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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@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