aa74c69
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Aug 20 13:46:03 2014 +0200

    QtGUI prints log to console (qDebug) as well.
    
    - removed in --disable-debug builds.

commit d93b4b3101d0910efc6b9f530a4cf26005c926dc
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Aug 18 20:22:07 2014 +0200

    FIX: ActionQueue::run() did not use boost::thread::sleep_for() correctly.

commit e9e86f755ec91600316ac1b266d68b3244700842
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Aug 17 23:31:27 2014 +0200

    FIX: UnitTestMain placed into convenience libUnitTest.
    
    - removed UnitTestMain.cpp from all .._SOURCES (except LinearAlgebra).
    - this is due to subdir-objects: we cannot use absolute paths anymore.
      automake tries to place .deps folder in the respective source path.
      Wrapping it up in a library removes this.

commit 09806af7c430c059fd0504fee221f5f8ec4ef155
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Aug 17 22:54:27 2014 +0200

    FIX: Interfragmenter had iter collision.

commit fe77dfcd3989b18314077cda402ac1c63695674a
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Aug 17 22:53:55 2014 +0200

    FIX: ReceiveResultContainer could not find functions from base class.

commit 0c74aa19d73454589c9ebbe8d61ee3397bca338f
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Aug 17 22:53:28 2014 +0200

    FIX: Fixes to Action_impl_python, lacked boost preprocessor includes.

commit 3b35e715f8f1469cc9d18d99c6e43aa47954d613
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Aug 17 21:07:34 2014 +0200

    Fixes due to update to Ubuntu 14.04.
    
    - subdir-objects is default behavior for automake.
    - INCLUDES is deprecated (in favor of AM_CPPFLAGS), made sure that every
      .._CPPFLAGS includes AM_CPPFLAGS.
    - updated boost.m4 (serial 22), re-added missing macros.
    - qwt.m4 does not use QString in constructor, as it pulls in QtCore dependency.
    - VectorUnitTest lacked libboost_system dep.

commit 3a33e3e227123ea24a3af9bdd665a5a2c9a43f65
Author: Frederik Heber <heber@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 45cdce6c6da7af45f28e4182d6539fe1c678f87a
Author: Frederik Heber <heber@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 4e65af7c5036d532974d84f76366a623f2c42571
Author: Frederik Heber <heber@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 7f833c8983a8e1024fff641289db472c6d79c3c7
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Aug 11 19:56:03 2014 +0200

    Giving the maximum components over all force vectors in ForceAnnealing.

commit f149722846dcf0a89078f551cedb518a9bef5686
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Aug 10 14:47:43 2014 +0200

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

commit e5f61ba098def1991ab9372e13b7d6740dedddc6
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sat Aug 2 18:22:46 2014 +0200

    Added MakroAction StructureOptimizationAction.
    
    - performs similarly as MolecularDynamicsAction only using ForceAnnealing.

commit ff3edf390edf783afaf6240fd0ef8e87e4412b91
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sat Aug 16 17:40:44 2014 +0200

    FIX: MolecularDynamicsAction works also without JobMarket.
    
    - since FragmentationAutomation works without.

commit 1a48d2c8c2b6ea08ac53c8fc5998d19145e4eeb8
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Aug 20 14:49:32 2014 +0200

    Added ForceAnnealingAction.
    
    - also added regression test.
    - performs a single optimization step.
    - added output-every-step for debugging.

commit d5f7b82f4661b07c35988437ed7f4a1719b312b1
Author: Frederik Heber <heber@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 1e45f1fb84ae30e44c393f19156012e19f962ac3
Author: Frederik Heber <heber@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 7e51e12e82c5637d2660d794f1e024fda52a5aa6
Author: Frederik Heber <heber@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 4424959d82789202040886c380e14457ae068293
Author: Frederik Heber <heber@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 51cdfdda92308eff94ae477deb3170f9bd1b79a1
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Aug 20 14:50:41 2014 +0200

    Extracted common functions from VerletForceIntegration into AtomicForceManipulator.
    
    - AtomicForceManipulator contains e.g. parsing forces from file.
    - removed performConstraintMinimization from VerletForceIntegration.
    - this is preparatory for ForceAnnealing, also derived from
      AtomicForceManipulator.
    - FIX: MoleculeVerletIntegrationAction checks whether atoms are selected and
      increments WorldTime only in success case.

commit 343c5aa67b8af4355dabe12bc32e94678574ee19
Author: Frederik Heber <heber@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@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@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@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@ins.uni-bonn.de>
Date:   Wed Jul 23 23:50:08 2014 +0200

    Added new Vector::IsParallelTo().

commit 98a293b9263c73baadd2152296722d9dd0d401e9
Author: Frederik Heber <heber@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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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