# # ChangeLog for src # # Generated by Trac 1.6 # May 24, 2025, 3:24:09 PM Thu, 22 Jul 2010 20:09:33 GMT Frederik Heber [2dfeeb] * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/HelpAction.hpp (modified) converted HelpAction to new createDialog() and implemented trivial ... Thu, 22 Jul 2010 20:07:51 GMT Frederik Heber [1d2d177] * src/Actions/CmdAction/VerboseAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.hpp (modified) converted VerboseAction to new createDialog() and implemented Undo/Redo. Thu, 22 Jul 2010 20:03:45 GMT Frederik Heber [ccf31f] * src/Actions/CmdAction/FastParsingAction.cpp (modified) * src/Actions/CmdAction/FastParsingAction.hpp (modified) converted FastParsingAction to new createDialog() and implemented ... Thu, 22 Jul 2010 19:59:36 GMT Frederik Heber [a12e8e] * src/Actions/CmdAction/ElementDbAction.cpp (modified) * src/Actions/CmdAction/ElementDbAction.hpp (modified) converted ElementDbAction to new createDialog(). Thu, 22 Jul 2010 19:57:57 GMT Frederik Heber [bb2b2c] * src/Actions/CmdAction/BondLengthTableAction.cpp (modified) * src/Actions/CmdAction/BondLengthTableAction.hpp (modified) converted BondLengthTableAction to new createDialog(). Thu, 22 Jul 2010 19:56:02 GMT Frederik Heber [5cb3cb] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.hpp (modified) converted RemoveAction to new createDialog() and uses selectedAtoms. Thu, 22 Jul 2010 19:55:55 GMT Frederik Heber [454065] * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.hpp (modified) Changed ChangeElementAction to new createDialog() and uses selectedAtoms. Thu, 22 Jul 2010 19:45:26 GMT Frederik Heber [9d33ba] * 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/AddAction.hpp (modified) * src/UIElements/ValueStorage.cpp (modified) * src/UIElements/ValueStorage.hpp (modified) Added ValueStorage::getDescription(), i.e. now all occurences of ... Thu, 22 Jul 2010 19:38:03 GMT Frederik Heber [ca1ba5] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) Adapted dialog->query...() calls of all CorrelationAction()s to ... Thu, 22 Jul 2010 19:37:46 GMT Frederik Heber [75dc28] * 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/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/ValueStorage.cpp (added) * src/UIElements/ValueStorage.hpp (added) Dialog->query...() don't need a _target anymore, - new class ... Thu, 22 Jul 2010 19:11:35 GMT Frederik Heber [d02e07] * 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/SurfaceCorrelationAction.cpp (added) * src/Actions/AnalysisAction/SurfaceCorrelationAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) Split PairCorrelation into Pair, Point and SurfaceCorrelation. - ... Thu, 22 Jul 2010 17:57:15 GMT Frederik Heber [0c9cc3] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (modified) MolecularVolumeAction rewritten to new createDialog(). 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 17:53:21 GMT Frederik Heber [ba7418] * src/Actions/Action.hpp (modified) new virtual function Action::createDialog(). Tue, 20 Jul 2010 13:01:11 GMT Frederik Heber [be97a8] * src/Actions/ActionRegistry.hpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.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/ConfigFileBuffer.cpp (modified) * src/ConfigFileBuffer.hpp (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/Exceptions/CustomException.cpp (modified) * src/Exceptions/CustomException.hpp (modified) * src/Exceptions/NotInvertibleException.cpp (added) * src/Exceptions/NotInvertibleException.hpp (added) * src/Helpers/Assert.hpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Line.cpp (modified) * src/Line.hpp (modified) * src/Makefile.am (modified) * src/Matrix.cpp (added) * src/Matrix.hpp (added) * src/MatrixContent.hpp (added) * src/Parser/MpqcParser.hpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedContainer.hpp (added) * src/Patterns/ObservedContainer_impl.hpp (added) * src/Patterns/ObservedIterator.hpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.hpp (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/QT4/QTMainWindow.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/UIElements/TextUI/TextWindow.hpp (modified) * src/UIElements/Views/StreamStringView.hpp (modified) * src/VectorContent.hpp (added) * src/VectorSet.cpp (deleted) * src/VectorSet.hpp (modified) * src/World.cpp (modified) * src/World.hpp (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.hpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/atom_trajectoryparticle.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/datacreator.cpp (modified) * src/datacreator.hpp (modified) * src/defs.hpp (modified) * src/element.hpp (modified) * src/ellipsoid.cpp (modified) * src/errorlogger.cpp (modified) * src/errorlogger.hpp (modified) * src/graph.cpp (modified) * src/graph.hpp (modified) * src/gslvector.cpp (modified) * src/gslvector.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/logger.cpp (modified) * src/logger.hpp (modified) * src/memoryallocator.cpp (deleted) * src/memoryallocator.hpp (deleted) * src/memoryusageobserver.cpp (deleted) * src/memoryusageobserver.hpp (deleted) * 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.hpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/LineUnittest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MatrixUnittest.cpp (added) * src/unittests/MatrixUnittest.hpp (added) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/ShapeUnittest.cpp (added) * src/unittests/ShapeUnittest.hpp (added) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.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) * src/verbose.cpp (modified) * src/verbose.hpp (modified) * test_all.sh (modified) * tests/Tesselations/defs.in (modified) * tests/Tesselations/heptan/1.5/NonConvexEnvelope-heptan.dat (modified) * tests/regression/Domain/4/post/test.conf (modified) * tests/regression/testsuite-analysis.at (modified) Merge branch 'StructureRefactoring' into stable Conflicts: ... Tue, 20 Jul 2010 10:20:49 GMT Frederik Heber [818eda] * src/Descriptors/MoleculeSelectionDescriptor.cpp (added) * src/Descriptors/MoleculeSelectionDescriptor.hpp (added) * src/Descriptors/MoleculeSelectionDescriptor_impl.hpp (added) Till forgot to add new MoleculeSelectionDescriptor files. 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 Fri, 16 Jul 2010 12:46:42 GMT Tillmann Crueger [8cce2b] * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor_impl.hpp (modified) Made the MoleculeDescriptor and AtomDescriptor use faster STL- ... Fri, 16 Jul 2010 11:07:08 GMT Tillmann Crueger [a1e0b6] * src/Descriptors/MoleculeDescriptor.cpp (modified) Improved speed of MoleculeDescriptor by using reference to MoleculeSet Fri, 16 Jul 2010 10:58:56 GMT Tillmann Crueger [41aa39] * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/World.hpp (modified) Made MoleculeIdDescriptor and AtomIdDescriptor faster by avoiding ... Fri, 16 Jul 2010 10:43:38 GMT Tillmann Crueger [3839e5] * src/World.cpp (modified) * src/World.hpp (modified) Added iterators over selected atoms and molecules Fri, 16 Jul 2010 10:34:12 GMT Tillmann Crueger [61d655e] * src/World.cpp (modified) * src/World.hpp (modified) Added methods for unselecting molecules and atoms Thu, 15 Jul 2010 15:30:55 GMT Tillmann Crueger [90c4280] * src/World.cpp (modified) * src/World.hpp (modified) Added several methods for selecting specific atoms in the World Thu, 15 Jul 2010 15:21:06 GMT Tillmann Crueger [c084cc] * src/atom.cpp (modified) * src/atom.hpp (modified) Added a method to query the molecule an atom belongs to. Thu, 15 Jul 2010 14:24:04 GMT Tillmann Crueger [1a76a6] * src/World.hpp (modified) Removed public direct access to Atoms from world Thu, 15 Jul 2010 14:14:42 GMT Tillmann Crueger [3bf9e2] * src/Box.cpp (modified) Replaced check for Symmetric matrix in Box class with check for ... Wed, 14 Jul 2010 12:00:29 GMT Tillmann Crueger [5d880e] * src/World.cpp (modified) * src/World.hpp (modified) Allowed observed access to iterators on Molecules Wed, 14 Jul 2010 11:53:16 GMT Tillmann Crueger [e3d865] * src/Patterns/ObservedContainer.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Madet the internal iterators provided by the world unobserved Wed, 14 Jul 2010 10:36:29 GMT Tillmann Crueger [51be2a] * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Made iterator access to the molecules observed Wed, 14 Jul 2010 10:27:19 GMT Tillmann Crueger [8774c5] * src/Patterns/ObservedIterator.hpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) Added operator-> for Observed Iterators Sat, 10 Jul 2010 14:55:16 GMT Tillmann Crueger [b99bf3] * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Patterns/ObservedContainer.hpp (added) * src/Patterns/ObservedContainer_impl.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) Moved the observedContainer templates to the Pattern directory Sat, 10 Jul 2010 14:46:51 GMT Tillmann Crueger [4ef9b7] * src/World.hpp (modified) Made the observed sets for Atoms more abstract using template mechanisms Sat, 10 Jul 2010 14:22:25 GMT Tillmann Crueger [4d7462] * src/Descriptors/AtomDescriptor.cpp (modified) FIX: Repaired broken optimized builds Thu, 08 Jul 2010 16:04:11 GMT Tillmann Crueger [127a8e] * src/World.cpp (modified) * src/World.hpp (modified) * src/defs.hpp (modified) Improved managing of Ids in the World - Improved algorithm for ... Thu, 08 Jul 2010 12:57:07 GMT Tillmann Crueger [40f928] * src/Patterns/Observer.hpp (modified) Fixed a small misnaming of a variable Thu, 08 Jul 2010 12:51:15 GMT Tillmann Crueger [fa0b18] * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added Observed and Selectiv iterators over internal Structures of the ... Thu, 08 Jul 2010 11:36:38 GMT Tillmann Crueger [61ea5b] * src/Patterns/Observer.hpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) Added a macro that allows locking observer from outside of the observer Thu, 08 Jul 2010 11:25:54 GMT Tillmann Crueger [77a570] * src/VectorSet.cpp (deleted) Removed unused VectorSet.cpp 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: ... Wed, 07 Jul 2010 15:55:33 GMT Tillmann Crueger [5630bd] * src/unittests/MatrixUnittest.cpp (added) * src/unittests/MatrixUnittest.hpp (added) Added Unittests for the matrix class Wed, 07 Jul 2010 13:57:05 GMT Tillmann Crueger [0eb2dc] * src/Matrix.cpp (modified) * src/Matrix.hpp (modified) * src/unittests/Makefile.am (modified) Added comparison Operator to matrix class Wed, 07 Jul 2010 13:46:59 GMT Frederik Heber [ed6dd8] * src/Actions/ParserAction/LoadXyzAction.cpp (modified) FIX: newly parsed-in atoms should always end up in their own molecule ... Wed, 07 Jul 2010 13:11:46 GMT Tillmann Crueger [3dbb9d] * src/Matrix.cpp (modified) * src/Matrix.hpp (modified) * src/VectorContent.hpp (modified) Added methods to matrix to create vectors for rows and columns Wed, 07 Jul 2010 12:43:34 GMT Tillmann Crueger [8e17d6] * src/Matrix.hpp (modified) * src/VectorContent.hpp (modified) * src/vector.hpp (modified) Added VectorContent types that allow making vectors from views Wed, 07 Jul 2010 12:26:05 GMT Tillmann Crueger [5e8e02] * src/Exceptions/CustomException.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/gslvector.cpp (modified) * src/verbose.cpp (modified) Repaired broken NO_MEMDEBUG build-path Wed, 07 Jul 2010 11:53:05 GMT Frederik Heber [86cff86] * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParserStorage.hpp (modified) * src/Parser/XyzParser.cpp (modified) * src/unittests/ParserUnitTest.cpp (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-domain.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) InputAction now parses all possible formats, not only pcp. - new ... Wed, 07 Jul 2010 11:51:34 GMT Tillmann Crueger [9d5ddf] * src/VectorContent.hpp (modified) * src/vector.cpp (modified) Added constructor and destructor to VectorContent struct Wed, 07 Jul 2010 08:35:30 GMT Frederik Heber [192f6e] * src/CommandLineParser.cpp (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) FIX: Removed positional action "input". - BUG: This caused that ... Tue, 06 Jul 2010 15:50:04 GMT Frederik Heber [b540f3] * src/Actions/MapOfActions.cpp (modified) * tests/regression/testsuite-analysis.at (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-filling.at (modified) * tests/regression/testsuite-molecules.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) changed validate() for VectorValue, parsing not 10. 10. 10. but "10., ... 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): ... Mon, 05 Jul 2010 17:03:53 GMT Frederik Heber [361ba7] * src/Actions/Makefile.am (modified) Trailing whitespace in src/Actions/Makefile.am Sat, 03 Jul 2010 14:02:50 GMT Frederik Heber [2a374e] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) MEMFIX: AnalysisPairCorrelationAction::performCall() did not free ... Sat, 03 Jul 2010 14:02:26 GMT Frederik Heber [c27778] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) MEMFIXES: ListOfLocalAtoms in molecule::FragmentMolecule() was not ... Fri, 02 Jul 2010 16:00:59 GMT Tillmann Crueger [08d9595] * src/tesselationhelpers.hpp (modified) removed GSL-Headers from tesselationhelpers.hpp Fri, 02 Jul 2010 15:58:53 GMT Tillmann Crueger [797126] * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) Removed two more unused functions Fri, 02 Jul 2010 15:32:22 GMT Tillmann Crueger [417813] * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) Removed unused DetGet() method Fri, 02 Jul 2010 15:29:21 GMT Tillmann Crueger [04ef48] * src/tesselationhelpers.cpp (modified) Made the GetSphere() function use matrix objects Fri, 02 Jul 2010 15:11:22 GMT Tillmann Crueger [fee079] * src/Matrix.cpp (modified) * src/Matrix.hpp (modified) * src/MatrixContent.hpp (added) Added a "forward declaration" of the gsl_matrix struct in file Matrix.hpp Fri, 02 Jul 2010 14:58:40 GMT Tillmann Crueger [aafd77] * src/atom_trajectoryparticle.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) Removed all inclusions of GSL-Headers from molecule.hpp Fri, 02 Jul 2010 14:58:40 GMT Tillmann Crueger [962d8d] * src/molecule.hpp (modified) Added forgotten inclusion of config.h in molecule.hpp Fri, 02 Jul 2010 14:58:39 GMT Tillmann Crueger [d4103c8] * src/graph.hpp (modified) * src/molecule.hpp (modified) Removed opening of namespace from molecule.hpp Fri, 02 Jul 2010 14:58:39 GMT Tillmann Crueger [c37386] * src/graph.hpp (modified) Replaced several defines in Graph.hpp with typedefs Fri, 02 Jul 2010 14:58:25 GMT Tillmann Crueger [ce3d2b] * src/Matrix.cpp (modified) * src/VectorContent.hpp (added) * src/gslvector.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Added a "forward declaration" to the gsl_vector struct to avoid ... Fri, 02 Jul 2010 13:44:23 GMT Frederik Heber [b9c847] * src/Actions/Makefile.am (modified) * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.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/Actions/WorldAction/SetOutputFormatsAction.cpp (added) * src/Actions/WorldAction/SetOutputFormatsAction.hpp (added) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/World.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) * tests/regression/testsuite-tesselation.at (modified) New SetOutputFormatsAction introduced. Fixes: - World::setDomain() ... Fri, 02 Jul 2010 13:19:32 GMT Tillmann Crueger [986ed3] * src/Actions/ActionRegistry.hpp (modified) * src/Actions/AtomsCalculation_impl.hpp (modified) * src/Actions/MapOfActions.cpp (modified) * src/ConfigFileBuffer.hpp (modified) * src/Exceptions/CustomException.hpp (modified) * src/Helpers/Assert.hpp (modified) * src/Matrix.hpp (modified) * src/Parser/MpqcParser.hpp (modified) * src/Parser/PcpParser.hpp (modified) * src/Patterns/Cacheable.hpp (modified) * src/Plane.hpp (modified) * src/UIElements/Views/StreamStringView.hpp (modified) * src/atom.hpp (modified) * src/atom_particleinfo.hpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/datacreator.hpp (modified) * src/element.hpp (modified) * src/errorlogger.cpp (modified) * src/errorlogger.hpp (modified) * src/gslvector.hpp (modified) * src/helpers.cpp (modified) * src/logger.cpp (modified) * src/logger.hpp (modified) * src/molecule_graph.cpp (modified) * src/periodentafel.hpp (modified) * src/tesselationhelpers.hpp (modified) * src/vector.hpp (modified) * src/verbose.hpp (modified) COMPILE_SPEEDUP: Replaced all implicit inclusions of iostream with ... Fri, 02 Jul 2010 13:09:37 GMT Tillmann Crueger [36166d] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/QT4/QTMainWindow.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_graphnodeinfo.cpp (modified) * src/atom_particleinfo.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/graph.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/memoryallocator.cpp (deleted) * src/memoryallocator.hpp (deleted) * src/memoryusageobserver.cpp (deleted) * src/memoryusageobserver.hpp (deleted) * 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/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Removed left over parts from old memory-tracker Fri, 02 Jul 2010 13:07:29 GMT Frederik Heber [4a611e] * src/Actions/WorldAction/OutputAction.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) OutputAction written and used in TextWindow::TextWindow(). ... Fri, 02 Jul 2010 13:05:08 GMT Frederik Heber [cd8e55] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (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) New StringsQuery that returns space-separated vector of strings. ... Fri, 02 Jul 2010 11:29:56 GMT Frederik Heber [edb454] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) MEMFIX: correlationmap was not free'd correctly in ... 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 ... Fri, 02 Jul 2010 09:36:29 GMT Tillmann Crueger [7ac4af] * src/Box.cpp (modified) * src/Box.hpp (modified) Added an optimized version of the Box::explode() method for n=1 Fri, 02 Jul 2010 09:28:10 GMT Tillmann Crueger [a630fd] * src/Box.cpp (modified) * src/Box.hpp (modified) Made the Box::explode() method take an aditional parameters ... Fri, 02 Jul 2010 09:12:10 GMT Tillmann Crueger [abd8f7] * src/Box.hpp (modified) Added comments for Box class Fri, 02 Jul 2010 09:00:17 GMT Tillmann Crueger [cd82ec] * src/Matrix.hpp (modified) Improved comments of matrix class 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 14:48:50 GMT Tillmann Crueger [4b94bb] * src/Matrix.cpp (modified) * src/Matrix.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Moved Vector-Matrix operations to matrix class Thu, 01 Jul 2010 14:37:53 GMT Tillmann Crueger [c550dd] * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/unittests/vectorunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Removed the VectorIsInParallelepiped in favor of more general methods ... Thu, 01 Jul 2010 14:33:13 GMT Frederik Heber [bdc91e] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/linkedcell.cpp (modified) * src/molecule_geometry.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) MEMFIXES: Tesselation routines were leaking memory. - ... Thu, 01 Jul 2010 14:29:52 GMT Tillmann Crueger [205d9b] * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) Added missing const to Shape::isInside() method Thu, 01 Jul 2010 14:24:25 GMT Tillmann Crueger [5e588b5] * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps.hpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) Added more Shape operations Thu, 01 Jul 2010 14:10:14 GMT Tillmann Crueger [b5bf84] * src/vector.cpp (modified) * src/vector.hpp (modified) Added a method that allows to scale all components of one vector with ... 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 Thu, 01 Jul 2010 13:44:39 GMT Tillmann Crueger [014475] * src/Box.cpp (modified) * src/Box.hpp (modified) * src/VectorSet.hpp (modified) * src/analysis_correlation.cpp (modified) * src/molecule_graph.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Made all places use the periodicDistance() and ... Thu, 01 Jul 2010 12:44:37 GMT Tillmann Crueger [12cf773] * src/Box.cpp (modified) * src/Box.hpp (modified) * src/VectorSet.hpp (modified) Added a define that makes the definition of VectorSets simpler Wed, 30 Jun 2010 16:46:53 GMT Tillmann Crueger [527de2] * src/Box.cpp (modified) * src/Box.hpp (modified) Added a function that allows to find the closest periodic point in a Box Wed, 30 Jun 2010 16:46:44 GMT Tillmann Crueger [ec7f5c] * src/VectorSet.hpp (modified) Added a method that allows the calculation of the minimum distance of ... Wed, 30 Jun 2010 16:17:24 GMT Tillmann Crueger [89e820] * src/Box.cpp (modified) * src/Box.hpp (modified) Added a function that allows an expansion of a Point into its 27 ... Wed, 30 Jun 2010 15:39:55 GMT Tillmann Crueger [f429d7] * src/Box.cpp (modified) * src/Box.hpp (modified) * src/molecule_geometry.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Move Vector::WrapPeriodically to Box class Wed, 30 Jun 2010 15:16:10 GMT Tillmann Crueger [3dcb1f] * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/unittests/LineUnittest.cpp (modified) * src/unittests/PlaneUnittest.cpp (modified) * src/unittests/linearsystemofequationsunittest.cpp (modified) * src/vector.hpp (modified) * src/vector_ops.cpp (modified) Added two functions to Box class to translate Vectors from Box-Space ... Wed, 30 Jun 2010 14:41:46 GMT Tillmann Crueger [6e00dd] * src/Box.cpp (modified) Added check for symmetricity in Box::setM() Wed, 30 Jun 2010 14:37:40 GMT Tillmann Crueger [ac2724] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) FIX: RepeatBoxAction was using a reference to the Box size instead of ... Wed, 30 Jun 2010 14:03:43 GMT Tillmann Crueger [082215] * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) FIX: ScaleBoxAction did not set the new Box Matrix in the World Wed, 30 Jun 2010 13:55:42 GMT Tillmann Crueger [84c494] * 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/Parser/PcpParser.cpp (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/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/analysis_correlation.cpp (modified) * src/boundary.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) Made the world store the cell_size within a Box object. Wed, 30 Jun 2010 12:20:34 GMT Tillmann Crueger [9df5c6] * src/atom.cpp (modified) * src/atom.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Made the Vector::IsInParallelepiped() method take a matrix instead of ... Wed, 30 Jun 2010 10:47:06 GMT Tillmann Crueger [4b0cbb] * src/molecule_graph.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Made the Vector::PeriodicDistance() and ... Wed, 30 Jun 2010 10:21:12 GMT Tillmann Crueger [7579a4b] * src/Box.cpp (modified) * src/Box.hpp (modified) Added Copy constructor and Assignment operator to Box class 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 ... Wed, 30 Jun 2010 09:41:55 GMT Tillmann Crueger [c49c96] * src/Matrix.cpp (modified) * src/Matrix.hpp (modified) Added an output function for matrices Wed, 30 Jun 2010 09:08:19 GMT Tillmann Crueger [1da5f5] * src/Matrix.cpp (modified) * src/Matrix.hpp (modified) Added method that allows fast construction of Unity matrices