September 2014 - Molecuilder-devel

[SCM] MoleCuilder branch Candidate_v1.4.9 created. v1.4.8-21-g78c9509
by git＠ins.uni-bonn.de 26 Sep '14

26 Sep '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_v1.4.9 has been created at 78c9509cba8ec6569d3fee2987607785743b7e09 (commit) - Log ----------------------------------------------------------------- ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Fix_ConvexizeNonconexEnvelope created. v1.4.8-30-gab72314
by git＠ins.uni-bonn.de 26 Sep '14

26 Sep '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_ConvexizeNonconexEnvelope has been created at ab72314934e071f1c33d4d2875f9d27458fb67da (commit) - Log ----------------------------------------------------------------- commit ab72314934e071f1c33d4d2875f9d27458fb67da Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 21:13:43 2014 +0200 Changed verbosities in tesselation a lot to make readable. commit 743052c22b9d7f7591cac44bd5eb2e484a5c3e42 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:26:20 2014 +0200 FIX: Changed all performCriticalExit() into ASSERT() in tesselation. commit d4f9bb3aba23969df122e85d3f5307a0398e5c3f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:26:03 2014 +0200 Changed some verbosities in Tesselation code. commit a07e7053630cf9faa4f5fc18481901cc4f79ab96 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:24:52 2014 +0200 FIX: RemoveTesselationLine() needs to erase line from OpenLines if present. commit 8e3d9d4f8f83fa748239e028a866abd8ab8c70d0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 20:23:50 2014 +0200 FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex. commit 10a01718c3a6190cfc9de345527be832011b1f87 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 18:25:23 2014 +0200 FIX: AddTesselationLine() would onl work in initial tesselation phase. - the CandidateForTesselation instance is NULL when we convexize and this was not correctly processed by AddTesselationLine(). commit e13991dce439602624fbb51421d9bf3c0a816396 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 25 18:24:30 2014 +0200 Added SphereRadius parameter to ConvexEnvelopeAction. commit 128616612a611878bc0a942bbc2f1eecab5d0c9a Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 23 18:14:18 2014 +0200 FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad. - causes segfault when notification informs about change and _lastchangeaction is still NULL (as the very first Action failed). - we now only notify when action succeeded. commit 56eee6e652088e82274fd47b6fd2b3b70e898feb Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 22 22:10:11 2014 +0200 FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized. commit 78c9509cba8ec6569d3fee2987607785743b7e09 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 19 13:19:18 2014 +0200 FIX: QtHomologyList's plot widget was too high (and fixed). - also the sizes of splitter's children in QtHomologyList are now stored to settings (as QsizePolicy does not have an effect on a splitter). commit 71350daef4a36bbd039aa43a5712363fddfc5a00 Merge: 14bede3 c7fe90c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 19 09:13:05 2014 +0200 Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9 Conflicts: doc/userguide/userguide.xml tests/regression/Atoms/testsuite-atoms.at - mirror-atoms and translate-to-origins occupied the same places. commit 14bede3ba3e8e2630b00858a76285e0e0439b26a Merge: 5340768 46ce1c8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 19 09:11:02 2014 +0200 Merge branch 'DynamicMolecules' into Candidate_v1.4.9 commit 5340768e903e79d978c07f327466f51ba993a139 Merge: 2ed3bf3 9d1320c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 19 09:10:10 2014 +0200 Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9 commit 2ed3bf3dd38da578e40e717928f565e66746d252 Merge: 7acbfc4 bbf6dcd Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 19 09:10:04 2014 +0200 Merge branch 'MirrorAtoms' into Candidate_v1.4.9 commit 7acbfc4fee584acd54942911e6d4b9c73149b2c7 Merge: 9bce964 054d47f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 19 09:09:53 2014 +0200 Merge branch 'ActionFixes' into Candidate_v1.4.9 commit bbf6dcd010a0439f2e1a441678550e5a56e1cf30 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Wed Sep 10 01:55:39 2014 +0200 Added AtomMirrorAction. - also added regression tests. commit 9d1320cc5a22b299fc35b50bb519d8bd8b13bc21 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 12 09:54:12 2014 +0200 Extracted SavePotentialsAction. - PotentialTrainer::StorePotentials removed. - Fit...Actions do not store anymore. - TESTFIX: potential regression tests now use save-potentials and compare against stored file. commit 5c6b432e38763ef95f591b8dae5078375f60c46c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Fri Sep 12 09:39:58 2014 +0200 Extracted ParsePotentialsAction from FitCompoundPotentialAction. commit 21c1c5cb23b27248af841d0fb4f026616b41b8c5 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 11 22:38:05 2014 +0200 Split FitPotentialAction into two actions. - FitPotentialAction fits just a single potential. - new FitCompoundPotentialAction fits via a potential file. - PotentialTrainer contains all helper functions and common code. commit 46ce1c8a9f9a6af80b7fcf736dcf57f11b47f8b7 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 20:30:46 2014 +0200 FIX: World::setTime() now first copies Bondgraph and then sets the time. - thus we do not cause GUI updates with each addBond(). commit 8cc22fe4af9577450a3d00a92ea000018b14b366 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 00:56:59 2014 +0200 Changed how trajectories are stored, not as vecor but as map. - AtomInfo and atom_bondedparticleinfo now store map<unsigned int, ...> instead of vector<...>. - UpdateSteps() -> UpdateStep(unsigned int), same with RemoveSteps() and AppendTrajectorySteps() and RemoveTrajectorySteps(). - made changes necessary to UndoRedoHelpers and two Actions. - TESTFIX: AtomObserverUnitTest failed as we longer "notify" in case already set element is set again. We now check that setType() sets to different element. commit c7fe90cd467a73a0ef32b5c631534b2928c0b926 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Aug 14 22:03:53 2014 +0200 Added TranslateToOriginAction. - also added regression test. commit f4b626a1fbf68b80e642bace1770e5577aeed6d8 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Aug 26 10:48:59 2014 +0200 Added AverageMoleculeForceAction for measuring average force acting on a molecule. commit 7a7b3408459dae333637248d2b3e0bebed301975 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Aug 17 12:10:08 2014 +0200 FIX: atom's copy cstor does not need to copy positions, ... again. commit 054d47f3558f3549e6480280882111c4df74ad9f Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Thu Sep 11 09:31:52 2014 +0200 FIX: (Not)AtomByIdAction would fail with assert if not atoms are present. - none are selected, we just fail the Action but removed assert. commit 9bce96471db8bac23510c29ddaa7dbcabf15d765 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 14 21:26:46 2014 +0200 DOCU: Fixed all missing links in userguide. - each section now has a linkname. commit f73e0644af36b981af22685b57300f77cb7b0937 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 14 20:25:06 2014 +0200 DOCU: Added all missing Actions to userguide. - removed XFAIL from associated CodeChecks test. commit c62e275561001d2ecd22b8489ac47810fd64e5ce Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 14 18:23:41 2014 +0200 Added CodeChecks test that every action appears in the userguide. - test is marked as XFAIL for the moment. commit 2a6d8c7977c1f749091ead256bcca349538a8b59 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 14 20:24:38 2014 +0200 DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer. commit ced7f04bae3c2939e0888dfb7559e4b0f342a808 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Sun Sep 14 20:24:23 2014 +0200 VersionAction also prints to log, not only to status. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch ThreadFixes created. v1.4.7-20-gca890d1
by git＠ins.uni-bonn.de 18 Sep '14

18 Sep '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 ca890d10159865475183bd08e46c1d304c75cc3f (commit) - Log ----------------------------------------------------------------- commit ca890d10159865475183bd08e46c1d304c75cc3f 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 13102c09392ef451c7547ec206917e96beeb1fad 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 bc2d4676ddd23758665398fbacb74e40e7fdb45b 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-g2b11dfb
by git＠ins.uni-bonn.de 18 Sep '14

18 Sep '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 2b11dfbc1e1e35a26b0f0634b74d579dc3fc208b ----------------------------------------------------------------------- 2b11dfbc1e1e35a26b0f0634b74d579dc3fc208b Cleaned up use of mutexes in ActionQueue. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Cleanup_old_code deleted. v1.4.7-13-g5a9f4c1
by git＠ins.uni-bonn.de 18 Sep '14

18 Sep '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, Cleanup_old_code has been deleted was 5a9f4c1e1caa72f88ad756fdaa11851f54a9426b ----------------------------------------------------------------------- 5a9f4c1e1caa72f88ad756fdaa11851f54a9426b Removed lots of commented-out code from GLWorldView. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch MemFixes deleted. v1.4.7-17-g5524ae9
by git＠ins.uni-bonn.de 18 Sep '14

18 Sep '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, MemFixes has been deleted was 5524ae96797a4fa7244c906512ec2bde76c952b3 ----------------------------------------------------------------------- 5524ae96797a4fa7244c906512ec2bde76c952b3 DOCU: Update on test policy with respect to now working valgrind tests. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch GUI_Fixes deleted. v1.4.7-18-g8859b5e
by git＠ins.uni-bonn.de 18 Sep '14

18 Sep '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_Fixes has been deleted was 8859b5e80aaacf810ed6de2750789019357f0fa0 ----------------------------------------------------------------------- 8859b5e80aaacf810ed6de2750789019357f0fa0 Added QtFavoriteActions to QtToolBar to spawn placeholder icons of most favorite Actions. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 deleted. v1.4.7-54-g4d966a0
by git＠ins.uni-bonn.de 18 Sep '14

18 Sep '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_v1.4.8 has been deleted was 4d966a045dba17945ab7e6433ebf4faea3d73b17 ----------------------------------------------------------------------- 4d966a045dba17945ab7e6433ebf4faea3d73b17 Set version to 1.4.8. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder annotated tag v1.4.8 created. v1.4.8
by git＠ins.uni-bonn.de 17 Sep '14

17 Sep '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, v1.4.8 has been created at c6204d0e3a45cbcb6116e4a45ea9853eba248be5 (tag) tagging 7f6a2fc9f64c88371654df745552167f0e0e3a9c (commit) replaces v1.4.7 tagged by Frederik Heber on Wed Sep 17 21:39:28 2014 +0200 - Log ----------------------------------------------------------------- Valgrind-checked the code and eliminated all memory leaks. First step of cleaning out old code (molecuilder_geometry and old fill Actions) GUI is a lot more useful (empty dialogs do not show up, i.e. easy clicking with all selection actions, undo/redo, ..., bonds are properly updated when atoms move, tooltips for every option in dialogs, homology tab working, suffixes as filters in filedialogs) This version contains the following branches: 7f6a2fc Candidate_v1.4.8 (Fixes after merge and version) 8859b5e GUI_Fixes (Lots of fixes to ease and enhance GUI usage) 5a9f4c1 Cleanup_old_code (throwing out old pieces of code, especially filler) 5524ae9 MemFixes (enable-valgrind now runs through without a glitch (except Python-related regression tests)) Frederik Heber (54): FIX: Process' dstor would always stop() even if not start()ed. FIX: FitPotentialAction's getFirstGraphwithSpecifiedElements() access key_end(). FIX: Box::setM() did not use const ref as argument. FIX: regression test add atoms outside boundary had given boundary conditions wrong in arguments. FIX: Made checks in random number engine and distribution regression tests more robust. MEMFIX: World's homologies not deleted. MEMFIX: Mismatched delete in PdbParser::Save(). MEMFIX: ActionQueue would loose memory when action failed. MEMFIX: RealSpaceMatrix's and MatrixContent's serialization leaked memory. MEMFIX: SaturationDistanceMaximizer::operator() did not delete Advocate. MEMFIX: PotentialRegistry's dstor forgot cleanup(). MEMFIX: PartialNucleiChargeFitter lost memory. MEMFIX: Many analysis_correlation function allocated return map twice. MEMFIX: Tesselation::operator() did not free linkedlist. FIX: molecule::Translate() uses AtomSet directly. Added option keep-bondgraph to MolecularDynamicsAction and StructuralOptimizationAction. World::setTime() now only copies bond graph, does not re-create it. FIX: Removed some misleading output of CorrectBondDegreeAction. FIX: BondGraph::cleanAdjacencyList() killed bonds of time steps before. FIX: GLMoleculeObject_shape might use empty point list for tesselation. FIX: Added update mechanism to GLWorldScene when WorldTime changes. FileQtQuery retrieves valid suffixes from validators. FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), CenterPeriodic(), and CenterAtVector(). FIX: Changes to function signatures in molecule_geometry. Added FileSuffixValidator to all Actions where missing but appropriate. In QTUI empty dialogs no longer have to be confirmed. FIX: Querys now have own description as tooltip, not Action's. In QTUI Dialog window now has a meaningful title. QMenu extended for tooltips, but not working yet. FIX: new item is just to some default values in QtMoleculeList, filled later anway. FIX: FillRegularGridAction requires filler molecule at origin. Extracted filler preparing functionality from FillRegularGridAction. FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in Filling/. Added FillVolumeAction for filling a Shape's volume. Refactored FillSurfaceAction to also use FillerPreparators. Removed FillVoidWithMolecule and FillWithMolecule actions. Removed FillBoxWithMolecule(), FillVoidWithMolecule, and helper functions. Moved and renamed SuspendInWaterAction from Molecule.. to FillAction/SuspendInMoleculeAction. Removed PrepareClustersInWater(). Removed lots of commented-out code from GLWorldView. FIX: QtQueryList now works with pointers, FileQtQuery gives name of file. FIX: QSeisPlotPage takes up all remaining space in QtHomologyList. FIX: QtHomologyList lacked use of FunctionModel::filter_t to split up arguments. Made ActionQueue observable. Added QtFavoriteActions to QtToolBar to spawn placeholder icons of most favorite Actions. MEMFIX: ActionQueue was not stopped() when argument parsing failed. MEMFIX: ElementDbAction would loose memory when parsing command-line arguments failed. DOCU: Update on test policy with respect to now working valgrind tests. Merge branch 'Cleanup_old_code' into stable Merge branch 'MemFixes' into stable Merge branch 'GUI_Fixes' into stable MEMFIX: Thrown ParserException causes mem leak in LoadAction FIX: CommandLineParser causes idling thread when parsing goes wrong. Set version to 1.4.8. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch stable updated. v1.4.7-54-g7f6a2fc
by git＠ins.uni-bonn.de 17 Sep '14

17 Sep '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 7f6a2fc9f64c88371654df745552167f0e0e3a9c (commit) via 06b5dfa95337fee961ce3018c5e56e6b64c06454 (commit) via 7e1a886b77240a61da6f1d0f312f69d0910ff9f0 (commit) via 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91 (commit) via b73545e66c148c8d0fce990a5e3138a99fadcc28 (commit) via 55736be799388502de9a57ac542d215e5ce0565a (commit) via 5524ae96797a4fa7244c906512ec2bde76c952b3 (commit) via 8d4eaa3c9914c99397ccf2583e276838c176a082 (commit) via 11d433d190a134a3015b4de85d3738c20a307688 (commit) via 8859b5e80aaacf810ed6de2750789019357f0fa0 (commit) via 29b52b1607551f45b84d99fb44f6e5e121221626 (commit) via 9bdcc9b9d75a09f2bb7ddfba50b34f7ad62a7e68 (commit) via 0ac3e3aeb53bc6b57899974dd8ec414158ffaccc (commit) via f8bccc9d2f41fb1866651aadba4beab9fe0bea1d (commit) via 5a9f4c1e1caa72f88ad756fdaa11851f54a9426b (commit) via 2b7375290eb8729da103864ee7aab10467ed3346 (commit) via aa55d00dbcc8c34ecf6c22c2d29232d84d0cc262 (commit) via 2528d8462c54c9cdfb2d41b92bd6e34d9fd0c364 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29b35efc972c36f104ccae2ad8b50ce095b475e8 (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 7f6a2fc9f64c88371654df745552167f0e0e3a9c Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:06:47 2014 +0200 Set version to 1.4.8. - MoleCuilder library is now 14:1:0. - Codename "Correction Enterprises" (Paragraph 148-128 of US law decrees enterprises employing incarcerated offenders have to be known as such). ----------------------------------------------------------------------- Summary of changes: LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp | 2 +- LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp | 2 + .../src/LinearAlgebra/RealSpaceMatrix.hpp | 5 +- LinearAlgebra/src/LinearAlgebra/VectorContent.cpp | 4 +- configure.ac | 6 +- src/Actions/Action.cpp | 2 +- src/Actions/ActionQueue.cpp | 65 +- src/Actions/ActionQueue.hpp | 40 +- src/Actions/Action_impl_pre.hpp | 8 +- .../DipoleAngularCorrelationAction.cpp | 4 +- .../AnalysisAction/DipoleCorrelationAction.cpp | 4 +- .../AnalysisAction/PairCorrelationAction.cpp | 4 +- .../AnalysisAction/PointCorrelationAction.cpp | 4 +- .../AnalysisAction/SurfaceCorrelationAction.cpp | 4 +- .../CommandAction/BondLengthTableAction.def | 4 +- src/Actions/CommandAction/ElementDbAction.cpp | 8 +- src/Actions/CommandAction/ElementDbAction.def | 1 + src/Actions/CommandAction/LoadSessionAction.def | 4 +- src/Actions/CommandAction/StoreSessionAction.def | 4 +- src/Actions/FillAction/FillRegularGridAction.cpp | 162 +- src/Actions/FillAction/FillSurfaceAction.cpp | 79 +- src/Actions/FillAction/FillSurfaceAction.def | 15 +- src/Actions/FillAction/FillVolumeAction.cpp | 225 ++ src/Actions/FillAction/FillVolumeAction.def | 52 + src/Actions/FillAction/FillVolumeAction.hpp | 22 + src/Actions/FillAction/SuspendInMoleculeAction.cpp | 333 +++ src/Actions/FillAction/SuspendInMoleculeAction.def | 52 + src/Actions/FillAction/SuspendInMoleculeAction.hpp | 22 + .../ClearFragmentationResultsAction.def | 8 - .../MolecularDynamicsAction.cpp | 23 + .../MolecularDynamicsAction.def | 11 +- .../StructuralOptimizationAction.cpp | 23 + .../StructuralOptimizationAction.def | 11 +- src/Actions/GlobalListOfActions.hpp | 5 +- .../GraphAction/CorrectBondDegreeAction.cpp | 8 - src/Actions/Makefile.am | 21 +- src/Actions/MoleculeAction/CopyAction.cpp | 7 +- .../MoleculeAction/FillVoidWithMoleculeAction.cpp | 166 -- .../MoleculeAction/FillVoidWithMoleculeAction.def | 49 - .../MoleculeAction/FillVoidWithMoleculeAction.hpp | 22 - .../MoleculeAction/FillWithMoleculeAction.cpp | 170 -- .../MoleculeAction/FillWithMoleculeAction.def | 53 - .../MoleculeAction/FillWithMoleculeAction.hpp | 22 - .../MoleculeAction/ForceAnnealingAction.def | 3 +- src/Actions/MoleculeAction/LoadAction.cpp | 10 +- .../RotateAroundSelfByAngleAction.cpp | 21 +- .../MoleculeAction/SuspendInWaterAction.cpp | 92 - .../MoleculeAction/SuspendInWaterAction.def | 37 - .../MoleculeAction/SuspendInWaterAction.hpp | 22 - .../MoleculeAction/VerletIntegrationAction.def | 2 +- src/Actions/PotentialAction/FitPotentialAction.cpp | 10 +- src/Actions/PotentialAction/FitPotentialAction.def | 5 +- src/Actions/Process.cpp | 5 +- src/Actions/WorldAction/InputAction.cpp | 9 +- src/Actions/unittests/stubs/DummyUI.hpp | 6 +- src/Analysis/analysis_correlation.cpp | 7 - src/Analysis/unittests/CountBondsUnitTest.cpp | 52 +- src/Box.cpp | 2 +- src/Box.hpp | 2 +- src/Filling/Inserter/SurfaceRandomInserter.cpp | 100 + src/Filling/Inserter/SurfaceRandomInserter.hpp | 48 + src/Filling/Makefile.am | 15 +- src/Filling/Mesh/MeshAdaptor.hpp | 1 + src/Filling/Preparators/BaseFillerPreparator.cpp | 140 + src/Filling/Preparators/BaseFillerPreparator.hpp | 75 + src/Filling/Preparators/BoxFillerPreparator.cpp | 57 + src/Filling/Preparators/BoxFillerPreparator.hpp | 42 + .../Preparators/ShapeSurfaceFillerPreparator.cpp | 96 + .../Preparators/ShapeSurfaceFillerPreparator.hpp | 49 + .../Preparators/ShapeVolumeFillerPreparator.cpp | 64 + .../Preparators/ShapeVolumeFillerPreparator.hpp | 37 + .../Exporters/SaturationDistanceMaximizer.cpp | 5 +- src/Fragmentation/Homology/HomologyContainer.hpp | 7 + src/Graph/BondGraph.hpp | 12 +- src/LinkedCell/linkedcell.cpp | 13 +- src/LinkedCell/unittests/linkedcellUnitTest.cpp | 2 +- src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp | 2 +- src/Parameters/Makefile.am | 27 +- src/Parameters/Specifics/Value_atom.cpp | 76 + src/Parameters/Specifics/Value_atom.hpp | 33 + src/Parameters/Specifics/Value_element.cpp | 73 + src/Parameters/Specifics/Value_element.hpp | 33 + src/Parameters/Specifics/Value_molecule.cpp | 76 + src/Parameters/Specifics/Value_molecule.hpp | 33 + src/Parameters/Specifics/Value_string.cpp | 57 + src/Parameters/Specifics/Value_string.hpp | 29 + src/Parameters/Validators/Ops_Validator_impl.hpp | 10 + .../Validators/Specific/FileSuffixValidator.hpp | 3 + .../Validators/Specific/ParserFileValidator.cpp | 10 +- .../Validators/Specific/ParserFileValidator.hpp | 3 + src/Parameters/Validators/Validator.hpp | 1 - .../getFlatListFromHierarchyOfValidators.hpp | 59 + src/Parameters/Value.hpp | 5 +- src/Parameters/Value_string.cpp | 51 - src/Parameters/Value_string.hpp | 26 - src/Parser/PdbParser.cpp | 2 +- src/Potentials/PartialNucleiChargeFitter.cpp | 16 +- src/Potentials/PotentialRegistry.cpp | 4 + src/Potentials/PotentialRegistry.hpp | 2 +- src/Potentials/SerializablePotential.hpp | 2 +- src/Tesselation/CandidateForTesselation.cpp | 2 +- src/Tesselation/boundary.cpp | 789 +------ src/Tesselation/boundary.hpp | 3 - src/Tesselation/tesselation.cpp | 18 +- src/UIElements/CommandLineUI/CommandLineDialog.cpp | 3 +- src/UIElements/CommandLineUI/CommandLineDialog.hpp | 2 +- src/UIElements/CommandLineUI/CommandLineParser.cpp | 40 +- src/UIElements/CommandLineUI/CommandLineParser.hpp | 2 +- .../CommandLineUI/CommandLineUIFactory.cpp | 4 +- .../CommandLineUI/CommandLineUIFactory.hpp | 2 +- src/UIElements/Dialog.cpp | 11 +- src/UIElements/Dialog.hpp | 2 +- src/UIElements/Makefile.am | 2 + src/UIElements/Menu/Menu.cpp | 7 +- src/UIElements/Menu/Menu.hpp | 43 +- src/UIElements/Menu/Qt4/QMenu_tooltip.hpp | 48 + src/UIElements/Menu/Qt4/QtMenu.hpp | 11 +- src/UIElements/Qt4/QtDialog.cpp | 6 +- src/UIElements/Qt4/QtDialog.hpp | 2 +- src/UIElements/Qt4/QtMainWindow.cpp | 1 + src/UIElements/Qt4/QtUIFactory.cpp | 4 +- src/UIElements/Qt4/QtUIFactory.hpp | 2 +- src/UIElements/Qt4/Query/AtomsQtQuery.cpp | 2 +- src/UIElements/Qt4/Query/DoublesQtQuery.cpp | 2 +- src/UIElements/Qt4/Query/ElementsQtQuery.cpp | 2 +- src/UIElements/Qt4/Query/FileQtQuery.cpp | 52 +- src/UIElements/Qt4/Query/FilesQtQuery.cpp | 2 +- src/UIElements/Qt4/Query/IntsQtQuery.cpp | 2 +- src/UIElements/Qt4/Query/MoleculesQtQuery.cpp | 2 +- src/UIElements/Qt4/Query/QtQuery.hpp | 2 + src/UIElements/Qt4/Query/QtQueryList.hpp | 6 +- src/UIElements/Qt4/Query/StringsQtQuery.cpp | 2 +- src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp | 2 +- src/UIElements/Qt4/Query/VectorsQtQuery.cpp | 2 +- src/UIElements/TextUI/TextDialog.cpp | 3 +- src/UIElements/TextUI/TextDialog.hpp | 2 +- src/UIElements/TextUI/TextUIFactory.cpp | 4 +- src/UIElements/TextUI/TextUIFactory.hpp | 2 +- src/UIElements/UIFactory.hpp | 2 +- src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp | 2 +- .../Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp | 17 - .../Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp | 7 +- .../Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp | 5 + .../Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp | 91 +- src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp | 136 +- src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp | 6 + src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp | 998 +------- src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp | 130 +- src/UIElements/Views/Qt4/QtHomologyList.cpp | 44 +- src/UIElements/Views/Qt4/QtMoleculeList.cpp | 6 +- src/UIElements/Views/Qt4/QtToolBar.cpp | 16 +- src/UIElements/Views/Qt4/QtToolBar.hpp | 74 +- .../Views/Qt4/QtToolBar_QtFavoriteActions.cpp | 199 ++ src/World.cpp | 47 +- src/builder.cpp | 5 +- src/cleanUp.cpp | 5 + src/documentation/constructs/filling.dox | 14 +- src/documentation/tests/tests.dox | 14 +- src/molecule.cpp | 11 - src/molecule.hpp | 20 +- src/molecule_geometry.cpp | 194 +- src/moleculelist.cpp | 12 +- tests/Python/AllActions/options.dat | 3 +- ...-analysis-dipole-correlation-discrete-angles.at | 6 +- .../testsuite-analysis-dipole-correlation-empty.at | 2 +- tests/regression/Atoms/Add/testsuite-atoms-add.at | 4 +- .../post/tensid-undo.data | 0 .../post/tensid.data | 0 .../Filling/FillSurface/post/water_cube.xyz | 80 + .../Filling/FillSurface/post/water_cylinder.xyz | 98 + .../Filling/FillSurface/post/water_sphere.xyz | 62 + .../Filling/FillSurface/post/water_undo.xyz | 5 + .../pre/tensid.data | 0 .../pre/tensid.potentials | 0 tests/regression/Filling/FillSurface/pre/water.xyz | 5 + .../FillSurface/testsuite-fill-surface-cube.at | 102 + .../FillSurface/testsuite-fill-surface-cylinder.at | 102 + .../testsuite-fill-surface-everywhere.at | 46 + .../FillSurface/testsuite-fill-surface-micelle.at | 105 + .../FillSurface/testsuite-fill-surface-nowhere.at | 45 + .../FillSurface/testsuite-fill-surface-sphere.at | 102 + .../Filling/FillVoidWithMolecule/post/propane.xyz | 13 - .../Filling/FillVoidWithMolecule/post/tensid.data | 2769 -------------------- .../Filling/FillVoidWithMolecule/post/test.conf | 1077 -------- .../Filling/FillVoidWithMolecule/post/test.xyz | 932 ------- .../Filling/FillVoidWithMolecule/pre/tensid.data | 59 - .../FillVoidWithMolecule/pre/tensid.potentials | 1546 ----------- .../Filling/FillVoidWithMolecule/pre/test.conf | 83 - .../Filling/FillVoidWithMolecule/pre/water.data | 4 - .../testsuite-fill-void-with-molecule.at | 69 - .../testsuite-fill-void-with-tenside-molecule.at | 57 - .../Filling/FillVolume/post/water_cylinder.xyz | 14 + .../Filling/FillVolume/post/water_undo.xyz | 5 + tests/regression/Filling/FillVolume/pre/water.xyz | 5 + .../FillVolume/testsuite-fill-volume-cube.at | 43 + .../FillVolume/testsuite-fill-volume-cylinder.at | 92 + .../FillVolume/testsuite-fill-volume-everywhere.at | 43 + .../FillVolume/testsuite-fill-volume-nowhere.at | 42 + .../FillVolume/testsuite-fill-volume-sphere.at | 43 + .../Filling/FillWithMolecule/post/propane.xyz | 13 - .../Filling/FillWithMolecule/post/test.conf | 1089 -------- .../Filling/FillWithMolecule/pre/test.conf | 83 - .../testsuite-fill-with-molecule.at | 72 - .../RegularGrid/post/solved_double_sles.data | 708 +++--- .../RegularGrid/post/solved_single_sles.data | 1332 +++++----- ...=> testsuite-fill-regular-grid-with-surface.at} | 0 ...ular-grid.at => testsuite-fill-regular-grid.at} | 0 .../testsuite-molecules-fill-spherical-surface.at | 57 - tests/regression/Filling/testsuite-filling.at | 27 +- tests/regression/Makefile.am | 19 +- .../testsuite-options-invalid-commands.at | 13 +- .../Options/Warranty/testsuite-options-warranty.at | 1 - .../Parser/Mpqc/testsuite-parser-mpqc-load.at | 2 +- .../testsuite-set-random-number-distribution.at | 8 +- .../Engine/testsuite-set-random-number-engine.at | 8 +- 215 files changed, 5391 insertions(+), 12269 deletions(-) create mode 100644 src/Actions/FillAction/FillVolumeAction.cpp create mode 100644 src/Actions/FillAction/FillVolumeAction.def create mode 100644 src/Actions/FillAction/FillVolumeAction.hpp create mode 100644 src/Actions/FillAction/SuspendInMoleculeAction.cpp create mode 100644 src/Actions/FillAction/SuspendInMoleculeAction.def create mode 100644 src/Actions/FillAction/SuspendInMoleculeAction.hpp delete mode 100644 src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp delete mode 100644 src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def delete mode 100644 src/Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp delete mode 100644 src/Actions/MoleculeAction/FillWithMoleculeAction.cpp delete mode 100644 src/Actions/MoleculeAction/FillWithMoleculeAction.def delete mode 100644 src/Actions/MoleculeAction/FillWithMoleculeAction.hpp delete mode 100644 src/Actions/MoleculeAction/SuspendInWaterAction.cpp delete mode 100644 src/Actions/MoleculeAction/SuspendInWaterAction.def delete mode 100644 src/Actions/MoleculeAction/SuspendInWaterAction.hpp create mode 100644 src/Filling/Inserter/SurfaceRandomInserter.cpp create mode 100644 src/Filling/Inserter/SurfaceRandomInserter.hpp create mode 100644 src/Filling/Preparators/BaseFillerPreparator.cpp create mode 100644 src/Filling/Preparators/BaseFillerPreparator.hpp create mode 100644 src/Filling/Preparators/BoxFillerPreparator.cpp create mode 100644 src/Filling/Preparators/BoxFillerPreparator.hpp create mode 100644 src/Filling/Preparators/ShapeSurfaceFillerPreparator.cpp create mode 100644 src/Filling/Preparators/ShapeSurfaceFillerPreparator.hpp create mode 100644 src/Filling/Preparators/ShapeVolumeFillerPreparator.cpp create mode 100644 src/Filling/Preparators/ShapeVolumeFillerPreparator.hpp create mode 100644 src/Parameters/Specifics/Value_atom.cpp create mode 100644 src/Parameters/Specifics/Value_atom.hpp create mode 100644 src/Parameters/Specifics/Value_element.cpp create mode 100644 src/Parameters/Specifics/Value_element.hpp create mode 100644 src/Parameters/Specifics/Value_molecule.cpp create mode 100644 src/Parameters/Specifics/Value_molecule.hpp create mode 100644 src/Parameters/Specifics/Value_string.cpp create mode 100644 src/Parameters/Specifics/Value_string.hpp create mode 100644 src/Parameters/Validators/getFlatListFromHierarchyOfValidators.hpp delete mode 100644 src/Parameters/Value_string.cpp delete mode 100644 src/Parameters/Value_string.hpp create mode 100644 src/UIElements/Menu/Qt4/QMenu_tooltip.hpp create mode 100644 src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp rename tests/regression/Filling/{SphericalSurface => FillSurface}/post/tensid-undo.data (100%) rename tests/regression/Filling/{SphericalSurface => FillSurface}/post/tensid.data (100%) create mode 100644 tests/regression/Filling/FillSurface/post/water_cube.xyz create mode 100644 tests/regression/Filling/FillSurface/post/water_cylinder.xyz create mode 100644 tests/regression/Filling/FillSurface/post/water_sphere.xyz create mode 100644 tests/regression/Filling/FillSurface/post/water_undo.xyz rename tests/regression/Filling/{SphericalSurface => FillSurface}/pre/tensid.data (100%) rename tests/regression/Filling/{SphericalSurface => FillSurface}/pre/tensid.potentials (100%) create mode 100644 tests/regression/Filling/FillSurface/pre/water.xyz create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-cube.at create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-cylinder.at create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-everywhere.at create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-micelle.at create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-nowhere.at create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-sphere.at delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/post/propane.xyz delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/post/tensid.data delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/post/test.conf delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/post/test.xyz delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/pre/tensid.potentials delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/pre/test.conf delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/pre/water.data delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at create mode 100644 tests/regression/Filling/FillVolume/post/water_cylinder.xyz create mode 100644 tests/regression/Filling/FillVolume/post/water_undo.xyz create mode 100644 tests/regression/Filling/FillVolume/pre/water.xyz create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-cube.at create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-cylinder.at create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-everywhere.at create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-nowhere.at create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-sphere.at delete mode 100644 tests/regression/Filling/FillWithMolecule/post/propane.xyz delete mode 100644 tests/regression/Filling/FillWithMolecule/post/test.conf delete mode 100644 tests/regression/Filling/FillWithMolecule/pre/test.conf delete mode 100644 tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at rename tests/regression/Filling/RegularGrid/{testsuite-molecules-fill-regular-grid-with-surface.at => testsuite-fill-regular-grid-with-surface.at} (100%) rename tests/regression/Filling/RegularGrid/{testsuite-molecules-fill-regular-grid.at => testsuite-fill-regular-grid.at} (100%) delete mode 100644 tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at hooks/post-receive -- MoleCuilder

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