- Molecuilder-devel

[SCM] MoleCuilder branch Fixes_Ubuntu14_04 deleted. v1.4.6-42-g2d8d5e9
by git＠ins.uni-bonn.de 21 Aug '14

21 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fixes_Ubuntu14_04 has been deleted was 2d8d5e9111050d81934f23f9e866e84df342b172 ----------------------------------------------------------------------- 2d8d5e9111050d81934f23f9e866e84df342b172 FIX: FragmentationAutomationAction did not fail correctly with JobMarket in debug mode. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fixes_Ubuntu14_04 created. v1.4.6-42-g2d8d5e9
by git＠ins.uni-bonn.de 21 Aug '14

21 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fixes_Ubuntu14_04 has been created at 2d8d5e9111050d81934f23f9e866e84df342b172 (commit) - Log ----------------------------------------------------------------- commit 2d8d5e9111050d81934f23f9e866e84df342b172 Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Sun Aug 17 22:54:27 2014 +0200 FIX: Interfragmenter had iter collision. commit 76d073cbf283b3d3f177a555c2681968688e7091 Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Sun Aug 10 15:17:52 2014 +0200 FIX: typos in AtomicForceManipulator.hpp. commit 51cfda11221ab02d7db630f150d0ba120ec6dff3 Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Wed Jul 23 23:50:08 2014 +0200 Added new Vector::IsParallelTo(). commit 98a293b9263c73baadd2152296722d9dd0d401e9 Author: Frederik Heber <heber(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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(a)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

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[SCM] MoleCuilder branch Fixes_Ubuntu14_04 deleted. v1.4.6-42-g26fd867
by git＠ins.uni-bonn.de 21 Aug '14

21 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fixes_Ubuntu14_04 has been deleted was 26fd8670f3f4e786bcb4a529c8d6e008d1a406e8 ----------------------------------------------------------------------- 26fd8670f3f4e786bcb4a529c8d6e008d1a406e8 FIX: FragmentationAutomationAction did not fail correctly with JobMarket in debug mode. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fixes_Ubuntu14_04a deleted. v1.4.6-42-g26fd867
by git＠ins.uni-bonn.de 20 Aug '14

20 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fixes_Ubuntu14_04a has been deleted was 26fd8670f3f4e786bcb4a529c8d6e008d1a406e8 ----------------------------------------------------------------------- 26fd8670f3f4e786bcb4a529c8d6e008d1a406e8 FIX: FragmentationAutomationAction did not fail correctly with JobMarket in debug mode. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fixes_Ubuntu14_04a created. v1.4.6-42-g26fd867
by git＠ins.uni-bonn.de 20 Aug '14

20 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fixes_Ubuntu14_04a has been created at 26fd8670f3f4e786bcb4a529c8d6e008d1a406e8 (commit) - Log ----------------------------------------------------------------- ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.7 deleted. v1.4.6-34-g8e20e36
by git＠ins.uni-bonn.de 20 Aug '14

20 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Candidate_v1.4.7 has been deleted was 8e20e36dcc35c56d5a90a9967b3b89ff17846858 ----------------------------------------------------------------------- 8e20e36dcc35c56d5a90a9967b3b89ff17846858 FIX: QtTimeLine::recieveNotification() checked falsely against AtomObserver. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch findBestMatching_HigherBondDegrees deleted. v1.4.6-35-g74c4846
by git＠ins.uni-bonn.de 20 Aug '14

20 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, findBestMatching_HigherBondDegrees has been deleted was 74c4846adeb2221e23f1677599fd7e537726cdf2 ----------------------------------------------------------------------- 74c4846adeb2221e23f1677599fd7e537726cdf2 recurseMatching() now takes connections into account. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fixes_Ubuntu14_04 created. v1.4.6-42-g26fd867
by git＠ins.uni-bonn.de 19 Aug '14

19 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fixes_Ubuntu14_04 has been created at 26fd8670f3f4e786bcb4a529c8d6e008d1a406e8 (commit) - Log ----------------------------------------------------------------- commit 26fd8670f3f4e786bcb4a529c8d6e008d1a406e8 Author: Frederik Heber <heber(a)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 e80acc99539937726b2f80303d89769b11ae651a Author: Frederik Heber <heber(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Sun Aug 17 22:54:27 2014 +0200 FIX: Interfragmenter had iter collision. commit 76d073cbf283b3d3f177a555c2681968688e7091 Author: Frederik Heber <heber(a)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(a)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(a)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. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fixes_Ubuntu14_04 deleted. v1.4.6-42-gc07189e
by git＠ins.uni-bonn.de 19 Aug '14

19 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fixes_Ubuntu14_04 has been deleted was c07189e9cf2a546c8207dd108d7825ec4c013889 ----------------------------------------------------------------------- c07189e9cf2a546c8207dd108d7825ec4c013889 FIX: FragmentationAutomationAction did not fail correctly with JobMarket in debug mode. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fixes_Ubuntu14_04 created. v1.4.6-42-gc07189e
by git＠ins.uni-bonn.de 19 Aug '14

19 Aug '14

This is an automated email from the git hooks/post-receive script. It was generated because a ref change was pushed to the repository containing the project "MoleCuilder". The branch, Fixes_Ubuntu14_04 has been created at c07189e9cf2a546c8207dd108d7825ec4c013889 (commit) - Log ----------------------------------------------------------------- commit c07189e9cf2a546c8207dd108d7825ec4c013889 Author: Frederik Heber <heber(a)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 e80acc99539937726b2f80303d89769b11ae651a Author: Frederik Heber <heber(a)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(a)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(a)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(a)ins.uni-bonn.de> Date: Sun Aug 17 22:54:27 2014 +0200 FIX: Interfragmenter had iter collision. commit 76d073cbf283b3d3f177a555c2681968688e7091 Author: Frederik Heber <heber(a)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(a)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(a)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. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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