[Molecuilder-devel] [SCM] MoleCuilder branch Fixes_Ubuntu14_04 created. v1.4.6-42-g2d8d5e9

21 Aug 2014


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commit 2d8d5e9111050d81934f23f9e866e84df342b172
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 653cafe8f25cea59f1218832295b477b2e542c63
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 3fde3e9626a25ba69ea72441f4ad744fa9546633
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 4f7c3f0c1d06cd87ba17715600ab661c81f1b0e5
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 11dbbdae4295b8bef1dd34e7f4ba08e2ec42deba
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Aug 17 22:54:27 2014 +0200

    FIX: Interfragmenter had iter collision.

commit 76d073cbf283b3d3f177a555c2681968688e7091
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 dba1ff59d1e997e9cc3673e1e5e50a313b63d550
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 d9891ca002cdca60b287f3e50331af8ad464c4d4
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 8e20e36dcc35c56d5a90a9967b3b89ff17846858
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 fb55065f34f19f831cc839df4504c71af959e0ca
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 3df57f2e7d807f5db30f539726be285674ae8227
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 c7212c1d7bc21c1f8e7249d31eae711aa179115f
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 24b66db290e0f96f9b9eed3221e779ca570dc9da
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Aug 10 15:17:52 2014 +0200

    FIX: typos in AtomicForceManipulator.hpp.

commit 51cfda11221ab02d7db630f150d0ba120ec6dff3
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 622e44a48d1737a7ede7a36df157afdbef7f88c7
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 ffa509902bdaef0fce358b99bc31165d858391c7
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 75869021a53f72dfd0b76aa0d1d11b0dcae8f5f8
Author: Frederik Heber <heber@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@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@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@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@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@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@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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[Molecuilder-devel] [SCM] MoleCuilder branch Fixes_Ubuntu14_04 created. v1.4.6-42-g2d8d5e9

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