# # ChangeLog for src/Makefile.am # # Generated by Trac 1.4.4 # Jan 14, 2025, 11:31:11 PM Wed, 02 Mar 2011 21:48:20 GMT Frederik Heber [435065] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Dynamics/VerletForceIntegration.hpp (added) * src/Makefile.am (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * tests/regression/Molecules/VerletIntegration/post/test.conf (moved) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) Rewrote VerletForceIntegration into a functor in Dynamics/. - we ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [8009ce] * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (modified) * src/AtomSet.hpp (modified) * src/Dynamics/OutputTemperature.hpp (added) * src/Makefile.am (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * tests/regression/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at (modified) Rewrote OutputTemperature into a functor in Dynamics/ - formerly ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [20943b] * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (added) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) Rewrote LinearInterpolationBetweenSteps into a functor in Dynamics/ ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [9e23a3] * src/Dynamics/MinimiseConstrainedPotential.cpp (added) * src/Dynamics/MinimiseConstrainedPotential.hpp (added) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) Rewrote MinimiseConstrainedPotential into a functor in Dynamics/. - ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [632508] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Graph/BondGraph.cpp (moved) * src/Graph/BondGraph.hpp (moved) * src/Makefile.am (modified) * src/World.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisBondsUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) Moved files bondgraph.?pp -> Graph/BondGraph.?pp. Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [5702cdb] * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_pointcloud.cpp (deleted) Removed molecule_pointcloud.cpp. Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [34c43a] * configure.ac (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/IPointCloud.hpp (added) * src/Makefile.am (modified) * src/PointCloud.cpp (deleted) * src/PointCloud.hpp (deleted) * src/PointCloudAdaptor.hpp (added) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/ellipsoid.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/TesselationUnitTest.hpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) Bigger change: Replaced PointCloud by PointCloudAdaptor. - ... Thu, 24 Feb 2011 19:43:03 GMT Frederik Heber [03c77c] * src/ConfigFileBuffer.cpp (modified) * src/Makefile.am (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/bond.cpp (modified) * src/bond.hpp (modified) * src/config.cpp (modified) * src/graph.hpp (modified) * src/lists.hpp (deleted) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) bonds::previous and ::next removed, lists.hpp deleted. - the last ... Thu, 24 Feb 2011 17:46:46 GMT Frederik Heber [6625c3] * src/AtomSet.hpp (modified) * src/Makefile.am (modified) * src/Parser/PcpParser.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/Langevin.hpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_trajectoryparticle.cpp (deleted) * src/atom_trajectoryparticle.hpp (deleted) * src/atom_trajectoryparticleinfo.cpp (deleted) * src/atom_trajectoryparticleinfo.hpp (deleted) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_geometry.cpp (modified) Removed atom_trajectoryparticle*, replaced by AtomInfo class now ... Thu, 24 Feb 2011 16:05:50 GMT Frederik Heber [6bb605] * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Makefile.am (modified) * src/WorldTime.cpp (modified) * src/WorldTime.hpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) Worldtime now has static CurrentTime and static (inline) ... Thu, 24 Feb 2011 15:54:52 GMT Frederik Heber [f649de] * src/Makefile.am (modified) * src/WorldTime.cpp (added) * src/WorldTime.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/WorldTimeUnitTest.cpp (added) * src/unittests/WorldTimeUnitTest.hpp (added) Implemented class WorldTime. - WorldTime contains the current, ... Thu, 03 Feb 2011 09:59:28 GMT Frederik Heber [1ee3b8d] * configure.ac (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/LinearAlgebra/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (added) * src/RandomNumbers/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Made RandomNumbers sources into its own library ... Thu, 03 Feb 2011 09:51:19 GMT Frederik Heber [081e5d] * src/Makefile.am (modified) * src/RandomNumbers/RandomNumberDistribution.hpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.def (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (added) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.hpp (modified) * src/RandomNumbers/RandomNumberEngine.hpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.def (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (added) * src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.def (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) Implemented all possible parameter functions for engine and ... Thu, 03 Feb 2011 09:51:19 GMT Frederik Heber [15911c] * src/Makefile.am (modified) * src/RandomNumbers/RandomNumberDistribution.hpp (modified) * src/RandomNumbers/RandomNumberEngine.hpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.hpp (modified) * src/RandomNumbers/RandomNumberGenerator_Encapsulation.hpp (modified) * src/RandomNumbers/unittests/Makefile.am (modified) Made some cstor of RandomNumber... protected. - ... Thu, 03 Feb 2011 09:51:19 GMT Frederik Heber [1d5a871] * configure.ac (modified) * src/Makefile.am (modified) * src/RandomNumbers/Creator_impl.hpp (deleted) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.def (modified) * src/RandomNumbers/RandomNumberDistributionFactory.hpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.undef (modified) * src/RandomNumbers/RandomNumberDistribution_Creator.hpp (deleted) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.hpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.def (modified) * src/RandomNumbers/RandomNumberEngineFactory.hpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.undef (modified) * src/RandomNumbers/RandomNumberEngine_Creator.hpp (deleted) * src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.def (added) * src/RandomNumbers/RandomNumberGeneratorFactory.hpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.undef (added) * src/RandomNumbers/RandomNumberGenerator_Creator.hpp (deleted) * src/RandomNumbers/RandomNumberGenerator_Encapsulation.hpp (modified) * src/RandomNumbers/TemplatePowerSetGenerator.hpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/builder_init.cpp (modified) Factored out Factory pattern (no pun intended). - the Factory ... Thu, 03 Feb 2011 09:51:19 GMT Frederik Heber [c9bc2b7] * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Makefile.am (modified) * src/RandomNumbers/Creator_impl.hpp (added) * src/RandomNumbers/EmptyPrototypeTable.hpp (added) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (added) * src/RandomNumbers/RandomNumberDistributionFactory.def (added) * src/RandomNumbers/RandomNumberDistributionFactory.hpp (added) * src/RandomNumbers/RandomNumberDistributionFactory.undef (added) * src/RandomNumbers/RandomNumberDistribution_Creator.hpp (added) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.hpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (added) * src/RandomNumbers/RandomNumberEngineFactory.def (moved) * src/RandomNumbers/RandomNumberEngineFactory.hpp (added) * src/RandomNumbers/RandomNumberEngineFactory.undef (added) * src/RandomNumbers/RandomNumberEngine_Creator.hpp (added) * src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.hpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.undef (deleted) * src/RandomNumbers/RandomNumberGenerator_Creator.hpp (added) * src/RandomNumbers/RandomNumberGenerator_Encapsulation.hpp (modified) * src/RandomNumbers/TemplatePowerSetGenerator.hpp (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (added) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.hpp (added) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (added) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.hpp (added) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.hpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (added) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.hpp (added) * src/builder_init.cpp (modified) Bigger rewrite of RandomNumbers ... due to cloning of prototypes. - ... Thu, 03 Feb 2011 09:51:19 GMT Frederik Heber [3f9eba] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (added) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.def (added) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.hpp (added) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (added) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.def (added) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.hpp (added) * src/Makefile.am (modified) * src/RandomNumbers/RandomNumberDistribution.hpp (added) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.hpp (added) * src/RandomNumbers/RandomNumberEngine.hpp (added) * src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (added) * src/RandomNumbers/RandomNumberGenerator.cpp (added) * src/RandomNumbers/RandomNumberGenerator.hpp (added) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (added) * src/RandomNumbers/RandomNumberGeneratorFactory.def (added) * src/RandomNumbers/RandomNumberGeneratorFactory.hpp (added) * src/RandomNumbers/RandomNumberGeneratorFactory.undef (added) * src/RandomNumbers/RandomNumberGenerator_Encapsulation.hpp (added) * src/RandomNumbers/TemplatePowerSetGenerator.hpp (added) * src/RandomNumbers/unittests/Makefile.am (added) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (added) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.hpp (added) * src/builder_init.cpp (modified) * src/unittests/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (added) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (added) * tests/regression/RandomNumbers/testsuite-randomnumbers.at (added) * tests/regression/testsuite.at (modified) New classes for random number generation. - we use boost::random as ... Thu, 03 Feb 2011 09:51:14 GMT Frederik Heber [e5bf2b] * src/Actions/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/LinearAlgebra/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/UIElements/Makefile.am (modified) removed CPPUNIT_LIBS/FLAGS from most Makefile.am and LIBS/libs -> ... Thu, 23 Dec 2010 17:41:54 GMT Frederik Heber [6d2207] * configure.ac (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (added) * src/Shapes/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Forgot Shapes/unittests and made Shapes into own library. - ... Thu, 23 Dec 2010 17:41:54 GMT Frederik Heber [acbe1b] * MoleCuilder.pc.in (added) * configure.ac (modified) * molecuilder.pc.in (deleted) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) All libraries don't have version in name anymore. - we used gained ... Thu, 23 Dec 2010 17:40:04 GMT Frederik Heber [a0064e] * configure.ac (modified) * m4/ax_codepatterns.m4 (added) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/Formula.hpp (modified) * src/Helpers/Assert.cpp (deleted) * src/Helpers/Assert.hpp (deleted) * src/Helpers/Info.cpp (deleted) * src/Helpers/Info.hpp (deleted) * src/Helpers/Log.cpp (deleted) * src/Helpers/Log.hpp (deleted) * src/Helpers/Makefile.am (deleted) * src/Helpers/MemDebug.cpp (deleted) * src/Helpers/MemDebug.hpp (deleted) * src/Helpers/Range.hpp (deleted) * src/Helpers/Verbose.cpp (deleted) * src/Helpers/Verbose.hpp (deleted) * src/Helpers/errorlogger.cpp (deleted) * src/Helpers/errorlogger.hpp (deleted) * src/Helpers/fast_functions.hpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/helpers.hpp (modified) * src/Helpers/logger.cpp (deleted) * src/Helpers/logger.hpp (deleted) * src/Helpers/toString.hpp (deleted) * src/Helpers/unittests/InfoUnitTest.cpp (deleted) * src/Helpers/unittests/InfoUnitTest.hpp (deleted) * src/Helpers/unittests/LogUnitTest.cpp (deleted) * src/Helpers/unittests/LogUnitTest.hpp (deleted) * src/Helpers/unittests/Makefile.am (deleted) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Patterns/Cacheable.hpp (deleted) * src/Patterns/ObservedContainer.hpp (deleted) * src/Patterns/ObservedContainer_impl.hpp (deleted) * src/Patterns/ObservedIterator.hpp (deleted) * src/Patterns/Observer.cpp (deleted) * src/Patterns/Observer.hpp (deleted) * src/Patterns/Registry.hpp (deleted) * src/Patterns/Registry_impl.hpp (deleted) * src/Patterns/Singleton.hpp (deleted) * src/Patterns/Singleton_impl.hpp (deleted) * src/Patterns/unittests/CacheableUnitTest.cpp (deleted) * src/Patterns/unittests/CacheableUnitTest.hpp (deleted) * src/Patterns/unittests/Makefile.am (deleted) * src/Patterns/unittests/ObserverUnitTest.cpp (deleted) * src/Patterns/unittests/ObserverUnitTest.hpp (deleted) * src/Patterns/unittests/RegistryUnitTest.cpp (deleted) * src/Patterns/unittests/RegistryUnitTest.hpp (deleted) * src/Patterns/unittests/SingletonUnitTest.cpp (deleted) * src/Patterns/unittests/SingletonUnitTest.hpp (deleted) * src/Shapes/unittests/Makefile.am (modified) * src/SubspaceFactorizer.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/SubspaceFactorizerUnitTest.cpp (modified) Moved stuff in src/Helpers and src/Patterns out to stand-alone ... Thu, 16 Dec 2010 17:32:23 GMT Frederik Heber [f4d063] * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Makefile.am (modified) * src/builder.cpp (modified) * src/builder_init.cpp (added) * src/builder_init.hpp (added) MEMFIX: MemDebug ignores all unknown sources. Removed all ... Thu, 16 Dec 2010 17:32:23 GMT Frederik Heber [c42e60] * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (added) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.hpp (added) * src/Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp (added) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (added) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.hpp (added) * src/Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp (added) * src/Makefile.am (modified) * tests/regression/Selection/Atoms/testsuite-selection-atoms-of-molecule.at (modified) * tests/regression/testsuite-molecules.at (modified) Two new descriptors: AtomOfMoleculeSelection, ... Thu, 16 Dec 2010 17:32:22 GMT Frederik Heber [92d756] * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByNameAction.cpp (added) * src/Actions/SelectionAction/MoleculeByNameAction.def (added) * src/Actions/SelectionAction/MoleculeByNameAction.hpp (added) * src/Actions/SelectionAction/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByOrderAction.def (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.def (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByNameAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByNameAction.def (added) * src/Actions/SelectionAction/NotMoleculeByNameAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByOrderAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByOrderAction.def (added) * src/Actions/SelectionAction/NotMoleculeByOrderAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (added) * src/Descriptors/MoleculeOrderDescriptor.hpp (added) * src/Descriptors/MoleculeOrderDescriptor_impl.hpp (added) * src/Makefile.am (modified) Larger update of selections. - new selections: - ... Mon, 06 Dec 2010 19:37:05 GMT Frederik Heber [a564be] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Makefile.am (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/stackclass.hpp (deleted) * src/unittests/Makefile.am (modified) * src/unittests/stackclassunittest.cpp (deleted) * src/unittests/stackclassunittest.hpp (deleted) Removed ancient StackClass, replaced by std::deque. - all PopLast ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [e828c0] * src/LinearAlgebra/Eigenspace.cpp (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/Subspace.cpp (modified) * src/LinearAlgebra/Subspace.hpp (modified) * src/LinearAlgebra/VectorContent.cpp (modified) * src/Makefile.am (modified) * src/SubspaceFactorizer.cpp (added) * src/unittests/SubspaceFactorizerUnittest.cpp (modified) * src/unittests/SubspaceFactorizerUnittest.hpp (modified) SubspaceFactorizer is now hierarchical. - higher order subspace ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [13d150] * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/leastsquaremin.cpp (moved) * src/LinearAlgebra/leastsquaremin.hpp (moved) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Makefile.am (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) Moved leastsquaremin.?pp to LinearAlgebra. - changed Makefile.am ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [e4fe8d] * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Descriptors/AtomIdDescriptor.hpp (modified) * src/Descriptors/AtomShapeDescriptor.hpp (modified) * src/Descriptors/MoleculeIdDescriptor.hpp (modified) * src/Descriptors/MoleculeNameDescriptor.hpp (modified) * src/Descriptors/MoleculePtrDescriptor.hpp (modified) * src/Helpers/Makefile.am (modified) * src/Helpers/defs.cpp (moved) * src/Helpers/defs.hpp (moved) * src/Helpers/fast_functions.hpp (modified) * src/Helpers/helpers.hpp (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.hpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/Vector.hpp (modified) * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/Makefile.am (modified) * src/Patterns/Singleton.hpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.hpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/World.cpp (modified) * src/analysis_correlation.hpp (modified) * src/boundary.hpp (modified) * src/element.hpp (modified) * src/linkedcell.hpp (modified) * src/molecule_graph.cpp (modified) * src/periodentafel.hpp (modified) * src/tesselationhelpers.hpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Moved defs.?pp to subdir (and library) Helpers. - hence, include ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [d5240d] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Exceptions/Makefile.am (modified) * src/Helpers/Makefile.am (modified) * src/LinearAlgebra/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Linking to non-system boost is working now. - FIX: ... Sat, 04 Dec 2010 23:44:19 GMT Frederik Heber [1e0861] * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Qt stuff is not compiled into libMolecuilder but libMolecuilderQtUI. Sat, 04 Dec 2010 23:44:19 GMT Frederik Heber [a5ddf0] * src/Makefile.am (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/QtQueryListPipe.hpp (modified) * src/UIElements/Qt4/Pipe/QtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.hpp (added) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.hpp (added) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) All Qt...QueryPipe now have their own header file. - Query just ... Sat, 04 Dec 2010 23:33:47 GMT Frederik Heber [b59da6] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Makefile.am (modified) * src/Patterns/Registry_impl.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/Menu.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuDescription.hpp (modified) * src/UIElements/Menu/MenuInterface.cpp (added) * src/UIElements/Menu/MenuInterface.hpp (added) * src/UIElements/Menu/Qt4/QtMenu.cpp (deleted) * src/UIElements/Menu/Qt4/QtMenu.hpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (added) * src/UIElements/Menu/Qt4/QtMenuPipe.hpp (added) * src/UIElements/Menu/SubMenuItem.hpp (deleted) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (moved) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (moved) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (moved) * src/UIElements/Menu/TextMenu/DisplayMenuItem.hpp (moved) * src/UIElements/Menu/TextMenu/MenuItem.cpp (moved) * src/UIElements/Menu/TextMenu/MenuItem.hpp (moved) * src/UIElements/Menu/TextMenu/SeperatorItem.cpp (moved) * src/UIElements/Menu/TextMenu/SeperatorItem.hpp (moved) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (moved) * src/UIElements/Menu/TextMenu/SubMenuItem.hpp (added) * src/UIElements/Menu/TextMenu/TextMenu.hpp (added) * src/UIElements/Menu/TextMenu/TxMenu.cpp (moved) * src/UIElements/Menu/TextMenu/TxMenu.hpp (moved) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/builder.cpp (modified) Refactoring of Menu structure for Qt and Text UI done. - Menu is ... Sat, 30 Oct 2010 20:42:44 GMT Frederik Heber [e4afb4] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionTraits.cpp (modified) * src/Actions/ActionTraits.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.def (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (modified) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.def (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpAction.def (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.def (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/VersionAction.def (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.def (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.def (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.def (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.def (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MapOfActions.cpp (deleted) * src/Actions/MapOfActions.hpp (deleted) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.def (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/OptionRegistry.cpp (added) * src/Actions/OptionRegistry.hpp (added) * src/Actions/OptionTrait.cpp (added) * src/Actions/OptionTrait.hpp (added) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.def (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.def (modified) * src/Actions/Process.cpp (modified) * src/Actions/Process.hpp (modified) * src/Actions/RedoAction.cpp (added) * src/Actions/RedoAction.def (added) * src/Actions/RedoAction.hpp (added) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.def (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.def (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.def (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.def (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.def (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.def (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.def (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.def (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (modified) * src/Actions/UndoAction.cpp (added) * src/Actions/UndoAction.def (moved) * src/Actions/UndoAction.hpp (added) * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.def (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.def (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.def (modified) * src/Actions/convert5.sh (added) * src/CommandLineParser.cpp (deleted) * src/Makefile.am (modified) * src/Patterns/Registry.hpp (modified) * src/Patterns/Registry_impl.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (added) * src/UIElements/CommandLineUI/CommandLineParser.hpp (moved) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (added) * src/UIElements/CommandLineUI/TypeEnumContainer.hpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuDescription.hpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/World_calculations.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MenuDescriptionUnitTest.cpp (modified) * src/unittests/MenuDescriptionUnitTest.hpp (modified) * src/unittests/RegistryUnitTest.cpp (added) * src/unittests/RegistryUnitTest.hpp (added) * src/unittests/atomsCalculationTest.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) Huge refactoring: Introduction of Traits to Actions. This change is ... Mon, 25 Oct 2010 17:16:19 GMT Frederik Heber [8df74d] * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (added) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/QtQueryListPipe.hpp (added) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (added) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (added) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (added) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (added) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (added) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (added) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (added) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (added) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (added) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (added) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (added) * src/UIElements/Qt4/Query/FileQtQuery.cpp (added) * src/UIElements/Qt4/Query/IntQtQuery.cpp (added) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (added) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (added) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (added) * src/UIElements/Qt4/Query/StringQtQuery.cpp (added) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (added) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (added) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (added) * src/UIElements/Query/AtomQuery.cpp (added) * src/UIElements/Query/AtomsQuery.cpp (added) * src/UIElements/Query/BooleanQuery.cpp (added) * src/UIElements/Query/BoxQuery.cpp (added) * src/UIElements/Query/DoubleQuery.cpp (added) * src/UIElements/Query/DoublesQuery.cpp (added) * src/UIElements/Query/ElementQuery.cpp (added) * src/UIElements/Query/ElementsQuery.cpp (added) * src/UIElements/Query/EmptyQuery.cpp (added) * src/UIElements/Query/FileQuery.cpp (added) * src/UIElements/Query/IntQuery.cpp (added) * src/UIElements/Query/IntsQuery.cpp (added) * src/UIElements/Query/MoleculeQuery.cpp (added) * src/UIElements/Query/MoleculesQuery.cpp (added) * src/UIElements/Query/Query.cpp (added) * src/UIElements/Query/StringQuery.cpp (added) * src/UIElements/Query/StringsQuery.cpp (added) * src/UIElements/Query/VectorQuery.cpp (added) * src/UIElements/Query/VectorsQuery.cpp (added) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (added) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (added) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (added) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (added) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (added) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (added) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (added) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (added) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (added) * src/UIElements/TextUI/Query/FileTextQuery.cpp (added) * src/UIElements/TextUI/Query/IntTextQuery.cpp (added) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (added) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (added) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (added) * src/UIElements/TextUI/Query/StringTextQuery.cpp (added) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (added) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (added) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (added) * src/UIElements/TextUI/TextDialog.cpp (modified) Split off all ...Query and ...Pipe boilerplate classes. - each ... Mon, 25 Oct 2010 17:13:30 GMT Frederik Heber [379b7e] * src/Makefile.am (modified) BUGFIX: Fixed wrong renaming of USE_GUI_QT to USE_GUI_Qt. Mon, 25 Oct 2010 12:08:39 GMT Frederik Heber [4cf323d] * src/Makefile.am (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Menu/Qt4/QtMenu.cpp (moved) * src/UIElements/Menu/Qt4/QtMenu.hpp (moved) * src/UIElements/Qt4/IntQtQuery.ui (moved) * src/UIElements/Qt4/IntsQtQuery.ui (moved) * src/UIElements/Qt4/QtDialog.cpp (moved) * src/UIElements/Qt4/QtDialog.hpp (moved) * src/UIElements/Qt4/QtMainWindow.cpp (moved) * src/UIElements/Qt4/QtMainWindow.hpp (moved) * src/UIElements/Qt4/QtUIFactory.cpp (moved) * src/UIElements/Qt4/QtUIFactory.hpp (moved) * src/UIElements/Views/Qt4/GLMoleculeView.cpp (moved) * src/UIElements/Views/Qt4/GLMoleculeView.hpp (moved) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (moved) * src/UIElements/Views/Qt4/QtMoleculeView.hpp (moved) * src/UIElements/Views/Qt4/QtStatusBar.cpp (moved) * src/UIElements/Views/Qt4/QtStatusBar.hpp (moved) * src/UIElements/Views/Qt4/QtWorldView.cpp (moved) * src/UIElements/Views/Qt4/QtWorldView.hpp (moved) * src/builder.cpp (modified) Renamed QT -> Qt in files, dirs, and class names. Fri, 22 Oct 2010 16:12:42 GMT Frederik Heber [e4decc] * configure.ac (modified) * src/Makefile.am (modified) * src/unittests/Makefile.am (modified) Changed a bit the sequence of adding BOOST_LIBs. Sat, 28 Aug 2010 03:21:11 GMT Frederik Heber [6c438f] * .gitignore (modified) * AUTHORS (modified) * COPYING (modified) * Makefile.am (modified) * README (modified) * TestRunnerClient.cpp (added) * TestRunnerClient.h (added) * autogen.sh (deleted) * bootstrap (added) * config/ltmain.sh (added) * configure.ac (modified) * doc/molecuilder_logo.png (added) * doc/molecuilder_logo.xcf (added) * libmolecuilder_config.h.in (added) * m4/gwqt4.m4 (modified) * molecuilder.pc.in (added) * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_header.hpp (added) * src/Actions/Action_impl_pre.hpp (added) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (added) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.def (added) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/Remove.def (added) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (added) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (added) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (added) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (added) * src/Actions/AtomAction/TranslateAction.cpp (added) * src/Actions/AtomAction/TranslateAction.def (added) * src/Actions/AtomAction/TranslateAction.hpp (added) * src/Actions/AtomsCalculation.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (deleted) * src/Actions/CmdAction/BondLengthTableAction.hpp (deleted) * src/Actions/CmdAction/ElementDbAction.cpp (deleted) * src/Actions/CmdAction/ElementDbAction.hpp (deleted) * src/Actions/CmdAction/FastParsingAction.cpp (deleted) * src/Actions/CmdAction/FastParsingAction.hpp (deleted) * src/Actions/CmdAction/HelpAction.cpp (deleted) * src/Actions/CmdAction/HelpAction.hpp (deleted) * src/Actions/CmdAction/VerboseAction.cpp (deleted) * src/Actions/CmdAction/VerboseAction.hpp (deleted) * src/Actions/CmdAction/VersionAction.cpp (deleted) * src/Actions/CmdAction/VersionAction.hpp (deleted) * src/Actions/CommandAction/BondLengthTableAction.cpp (added) * src/Actions/CommandAction/BondLengthTableAction.def (added) * src/Actions/CommandAction/BondLengthTableAction.hpp (added) * src/Actions/CommandAction/ElementDbAction.cpp (added) * src/Actions/CommandAction/ElementDbAction.def (added) * src/Actions/CommandAction/ElementDbAction.hpp (added) * src/Actions/CommandAction/FastParsingAction.cpp (added) * src/Actions/CommandAction/FastParsingAction.def (added) * src/Actions/CommandAction/FastParsingAction.hpp (added) * src/Actions/CommandAction/HelpAction.cpp (added) * src/Actions/CommandAction/HelpAction.def (added) * src/Actions/CommandAction/HelpAction.hpp (added) * src/Actions/CommandAction/VerboseAction.cpp (added) * src/Actions/CommandAction/VerboseAction.def (added) * src/Actions/CommandAction/VerboseAction.hpp (added) * src/Actions/CommandAction/VersionAction.cpp (added) * src/Actions/CommandAction/VersionAction.def (added) * src/Actions/CommandAction/VersionAction.hpp (added) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.def (added) * src/Actions/FragmentationAction/ConstructBondGraphAction.hpp (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.def (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.def (added) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.def (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (added) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (added) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (added) * src/Actions/MoleculeAction/CopyAction.def (added) * src/Actions/MoleculeAction/CopyAction.hpp (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (added) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.hpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (added) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (added) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (added) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (deleted) * src/Actions/MoleculeAction/TranslateAction.hpp (deleted) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (added) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.def (added) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.def (added) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.def (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (added) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.hpp (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.hpp (added) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.def (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (added) * src/Actions/SelectionAction/AtomByElementAction.def (added) * src/Actions/SelectionAction/AtomByElementAction.hpp (added) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.def (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (added) * src/Actions/SelectionAction/ClearAllAtomsAction.def (added) * src/Actions/SelectionAction/ClearAllAtomsAction.hpp (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.def (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.hpp (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.hpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.def (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (added) * src/Actions/SelectionAction/MoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/MoleculeOfAtomAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.hpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (added) * src/Actions/SelectionAction/NotAtomByElementAction.def (added) * src/Actions/SelectionAction/NotAtomByElementAction.hpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.def (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.def (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.hpp (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/ValueStorage.cpp (added) * src/Actions/ValueStorage.hpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (added) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (added) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (added) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (added) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.def (added) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (added) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (deleted) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (deleted) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (added) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (added) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (added) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.def (added) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.def (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/AtomSet.hpp (added) * src/AtomicInfo.cpp (added) * src/AtomicInfo.hpp (added) * src/BoundaryLineSet.cpp (added) * src/BoundaryLineSet.hpp (added) * src/BoundaryMaps.hpp (added) * src/BoundaryPointSet.cpp (added) * src/BoundaryPointSet.hpp (added) * src/BoundaryPolygonSet.cpp (added) * src/BoundaryPolygonSet.hpp (added) * src/BoundaryTriangleSet.cpp (added) * src/BoundaryTriangleSet.hpp (added) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/CandidateForTesselation.cpp (added) * src/CandidateForTesselation.hpp (added) * src/CommandLineParser.cpp (modified) * src/CommandLineParser.hpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.hpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/Makefile.am (added) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Formula.hpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Assert.hpp (modified) * src/Helpers/Info.cpp (moved) * src/Helpers/Info.hpp (moved) * src/Helpers/Log.cpp (moved) * src/Helpers/Log.hpp (moved) * src/Helpers/Makefile.am (added) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Helpers/Verbose.cpp (moved) * src/Helpers/Verbose.hpp (moved) * src/Helpers/errorlogger.cpp (moved) * src/Helpers/errorlogger.hpp (moved) * src/Helpers/helpers.cpp (moved) * src/Helpers/helpers.hpp (moved) * src/Helpers/logger.cpp (moved) * src/Helpers/logger.hpp (moved) * src/Legacy/oldmenu.cpp (deleted) * src/Legacy/oldmenu.hpp (deleted) * src/LinearAlgebra/BoxVector.cpp (added) * src/LinearAlgebra/BoxVector.hpp (added) * src/LinearAlgebra/Line.cpp (moved) * src/LinearAlgebra/Line.hpp (moved) * src/LinearAlgebra/LineSegment.cpp (moved) * src/LinearAlgebra/LineSegment.hpp (moved) * src/LinearAlgebra/LineSegmentSet.cpp (moved) * src/LinearAlgebra/LineSegmentSet.hpp (moved) * src/LinearAlgebra/Makefile.am (added) * src/LinearAlgebra/Matrix.cpp (moved) * src/LinearAlgebra/Matrix.hpp (moved) * src/LinearAlgebra/MatrixContent.hpp (moved) * src/LinearAlgebra/Plane.cpp (moved) * src/LinearAlgebra/Plane.hpp (moved) * src/LinearAlgebra/Space.cpp (moved) * src/LinearAlgebra/Space.hpp (moved) * src/LinearAlgebra/Vector.cpp (moved) * src/LinearAlgebra/Vector.hpp (moved) * src/LinearAlgebra/VectorContent.hpp (moved) * src/LinearAlgebra/VectorInterface.cpp (added) * src/LinearAlgebra/VectorInterface.hpp (added) * src/LinearAlgebra/VectorSet.hpp (moved) * src/LinearAlgebra/gslmatrix.cpp (moved) * src/LinearAlgebra/gslmatrix.hpp (moved) * src/LinearAlgebra/gslvector.cpp (moved) * src/LinearAlgebra/gslvector.hpp (moved) * src/LinearAlgebra/linearsystemofequations.cpp (moved) * src/LinearAlgebra/linearsystemofequations.hpp (moved) * src/LinearAlgebra/vector_ops.cpp (moved) * src/LinearAlgebra/vector_ops.hpp (moved) * src/Makefile.am (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/Makefile.am (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbParser.cpp (added) * src/Parser/PdbParser.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/ObservedContainer_impl.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Registry_impl.hpp (modified) * src/PointCloud.cpp (added) * src/PointCloud.hpp (added) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) * src/TesselPoint.cpp (added) * src/TesselPoint.hpp (added) * src/ThermoStatContainer.cpp (modified) * src/ThermoStatContainer.hpp (modified) * src/Thermostats/Berendsen.cpp (added) * src/Thermostats/Berendsen.hpp (added) * src/Thermostats/GaussianThermostat.cpp (added) * src/Thermostats/GaussianThermostat.hpp (added) * src/Thermostats/Langevin.cpp (added) * src/Thermostats/Langevin.hpp (added) * src/Thermostats/NoThermostat.cpp (added) * src/Thermostats/NoThermostat.hpp (added) * src/Thermostats/NoseHoover.cpp (added) * src/Thermostats/NoseHoover.hpp (added) * src/Thermostats/Thermostat.cpp (added) * src/Thermostats/Thermostat.hpp (added) * src/Thermostats/Woodcock.cpp (added) * src/Thermostats/Woodcock.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/QT4/QTMenu.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/QT4/IntQTQuery.ui (added) * src/UIElements/QT4/IntsQTQuery.ui (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTUIFactory.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/ValueStorage.cpp (deleted) * src/UIElements/ValueStorage.hpp (deleted) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/QT4/GLMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/UIElements/Views/QT4/QTWorldView.cpp (modified) * src/UIElements/Views/QT4/QTWorldView.hpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_bonds.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnode.hpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_graphnodeinfo.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (added) * src/defs.hpp (modified) * src/element.cpp (modified) * src/element.hpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (deleted) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/triangleintersectionlist.hpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/AtomDescriptorTest.hpp (modified) * src/unittests/BoxUnittest.cpp (added) * src/unittests/BoxUnittest.hpp (added) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/DummyUI.hpp (added) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MatrixUnittest.hpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/MoleculeDescriptorTest.hpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/ShapeUnittest.hpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/atomsCalculationTest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.hpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslmatrixunittest.hpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/manipulateAtomsTest.hpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/periodentafelTest.hpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.hpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/tesselationunittest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/version.h (modified) * test_all.sh (modified) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/defs.in (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/10/post/test-rotated-xYz20.xyz (added) * tests/regression/Molecules/10/post/test-rotated-z180.xyz (added) * tests/regression/Molecules/10/post/test-rotated-z360.xyz (added) * tests/regression/Molecules/10/post/test-rotated-z90.xyz (added) * tests/regression/Molecules/10/pre/test.xyz (added) * tests/regression/Molecules/11/post/test-copy.xyz (added) * tests/regression/Molecules/11/pre/test.xyz (added) * tests/regression/Molecules/2/post/test.adj (modified) * tests/regression/Molecules/8/post/test-rotated-xYz20.xyz (added) * tests/regression/Molecules/8/post/test-rotated-z180.xyz (added) * tests/regression/Molecules/8/post/test-rotated-z360.xyz (added) * tests/regression/Molecules/8/post/test-rotated-z90.xyz (added) * tests/regression/Molecules/8/pre/test-rotated-xYz20.xyz (added) * tests/regression/Molecules/8/pre/test-rotated-z180.xyz (added) * tests/regression/Molecules/8/pre/test-rotated-z360.xyz (added) * tests/regression/Molecules/8/pre/test-rotated-z90.xyz (added) * tests/regression/Molecules/9/post/test-rotated-xYz20.xyz (added) * tests/regression/Molecules/9/post/test-rotated-z180.xyz (added) * tests/regression/Molecules/9/post/test-rotated-z360.xyz (added) * tests/regression/Molecules/9/post/test-rotated-z90.xyz (added) * tests/regression/Molecules/9/pre/test.xyz (added) * tests/regression/Simple_configuration/2/post/test.pdb (added) * tests/regression/Simple_configuration/3/post/empty.conf (moved) * tests/regression/Simple_configuration/5/pre/test.conf (modified) * tests/regression/Simple_configuration/8/post/test-cuboid.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test-sphere.xyz-sorted (moved) * tests/regression/Simple_configuration/8/post/test-withoutcuboid.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test-withoutsphere.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test.xyz-sorted (modified) * tests/regression/Simple_configuration/8/pre/test.conf (deleted) * tests/regression/Simple_configuration/8/pre/test.xyz (added) * tests/regression/Simple_configuration/9/post/test-shifted.xyz (added) * tests/regression/Simple_configuration/9/post/test.xyz (added) * tests/regression/Simple_configuration/9/pre/test.xyz (added) * tests/regression/atlocal.in (modified) * tests/regression/molecuilder.in (modified) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-graph.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-standard_options.at (modified) * tests/regression/testsuite.at (modified) Merge branch 'StructureRefactoring' into Shapes Conflicts: ... Sat, 28 Aug 2010 01:45:13 GMT Frederik Heber [fd4905] * .gitignore (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/Action_impl_header.hpp (added) * src/Actions/Action_impl_pre.hpp (added) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (added) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.def (added) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/Remove.def (added) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.def (added) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (added) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.hpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (added) * src/Actions/AtomAction/TranslateAction.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (deleted) * src/Actions/CmdAction/BondLengthTableAction.hpp (deleted) * src/Actions/CmdAction/ElementDbAction.hpp (deleted) * src/Actions/CmdAction/FastParsingAction.cpp (deleted) * src/Actions/CmdAction/FastParsingAction.hpp (deleted) * src/Actions/CmdAction/HelpAction.cpp (deleted) * src/Actions/CmdAction/HelpAction.hpp (deleted) * src/Actions/CmdAction/VerboseAction.cpp (deleted) * src/Actions/CmdAction/VerboseAction.hpp (deleted) * src/Actions/CmdAction/VersionAction.cpp (deleted) * src/Actions/CmdAction/VersionAction.hpp (deleted) * src/Actions/CommandAction/BondLengthTableAction.cpp (added) * src/Actions/CommandAction/BondLengthTableAction.def (added) * src/Actions/CommandAction/BondLengthTableAction.hpp (added) * src/Actions/CommandAction/ElementDbAction.cpp (moved) * src/Actions/CommandAction/ElementDbAction.def (added) * src/Actions/CommandAction/ElementDbAction.hpp (added) * src/Actions/CommandAction/FastParsingAction.cpp (added) * src/Actions/CommandAction/FastParsingAction.def (added) * src/Actions/CommandAction/FastParsingAction.hpp (added) * src/Actions/CommandAction/HelpAction.cpp (added) * src/Actions/CommandAction/HelpAction.def (added) * src/Actions/CommandAction/HelpAction.hpp (added) * src/Actions/CommandAction/VerboseAction.cpp (added) * src/Actions/CommandAction/VerboseAction.def (added) * src/Actions/CommandAction/VerboseAction.hpp (added) * src/Actions/CommandAction/VersionAction.cpp (added) * src/Actions/CommandAction/VersionAction.def (added) * src/Actions/CommandAction/VersionAction.hpp (added) * src/Actions/ErrorAction.cpp (modified) * 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(added) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (added) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (added) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (added) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.def (added) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.def (added) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.def (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.def (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.def (added) * src/Actions/SelectionAction/AtomByElementAction.hpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.def (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.def (added) * src/Actions/SelectionAction/ClearAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.def (added) * src/Actions/SelectionAction/ClearAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/MoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.def (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/MoleculeOfAtomAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.def (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.def (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.def (added) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.hpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.def (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.def (added) * src/Actions/SelectionAction/NotAtomByElementAction.hpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.def (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.def (added) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.def (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.def (added) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.hpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.def (added) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.def (added) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (added) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.def (added) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.def (added) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (added) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (added) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (added) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (added) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.def (added) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.def (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/CommandLineParser.hpp (modified) * src/LinearAlgebra/BoxVector.cpp (added) * src/LinearAlgebra/BoxVector.hpp (added) * src/LinearAlgebra/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/Makefile.am (modified) * src/Parser/PdbParser.cpp (added) * src/Parser/PdbParser.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnode.hpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * tests/regression/Molecules/11/post/test-copy.xyz (added) * tests/regression/Molecules/11/pre/test.xyz (added) * tests/regression/Molecules/2/post/test.adj (modified) * tests/regression/Simple_configuration/2/post/test.pdb (added) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) Merge branch 'stable' into StructureRefactoring Sat, 28 Aug 2010 00:52:58 GMT Frederik Heber [9ee38b] * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_post.hpp (deleted) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/unittests/Makefile.am (modified) Extended macro framework. Extensions: - all central definitions ... Wed, 25 Aug 2010 12:25:28 GMT Tillmann Crueger [51c3e4] * AUTHORS (modified) * COPYING (modified) * README (modified) * autogen.sh (deleted) * bootstrap (added) * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/AtomicInfo.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Info.cpp (modified) * src/Helpers/Log.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/Verbose.cpp (modified) * src/Helpers/errorlogger.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/logger.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/gslvector.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Makefile.am (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/QT4/QTMenu.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTUIFactory.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/QT4/GLMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/UIElements/Views/QT4/QTWorldView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (modified) * src/element.cpp (modified) * src/element.hpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/BaseShapesUnittest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/version.h (modified) * test_all.sh (modified) * tests/regression/Makefile.am (modified) * tests/regression/atlocal.in (modified) * tests/regression/molecuilder.in (modified) * tests/regression/testsuite.at (modified) Merge branch 'stable' into StructureRefactoring Conflicts: ... Fri, 20 Aug 2010 11:43:39 GMT Tillmann Crueger [194649] * src/Makefile.am (modified) * src/Thermostats/Berendsen.cpp (added) * src/Thermostats/Berendsen.hpp (added) * src/Thermostats/GaussianThermostat.cpp (added) * src/Thermostats/GaussianThermostat.hpp (added) * src/Thermostats/Langevin.cpp (added) * src/Thermostats/Langevin.hpp (added) * src/Thermostats/NoThermostat.cpp (added) * src/Thermostats/NoThermostat.hpp (added) * src/Thermostats/NoseHoover.cpp (added) * src/Thermostats/NoseHoover.hpp (added) * src/Thermostats/Thermostat.cpp (added) * src/Thermostats/Thermostat.hpp (added) * src/Thermostats/Woodcock.cpp (added) * src/Thermostats/Woodcock.hpp (added) Added class structure to represent thermostats Tue, 17 Aug 2010 13:19:54 GMT Frederik Heber [5f8660a] * configure.ac (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Makefile.am (modified) * src/UIElements/QT4/QTUIFactory.cpp (modified) * src/builder.cpp (modified) * src/version.h (modified) Changed PACKAGENAME and version. - rename ESPACKVersion in ... Wed, 11 Aug 2010 11:47:46 GMT Frederik Heber [13e3c3] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/BoundaryLineSet.cpp (modified) * src/BoundaryMaps.hpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPolygonSet.cpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/CandidateForTesselation.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MissingValueException.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (modified) * src/Exceptions/ParseError.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Formula.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/Info.cpp (modified) * src/Helpers/Log.cpp (modified) * src/Helpers/Makefile.am (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/Verbose.cpp (modified) * src/Helpers/errorlogger.cpp (modified) * src/Helpers/helpers.cpp (modified) * src/Helpers/logger.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorInterface.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/gslvector.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Makefile.am (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Observer.cpp (modified) * src/PointCloud.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/TesselPoint.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/QT4/QTMenu.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTUIFactory.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/QT4/GLMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTMoleculeView.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/UIElements/Views/QT4/QTWorldView.cpp (modified) * src/UIElements/Views/QT4/QTWorldView.hpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/defs.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AtomDescriptorTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/FormulaUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/MapofActionsTest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MoleculeDescriptorTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/SingletonTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/atomsCalculationTest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) * src/unittests/gslmatrixunittest.cpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/memoryusageobserverunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Merge branch 'SmallFixes' into stable Conflicts: ... Wed, 11 Aug 2010 09:41:43 GMT Frederik Heber [b0b086] * src/Helpers/Makefile.am (modified) * src/Makefile.am (modified) BUGFIX: Fixed unity target. - MemDebug.cpp has to appear before any ... Tue, 10 Aug 2010 11:31:36 GMT Frederik Heber [e41c48] * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/AtomicInfo.cpp (added) * src/AtomicInfo.hpp (added) * src/Makefile.am (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * tests/regression/Simple_configuration/5/pre/test.conf (modified) * tests/regression/testsuite-simple_configuration.at (modified) RemoveAction has Undo/Redo capability. - FIX: atom::getMolecule() ... Mon, 09 Aug 2010 17:57:50 GMT Frederik Heber [1cc87e] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (added) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.hpp (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.cpp (added) * src/Actions/SelectionAction/AllAtomsInsideSphereAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsInsideSphereAction.hpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (deleted) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (deleted) * src/Makefile.am (modified) * tests/regression/Simple_configuration/8/post/test-cuboid.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test-sphere.xyz-sorted (moved) * tests/regression/Simple_configuration/8/post/test-withoutcuboid.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test-withoutsphere.xyz-sorted (added) * tests/regression/Simple_configuration/8/post/test.xyz-sorted (modified) * tests/regression/Simple_configuration/8/pre/test.conf (deleted) * tests/regression/Simple_configuration/8/pre/test.xyz (added) * tests/regression/testsuite-simple_configuration.at (modified) Added select-atoms-inside-sphere/cuboid and unselect-.. - new ... Sat, 07 Aug 2010 13:46:16 GMT Frederik Heber [88b400] * TestRunnerClient.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/BoundaryMaps.hpp (modified) * src/BoundaryTriangleSet.hpp (modified) * src/CandidateForTesselation.cpp (modified) * src/CandidateForTesselation.hpp (modified) * src/Makefile.am (modified) * src/ThermoStatContainer.hpp (modified) * src/analysis_bonds.hpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.hpp (modified) * src/defs.cpp (added) * src/defs.hpp (modified) * src/joiner.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/unittests/AtomDescriptorTest.hpp (modified) * src/unittests/MoleculeDescriptorTest.hpp (modified) * src/unittests/atomsCalculationTest.hpp (modified) * src/unittests/manipulateAtomsTest.hpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.hpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/tesselationunittest.hpp (modified) converted #define's to enums, consts and typedefs [Meyers, "Effective ... Sat, 07 Aug 2010 12:07:04 GMT Frederik Heber [8f4df1] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/AtomSet.hpp (modified) * src/BoundaryLineSet.cpp (added) * src/BoundaryLineSet.hpp (added) * src/BoundaryMaps.hpp (added) * src/BoundaryPointSet.cpp (added) * src/BoundaryPointSet.hpp (added) * src/BoundaryPolygonSet.cpp (added) * src/BoundaryPolygonSet.hpp (added) * src/BoundaryTriangleSet.cpp (added) * src/BoundaryTriangleSet.hpp (added) * src/CandidateForTesselation.cpp (added) * src/CandidateForTesselation.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/Vector.hpp (modified) * src/LinearAlgebra/VectorInterface.cpp (added) * src/LinearAlgebra/VectorInterface.hpp (added) * src/LinearAlgebra/vector_ops.cpp (moved) * src/LinearAlgebra/vector_ops.hpp (moved) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/PointCloud.cpp (added) * src/PointCloud.hpp (added) * src/TesselPoint.cpp (added) * src/TesselPoint.hpp (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/atom_graphnodeinfo.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/triangleintersectionlist.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) Merge branch 'AtomicPositionEncapsulation' into stable Conflicts: ... Fri, 06 Aug 2010 13:32:00 GMT Frederik Heber [6e5084] * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Makefile.am (modified) * src/boundary.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * tests/regression/testsuite-molecules.at (modified) Fixed PrincipalAxisSystemAction. - ... Fri, 06 Aug 2010 09:34:59 GMT Frederik Heber [d223d5] * Makefile.am (modified) * TestRunnerClient.cpp (added) * TestRunnerClient.h (added) * config/ltmain.sh (added) * configure.ac (modified) * libmolecuilder_config.h.in (added) * m4/gwqt4.m4 (modified) * molecuilder.pc.in (added) * src/Actions/Action.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (moved) * src/Actions/ValueStorage.hpp (moved) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Exceptions/Makefile.am (added) * src/Formula.hpp (modified) * src/Helpers/Info.cpp (moved) * src/Helpers/Info.hpp (moved) * src/Helpers/Log.cpp (moved) * src/Helpers/Log.hpp (moved) * src/Helpers/Makefile.am (added) * src/Helpers/MemDebug.hpp (modified) * src/Helpers/Verbose.cpp (moved) * src/Helpers/Verbose.hpp (moved) * src/Helpers/errorlogger.cpp (moved) * src/Helpers/errorlogger.hpp (moved) * src/Helpers/helpers.cpp (moved) * src/Helpers/helpers.hpp (moved) * src/Helpers/logger.cpp (moved) * src/Helpers/logger.hpp (moved) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Line.cpp (moved) * src/LinearAlgebra/Line.hpp (moved) * src/LinearAlgebra/Makefile.am (added) * src/LinearAlgebra/Matrix.cpp (moved) * src/LinearAlgebra/Matrix.hpp (moved) * src/LinearAlgebra/MatrixContent.hpp (moved) * src/LinearAlgebra/Plane.cpp (moved) * src/LinearAlgebra/Plane.hpp (moved) * src/LinearAlgebra/Space.cpp (moved) * src/LinearAlgebra/Space.hpp (moved) * src/LinearAlgebra/Vector.cpp (moved) * src/LinearAlgebra/Vector.hpp (moved) * src/LinearAlgebra/VectorContent.hpp (moved) * src/LinearAlgebra/VectorSet.hpp (moved) * src/LinearAlgebra/gslmatrix.cpp (moved) * src/LinearAlgebra/gslmatrix.hpp (moved) * src/LinearAlgebra/gslvector.cpp (moved) * src/LinearAlgebra/gslvector.hpp (moved) * src/LinearAlgebra/linearsystemofequations.cpp (moved) * src/LinearAlgebra/linearsystemofequations.hpp (moved) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/Makefile.am (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/QT4/IntQTQuery.ui (added) * src/UIElements/QT4/IntsQTQuery.ui (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/ShapeUnittest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.hpp (modified) * src/unittests/gslmatrixunittest.hpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.hpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector_ops.cpp (modified) Merge branch 'SharedLibraries' into stable - BUGFIX: MemDebug.cpp ... Thu, 05 Aug 2010 19:46:21 GMT Frederik Heber [255971] * src/Makefile.am (modified) * src/unittests/Makefile.am (modified) Converted libMolecuilder to shared lib via libtool. - joiner and ... Thu, 05 Aug 2010 19:46:06 GMT Frederik Heber [b37436] * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/Makefile.am (modified) Converted libMolecuilderUI to shared lib via libtool. Thu, 05 Aug 2010 19:41:21 GMT Frederik Heber [952f38] * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/SelectiveIterator_impl.hpp (modified) * src/Helpers/Info.cpp (moved) * src/Helpers/Info.hpp (moved) * src/Helpers/Log.cpp (moved) * src/Helpers/Log.hpp (moved) * src/Helpers/Makefile.am (added) * src/Helpers/Verbose.cpp (moved) * src/Helpers/Verbose.hpp (moved) * src/Helpers/errorlogger.cpp (moved) * src/Helpers/errorlogger.hpp (moved) * src/Helpers/helpers.cpp (moved) * src/Helpers/helpers.hpp (moved) * src/Helpers/logger.cpp (moved) * src/Helpers/logger.hpp (moved) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/Views/QT4/QTStatusBar.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/ellipsoid.cpp (modified) * src/graph.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/infounittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector_ops.cpp (modified) created LibMolecuilderHelpers. - is shared - renamed log.[ch]pp -> ... Thu, 05 Aug 2010 19:28:52 GMT Frederik Heber [57f243] * configure.ac (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/LinearAlgebra/Line.cpp (moved) * src/LinearAlgebra/Line.hpp (moved) * src/LinearAlgebra/Makefile.am (added) * src/LinearAlgebra/Matrix.cpp (moved) * src/LinearAlgebra/Matrix.hpp (moved) * src/LinearAlgebra/MatrixContent.hpp (moved) * src/LinearAlgebra/Plane.cpp (moved) * src/LinearAlgebra/Plane.hpp (moved) * src/LinearAlgebra/Space.cpp (moved) * src/LinearAlgebra/Space.hpp (moved) * src/LinearAlgebra/Vector.cpp (moved) * src/LinearAlgebra/Vector.hpp (moved) * src/LinearAlgebra/VectorContent.hpp (moved) * src/LinearAlgebra/VectorSet.hpp (moved) * src/LinearAlgebra/gslmatrix.cpp (moved) * src/LinearAlgebra/gslmatrix.hpp (moved) * src/LinearAlgebra/gslvector.cpp (moved) * src/LinearAlgebra/gslvector.hpp (moved) * src/LinearAlgebra/linearsystemofequations.cpp (moved) * src/LinearAlgebra/linearsystemofequations.hpp (moved) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/World.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/ShapeUnittest.cpp (modified) * src/unittests/ShapeUnittest.hpp (modified) * src/unittests/gslmatrixsymmetricunittest.hpp (modified) * src/unittests/gslmatrixunittest.hpp (modified) * src/unittests/gslvectorunittest.hpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector_ops.cpp (modified) Created libMolecuilderLinearAlgebra. - is shared. - contains the ... Thu, 05 Aug 2010 19:28:39 GMT Frederik Heber [f4b5b7] * configure.ac (modified) * src/Exceptions/Makefile.am (added) * src/Makefile.am (modified) * src/unittests/Makefile.am (modified) Created LibMolecuilderExceptions. - is shared. - contains all ... Thu, 05 Aug 2010 15:48:55 GMT Frederik Heber [861874] * Makefile.am (modified) * TestRunnerClient.cpp (added) * TestRunnerClient.h (added) * config/ltmain.sh (added) * configure.ac (modified) * libmolecuilder_config.h.in (added) * m4/gwqt4.m4 (modified) * molecuilder.pc.in (added) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/ValueStorage.cpp (moved) * src/Actions/ValueStorage.hpp (moved) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/QT4/IntQTQuery.ui (added) * src/UIElements/QT4/IntsQTQuery.ui (added) * src/unittests/Makefile.am (modified) libMolecuilderAction is now a shared lib via libtool. This is all ... Wed, 04 Aug 2010 13:25:25 GMT Tillmann Crueger [796aa6] * Makefile.am (modified) * src/Actions/Makefile.am (modified) * src/Helpers/Assert.cpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) Added faster unity build target to makefiles - unity build means a ... Wed, 04 Aug 2010 12:37:50 GMT Tillmann Crueger [d193a2] * src/Makefile.am (modified) Simplyfied building of QT4 mocfiles needed for GUI Wed, 04 Aug 2010 12:27:21 GMT Tillmann Crueger [ca275d] * src/Makefile.am (modified) * src/unittests/Makefile.am (modified) Seperated some basic parts of the molecuilder inside their own library Sat, 31 Jul 2010 15:23:10 GMT Frederik Heber [d74077] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/BoundaryLineSet.cpp (added) * src/BoundaryLineSet.hpp (added) * src/BoundaryMaps.hpp (added) * src/BoundaryPointSet.cpp (added) * src/BoundaryPointSet.hpp (added) * src/BoundaryPolygonSet.cpp (added) * src/BoundaryPolygonSet.hpp (added) * src/BoundaryTriangleSet.cpp (added) * src/BoundaryTriangleSet.hpp (added) * src/CandidateForTesselation.cpp (added) * src/CandidateForTesselation.hpp (added) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/PointCloud.cpp (added) * src/PointCloud.hpp (added) * src/TesselPoint.cpp (added) * src/TesselPoint.hpp (added) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/VectorInterface.cpp (added) * src/VectorInterface.hpp (added) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_bondedparticleinfo.hpp (modified) * src/atom_graphnodeinfo.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticle.hpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/triangleintersectionlist.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Member variable Vector and element of class atom are now private. - ... Thu, 29 Jul 2010 12:23:21 GMT Tillmann Crueger [112f90] * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/manipulateAtomsTest.cpp (modified) Fixed ActionSequenceTest and ManipulateAtomsTest Wed, 28 Jul 2010 09:35:44 GMT Tillmann Crueger [400170] * .gitignore (added) * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (added) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.hpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.hpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.hpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/HelpAction.hpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.hpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/CmdAction/VersionAction.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (added) * src/Actions/SelectionAction/AllMoleculesAction.cpp (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (added) * src/Actions/SelectionAction/AtomByIdAction.cpp (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/Values.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/CommandLineParser.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (added) * src/Exceptions/IllegalTypeException.hpp (added) * src/Exceptions/MissingValueException.cpp (added) * src/Exceptions/MissingValueException.hpp (added) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/ValueStorage.cpp (added) * src/UIElements/ValueStorage.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * test_all.sh (modified) * tests/Tesselations/defs.in (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (modified) * tests/regression/Simple_configuration/3/post/test2.conf (deleted) * tests/regression/Simple_configuration/3/post/test2.in (deleted) * tests/regression/Simple_configuration/3/post/test2.xyz (deleted) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-filling.at (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-tesselation.at (modified) Merge branch 'StructureRefactoring' into Shapes Wed, 28 Jul 2010 09:21:14 GMT Tillmann Crueger [677e13] * .gitignore (added) * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (added) * src/Actions/AnalysisAction/PointCorrelationAction.hpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (added) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.hpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.hpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.hpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.hpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/HelpAction.hpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.hpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/CmdAction/VersionAction.hpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/ErrorAction.hpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.hpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.hpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.hpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.hpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.hpp (modified) * src/Actions/SelectionAction/AllAtomsAction.cpp (added) * src/Actions/SelectionAction/AllAtomsAction.hpp (added) * src/Actions/SelectionAction/AllMoleculesAction.cpp (added) * src/Actions/SelectionAction/AllMoleculesAction.hpp (added) * src/Actions/SelectionAction/AtomByIdAction.cpp (added) * src/Actions/SelectionAction/AtomByIdAction.hpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/MoleculeByIdAction.hpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.cpp (added) * src/Actions/SelectionAction/NotAllAtomsAction.hpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.cpp (added) * src/Actions/SelectionAction/NotAllMoleculesAction.hpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.cpp (added) * src/Actions/SelectionAction/NotAtomByIdAction.hpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.cpp (added) * src/Actions/SelectionAction/NotMoleculeByIdAction.hpp (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (modified) * src/Actions/Values.hpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.hpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.hpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/InputAction.hpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.hpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.hpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.hpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.hpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/CommandLineParser.cpp (modified) * src/Exceptions/IllegalTypeException.cpp (added) * src/Exceptions/IllegalTypeException.hpp (added) * src/Exceptions/MissingValueException.cpp (added) * src/Exceptions/MissingValueException.hpp (added) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/Menu/TextMenu.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/ValueStorage.cpp (added) * src/UIElements/ValueStorage.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * test_all.sh (modified) * tests/Tesselations/defs.in (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (modified) * tests/regression/Simple_configuration/3/post/test2.conf (deleted) * tests/regression/Simple_configuration/3/post/test2.in (deleted) * tests/regression/Simple_configuration/3/post/test2.xyz (deleted) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-filling.at (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-tesselation.at (modified) Merge branch 'stable' into StructureRefactoring Conflicts: ... Fri, 23 Jul 2010 16:28:28 GMT Frederik Heber [4e145c] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Makefile.am (modified) Actions can now be called non-interactively, MissingValueException ... Fri, 23 Jul 2010 14:43:02 GMT Tillmann Crueger [ed476e] * src/LineSegmentSet.cpp (added) * src/LineSegmentSet.hpp (added) * src/Makefile.am (modified) Added a Class that allows description of sets of LineSegments from ... Fri, 23 Jul 2010 14:07:10 GMT Tillmann Crueger [49d3d39] * src/Descriptors/MoleculeFormulaDescriptor.cpp (added) * src/Descriptors/MoleculeFormulaDescriptor.hpp (added) * src/Descriptors/MoleculeFormulaDescriptor_impl.hpp (added) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Exceptions/ParseError.cpp (added) * src/Exceptions/ParseError.hpp (added) * src/Formula.cpp (added) * src/Formula.hpp (added) * src/Helpers/Range.hpp (added) * src/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/unittests/FormulaUnittest.cpp (added) * src/unittests/FormulaUnittest.hpp (added) * src/unittests/Makefile.am (modified) * test_all.sh (modified) Merge branch 'StructureRefactoring' into Shapes Conflicts: ... Fri, 23 Jul 2010 14:01:40 GMT Tillmann Crueger [a4e9bb] * src/LineSegment.cpp (added) * src/LineSegment.hpp (added) * src/Makefile.am (modified) Added a class that allows specifying Segments of a Line Thu, 22 Jul 2010 17:53:44 GMT Frederik Heber [ab9a27] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Exceptions/IllegalTypeException.cpp (added) * src/Exceptions/IllegalTypeException.hpp (added) * src/Makefile.am (modified) MapOfActions::TypeMap now contains type_info. We are going to use ... Thu, 22 Jul 2010 11:46:18 GMT Tillmann Crueger [6d858c] * src/Descriptors/AtomShapeDescriptor.cpp (added) * src/Descriptors/AtomShapeDescriptor.hpp (added) * src/Descriptors/AtomShapeDescriptor_impl.hpp (added) * src/Makefile.am (modified) Added Descriptor that allows specifying atoms within a given ... Thu, 22 Jul 2010 11:14:08 GMT Tillmann Crueger [6e7147] * src/Descriptors/MoleculeFormulaDescriptor.cpp (added) * src/Descriptors/MoleculeFormulaDescriptor.hpp (added) * src/Descriptors/MoleculeFormulaDescriptor_impl.hpp (added) * src/Makefile.am (modified) Added a Descriptor that allows querying molecules by their Formula Wed, 21 Jul 2010 13:17:18 GMT Tillmann Crueger [574ddc1] * src/Exceptions/ParseError.cpp (added) * src/Exceptions/ParseError.hpp (added) * src/Makefile.am (modified) Added an exception to indicate failures in parsing. Wed, 21 Jul 2010 13:09:11 GMT Tillmann Crueger [6f43ab] * src/Formula.cpp (added) * src/Formula.hpp (added) * src/Makefile.am (modified) Added a class that allow simple handling of molecules formulas Wed, 21 Jul 2010 07:49:33 GMT Tillmann Crueger [3d078d] * COPYING (modified) * ChangeLog (modified) * README (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (added) * src/Descriptors/AtomSelectionDescriptor.hpp (added) * src/Descriptors/AtomSelectionDescriptor_impl.hpp (added) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (added) * src/Descriptors/MoleculeSelectionDescriptor.hpp (added) * src/Descriptors/MoleculeSelectionDescriptor_impl.hpp (added) * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * tests/Tesselations/defs.in (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (modified) * tests/regression/Domain/6/post/test-x.xyz (moved) * tests/regression/Domain/6/post/test-y.xyz (moved) * tests/regression/Domain/6/post/test-z.xyz (moved) * tests/regression/Domain/6/post/test.xyz (moved) * tests/regression/Fragmentation/2/post/BondFragment0.xyz (moved) * tests/regression/Fragmentation/2/post/BondFragment1.xyz (moved) * tests/regression/Fragmentation/2/post/BondFragment2.xyz (moved) * tests/regression/Fragmentation/2/post/BondFragment3.xyz (moved) * tests/regression/Fragmentation/2/post/BondFragment4.xyz (moved) * tests/regression/Molecules/6/post/test2.conf (moved) * tests/regression/Molecules/6/pre/test2.conf (added) * tests/regression/Simple_configuration/2/post/test.in (moved) * tests/regression/Simple_configuration/2/post/test.xyz (moved) * tests/regression/Simple_configuration/3/post/test.in (moved) * tests/regression/Simple_configuration/3/post/test.xyz (moved) * tests/regression/Simple_configuration/3/post/test2.conf (moved) * tests/regression/Simple_configuration/3/post/test2.in (added) * tests/regression/Simple_configuration/3/post/test2.xyz (added) * tests/regression/Simple_configuration/4/post/test.conf.xyz (deleted) * tests/regression/Simple_configuration/4/post/test.xyz (added) * tests/regression/Simple_configuration/4/pre/test.xyz (added) * tests/regression/Simple_configuration/5/post/test.in (moved) * tests/regression/Simple_configuration/5/post/test.xyz (moved) * tests/regression/Simple_configuration/8/post/test.xyz (moved) * tests/regression/Simple_configuration/8/post/test.xyz-sorted (added) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) Merge branch 'stable' into Shapes Fri, 16 Jul 2010 13:11:45 GMT Tillmann Crueger [cf0ca1] * src/Makefile.am (modified) * src/World.hpp (modified) Added Descriptors that allow description of all Selected molecules Fri, 16 Jul 2010 13:02:31 GMT Tillmann Crueger [48dcbd] * src/Descriptors/AtomSelectionDescriptor.cpp (added) * src/Descriptors/AtomSelectionDescriptor.hpp (added) * src/Descriptors/AtomSelectionDescriptor_impl.hpp (added) * src/Makefile.am (modified) Added descriptors that allow description of all selected atoms Wed, 14 Jul 2010 14:48:58 GMT Tillmann Crueger [06300d] * src/Exceptions/NotOnSurfaceException.cpp (added) * src/Exceptions/NotOnSurfaceException.hpp (added) * src/Exceptions/ShapeException.cpp (added) * src/Exceptions/ShapeException.hpp (added) * src/Makefile.am (modified) Added some Exceptions that can be used by shapes to indicate various ... Wed, 07 Jul 2010 16:08:32 GMT Tillmann Crueger [4e10f5] * COPYING (added) * INSTALL (added) * README (modified) * config/config.guess (added) * config/config.sub (added) * config/depcomp (added) * config/install-sh (added) * config/missing (added) * configure.ac (modified) * m4/ax_lang_compiler_ms.m4 (added) * m4/cppunit.m4 (added) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/SetOutputFormatsAction.cpp (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * tests/Tesselations/defs.in (modified) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-filling.at (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-graph.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-specifics.at (modified) * tests/regression/testsuite-standard_options.at (modified) * tests/regression/testsuite-tesselation.at (modified) Merge branch 'stable' into StructureRefactoring Conflicts: ... Tue, 06 Jul 2010 11:48:01 GMT Ralf Wildenhues [f8be39] * src/Makefile.am (modified) Fix .git-version rule. * src/Makefile.am ($(srcdir)/.git-version): ... Fri, 02 Jul 2010 09:51:01 GMT Tillmann Crueger [5ec8e3] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (added) * src/Box.hpp (added) * src/Exceptions/NotInvertibleException.cpp (added) * src/Exceptions/NotInvertibleException.hpp (added) * src/Line.cpp (modified) * src/Line.hpp (modified) * src/Makefile.am (modified) * src/Matrix.cpp (added) * src/Matrix.hpp (added) * src/Parser/PcpParser.cpp (modified) * src/Shapes/BaseShapes.cpp (added) * src/Shapes/BaseShapes.hpp (added) * src/Shapes/BaseShapes_impl.hpp (added) * src/Shapes/Shape.cpp (added) * src/Shapes/Shape.hpp (added) * src/Shapes/ShapeOps.cpp (added) * src/Shapes/ShapeOps.hpp (added) * src/Shapes/ShapeOps_impl.hpp (added) * src/Shapes/Shape_impl.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/VectorSet.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (added) * src/unittests/ShapeUnittest.hpp (added) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) * tests/regression/Domain/4/post/test.conf (modified) Merge branch 'VectorRefactoring' into StructureRefactoring ... Thu, 01 Jul 2010 14:57:02 GMT Tillmann Crueger [456341] * src/Makefile.am (modified) Moved all Exceptions and Matrix class from LinAlg module back to main ... Thu, 01 Jul 2010 13:55:08 GMT Tillmann Crueger [8f822c] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (added) * src/Actions/WorldAction/InputAction.hpp (added) * src/Actions/WorldAction/OutputAction.cpp (added) * src/Actions/WorldAction/OutputAction.hpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (added) * src/Box.hpp (added) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (added) * src/ConfigFileBuffer.hpp (added) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Exceptions/NotInvertibleException.cpp (added) * src/Exceptions/NotInvertibleException.hpp (added) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Matrix.cpp (added) * src/Matrix.hpp (added) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (added) * src/Parser/FormatParserStorage.hpp (added) * src/Parser/MpqcParser.cpp (added) * src/Parser/MpqcParser.hpp (added) * src/Parser/PcpParser.cpp (added) * src/Parser/PcpParser.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/Patterns/Singleton.hpp (modified) * src/Patterns/Singleton_impl.hpp (modified) * src/ThermoStatContainer.cpp (added) * src/ThermoStatContainer.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/VectorSet.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/ellipsoid.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/ParserUnitTest.hpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) * tests/regression/Domain/4/post/test.conf (modified) * tests/regression/Domain/6/post/test-x.conf.xyz (modified) * tests/regression/Domain/6/post/test-y.conf.xyz (modified) * tests/regression/Domain/6/post/test-z.conf.xyz (modified) * tests/regression/Domain/6/post/test.conf.xyz (modified) * tests/regression/Filling/1/post/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/3/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/4/post/test.conf (modified) * tests/regression/Simple_configuration/4/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/5/post/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf.xyz (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-standard_options.at (modified) Merge branch 'VectorRefactoring' into Shapes Wed, 30 Jun 2010 09:42:58 GMT Tillmann Crueger [83c09a] * src/Box.cpp (added) * src/Box.hpp (added) * src/Makefile.am (modified) Added a basic Box class to store cell_size as well as inverse of ... Sat, 26 Jun 2010 22:14:22 GMT Frederik Heber [b0acc3] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/builder.cpp (modified) Merge branch 'stable' into QT4Refactoring Conflicts: ... Fri, 25 Jun 2010 15:54:48 GMT Tillmann Crueger [33d774] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/builder.cpp (modified) Merge branch 'StructureRefactoring' into VectorRefactoring ... Fri, 25 Jun 2010 13:44:07 GMT Tillmann Crueger [325390] * src/Exceptions/NotInvertibleException.cpp (added) * src/Exceptions/NotInvertibleException.hpp (added) * src/Makefile.am (modified) * src/Matrix.cpp (added) * src/Matrix.hpp (added) * src/vector.cpp (modified) * src/vector.hpp (modified) Started work on basic matrix class to be used with Vector class Fri, 25 Jun 2010 13:04:13 GMT Frederik Heber [326bbe] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/builder.cpp (modified) Legacy/oldmenu is no more. - TextWindow::TextWindow() now properly ... Fri, 25 Jun 2010 09:57:15 GMT Tillmann Crueger [04488a] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (added) * src/Actions/WorldAction/InputAction.hpp (added) * src/Actions/WorldAction/OutputAction.cpp (added) * src/Actions/WorldAction/OutputAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/ConfigFileBuffer.cpp (added) * src/ConfigFileBuffer.hpp (added) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ChangeTracker.hpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParserStorage.cpp (added) * src/Parser/FormatParserStorage.hpp (added) * src/Parser/MpqcParser.cpp (added) * src/Parser/MpqcParser.hpp (added) * src/Parser/PcpParser.cpp (added) * src/Parser/PcpParser.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/Patterns/Singleton.hpp (modified) * src/Patterns/Singleton_impl.hpp (modified) * src/ThermoStatContainer.cpp (added) * src/ThermoStatContainer.hpp (added) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/ParserUnitTest.hpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * tests/regression/Domain/6/post/test-x.conf.xyz (modified) * tests/regression/Domain/6/post/test-y.conf.xyz (modified) * tests/regression/Domain/6/post/test-z.conf.xyz (modified) * tests/regression/Domain/6/post/test.conf.xyz (modified) * tests/regression/Filling/1/post/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/3/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/4/post/test.conf (modified) * tests/regression/Simple_configuration/4/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/5/post/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf.xyz (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-standard_options.at (modified) Merge branch 'StructureRefactoring' into QT4Refactoring Conflicts: ... Fri, 25 Jun 2010 08:11:20 GMT Frederik Heber [4f7f34e] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (added) * src/Actions/WorldAction/InputAction.hpp (added) * src/Actions/WorldAction/OutputAction.cpp (added) * src/Actions/WorldAction/OutputAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-standard_options.at (modified) ParseCommandLineOptions() is not used anymore. - new Actions ... Wed, 23 Jun 2010 15:52:50 GMT Frederik Heber [35b698] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/Makefile.am (modified) * tests/regression/Domain/6/post/test-x.conf.xyz (modified) * tests/regression/Domain/6/post/test-y.conf.xyz (modified) * tests/regression/Domain/6/post/test-z.conf.xyz (modified) * tests/regression/Domain/6/post/test.conf.xyz (modified) * tests/regression/Filling/1/post/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/3/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/4/post/test.conf (modified) * tests/regression/Simple_configuration/4/post/test.conf.xyz (modified) * tests/regression/Simple_configuration/5/post/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf.xyz (modified) * tests/regression/testsuite-fragmentation.at (modified) BIG CHANGE: config::load and config::save in ... Tue, 22 Jun 2010 14:09:14 GMT Frederik Heber [52baf9] * src/Makefile.am (modified) * src/Parser/FormatParserStorage.cpp (added) * src/Parser/FormatParserStorage.hpp (added) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) new class FormatParserStorage takes care of allocation, uniqueness ... Mon, 21 Jun 2010 07:56:00 GMT Frederik Heber [55240c4] * doc/Doxyfile (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/CommandLineParser.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/MultipleSolutionsException.hpp (added) * src/Exceptions/SkewException.cpp (added) * src/Exceptions/SkewException.hpp (added) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Hbondangle.db (modified) * src/Hbonddistance.db (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Line.cpp (modified) * src/Line.hpp (modified) * src/Makefile.am (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (modified) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/Space.cpp (modified) * src/Space.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuItem.cpp (modified) * src/UIElements/Menu/SeperatorItem.cpp (modified) * src/UIElements/Menu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextUIFactory.hpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/VectorSet.cpp (added) * src/VectorSet.hpp (added) * src/World.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/atom_trajectoryparticleinfo.hpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/elements_db.cpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslmatrix.cpp (modified) * src/gslvector.cpp (modified) * src/gslvector.hpp (modified) * src/helpers.cpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/log.cpp (modified) * src/logger.cpp (modified) * src/memoryallocator.cpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/orbitals.db (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/LineUnittest.cpp (added) * src/unittests/LineUnittest.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/PlaneUnittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/valence.db (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) * src/vector_ops.hpp (modified) * src/verbose.cpp (modified) * tests/regression/Domain/2/post/test.conf (modified) * tests/regression/Domain/3/post/test.conf (modified) * tests/regression/Domain/4/post/test.conf (modified) * tests/regression/Domain/5/post/test.conf (modified) * tests/regression/Filling/1/post/test.conf (modified) * tests/regression/Filling/1/pre/test.conf (modified) * tests/regression/Molecules/6/post/test.conf (modified) * tests/regression/Molecules/6/pre/test.conf (modified) * tests/regression/Molecules/7/post/test.conf (modified) * tests/regression/Molecules/7/pre/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.conf (modified) * tests/regression/Simple_configuration/3/post/test.conf (modified) * tests/regression/Simple_configuration/4/post/test.conf (modified) * tests/regression/Simple_configuration/5/post/test.conf (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) * tests/regression/testsuite-tesselation.at (modified) Merge branch 'stable' into PcpAndMpqcParser Conflicts: ... Fri, 18 Jun 2010 10:44:04 GMT Tillmann Crueger [e09b70] * src/Makefile.am (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (added) * src/Shapes/ShapeOps.hpp (added) * src/Shapes/ShapeOps_impl.hpp (added) * src/Shapes/Shape_impl.hpp (modified) Added basic operations on shapes Fri, 18 Jun 2010 10:18:10 GMT Tillmann Crueger [e38447] * src/Makefile.am (modified) * src/Shapes/BaseShapes.cpp (added) * src/Shapes/BaseShapes.hpp (added) * src/Shapes/BaseShapes_impl.hpp (added) Added some basic shapes to the shape framework Fri, 18 Jun 2010 10:03:23 GMT Tillmann Crueger [997784] * src/Makefile.am (modified) * src/Shapes/Shape.cpp (added) * src/Shapes/Shape.hpp (added) * src/Shapes/Shape_impl.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/ShapeUnittest.cpp (added) * src/unittests/ShapeUnittest.hpp (added) Added basic structure for definition of geometric 3D shapes. Thu, 17 Jun 2010 14:55:56 GMT Tillmann Crueger [257c77] * Makefile.am (modified) * configure.ac (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (added) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (added) * src/Actions/AtomAction/AddAction.cpp (added) * src/Actions/AtomAction/AddAction.hpp (added) * src/Actions/AtomAction/ChangeElementAction.cpp (added) * src/Actions/AtomAction/ChangeElementAction.hpp (added) * src/Actions/AtomAction/RemoveAction.cpp (added) * src/Actions/AtomAction/RemoveAction.hpp (added) * src/Actions/CmdAction/BondLengthTableAction.cpp (added) * src/Actions/CmdAction/BondLengthTableAction.hpp (added) * src/Actions/CmdAction/ElementDbAction.cpp (added) * src/Actions/CmdAction/ElementDbAction.hpp (added) * src/Actions/CmdAction/FastParsingAction.cpp (added) * src/Actions/CmdAction/FastParsingAction.hpp (added) * src/Actions/CmdAction/HelpAction.cpp (added) * src/Actions/CmdAction/HelpAction.hpp (added) * src/Actions/CmdAction/VerboseAction.cpp (added) * src/Actions/CmdAction/VerboseAction.hpp (added) * src/Actions/CmdAction/VersionAction.cpp (added) * src/Actions/CmdAction/VersionAction.hpp (added) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (added) * src/Actions/FragmentationAction/FragmentationAction.cpp (added) * src/Actions/FragmentationAction/FragmentationAction.hpp (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (added) * src/Actions/Makefile.am (added) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (added) * src/Actions/MapOfActions.hpp (added) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (added) * src/Actions/MoleculeAction/BondFileAction.hpp (added) * src/Actions/MoleculeAction/ChangeNameAction.cpp (added) * src/Actions/MoleculeAction/ChangeNameAction.hpp (moved) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (added) * src/Actions/MoleculeAction/SaveBondsAction.cpp (added) * src/Actions/MoleculeAction/SaveBondsAction.hpp (added) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (added) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (added) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (added) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (added) * src/Actions/MoleculeAction/TranslateAction.cpp (added) * src/Actions/MoleculeAction/TranslateAction.hpp (added) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (added) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (added) * src/Actions/ParserAction/LoadXyzAction.cpp (added) * src/Actions/ParserAction/LoadXyzAction.hpp (added) * src/Actions/ParserAction/SaveXyzAction.cpp (added) * src/Actions/ParserAction/SaveXyzAction.hpp (added) * src/Actions/Process.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (added) * src/Actions/Values.hpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (added) * src/Actions/WorldAction/BoundInBoxAction.cpp (added) * src/Actions/WorldAction/BoundInBoxAction.hpp (added) * src/Actions/WorldAction/CenterInBoxAction.cpp (added) * src/Actions/WorldAction/CenterInBoxAction.hpp (added) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (added) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (added) * src/Actions/WorldAction/ChangeBoxAction.cpp (added) * src/Actions/WorldAction/ChangeBoxAction.hpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (added) * src/Actions/WorldAction/RepeatBoxAction.cpp (added) * src/Actions/WorldAction/RepeatBoxAction.hpp (added) * src/Actions/WorldAction/ScaleBoxAction.cpp (added) * src/Actions/WorldAction/ScaleBoxAction.hpp (added) * src/Actions/WorldAction/SetDefaultNameAction.cpp (added) * src/Actions/WorldAction/SetDefaultNameAction.hpp (added) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (added) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (added) * src/Actions/small_actions.cpp (deleted) * src/CommandLineParser.cpp (added) * src/CommandLineParser.hpp (added) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (added) * src/Descriptors/MoleculeNameDescriptor.hpp (added) * src/Descriptors/MoleculeNameDescriptor_impl.hpp (added) * src/Descriptors/MoleculePtrDescriptor.cpp (added) * src/Descriptors/MoleculePtrDescriptor.hpp (added) * src/Descriptors/MoleculePtrDescriptor_impl.hpp (added) * src/Exceptions/CustomException.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (modified) * src/Exceptions/MathException.cpp (modified) * src/Exceptions/SkewException.cpp (modified) * src/Exceptions/ZeroVectorException.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Line.cpp (modified) * src/Makefile.am (modified) * src/Menu/QT4/QTMenu.cpp (deleted) * src/Menu/QT4/QTMenu.hpp (deleted) * src/Parser/ChangeTracker.cpp (added) * src/Parser/ChangeTracker.hpp (added) * src/Parser/FormatParser.cpp (added) * src/Parser/FormatParser.hpp (added) * src/Parser/TremoloParser.cpp (added) * src/Parser/TremoloParser.hpp (added) * src/Parser/XyzParser.cpp (added) * src/Parser/XyzParser.hpp (added) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (added) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.cpp (modified) * src/Space.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (added) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (added) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (added) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (added) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (added) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (added) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/Makefile.am (added) * src/UIElements/Menu/ActionMenuItem.cpp (moved) * src/UIElements/Menu/ActionMenuItem.hpp (moved) * src/UIElements/Menu/DisplayMenuItem.cpp (moved) * src/UIElements/Menu/DisplayMenuItem.hpp (moved) * src/UIElements/Menu/Menu.cpp (moved) * src/UIElements/Menu/Menu.hpp (moved) * src/UIElements/Menu/MenuItem.cpp (moved) * src/UIElements/Menu/MenuItem.hpp (moved) * src/UIElements/Menu/SeperatorItem.cpp (moved) * src/UIElements/Menu/SeperatorItem.hpp (moved) * src/UIElements/Menu/SubMenuItem.cpp (moved) * src/UIElements/Menu/SubMenuItem.hpp (moved) * src/UIElements/Menu/TextMenu.cpp (moved) * src/UIElements/Menu/TextMenu.hpp (moved) * src/UIElements/QT4/QTDialog.cpp (modified) * src/UIElements/QT4/QTDialog.hpp (modified) * src/UIElements/QT4/QTMainWindow.cpp (modified) * src/UIElements/QT4/QTMainWindow.hpp (modified) * src/UIElements/QT4/QTUIFactory.cpp (modified) * src/UIElements/QT4/QTUIFactory.hpp (modified) * src/UIElements/TextDialog.cpp (deleted) * src/UIElements/TextDialog.hpp (deleted) * src/UIElements/TextUI/TextDialog.cpp (added) * src/UIElements/TextUI/TextDialog.hpp (added) * src/UIElements/TextUI/TextStatusIndicator.cpp (moved) * src/UIElements/TextUI/TextStatusIndicator.hpp (moved) * src/UIElements/TextUI/TextUIFactory.cpp (moved) * src/UIElements/TextUI/TextUIFactory.hpp (moved) * src/UIElements/TextUI/TextWindow.cpp (moved) * src/UIElements/TextUI/TextWindow.hpp (moved) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/UIElements/Views/MethodStringView.cpp (moved) * src/UIElements/Views/MethodStringView.hpp (moved) * src/UIElements/Views/StreamStringView.cpp (moved) * src/UIElements/Views/StreamStringView.hpp (moved) * src/UIElements/Views/StringView.cpp (moved) * src/UIElements/Views/StringView.hpp (moved) * src/UIElements/Views/View.cpp (moved) * src/UIElements/Views/View.hpp (moved) * src/Views/QT4/GLMoleculeView.cpp (deleted) * src/Views/QT4/GLMoleculeView.hpp (deleted) * src/Views/QT4/QTMoleculeView.cpp (deleted) * src/Views/QT4/QTMoleculeView.hpp (deleted) * src/Views/QT4/QTStatusBar.cpp (deleted) * src/Views/QT4/QTStatusBar.hpp (deleted) * src/Views/QT4/QTWorldView.cpp (deleted) * src/Views/QT4/QTWorldView.hpp (deleted) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_bonds.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_atominfo.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_bondedparticleinfo.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/atom_trajectoryparticleinfo.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/elements.db (modified) * src/elements_db.cpp (added) * src/elements_db.hpp (added) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/graph.cpp (modified) * src/gslmatrix.cpp (modified) * src/gslvector.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/info.cpp (modified) * src/joiner.cpp (modified) * src/leastsquaremin.cpp (modified) * src/linearsystemofequations.cpp (modified) * src/linkedcell.cpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/log.cpp (modified) * src/logger.cpp (modified) * src/memoryallocator.cpp (added) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * src/unittests/CacheableTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.hpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MapofActionsTest.cpp (added) * src/unittests/MapofActionsTest.hpp (added) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/ParserUnitTest.cpp (added) * src/unittests/ParserUnitTest.hpp (added) * src/unittests/SingletonTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/analysisbondsunittest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/periodentafelTest.cpp (added) * src/unittests/periodentafelTest.hpp (added) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector_ops.cpp (modified) * src/verbose.cpp (modified) * tests/Makefile.am (modified) * tests/Tesselations/defs.in (modified) * tests/regression/Analysis/1/post/bin_output.csv (added) * tests/regression/Analysis/1/post/output.csv (added) * tests/regression/Analysis/1/pre/test.conf (added) * tests/regression/Analysis/2/post/bin_output-10.csv (added) * tests/regression/Analysis/2/post/bin_output-20.csv (added) * tests/regression/Analysis/2/post/bin_output-5.csv (added) * tests/regression/Analysis/2/post/output-10.csv (added) * tests/regression/Analysis/2/post/output-20.csv (added) * tests/regression/Analysis/2/post/output-5.csv (added) * tests/regression/Analysis/2/pre/test.conf (added) * tests/regression/Analysis/3/post/bin_output.csv (added) * tests/regression/Analysis/3/post/output.csv (added) * tests/regression/Analysis/3/pre/test.conf (added) * tests/regression/Analysis/4/post/bin_output.csv (added) * tests/regression/Analysis/4/post/output.csv (added) * tests/regression/Analysis/4/pre/test.conf (added) * tests/regression/Analysis/5/pre/test.conf (added) * tests/regression/Domain/1/post/test.conf (added) * tests/regression/Domain/2/post/test.conf (moved) * tests/regression/Domain/2/pre/test.conf (added) * tests/regression/Domain/3/post/test.conf (moved) * tests/regression/Domain/3/pre/test.conf (added) * tests/regression/Domain/4/post/test.conf (moved) * tests/regression/Domain/4/pre/test.conf (added) * tests/regression/Domain/5/post/test.conf (moved) * tests/regression/Domain/5/pre/test.conf (added) * tests/regression/Domain/6/post/test-x.conf.xyz (added) * tests/regression/Domain/6/post/test-y.conf.xyz (added) * tests/regression/Domain/6/post/test-z.conf.xyz (added) * tests/regression/Domain/6/post/test.conf.xyz (moved) * tests/regression/Domain/6/pre/test.conf (added) * tests/regression/Filling/1/post/test.conf (added) * tests/regression/Filling/1/pre/test.conf (added) * tests/regression/Filling/2/pre/test.conf (added) * tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (deleted) * tests/regression/Graph/2/pre/test.conf (added) * tests/regression/Makefile.am (added) * tests/regression/Molecules/1/pre/test.conf (added) * tests/regression/Molecules/1/pre/test.dbond (added) * tests/regression/Molecules/2/post/test.adj (added) * tests/regression/Molecules/2/post/test.dbond (added) * tests/regression/Molecules/2/pre/test.conf (moved) * tests/regression/Molecules/3/post/test.ekin (added) * tests/regression/Molecules/3/pre/test.conf (added) * tests/regression/Molecules/4/post/test.conf (added) * tests/regression/Molecules/4/pre/test.conf (added) * tests/regression/Molecules/5/pre/test.conf (added) * tests/regression/Molecules/5/pre/test.forces (added) * tests/regression/Molecules/6/post/test.conf (added) * tests/regression/Molecules/6/pre/test.conf (added) * tests/regression/Molecules/7/post/test.conf (added) * tests/regression/Molecules/7/pre/test.conf (added) * tests/regression/Molecules/8/pre/test.conf (added) * tests/regression/Simple_configuration/2/post/test.conf.in (added) * tests/regression/Simple_configuration/3/post/test.conf.in (added) * tests/regression/Simple_configuration/5/post/test.conf.in (added) * tests/regression/Simple_configuration/8/post/test.conf.xyz (added) * tests/regression/Simple_configuration/8/pre/test.conf (added) * tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) * tests/regression/atlocal.in (moved) * tests/regression/molecuilder.in (moved) * tests/regression/testsuite-analysis.at (added) * tests/regression/testsuite-domain.at (added) * tests/regression/testsuite-filling.at (added) * tests/regression/testsuite-fragmentation.at (added) * tests/regression/testsuite-graph.at (added) * tests/regression/testsuite-molecules.at (added) * tests/regression/testsuite-simple_configuration.at (added) * tests/regression/testsuite-specifics.at (added) * tests/regression/testsuite-standard_options.at (added) * tests/regression/testsuite-tesselation.at (added) * tests/regression/testsuite.at (added) * tests/testsuite.at (deleted) Merge branch 'stable' into QT4Refactoring Conflicts: ... Wed, 16 Jun 2010 12:24:21 GMT Tillmann Crueger [e6317b] * configure.ac (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp (deleted) * src/Actions/AnalysisAction/PairCorrelationToPointAction.hpp (deleted) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (deleted) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp (deleted) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/Values.hpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (modified) * src/CommandLineParser.cpp (modified) * src/CommandLineParser.hpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (added) * src/Descriptors/MoleculeNameDescriptor.hpp (added) * src/Descriptors/MoleculeNameDescriptor_impl.hpp (added) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * tests/Tesselations/defs.in (modified) * tests/regression/Analysis/3/post/bin_output.csv (modified) * tests/regression/Fragmentation/3/pre/BondFragment0.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragment4.conf (deleted) * tests/regression/Fragmentation/3/pre/BondFragment4.conf.xyz (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (deleted) * tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (deleted) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-filling.at (modified) * tests/regression/testsuite-fragmentation.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-standard_options.at (modified) * tests/regression/testsuite-tesselation.at (modified) Broken: Merge commit 'Gitosis/stable' into stable Conflicts: ... Sat, 12 Jun 2010 15:54:26 GMT Frederik Heber [43dad6] * src/ConfigFileBuffer.cpp (modified) * src/ConfigFileBuffer.hpp (modified) * src/Makefile.am (modified) * src/Parser/MpqcParser.cpp (added) * src/Parser/MpqcParser.hpp (added) * src/Parser/PcpParser.cpp (added) * src/Parser/PcpParser.hpp (added) * src/ThermoStatContainer.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.cpp (modified) Introducing (but not yet incorporated) FormatParser specializations ... Sat, 12 Jun 2010 13:12:51 GMT Frederik Heber [a3fded] * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/ConfigFileBuffer.hpp (modified) * src/Makefile.am (modified) * src/ThermoStatContainer.cpp (added) * src/ThermoStatContainer.hpp (added) * src/atom_trajectoryparticle.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/moleculelist.cpp (modified) New class ThermoStatContainer containing all parameters and changes ... Sat, 12 Jun 2010 11:12:20 GMT Frederik Heber [88104f] * src/ConfigFileBuffer.cpp (added) * src/ConfigFileBuffer.hpp (added) * src/Makefile.am (modified) * src/config.cpp (modified) * src/config.hpp (modified) Placed class ConfigFileBuffer into its own module. - this is a ...