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The branch, Candidate_v1.4.7 has been created at 8e20e36dcc35c56d5a90a9967b3b89ff17846858 (commit) - Log ----------------------------------------------------------------- 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. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder