- Molecuilder-devel

[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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[SCM] MoleCuilder branch Candidate_v1.4.8 created. v1.4.7-54-g4d966a0
by git＠ins.uni-bonn.de 16 Sep '14

16 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 created at 4d966a045dba17945ab7e6433ebf4faea3d73b17 (commit) - Log ----------------------------------------------------------------- commit 4d966a045dba17945ab7e6433ebf4faea3d73b17 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 "" (). commit 06b5dfa95337fee961ce3018c5e56e6b64c06454 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 16 02:09:36 2014 +0200 FIX: CommandLineParser causes idling thread when parsing goes wrong. - CommandLineParser::Parse() now returns bool to give status of parsing, only when true is scanForArguments() called, which fills the ActionQueue's queue which is not executed anymore because the run thread was already stopped by the caught exception from the parse failure. commit 7e1a886b77240a61da6f1d0f312f69d0910ff9f0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 23:29:05 2014 +0200 MEMFIX: Thrown ParserException causes mem leak in LoadAction - also added catching of exception to both LoadAction and InputAction. commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91 Merge: b73545e 8859b5e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:05:28 2014 +0200 Merge branch 'GUI_Fixes' into stable commit b73545e66c148c8d0fce990a5e3138a99fadcc28 Merge: 55736be 5524ae9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:28:50 2014 +0200 Merge branch 'MemFixes' into stable Conflicts: src/Tesselation/boundary.cpp - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly also affected during MemFixes. commit 55736be799388502de9a57ac542d215e5ce0565a Merge: 29b35ef 5a9f4c1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:22:29 2014 +0200 Merge branch 'Cleanup_old_code' into stable ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 deleted. v1.4.7-54-g586f10c
by git＠ins.uni-bonn.de 16 Sep '14

16 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 586f10c83860e32bd4385827fe0c3e97d2ba55cf ----------------------------------------------------------------------- 586f10c83860e32bd4385827fe0c3e97d2ba55cf Set version to 1.4.8. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 created. v1.4.7-54-g586f10c
by git＠ins.uni-bonn.de 16 Sep '14

16 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 created at 586f10c83860e32bd4385827fe0c3e97d2ba55cf (commit) - Log ----------------------------------------------------------------- commit 586f10c83860e32bd4385827fe0c3e97d2ba55cf 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 "" (). commit ddfbd403ac839c27e59df6bc1810504ffec4fa86 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Tue Sep 16 02:09:36 2014 +0200 FIX: CommandLineParser causes idling thread when parsing goes wrong. - CommandLineParser::Parse() now returns bool to give status of parsing, only when true is scanForArguments() called, which fills the ActionQueue's queue which is not executed anymore because the run thread was already stopped by the caught exception from the parse failure. commit 7e1a886b77240a61da6f1d0f312f69d0910ff9f0 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 23:29:05 2014 +0200 MEMFIX: Thrown ParserException causes mem leak in LoadAction - also added catching of exception to both LoadAction and InputAction. commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91 Merge: b73545e 8859b5e Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 17:05:28 2014 +0200 Merge branch 'GUI_Fixes' into stable commit b73545e66c148c8d0fce990a5e3138a99fadcc28 Merge: 55736be 5524ae9 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:28:50 2014 +0200 Merge branch 'MemFixes' into stable Conflicts: src/Tesselation/boundary.cpp - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly also affected during MemFixes. commit 55736be799388502de9a57ac542d215e5ce0565a Merge: 29b35ef 5a9f4c1 Author: Frederik Heber <heber(a)ins.uni-bonn.de> Date: Mon Sep 15 16:22:29 2014 +0200 Merge branch 'Cleanup_old_code' into stable ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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[SCM] MoleCuilder branch Candidate_v1.4.8 deleted. v1.4.7-53-g05341a0
by git＠ins.uni-bonn.de 16 Sep '14

16 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 05341a09115eb72edd1ad3c7350702234bb2fa73 ----------------------------------------------------------------------- 05341a09115eb72edd1ad3c7350702234bb2fa73 Set version to 1.4.8. ----------------------------------------------------------------------- hooks/post-receive -- MoleCuilder

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