- Molecuilder-devel

[SCM] MoleCuilder branch ThreadFixes created. v1.4.9-3-gfff8fcb
by git＠ins.uni-bonn.de 26 Oct '14

26 Oct '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, ThreadFixes has been created at fff8fcbd58abd7059236c3fbddafc1000d300ae9 (commit) - Log ----------------------------------------------------------------- commit fff8fcbd58abd7059236c3fbddafc1000d300ae9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 3 21:26:17 2014 +0200 Cleaned up use of mutexes in ActionQueue. - tempqueue now has its own mutex. - more often using lock_guard. - run_thread_isIdle has own mutex. commit 9a4949ffbc4c1ce8a083f8878c8ff61e484e6e79 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 3 19:21:08 2014 +0200 Added extra flag run_thread_running to ActionQueue. - helgrind admonished race conditions when thread is joined. This did not fix them but should be safer as we cannot know whether the other thread has already been started when suddenly shutting down molecuilder due to an exception. commit 23b6cf7ccc51b9a98424d0793c25f776ae063e5f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Aug 29 11:46:02 2014 +0200 THREADFIX: Fixed ActionQueue with respect to mutex and threads. - run_thread is now last member variable, hence started after all other variables are initialized. - separated accesses to queues and to run_thread_isIdle flag. Also renamed its mutex for easier association with it. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch ThreadFixes deleted. v1.4.7-20-gca890d1
by git＠ins.uni-bonn.de 26 Oct '14

26 Oct '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, ThreadFixes has been deleted was ca890d10159865475183bd08e46c1d304c75cc3f ----------------------------------------------------------------------- ca890d10159865475183bd08e46c1d304c75cc3f Cleaned up use of mutexes in ActionQueue. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_smallchanges created. v1.4.9-2-g7305d52
by git＠ins.uni-bonn.de 26 Oct '14

26 Oct '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, GUI_smallchanges has been created at 7305d5268402221ff02978b5f2ec39cb12bbd238 (commit) - Log ----------------------------------------------------------------- commit 7305d5268402221ff02978b5f2ec39cb12bbd238 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 17 18:04:58 2014 +0200 Removed extra option actionname from HelpAction. - this shortens the way to getting help a lot. - TESTFIX: regression potentials fixed due to removed actionname. commit fe02bf3a9081343f5898f5348bfea7aa2dd6e3de Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 17 18:50:10 2014 +0200 CommandLineParser adds Action's default values as implicit. - this allows to have action's token as option with both empty (then default is used) and some given argument. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fix_VMGForces created. v1.4.9-15-g080a424
by git＠ins.uni-bonn.de 26 Oct '14

26 Oct '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, Fix_VMGForces has been created at 080a424203e0ebca556daa66aeee341639f7c857 (commit) - Log ----------------------------------------------------------------- commit 080a424203e0ebca556daa66aeee341639f7c857 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Oct 26 00:01:51 2014 +0200 tempcommit: Some changes to InterfaceVMGJob on force summation. - added some debug output. commit a9b2563e739c20b2dbe939a7c5246a57b7fa06e2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Oct 26 00:00:30 2014 +0200 MPQCData now also uses FragmentForces (instead of typedef forcevector). - required small changes to MPQCCommandJob due to changed typedef. commit e99b6854ddb97a11c933537772a31331beb695d5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Oct 26 00:00:05 2014 +0200 tempcommit: Removed += and -= operators again from FragmentForces. commit 7b1bee90e5dc6cbda55f0799628df9f04a0a25e3 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 23:56:32 2014 +0200 Again changes to obtain correct longrange forces. - renamed particle_forces -> forces to make it consistent with MPQCData_Fused. - MPQCData_Fused and VMGData_Fused are structs and no longer namespace as the latter cannot serve as template arguments. - split off forces in VMGData into VMGDataForceMap_t and VMGDataForceVector_t. - changed ConvertMPQCDataToForceMap() into template function ConvertDataToForceMap(), working also on VMGDataForceMap_t. - this required changes in FragmentationShortRangeResults. - FragmentationLongRangeResults now also converts the longrange forces correctly. - AnalyseFragmentResults now prints also a ..VMGForces.dat file. commit 001ff0e359be41e9130809c0b1b3acb4483165df Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 12:49:02 2014 +0200 Split off sampled_potential im VMGDataMap_t into separate fusion container. - this should correct the output in ..._VMGEnergy.dat commit 72c797595c5e794f89a48a37bca44c1f7834f850 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 09:56:46 2014 +0200 tempcommit: FragmentForces was missing in some parts. commit 1d9591267e76f1e0ced09ce7f8c309c384007294 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 09:54:37 2014 +0200 FIX: Shared libraries's Makefile.am rules are now consistent. - pkgconfig is just given once (in src/Makefile.am). - all have version information, including now pyMoleCuilder.so. commit 307f15aa52220dace3dc7f00c0ad7699e70cd2c2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 24 19:49:08 2014 +0200 tempcommit: Fixes to InterfaceVMGJob. commit 48efe779baefa7303b2d6478f91585da471e2b2e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 24 19:37:21 2014 +0200 Added new SetValues FragmentForces. commit d16a3ccd3112252652ee21663b63528d5c216823 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 24 19:36:38 2014 +0200 tempcommit: Merge with 940da75c commit e28a70c22648ae28dce0acbf4b507bbb99b7bba9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 24 19:34:31 2014 +0200 tempcommit: Merge with d302c57b commit 7ba727725051002d1b7602f8fdc9f567f13c4a4d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 23 19:09:06 2014 +0200 tempcommit: Fix. Merge with d302c57b commit 6e0506ff9f4acaada53ea1a545ee688456c4be4b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 17 19:29:19 2014 +0200 FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob. - note that so far domains needs to be cubic. commit d302c57b6c1c3d75803d9a2b0ad332dd5c11a911 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 20 18:31:42 2014 +0100 Added particle_forces entity to VMGData. - needs to get filled yet. commit 940da75c02ac96c8907eed986c8467a38fccea32 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 20 18:30:19 2014 +0100 Added extraction of long-range forces from VMGData's array f. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fix_VMGForces deleted. v1.4.9-11-g2c2d023
by git＠ins.uni-bonn.de 26 Oct '14

26 Oct '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, Fix_VMGForces has been deleted was 2c2d0231a7e6dfbdddb7194afd82d5edfb85e7c9 ----------------------------------------------------------------------- 2c2d0231a7e6dfbdddb7194afd82d5edfb85e7c9 Split off sampled_potential im VMGDataMap_t into separate fusion container. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fix_VMGForces updated. v1.4.9-11-g2c2d023
by git＠ins.uni-bonn.de 25 Oct '14

25 Oct '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, Fix_VMGForces has been updated via 2c2d0231a7e6dfbdddb7194afd82d5edfb85e7c9 (commit) via 72c797595c5e794f89a48a37bca44c1f7834f850 (commit) via 1d9591267e76f1e0ced09ce7f8c309c384007294 (commit) from 307f15aa52220dace3dc7f00c0ad7699e70cd2c2 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 2c2d0231a7e6dfbdddb7194afd82d5edfb85e7c9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 12:49:02 2014 +0200 Split off sampled_potential im VMGDataMap_t into separate fusion container. - this should correct the output in ..._VMGEnergy.dat commit 72c797595c5e794f89a48a37bca44c1f7834f850 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 09:56:46 2014 +0200 tempcommit: FragmentForces was missing in some parts. commit 1d9591267e76f1e0ced09ce7f8c309c384007294 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sat Oct 25 09:54:37 2014 +0200 FIX: Shared libraries's Makefile.am rules are now consistent. - pkgconfig is just given once (in src/Makefile.am). - all have version information, including now pyMoleCuilder.so. ----------------------------------------------------------------------- Summary of changes: .../AnalyseFragmentationResultsAction.cpp | 12 +++-- .../FragmentationAutomationAction.cpp | 1 + src/Fragmentation/Makefile.am | 7 --- .../Containers/FragmentationLongRangeResults.cpp | 9 +++- .../Containers/FragmentationLongRangeResults.hpp | 4 ++ src/Fragmentation/Summation/Containers/VMGData.cpp | 1 + src/Fragmentation/Summation/Containers/VMGData.hpp | 2 +- .../Summation/Containers/VMGDataMap.hpp | 14 +++++-- .../Summation/Converter/DataConverter.hpp | 21 +++++++++- src/Fragmentation/Summation/Makefile.am | 7 --- .../Summation/SetValues/FragmentForces.cpp | 8 ++++ .../Summation/SetValues/FragmentForces.hpp | 2 +- src/Jobs/Makefile.am | 7 --- src/Makefile.am | 2 +- src/UIElements/Makefile.am | 42 ++++++++++++++----- src/UIElements/Views/Qt4/Plotting/Makefile.am | 30 +++++++++++++- 16 files changed, 118 insertions(+), 51 deletions(-) hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fix_VMGForces created. v1.4.9-8-g307f15a
by git＠ins.uni-bonn.de 24 Oct '14

24 Oct '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, Fix_VMGForces has been created at 307f15aa52220dace3dc7f00c0ad7699e70cd2c2 (commit) - Log ----------------------------------------------------------------- commit 307f15aa52220dace3dc7f00c0ad7699e70cd2c2 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 24 19:49:08 2014 +0200 tempcommit: Fixes to InterfaceVMGJob. commit 48efe779baefa7303b2d6478f91585da471e2b2e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 24 19:37:21 2014 +0200 Added new SetValues FragmentForces. commit d16a3ccd3112252652ee21663b63528d5c216823 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 24 19:36:38 2014 +0200 tempcommit: Merge with 940da75c commit e28a70c22648ae28dce0acbf4b507bbb99b7bba9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 24 19:34:31 2014 +0200 tempcommit: Merge with d302c57b commit 7ba727725051002d1b7602f8fdc9f567f13c4a4d Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 23 19:09:06 2014 +0200 tempcommit: Fix. Merge with d302c57b commit 6e0506ff9f4acaada53ea1a545ee688456c4be4b Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Oct 17 19:29:19 2014 +0200 FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob. - note that so far domains needs to be cubic. commit d302c57b6c1c3d75803d9a2b0ad332dd5c11a911 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 20 18:31:42 2014 +0100 Added particle_forces entity to VMGData. - needs to get filled yet. commit 940da75c02ac96c8907eed986c8467a38fccea32 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Mar 20 18:30:19 2014 +0100 Added extraction of long-range forces from VMGData's array f. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch stable updated. v1.4.9
by git＠ins.uni-bonn.de 23 Oct '14

23 Oct '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, stable has been updated via 7b38d3ce5a4b0f857769b4fa0009f95a8f574d78 (commit) from 42344903478721db21dff3e7385e7c5f037aff66 (commit) Those revisions listed above that are new to this repository have not appeared on any other notification email; so we list those revisions in full, below. - Log ----------------------------------------------------------------- commit 7b38d3ce5a4b0f857769b4fa0009f95a8f574d78 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Oct 23 00:19:36 2014 +0200 Set version to 1.4.9. - MoleCuilder library is now 14:2:0. - Codename "Squares" (1,2, and 3 squared) ----------------------------------------------------------------------- Summary of changes: configure.ac | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder annotated tag v1.4.9 created. v1.4.9
by git＠ins.uni-bonn.de 23 Oct '14

23 Oct '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 annotated tag, v1.4.9 has been created at ac3336b2fd7cdc1a9122e0a901e3b2e4b22a3406 (tag) tagging 7b38d3ce5a4b0f857769b4fa0009f95a8f574d78 (commit) replaces v1.4.8 tagged by Frederik Heber on Thu Oct 23 00:21:22 2014 +0200 - Log ----------------------------------------------------------------- Convex envelopes and thereby volume measurments are fully working. Trajectories no longer need to be consecutive (we store time step and position) Some new actions and small fixes. Userguide now contains explanation of every present Action. This version contains the following branches: 4234490 Candidate_v1.4.9 (version setting and mem and distcheck fixes) 33ee996 Fix_ConvexizeNonconvexEnvelope (volumes can now sensibly be measured) 78c9509 GUI_Enhancements (fixed appearance of QtHomologyList widget) c7fe90c Experiment_AmyloseWater (new TranslateToOriginAction eases rotations) 46ce1c8 Dynamic_Molecules (trajectories stored as map, not vector) 0ea063b Refactoring_PotentialActions (split FitPotentialAction, extracted save and load potentials) bbf6dcd MirrorAtoms (new MirrorAtoms action) 054d47f ActionFixes (fixing AtomByIdAction) 9bce964 CodeCheck_ActionInUserguide (check that every Action appears in user guide) Frederik Heber (57): VersionAction also prints to log, not only to status. DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer. Added CodeChecks test that every action appears in the userguide. DOCU: Added all missing Actions to userguide. DOCU: Fixed all missing links in userguide. FIX: (Not)AtomByIdAction would fail with assert if not atoms are present. FIX: atom's copy cstor does not need to copy positions, ... again. Added AverageMoleculeForceAction for measuring average force acting on a molecule. Added TranslateToOriginAction. Changed how trajectories are stored, not as vecor but as map. FIX: World::setTime() now first copies Bondgraph and then sets the time. Added AtomMirrorAction. Merge branch 'ActionFixes' into Candidate_v1.4.9 Merge branch 'MirrorAtoms' into Candidate_v1.4.9 Split FitPotentialAction into two actions. Extracted ParsePotentialsAction from FitCompoundPotentialAction. Extracted SavePotentialsAction. Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9 Merge branch 'DynamicMolecules' into Candidate_v1.4.9 Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9 FIX: QtHomologyList's plot widget was too high (and fixed). FIX: Added Boost::MultiIndexContainer check for MemDebug. MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d. FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized. FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad. FIX: Raster3D needs header.r3d, which had been missing so far. FIX: Changed all performCriticalExit() into ASSERT() in tesselation. FIX: AddTesselationLine() would only work in initial tesselation phase. FIX: RemoveTesselationLine() needs to erase line from OpenLines if present. FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex. DOCUFIX: Corrected formula for general tetrahedron in docu. Changed some verbosities in Tesselation code. FIX: Reduced verbosity noise from Line::getIntersection(). FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly. FIX: Filling of non-convex polygon with only minimal angles did not work. Added Tesselation::IsPointBelowSurroundingPolygon(). FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong. FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong. FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector. FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface(). Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface() FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop. Rewrote ConvexizeNonconvexEnvelope(). FIX: GainMap is used to store the concavity angle, we flip now always most concave. FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization. ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface(). Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction. DOCU: Added extensive explanation how convexization works. Added tcl scripts for viewing and debugging convexized surfaces. Added SphereRadius parameter to ConvexEnvelopeAction. Convex-envelope has debug parameter DoOutputEveryStep. TESTFIX: Regression test Tesselation/BigConvex is now working. TESTS: Extended Tesselations tests to convex case. Merge branch 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9 MEMFIX: PotentialTrainer::getFirstGraphwithSpecifiedElements() used olditer pointing nowhere. DISTFIX: POTENTIALSOURCES was overwritten, not added to. Set version to 1.4.9. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder annotated tag v1.4.9 deleted. v1.4.8-56-g4234490
by git＠ins.uni-bonn.de 23 Oct '14

23 Oct '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 annotated tag, v1.4.9 has been deleted was ed071df08976dd4a9e83a9dcd39827e1d10dc656 ----------------------------------------------------------------------- tag v1.4.9 Convex envelopes and thereby volume measurments are fully working. Trajectories no longer need to be consecutive (we store time step and position) Some new actions and small fixes. Userguide now contains explanation of every present Action. This version contains the following branches: 33ee996 Fix_ConvexizeNonconvexEnvelope (volumes can now sensibly be measured) 78c9509 GUI_Enhancements (fixed appearance of QtHomologyList widget) c7fe90c Experiment_AmyloseWater (new TranslateToOriginAction eases rotations) 46ce1c8 Dynamic_Molecules (trajectories stored as map, not vector) 9d1320c Refactoring_PotentialActions (split FitPotentialAction, extracted save and load potentials) bbf6dcd MirrorAtoms (new MirrorAtoms action) 054d47f ActionFixes (fixing AtomByIdAction) 9bce964 CodeCheck_ActionInUserguide (check that every Action appears in user guide) 42344903478721db21dff3e7385e7c5f037aff66 DISTFIX: POTENTIALSOURCES was overwritten, not added to. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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