# # ChangeLog for src # # Generated by Trac 1.4.4 # Apr 8, 2025, 1:14:26 PM Fri, 17 Dec 2010 14:20:26 GMT Frederik Heber [5d6f38] * src/Parser/TremoloAtomInfoContainer.cpp (modified) Merge branch 'Fix_TremoloAtomInfoContainer_MemDebug' into stable Fri, 17 Dec 2010 14:20:07 GMT Frederik Heber [dd97a9] * src/Parser/TremoloAtomInfoContainer.cpp (modified) Added missing MemDebug.hpp to TremoloAtomInfoContainer.cpp. Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber [f844ef] * src/LinearAlgebra/Subspace.hpp (modified) * src/periodentafel.hpp (modified) * src/unittests/AnalysisBondsUnitTest.cpp (moved) * src/unittests/AnalysisBondsUnitTest.hpp (moved) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (moved) * src/unittests/BondGraphUnitTest.hpp (moved) * src/unittests/BoxUnitTest.cpp (moved) * src/unittests/BoxUnitTest.hpp (moved) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (moved) * src/unittests/FormulaUnitTest.hpp (moved) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (moved) * src/unittests/ListOfBondsUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) * src/unittests/MapofActionsTest.cpp (deleted) * src/unittests/MapofActionsTest.hpp (deleted) * src/unittests/PeriodentafelUnitTest.cpp (moved) * src/unittests/PeriodentafelUnitTest.hpp (moved) * src/unittests/SubspaceFactorizerUnitTest.cpp (moved) * src/unittests/SubspaceFactorizerUnitTest.hpp (moved) * src/unittests/TesselationUnitTest.cpp (moved) * src/unittests/TesselationUnitTest.hpp (moved) * src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (moved) * src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (moved) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (moved) * src/unittests/Tesselation_InsideOutsideUnitTest.hpp (moved) * src/unittests/memoryallocatorunittest.cpp (deleted) * src/unittests/memoryallocatorunittest.hpp (deleted) * src/unittests/memoryusageobserverunittest.cpp (deleted) * src/unittests/memoryusageobserverunittest.hpp (deleted) Renamed all remaining unit tests in src/unittests to Capitalized ... Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber [dfafe7] * src/LinearAlgebra/unittests/Makefile.am (modified) * src/LinearAlgebra/unittests/VectorContentUnitTest.cpp (moved) * src/LinearAlgebra/unittests/VectorContentUnitTest.hpp (moved) * src/LinearAlgebra/unittests/VectorUnitTest.cpp (moved) * src/LinearAlgebra/unittests/VectorUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved VectorContentUnittest and vectorunittest to ... Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber [0b3cbdf] * src/Shapes/unittests/Makefile.am (added) * src/Shapes/unittests/ShapeUnitTest.cpp (moved) * src/Shapes/unittests/ShapeUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved ShapeUnittest to Shapes/unittests/ShapeUnitTest. Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber [57d976] * src/Patterns/unittests/Makefile.am (modified) * src/Patterns/unittests/RegistryUnitTest.cpp (moved) * src/Patterns/unittests/RegistryUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved RegistryUnitTest to Patterns/unittests/RegistryUnitTest. - ... Thu, 16 Dec 2010 23:47:45 GMT Frederik Heber [5bc8229] * src/LinearAlgebra/unittests/Makefile.am (modified) * src/LinearAlgebra/unittests/PlaneUnitTest.cpp (moved) * src/LinearAlgebra/unittests/PlaneUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved PlaneUnittest to LinearAlgebra/unittests/PlaneUnitTest. Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [f89024] * src/LinearAlgebra/unittests/LineUnitTest.cpp (moved) * src/LinearAlgebra/unittests/LineUnitTest.hpp (moved) * src/LinearAlgebra/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LineUnittest to LinearAlgebra/unittests/LineUnitTest. Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [41396a] * configure.ac (modified) * src/Parser/unittests/Makefile.am (added) * src/Parser/unittests/ParserCommonUnitTest.cpp (moved) * src/Parser/unittests/ParserCommonUnitTest.hpp (moved) * src/Parser/unittests/ParserTremoloUnitTest.cpp (moved) * src/Parser/unittests/ParserTremoloUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved Parser...UnitTest to Parser/unittests/Parser...UnitTest. Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [a2c4f3] * src/Patterns/unittests/Makefile.am (modified) * src/Patterns/unittests/ObserverUnitTest.cpp (moved) * src/Patterns/unittests/ObserverUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved ObserverTest to Patterns/unittests/ObserverUnitTest. Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [6c9adc] * src/Descriptors/unittests/Makefile.am (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (moved) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved MoleculeDescriptorTest to ... Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [0e2031] * configure.ac (modified) * src/UIElements/Menu/unittests/Makefile.am (added) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (moved) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved MenuDescriptionUnitTest to UIElements/Menu/unittests. Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [efd61b] * src/Actions/unittests/Makefile.am (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (moved) * src/Actions/unittests/ManipulateAtomsUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved manipulateAtomsTest to Actions/unittests/ManipulateAtomsUnitTest. Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [4076fcc] * src/Helpers/unittests/LogUnitTest.cpp (moved) * src/Helpers/unittests/LogUnitTest.hpp (moved) * src/Helpers/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved logunittest to Helpers/unittests/LogUnitTest. Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [78b593] * src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/LinearSystemOfEquationsUnitTest.cpp (moved) * src/LinearAlgebra/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * src/LinearAlgebra/unittests/Makefile.am (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/Makefile.am (modified) Moved linearsystemofequations to ... Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [fff54f] * configure.ac (modified) * src/Actions/unittests/Makefile.am (modified) * src/Helpers/unittests/InfoUnitTest.cpp (moved) * src/Helpers/unittests/InfoUnitTest.hpp (moved) * src/Helpers/unittests/Makefile.am (added) * src/LinearAlgebra/unittests/Makefile.am (added) * src/LinearAlgebra/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * src/LinearAlgebra/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * src/LinearAlgebra/unittests/MatrixContentUnitTest.cpp (moved) * src/LinearAlgebra/unittests/MatrixContentUnitTest.hpp (moved) * src/LinearAlgebra/unittests/MatrixUnitTest.cpp (moved) * src/LinearAlgebra/unittests/MatrixUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved all Matrix...Unittest to LinearAlgebra/unittests/Matrix...UnitTest. Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [3c8e8b] * src/Actions/unittests/AtomsCalculationUnitTest.cpp (moved) * src/Actions/unittests/AtomsCalculationUnitTest.hpp (moved) * src/Actions/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved atomsCalculationTest to Actions/unittests/AtomsCalculationUnitTest. Thu, 16 Dec 2010 23:47:44 GMT Frederik Heber [e7da1f] * src/Patterns/unittests/CacheableUnitTest.cpp (moved) * src/Patterns/unittests/CacheableUnitTest.hpp (moved) * src/Patterns/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved CacheableTest to Patterns/unittests/CacheableUnitTest. Thu, 16 Dec 2010 23:47:43 GMT Frederik Heber [d766b5] * configure.ac (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (moved) * src/Descriptors/unittests/AtomDescriptorUnitTest.hpp (moved) * src/Descriptors/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) Moved AtomDescriptorTest to Descriptors/unittests/AtomDescriptorUnitTest. Thu, 16 Dec 2010 23:45:30 GMT Frederik Heber [456e78] * src/molecule_dynamics.cpp (modified) * src/test/ActOnAlltest.hpp (deleted) * src/unittests/ActOnAllUnitTest.cpp (deleted) * src/unittests/ActOnAllUnitTest.hpp (deleted) * src/unittests/Makefile.am (modified) Removed ActOnAllUnitTest. - Till had replaced all ActOnAll by ... Thu, 16 Dec 2010 23:45:30 GMT Frederik Heber [f7c0c4] * src/Actions/unittests/ActionSequenceUnitTest.cpp (moved) * src/Actions/unittests/ActionSequenceUnitTest.hpp (moved) * src/Actions/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved ActionSequenceTest to Actions/unittests, renamed to ... Thu, 16 Dec 2010 23:45:27 GMT Frederik Heber [deddf6] * configure.ac (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (added) * src/Actions/unittests/ActionRegistryUnitTest.hpp (added) * src/Actions/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) New unit test for ActionRegistry. - checks whether a short form has ... Thu, 16 Dec 2010 23:32:21 GMT Frederik Heber [c0bccb] * configure.ac (modified) * src/Patterns/Singleton_impl.hpp (modified) * src/Patterns/unittests/Makefile.am (added) * src/Patterns/unittests/SingletonUnitTest.cpp (moved) * src/Patterns/unittests/SingletonUnitTest.hpp (moved) * src/unittests/Makefile.am (modified) Moved SingletonTest to Patterns/unittests/SingletonUnitTest. Thu, 16 Dec 2010 17:32:23 GMT Frederik Heber [2a0a9e3] * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) FIX: CommandLineParser::getShortFormToActionMap() const member ... Thu, 16 Dec 2010 17:32:23 GMT Frederik Heber [ad7270] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/ThermoStatContainer.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/Qt4/QtMenu.hpp (modified) * src/builder_init.cpp (modified) * src/periodentafel.cpp (modified) * tests/regression/testsuite-standard_options.at (modified) Reduced initial verbosity of code. FIX: - initUI() - no more ... 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 [ff237c] * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) FIX: Simplified SelectionNotMoleculeByFormulaAction::performCall() ... Thu, 16 Dec 2010 17:32:23 GMT Frederik Heber [1a0987] * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) BUGFIX: SelectionMoleculeByIdAction::performRedo() uses wrong ... 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 [fc5c3a] * src/Actions/MoleculeAction/SaveAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.def (modified) * tests/regression/testsuite-simple_configuration.at (modified) Molecule's SaveAction saves selected molecules, World's OutputAction ... Thu, 16 Dec 2010 17:32:22 GMT Frederik Heber [73916f] * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/SaveAction.cpp (modified) * src/Actions/MoleculeAction/SaveAction.def (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Parser/FormatParser.cpp (modified) * src/Parser/FormatParser.hpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/XyzParser.hpp (modified) * src/unittests/ParserCommonUnitTest.cpp (modified) * src/unittests/ParserTremoloUnitTest.cpp (modified) Extended FormatParser::save() to use vector to save. - This ... Thu, 16 Dec 2010 17:32:22 GMT Frederik Heber [125002] * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsAction.def (moved) * src/Actions/SelectionAction/Atoms/AllAtomsAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.def (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.def (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.def (moved) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AtomByElementAction.def (moved) * src/Actions/SelectionAction/Atoms/AtomByElementAction.hpp (moved) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AtomByIdAction.def (moved) * src/Actions/SelectionAction/Atoms/AtomByIdAction.hpp (moved) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (moved) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.def (moved) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.hpp (moved) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def (moved) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.hpp (moved) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (moved) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.def (moved) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.hpp (moved) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (moved) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.def (moved) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.hpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (moved) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.def (moved) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.def (moved) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.hpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def (moved) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.hpp (moved) Splitted SelectionAction modules into two groups - atoms, molecules - ... 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: - ... Thu, 16 Dec 2010 17:32:22 GMT Frederik Heber [0bbfa1] * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloAtomInfoContainer.hpp (modified) * src/Parser/TremoloParser.cpp (modified) BUGFIX: Parsing a second .data file failed. - atomIdMap was not ... Thu, 16 Dec 2010 17:32:22 GMT Frederik Heber [93fd43e] * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) new function PdbParser::getadditionalAtomData() that also adds new ... Thu, 16 Dec 2010 17:32:22 GMT Frederik Heber [1d02fe3] * src/Parser/PdbParser.cpp (modified) MEMFIX: PdbParser::readAtomDataLine() additionalAtomData entries ... Thu, 16 Dec 2010 17:32:18 GMT Frederik Heber [16462f] * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbAtomInfoContainer.hpp (modified) * src/Parser/PdbKey.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * tests/regression/Simple_configuration/2/post/test.pdb (modified) PdbParser is now complete with respect to additionalAtomData. - ... Thu, 16 Dec 2010 17:27:54 GMT Frederik Heber [031e2c6] * src/Parser/Makefile.am (modified) * src/Parser/TremoloAtomInfoContainer.cpp (added) * src/Parser/TremoloAtomInfoContainer.hpp (added) * src/Parser/TremoloKey.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) Splitted off classes TremoloKey and TremoloAtomInfoContainer into own ... Thu, 16 Dec 2010 17:27:54 GMT Frederik Heber [24f128] * src/Parser/TremoloParser.cpp (modified) MEMFIX: TremoloParser::readAtomDataLine() additionalAtomData entries. ... Mon, 06 Dec 2010 20:47:33 GMT Frederik Heber [4c1230] * src/Parser/PdbParser.cpp (modified) FIX: PdbParser::writeNeighbors() uses getAtomId not getSerial. - ... 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 ... Sun, 05 Dec 2010 00:20:42 GMT Frederik Heber [ca03c7] * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/MoleculeByOrderAction.cpp (added) * src/Actions/SelectionAction/MoleculeByOrderAction.def (added) * src/Actions/SelectionAction/MoleculeByOrderAction.hpp (added) Added select-molecule-by-order Action. Sun, 05 Dec 2010 00:20:07 GMT Frederik Heber [cabb46] * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/LoadAction.cpp (added) * src/Actions/MoleculeAction/LoadAction.def (moved) * src/Actions/MoleculeAction/LoadAction.hpp (moved) * src/Actions/MoleculeAction/SaveAction.cpp (moved) * src/Actions/MoleculeAction/SaveAction.def (moved) * src/Actions/MoleculeAction/SaveAction.hpp (moved) * src/Actions/ParserAction/LoadXyzAction.cpp (deleted) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.def (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/unittests/ParserCommonUnitTest.cpp (modified) * tests/regression/Simple_configuration/2/post/test.conf (modified) * tests/regression/Simple_configuration/2/post/test.pdb (modified) * tests/regression/Simple_configuration/2/pre/test.conf (added) * tests/regression/Simple_configuration/2/pre/test.pdb (added) * tests/regression/Simple_configuration/2/pre/test.xyz (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) Extended LoadXyz and SaveXyz to any format. - renamed ... Sun, 05 Dec 2010 00:01:43 GMT Frederik Heber [4fbca9c] * src/Parser/Makefile.am (modified) * src/Parser/PdbAtomInfoContainer.cpp (added) * src/Parser/PdbAtomInfoContainer.hpp (added) * src/Parser/PdbKey.hpp (added) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ParserCommonUnitTest.cpp (moved) * src/unittests/ParserCommonUnitTest.hpp (added) * src/unittests/ParserTremoloUnitTest.cpp (added) * src/unittests/ParserTremoloUnitTest.hpp (moved) PdbParser::save() fully working. - added UnitTest for PdbParser. - ... 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 23:56:28 GMT Frederik Heber [1fb318] * src/Helpers/toString.hpp (modified) Added helper template function: ConvertTo() that converts a string to ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [286af5f] * src/LinearAlgebra/Eigenspace.cpp (modified) * src/LinearAlgebra/Eigenspace.hpp (modified) * src/LinearAlgebra/Subspace.cpp (modified) * src/LinearAlgebra/Subspace.hpp (modified) * src/unittests/SubspaceFactorizerUnittest.cpp (modified) * src/unittests/SubspaceFactorizerUnittest.hpp (modified) SubspaceFactorizerUnittest::SubspaceTest() - fully working compared ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [7d059d] * src/LinearAlgebra/MatrixContent.cpp (modified) SMALLFIX: MatrixContent::setIdentity() - made cast from bool to ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [9f9b5a] * src/Helpers/toString.hpp (modified) Added some template operator<<() functions for ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [a06042] * src/LinearAlgebra/Eigenspace.cpp (modified) * src/LinearAlgebra/Eigenspace.hpp (modified) * src/LinearAlgebra/Subspace.cpp (modified) * src/LinearAlgebra/Subspace.hpp (modified) * src/unittests/SubspaceFactorizerUnittest.cpp (modified) SubspaceFactorizerUnittest::SubspaceTest() enhanced. - Now ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [586055] * src/LinearAlgebra/VectorContent.cpp (modified) Made VectorContent::operator=() ASSERT more verbose. Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [9c5296] * src/LinearAlgebra/Eigenspace.cpp (added) * src/LinearAlgebra/Eigenspace.hpp (added) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/Subspace.cpp (added) * src/LinearAlgebra/Subspace.hpp (added) * src/unittests/SubspaceFactorizerUnittest.cpp (modified) * src/unittests/SubspaceFactorizerUnittest.hpp (modified) New classes Eigenspace and Subspace that contain eigen(sub)spaces. ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [f5bca2] * src/unittests/SubspaceFactorizerUnittest.cpp (modified) * src/unittests/SubspaceFactorizerUnittest.hpp (modified) SubspaceFactorizer now has the matrix dimension as an enum. Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [742371] * src/LinearAlgebra/MatrixContent.cpp (modified) * src/unittests/SubspaceFactorizerUnittest.cpp (modified) * src/unittests/SubspaceFactorizerUnittest.hpp (modified) Subspace Factorizer is almost working. - for the testing (4x4) ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [a062e1] * src/LinearAlgebra/MatrixContent.cpp (modified) BUGFIX: MatrixContent::operator*=(MatrixContent&)'ASSIGNS were wrong. ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [14cce6] * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/VectorContent.hpp (modified) New getter for VectorContent::dimension. Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [aab177] * src/LinearAlgebra/MatrixContent.cpp (modified) BUGFIX: MatrixContent::getColumnVector() and ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [35fbef] * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) BUGFIX: MatrixContent::get...() not const member functions as should be. Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [3da2fb] * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/MatrixVector_ops.cpp (added) * src/LinearAlgebra/MatrixVector_ops.hpp (added) * src/LinearAlgebra/Vector.hpp (modified) * src/LinearAlgebra/VectorContent.hpp (modified) New module MatrixVector_ops that contains matrix vector products. - ... Sat, 04 Dec 2010 23:56:28 GMT Frederik Heber [694eae] * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/Vector.hpp (modified) Implemenation of Vector::Norm(), ... now depend on VectorContent. - ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [3dd9c7] * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/VectorContent.hpp (modified) New functions for VectorContent, partially copied from Vector. - ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [40be55] * src/unittests/SubspaceFactorizerUnittest.cpp (modified) * src/unittests/SubspaceFactorizerUnittest.hpp (modified) Current stable version of SubspaceFactorizer. can: - functions ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [0fd3f2] * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/VectorContent.hpp (modified) Scalar product operator implemented, taken from Vector. Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [f453d2] * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/VectorContent.hpp (modified) New VectorContent copy constructor for gsl_vector. Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [60dada] * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) Added getter for MatrixContent:rows and ::columns, and for ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [4c57fb] * src/Helpers/toString.hpp (modified) FIX: _object for toString() can and has to be const without any loss. Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [d85c28] * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) Added Hadamard product by overloading MatrixContent::operator&(..) ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [041462] * src/LinearAlgebra/VectorContent.cpp (modified) BUGFIX: operator<< for VectorContent placed "," at wrong position. Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [17fa81] * src/LinearAlgebra/MatrixContent.cpp (modified) MatrixContent::transformToEigenbasis() also working for non-symmetric ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [5eec98] * src/unittests/Makefile.am (modified) Subspacefactorizer can now be linked with just GSLLIBS. - i.e. we ... 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 [6d5a10] * src/Exceptions/MultipleSolutionsException.hpp (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) Added/Sorted some includes in LinearAlgebra and Exceptions. 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 23:56:27 GMT Frederik Heber [ef0c6b] * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/gslvector.cpp (deleted) * src/LinearAlgebra/gslvector.hpp (deleted) Deleted gslvector.?pp from repository. Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [8e9ce1] * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/VectorContent.hpp (modified) Added MatrixViewContent to allow views on blocks of a gsl_matrix. - ... Sat, 04 Dec 2010 23:56:27 GMT Frederik Heber [b4cf2b] * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/SubspaceFactorizerUnittest.cpp (added) * src/unittests/SubspaceFactorizerUnittest.hpp (added) First commit of SubspaceFactorizerUnitTest. Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [bbf1bd] * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/Vector.hpp (modified) * src/LinearAlgebra/VectorContent.cpp (added) * src/LinearAlgebra/VectorContent.hpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/linearsystemofequations.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixContentSymmetricUnittest.cpp (modified) * src/unittests/MatrixContentUnittest.cpp (modified) * src/unittests/VectorContentUnittest.cpp (moved) * src/unittests/VectorContentUnittest.hpp (moved) Extended VectorContent class. - VectorContent formerly has been ... Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [5ada94] * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/gslmatrix.cpp (deleted) * src/LinearAlgebra/gslmatrix.hpp (deleted) * src/LinearAlgebra/vector_ops.cpp (modified) Removed files gslmatrix.?pp. - also removed last include in ... Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [6c1cd1] * src/LinearAlgebra/MatrixContent.cpp (modified) tempfix: typo in MatrixContent::...pointer contained ref to GSLMatrix. Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [c134d9] * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) tempfix: removed transpose ... messages. Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [0d4424] * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/linearsystemofequations.cpp (modified) * src/LinearAlgebra/linearsystemofequations.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixContentSymmetricUnittest.cpp (moved) * src/unittests/MatrixContentSymmetricUnittest.hpp (moved) * src/unittests/MatrixContentUnittest.cpp (moved) * src/unittests/MatrixContentUnittest.hpp (moved) Made gslmatrix obsolete. - Transfered property and swap...() ... Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [cca9ef] * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * src/LinearAlgebra/Vector.hpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps.hpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/atom_atominfo.hpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.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/tesselationhelpers.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/BoxUnittest.hpp (modified) * src/unittests/MatrixUnittest.cpp (modified) * src/unittests/MatrixUnittest.hpp (modified) * src/unittests/vectorunittest.cpp (modified) Renamed Matrix to RealSpaceMatrix. - class Matrix only represents ... Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [3bc926] * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Matrix.hpp (modified) * src/LinearAlgebra/MatrixContent.cpp (added) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/Vector.hpp (modified) * src/LinearAlgebra/gslmatrix.cpp (modified) * src/LinearAlgebra/gslmatrix.hpp (modified) * src/unittests/MatrixUnittest.cpp (modified) Extended MatrixContent class. - MatrixContent formerly has been ... Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [9eb7580] * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/SelectionAction/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Box.cpp (modified) * src/LinearAlgebra/Matrix.cpp (modified) * src/LinearAlgebra/Matrix.hpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/unittests/BoxUnittest.cpp (modified) * src/unittests/MatrixUnittest.cpp (modified) Renamed Matrix setter functions to unify naming. - Matrix::one -> ... Sat, 04 Dec 2010 23:54:32 GMT Frederik Heber [cfc53b] * src/Helpers/Assert.hpp (modified) * src/Helpers/toString.hpp (added) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) Added template function toString(), is included in Assert.hpp. - ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [a01144] * src/UIElements/TextUI/TextWindow.cpp (modified) MEMFIX: quitAction is not free'd anymore. - this is done by ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [0e08d5] * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) MEMFIX: Submenus were not free'd. - introduced list of submenus to ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [b2151f5] * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.hpp (modified) Removed some virtual keywords in front of classes that are not base ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [c82d0c] * 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/builder.cpp (modified) * src/unittests/MenuDescriptionUnitTest.cpp (modified) MenuDescription is now a singleton. - also all Maps are static ... 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 23:47:35 GMT Frederik Heber [ae21cbd] * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/Vector.hpp (modified) * src/Patterns/Registry_impl.hpp (modified) * src/builder.cpp (modified) MEMFIX: new function AddStaticEntitiestoIgnoreList() for putting ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [41449c] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/builder.cpp (modified) MEMFIX: Action::success and Action::failure are not recognized by ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [052afe] * src/Helpers/errorlogger.cpp (modified) * src/Helpers/logger.cpp (modified) * src/builder.cpp (modified) MEMFIX: ofstreams in ...logger.hpp as static objects were not ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [694d84] * src/UIElements/UIFactory.cpp (modified) * src/unittests/ActionSequenceTest.cpp (modified) * src/unittests/ActionSequenceTest.hpp (modified) * src/unittests/manipulateAtomsTest.cpp (modified) * src/unittests/manipulateAtomsTest.hpp (modified) MEMFIX: static factories map of UIFactory was not clear()'ed in ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [95c0ab] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/Action_impl_pre.hpp (modified) MEMFIX: MemDebug was confused by const Action objects, changed to ... Sat, 04 Dec 2010 23:47:35 GMT Frederik Heber [d2b28f] * src/Actions/ActionTraits.cpp (modified) * src/AtomicInfo.cpp (modified) * src/Exceptions/NotOnSurfaceException.cpp (modified) * src/Exceptions/ShapeException.cpp (modified) * src/LinearAlgebra/BoxVector.cpp (modified) * src/LinearAlgebra/LineSegment.cpp (modified) * src/LinearAlgebra/LineSegmentSet.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) Added missing MemDebug include to various implementation files. Sat, 04 Dec 2010 23:44:19 GMT Frederik Heber [d754bb] * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) All TextQuery now show getDescription()+": " on handle() call. - ... Sat, 04 Dec 2010 23:44:19 GMT Frederik Heber [5eebbc] * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) FIX: FileTextQuery was not working properly. - somehow getline from ... Sat, 04 Dec 2010 23:44:19 GMT Frederik Heber [670cd1] * src/UIElements/Menu/TextMenu/TextMenu.hpp (modified) FIX: Missing MemDebug.hpp before TextMenu template declaration. 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.