[Molecuilder-devel] [SCM] MoleCuilder branch stable updated. v1.4.7-54-g7f6a2fc
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- Log -----------------------------------------------------------------
commit 7f6a2fc9f64c88371654df745552167f0e0e3a9c
Author: Frederik Heber <heber at 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
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