# # ChangeLog for src # # Generated by Trac 1.4.4 # Jan 1, 2025, 3:34:01 PM Mon, 18 Apr 2011 12:45:06 GMT Frederik Heber [455573] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Large Commit: SUBDIRS in src/Makefile.am replaced by include. - ... Mon, 18 Apr 2011 12:45:06 GMT Frederik Heber [ca2cfa] * src/Parser/TremoloParser.cpp (modified) FIX: TremoloParser writes neighbours as sorted list. - ... Fri, 08 Apr 2011 15:48:50 GMT Frederik Heber [bf4b9f] * LinearAlgebra/.gitignore (added) * LinearAlgebra/AUTHORS (added) * LinearAlgebra/COPYING (added) * LinearAlgebra/ChangeLog (added) * LinearAlgebra/INSTALL (added) * LinearAlgebra/LinearAlgebra-debug.pc.in (added) * LinearAlgebra/LinearAlgebra.pc.in (moved) * LinearAlgebra/Makefile.am (added) * LinearAlgebra/NEWS (added) * LinearAlgebra/README (added) * LinearAlgebra/bootstrap (added) * LinearAlgebra/build-aux/README (added) * LinearAlgebra/configure.ac (added) * LinearAlgebra/doc/Doxyfile (added) * LinearAlgebra/doc/Makefile.am (added) * LinearAlgebra/libLinearAlgebra_config.h.in (added) * LinearAlgebra/m4 (added) * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Line.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Makefile.am (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Space.hpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.cpp (moved) * LinearAlgebra/src/LinearAlgebra/Vector.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorContent.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorInterface.hpp (moved) * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (moved) * LinearAlgebra/src/LinearAlgebra/defs.hpp (moved) * LinearAlgebra/src/LinearAlgebra/fast_functions.hpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (moved) * LinearAlgebra/src/LinearAlgebra/leastsquaremin.hpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (moved) * LinearAlgebra/src/LinearAlgebra/vector_ops.hpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LineUnitTest.hpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (moved) * LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * LinearAlgebra/src/unittests/Makefile.am (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.cpp (moved) * LinearAlgebra/src/unittests/MatrixUnitTest.hpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved) * LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved) * LinearAlgebra/src/unittests/TestRunnerMain.cpp (added) * LinearAlgebra/src/unittests/UnitTestMain.cpp (added) * LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved) * LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved) * LinearAlgebra/tests/CodeChecks/Makefile.am (added) * LinearAlgebra/tests/CodeChecks/atlocal.in (added) * LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (added) * LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (added) * LinearAlgebra/tests/CodeChecks/testsuite.at (added) * Makefile.am (modified) * bootstrap (modified) * build-aux/README (added) * config/depcomp (deleted) * config/install-sh (deleted) * config/ltmain.sh (deleted) * config/missing (deleted) * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LinearAlgebra from folder src/ into distinct sub-package. - ... Wed, 06 Apr 2011 13:50:42 GMT Frederik Heber [3e2225f] * configure.ac (modified) * src/Actions/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Exceptions/CustomException.cpp (deleted) * src/Exceptions/CustomException.hpp (deleted) * src/Exceptions/Makefile.am (deleted) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Removed subdir Exceptions and libMolecuilderExceptions. - changes ... Wed, 06 Apr 2011 13:50:42 GMT Frederik Heber [336e33] * src/Actions/Action.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/Exceptions/Makefile.am (modified) * src/Exceptions/MissingValueException.cpp (deleted) * src/Exceptions/MissingValueException.hpp (deleted) Removed MissingValueException from Exceptions. - is now ... Wed, 06 Apr 2011 13:50:42 GMT Frederik Heber [882678] * src/Actions/ValueStorage.cpp (modified) * src/Actions/ValueStorage.hpp (modified) * src/Exceptions/IllegalTypeException.cpp (deleted) * src/Exceptions/IllegalTypeException.hpp (deleted) * src/Exceptions/Makefile.am (modified) * src/LinearAlgebra/Exceptions.hpp (modified) Removed IllegalTypeException from Exceptions. - is now ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [b94634] * src/Exceptions/Makefile.am (modified) * src/Exceptions/NotOnSurfaceException.cpp (deleted) * src/Exceptions/NotOnSurfaceException.hpp (deleted) * src/Exceptions/ShapeException.cpp (deleted) * src/Exceptions/ShapeException.hpp (deleted) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeExceptions.hpp (added) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) Removed NotOnSurfaceException and ShapeException from Exceptions. - ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [b88fe4] * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.hpp (modified) * src/Exceptions/FormulaStringParseException.cpp (deleted) * src/Exceptions/FormulaStringParseException.hpp (deleted) * src/Exceptions/Makefile.am (modified) * src/Formula.cpp (modified) * src/Formula.hpp (modified) Removed Exceptions/FormulaStringParseException. - is now ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [00bb38] * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/Makefile.am (modified) Removed libMolecuilderExceptions from LinearAlgebra. - now we may ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [783e88] * src/BoundaryTriangleSet.cpp (modified) * src/Exceptions/LinearDependenceException.cpp (deleted) * src/Exceptions/LinearDependenceException.hpp (deleted) * src/Exceptions/Makefile.am (modified) * src/Exceptions/MathException.cpp (deleted) * src/Exceptions/MathException.hpp (deleted) * src/Exceptions/MultipleSolutionsException.hpp (deleted) * src/LinearAlgebra/Exceptions.hpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Plane.hpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/unittests/LineUnitTest.cpp (modified) * src/LinearAlgebra/unittests/VectorUnitTest.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/molecule.cpp (modified) * src/tesselation.cpp (modified) Removed LinearDependenceException, MultipleSolutionsException and ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [8b9c43] * src/Exceptions/Makefile.am (modified) * src/Exceptions/ZeroVectorException.cpp (deleted) * src/Exceptions/ZeroVectorException.hpp (deleted) * src/LinearAlgebra/Exceptions.hpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/Plane.hpp (modified) * src/LinearAlgebra/unittests/PlaneUnitTest.cpp (modified) Removed Exceptions/ZeroVectorException. - is now ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [a700c4] * src/Exceptions/Makefile.am (modified) * src/Exceptions/NotInvertibleException.cpp (deleted) * src/Exceptions/NotInvertibleException.hpp (deleted) * src/LinearAlgebra/Exceptions.hpp (modified) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/unittests/MatrixUnitTest.cpp (modified) Removed Exceptions/NotInvertibleException. - is now a ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [3bfd78] * src/Exceptions/Makefile.am (modified) * src/Exceptions/SkewException.cpp (deleted) * src/Exceptions/SkewException.hpp (deleted) * src/LinearAlgebra/Exceptions.hpp (added) * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/unittests/LineUnitTest.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) LinearAlgebra now begins having its own exceptions derived from ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [255829] * configure.ac (modified) * src/BoundaryPolygonSet.cpp (modified) * src/ConfigFileBuffer.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/OutputTemperature.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Formula.hpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Helpers/Makefile.am (deleted) * src/Helpers/defs.hpp (modified) * src/Helpers/helpers.cpp (deleted) * src/Helpers/helpers.hpp (modified) * src/Makefile.am (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.hpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/tesselation.hpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) Removed Helpers.hpp, deleted Helpers.cpp and libMoleCuilderHelpers.la ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [8766e72] * src/boundary.cpp (modified) FIX: setRandomRotation() used probably faulty rotation matrix. - ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [b81f1c] * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.hpp (modified) * src/boundary.cpp (modified) Removed libMolecuilderRandomNumbers from LinearAlgebra. - added ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [819cbe] * src/LinearAlgebra/unittests/MatrixUnitTest.cpp (modified) FIX: MatrixTest::RotationTest() allowed also rotations matrices with ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [0a60ee] * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/Makefile.am (modified) Removed libMolecuilderHelpers from LIBADDs in LinearAlgebra. Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [71129f] * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/defs.hpp (modified) * src/LinearAlgebra/fast_functions.hpp (modified) * src/LinearAlgebra/unittests/LinearSystemOfEquationsUnitTest.cpp (modified) * src/LinearAlgebra/unittests/MatrixUnitTest.cpp (modified) * src/LinearAlgebra/unittests/PlaneUnitTest.cpp (modified) * src/LinearAlgebra/unittests/VectorUnitTest.cpp (modified) Removed inclusion of Helpers/...hpp from LinearAlgebra. - ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [5605793] * src/Helpers/helpers.hpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) Moved PLURAL_S from Helpers/helpers to UIElements/Views/Qt4/QtStatusBar. Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [0d0316] * src/Helpers/helpers.cpp (modified) * src/Helpers/helpers.hpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) Removed FixedDigitNumber from Helpers/helpers. - is now inlined ... Wed, 06 Apr 2011 13:50:41 GMT Frederik Heber [67acff] * src/Helpers/helpers.cpp (modified) * src/Helpers/helpers.hpp (modified) Removed debug and debug_in that are no longer used. Wed, 06 Apr 2011 13:50:40 GMT Frederik Heber [888743] * src/LinearAlgebra/VectorContent.cpp (modified) BUGFIX: VectorContent::free_content_on_exit not initialised for ... Wed, 06 Apr 2011 13:50:40 GMT Frederik Heber [cd406d] * src/Helpers/helpers.cpp (modified) * src/Helpers/helpers.hpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/fast_functions.hpp (modified) Moved sign() from Helpers/helpers to LinearAlgebra/fast_functions.hpp. Wed, 06 Apr 2011 13:50:40 GMT Frederik Heber [6f68d6] * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) * src/LinearAlgebra/unittests/MatrixContentUnitTest.cpp (modified) * src/LinearAlgebra/unittests/MatrixContentUnitTest.hpp (modified) Added possibility to parse MatrixContent from stream and to write to. ... Wed, 06 Apr 2011 13:50:40 GMT Frederik Heber [0e4aa4] * src/LinearAlgebra/MatrixContent.cpp (modified) FIX: MatrixContent::sortEigenbasis() sorted by magnitude not value. Wed, 06 Apr 2011 13:50:40 GMT Frederik Heber [abfb12] * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/VectorContent.hpp (modified) VectorContent also free's ::content when delivered by pointer. - ... Wed, 06 Apr 2011 13:50:40 GMT Frederik Heber [644d03] * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/MatrixContent.hpp (modified) Added operator+ and operator- for two MatrixContent's. - += and -= ... Wed, 06 Apr 2011 13:50:40 GMT Frederik Heber [a9c556] * src/LinearAlgebra/Eigenspace.cpp (deleted) * src/LinearAlgebra/Eigenspace.hpp (deleted) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/Subspace.cpp (deleted) * src/LinearAlgebra/Subspace.hpp (deleted) * src/Makefile.am (modified) * src/SubspaceFactorizer.cpp (deleted) * src/unittests/Makefile.am (modified) * src/unittests/SubspaceFactorizerUnitTest.cpp (deleted) * src/unittests/SubspaceFactorizerUnitTest.hpp (deleted) Removed Subspace stuff from this project. - has been relayed along ... Wed, 06 Apr 2011 13:50:30 GMT Frederik Heber [06aedc] * LinearAlgebra-debug.pc.in (added) * LinearAlgebra.pc.in (added) * configure.ac (modified) * src/Actions/Values.hpp (modified) * src/BoundaryTriangleSet.cpp (modified) * src/Box.cpp (modified) * src/Helpers/Makefile.am (modified) * src/Helpers/defs.hpp (modified) * src/Helpers/helpers.cpp (modified) * src/LinearAlgebra/BoxVector.cpp (modified) * src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.hpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/Vector.hpp (modified) * src/LinearAlgebra/defs.hpp (modified) * src/LinearAlgebra/fast_functions.hpp (moved) * src/LinearAlgebra/leastsquaremin.cpp (modified) * src/LinearAlgebra/unittests/MatrixUnitTest.cpp (modified) * src/LinearAlgebra/vector_ops.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.cpp (modified) * src/boundary.hpp (modified) * src/datacreator.cpp (modified) * src/element.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) libMolecuilderLinearAlgebra is now a self-contained library fit for ... Wed, 06 Apr 2011 13:10:31 GMT Frederik Heber [9b410d] * src/LinearAlgebra/Line.cpp (modified) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/MatrixContent.cpp (modified) * src/LinearAlgebra/Plane.cpp (modified) * src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * src/LinearAlgebra/Space.cpp (modified) * src/LinearAlgebra/Vector.cpp (modified) * src/LinearAlgebra/VectorContent.cpp (modified) * src/LinearAlgebra/defs.hpp (added) * src/LinearAlgebra/unittests/LinearSystemOfEquationsUnitTest.cpp (modified) * src/LinearAlgebra/unittests/MatrixUnitTest.cpp (modified) * src/LinearAlgebra/unittests/PlaneUnitTest.cpp (modified) * src/LinearAlgebra/unittests/VectorUnitTest.cpp (modified) Replace MYEPSILON in LinearAlgebra/ by LINALG_MYEPSILON. - this is ... Wed, 06 Apr 2011 13:10:11 GMT Frederik Heber [1be8a5] * src/LinearAlgebra/Vector.cpp (modified) Changed inclusion of LinearAlgebra/Vector.cpp. - Removed unneeded ... Fri, 11 Mar 2011 12:38:34 GMT Frederik Heber [61775a] * src/Helpers/helpers.hpp (modified) Removed templated CreateFatherLookupTable from helpers.hpp. Fri, 11 Mar 2011 12:38:30 GMT Frederik Heber [13a953] * src/Graph/CheckAgainstAdjacencyFile.cpp (added) * src/Graph/CheckAgainstAdjacencyFile.hpp (added) * src/Graph/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) Moved molecule::CheckAdjacencyAgainstFile() into functor in Graph/. ... Mon, 07 Mar 2011 11:40:27 GMT Frederik Heber [2d4334] * src/Graph/BuildInducedSubgraph.cpp (added) * src/Graph/BuildInducedSubgraph.hpp (added) * src/Graph/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) Moved BuildInducedSubgraph from molecule into functor in Graph/. - ... Mon, 07 Mar 2011 11:40:27 GMT Frederik Heber [dda246] * configure.ac (modified) * src/Helpers/Makefile.am (added) * src/LinearAlgebra/Makefile.am (modified) * src/LinearAlgebra/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Made Helpers into commodity library to prevent double inclusion. - ... Mon, 07 Mar 2011 11:40:27 GMT Frederik Heber [d09093] * src/Actions/GraphAction/CreateAdjacencyAction.cpp (moved) * src/Actions/GraphAction/CreateAdjacencyAction.def (moved) * src/Actions/GraphAction/CreateAdjacencyAction.hpp (moved) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (moved) * src/Actions/GraphAction/DepthFirstSearchAction.def (moved) * src/Actions/GraphAction/DepthFirstSearchAction.hpp (moved) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (moved) * src/Actions/GraphAction/SubgraphDissectionAction.def (moved) * src/Actions/GraphAction/SubgraphDissectionAction.hpp (moved) * src/Actions/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) Moved all graph-related Actions into own folder Actions/GraphAction/. ... Mon, 07 Mar 2011 11:40:27 GMT Frederik Heber [197e13] * src/UIElements/Menu/MenuDescription.hpp (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (added) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.hpp (added) Added MenuDescription_ActionRegistry_ConsistenyUnitTest to check ... Mon, 07 Mar 2011 11:40:27 GMT Frederik Heber [19290f] * configure.ac (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistenyUnitTest.cpp (added) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistenyUnitTest.hpp (added) * src/UIElements/CommandLineUI/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) Added CommandLineParser_ActionRegistry_ConsistenyUnitTest to check ... Mon, 07 Mar 2011 11:40:25 GMT Frederik Heber [c6e5eb] * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) FIX: CommandLineParser::setOptions() added option_descriptions hard- ... Wed, 02 Mar 2011 21:53:09 GMT Frederik Heber [137ae1] * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) FIX: Made MenuDescriptionTest::ConsistencyCheck()'s failure message a ... Wed, 02 Mar 2011 21:53:09 GMT Frederik Heber [7d8aa0] * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp (modified) Typo in protecting define for MenuDescriptionUnitTest. Wed, 02 Mar 2011 21:53:09 GMT Frederik Heber [efe516] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BreadthFirstSearchAdd.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) Removed bond::nr. - has only been used by BreadthFirstSearchAdd. - ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [49c059] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (added) * src/Graph/DepthFirstSearchAnalysis.hpp (added) * src/Graph/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * tests/Fragmentations/defs.in (modified) * tests/regression/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Molecules/MoleculeById/post/id4_missing.xyz (moved) * tests/regression/Selection/Molecules/MoleculeById/post/water_id4.xyz (moved) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-molecules-by-name.at (modified) Moved DepthFirstSearchAnalysis into functor in Graph/. Smaller ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [1a4d4fe] * src/Bond/bond.cpp (modified) FIX: bond::~bond() checks whether the bond is a ring circle, leftatom ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [e73ad9a] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Graph/CyclicStructureAnalysis.cpp (added) * src/Graph/CyclicStructureAnalysis.hpp (added) * src/Graph/Makefile.am (modified) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) Moved CyclicStructureAnalysis from molecule_graph.cpp into own ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [2e4105] * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/boundary.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) molecule::erase() is only used by atom::removeFromMolecule(). - ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [0d9546] * src/atom.cpp (modified) * src/atom.hpp (modified) new function atom::unsetMolecule(). - is meant along with ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [1363de] * src/atom.cpp (modified) * src/atom.hpp (modified) DOCUFIX: atom - Moved all doxygen documentation to header file. Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [09ac12] * src/Graph/ConnectedSubgraph.cpp (added) * src/Graph/ConnectedSubgraph.hpp (added) * src/Graph/Makefile.am (modified) Added new class ConnectedSubgraph. - inherits list. - will ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [111387] * src/Graph/BreadthFirstSearchAdd.hpp (modified) FIX: BreadthFirstSearchAdd header only includes GraphEdge, not bond ... Wed, 02 Mar 2011 21:53:08 GMT Frederik Heber [129204] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Bond/GraphEdge.cpp (added) * src/Bond/GraphEdge.hpp (added) * src/Bond/bond.cpp (moved) * src/Bond/bond.hpp (moved) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BreadthFirstSearchAdd.hpp (modified) * src/Makefile.am (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/graph.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisBondsUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) Moved bond.* to Bond/, new class GraphEdge which contains graph parts ... Wed, 02 Mar 2011 21:53:07 GMT Frederik Heber [766ba5] * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/bond.cpp (modified) * src/bond.hpp (modified) bond::GetColor() is now static function bond::getColorName(). Wed, 02 Mar 2011 21:53:07 GMT Frederik Heber [53d6b2] * configure.ac (modified) * src/Graph/BreadthFirstSearchAdd.cpp (added) * src/Graph/BreadthFirstSearchAdd.hpp (added) * src/Graph/Makefile.am (added) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) Moved unused function BreadthFirstSearchAdd and subfunctions into ... Wed, 02 Mar 2011 21:53:07 GMT Frederik Heber [99752a] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) Moved FillBondStructureFromReference from MoleculeLeafClass to molecule. Wed, 02 Mar 2011 21:53:07 GMT Frederik Heber [c6123b] * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) Moved FillListOfLocalAtoms() from MoleculeLeafClass to molecule. Wed, 02 Mar 2011 21:53:07 GMT Frederik Heber [341f22] * src/Makefile.am (modified) * src/molecule_dynamics.cpp (deleted) Removed molecule_dynamics.cpp Wed, 02 Mar 2011 21:48:20 GMT Frederik Heber [435065] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Dynamics/VerletForceIntegration.hpp (added) * src/Makefile.am (modified) * src/atom_atominfo.cpp (modified) * src/atom_atominfo.hpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * tests/regression/Molecules/VerletIntegration/post/test.conf (moved) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) Rewrote VerletForceIntegration into a functor in Dynamics/. - we ... Wed, 02 Mar 2011 21:40:51 GMT Frederik Heber [eb33c4] * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * tests/regression/Molecules/LinearInterpolationofTrajectories/post/teststep.conf (added) * tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at (modified) LinearInterpolationofTrajectoriesAction only interpolates, does not ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [e355762] * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.hpp (modified) * src/molecule_dynamics.cpp (modified) Rewrote MinimiseConstrainedPotential to just use std::map instead of ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [fe6f20] * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (added) * src/Actions/AtomAction/SaveSelectedAtomsAction.def (added) * src/Actions/AtomAction/SaveSelectedAtomsAction.hpp (moved) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (moved) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.def (moved) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.hpp (added) * tests/regression/Atoms/SaveSelectedAtoms/post/testsave.xyz (added) * tests/regression/Atoms/SaveSelectedAtoms/pre/test.xyz (added) * tests/regression/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/SaveSelectedMolecules/post/testsave.xyz (added) * tests/regression/Molecules/SaveSelectedMolecules/pre/test.xyz (added) * tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) New Action SaveSelectedAtoms and renamed SaveAction -> ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [8009ce] * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (modified) * src/AtomSet.hpp (modified) * src/Dynamics/OutputTemperature.hpp (added) * src/Makefile.am (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * tests/regression/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at (modified) Rewrote OutputTemperature into a functor in Dynamics/ - formerly ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [20943b] * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (added) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) Rewrote LinearInterpolationBetweenSteps into a functor in Dynamics/ ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [9e23a3] * src/Dynamics/MinimiseConstrainedPotential.cpp (added) * src/Dynamics/MinimiseConstrainedPotential.hpp (added) * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) Rewrote MinimiseConstrainedPotential into a functor in Dynamics/. - ... Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [632508] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Graph/BondGraph.cpp (moved) * src/Graph/BondGraph.hpp (moved) * src/Makefile.am (modified) * src/World.cpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/AnalysisBondsUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) Moved files bondgraph.?pp -> Graph/BondGraph.?pp. Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber [607eab] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) BondGraph::...MinMaxDistance() now return range instead of ... Tue, 01 Mar 2011 13:17:08 GMT Frederik Heber [cff66c] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) Removed bool is Angstroem from all BondGraph::...() member functions. ... Tue, 01 Mar 2011 13:17:08 GMT Frederik Heber [111f4a] * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) Const-ness and cosmetic fixes to class BondGraph. - made ... Tue, 01 Mar 2011 13:17:08 GMT Frederik Heber [0ec7fe] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) Removed BondGraph::max_distance along with getter and setter. - ... Tue, 01 Mar 2011 13:17:08 GMT Frederik Heber [300220] * configure.ac (modified) * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) BondGraph::..MinMaxDistance() changed to use range. - ... Tue, 01 Mar 2011 13:17:07 GMT Frederik Heber [0cbad2] * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.def (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * tests/regression/Molecules/BondFile/post/test.pdb (added) * tests/regression/Molecules/BondFile/pre/silica.dbond.0000 (added) * tests/regression/Molecules/BondFile/pre/silica.pov1.0000.pdb (added) * tests/regression/Molecules/BondFile/pre/test.dbond (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at (modified) Moved molecule::CreateAdjacencyListFromDbondFile() over to BondGraph ... Tue, 01 Mar 2011 12:49:28 GMT Frederik Heber [3738f0] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/AtomSet.hpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/AnalysisBondsUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * tests/Fragmentations/defs.in (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified) * tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified) Moved molecule::CreateAdjacencyList over to class BondGraph. to ... Tue, 01 Mar 2011 10:16:46 GMT Frederik Heber [ce5f05] * src/Helpers/defs.hpp (modified) * src/bond.cpp (modified) * src/bond.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) Moved Shading and EdgeType from defs.hpp to bond.hpp, getColor from ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [4092c5] * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) Changed BondGraph::...MinMaxDistance()'s parameters to const ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [b9772a] * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) Renamed function pointer in molecule::CreateAdjacencyList to ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [4b5cf8] * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) BondedParticle::OutputBondOfAtom() now takes stream to print to. Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [458c31] * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) molecule::BondCount is now Cachable and private. - renamed ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [d4a44c] * src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (moved) * src/Actions/FragmentationAction/CreateAdjacencyAction.def (moved) * src/Actions/FragmentationAction/CreateAdjacencyAction.hpp (moved) * src/Actions/Makefile.am (modified) * tests/regression/Graph/1/pre/test2.conf (deleted) Renamed ConstructBondGraphAction -> CreateAdjacencyAction. Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [715b67] * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/unittests/AnalysisBondsUnitTest.cpp (modified) * src/unittests/BondGraphUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) Renamed BondGraph::ConstructBondGraph -> CreateAdjacencyForMolecule. ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [7adf0f] * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) Removed molecule::BondDistance, replaced by ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [e7350d4] * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) DOCUFIX: BondGraph - moved doxygen comments from cpp to header. Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [72d90e] * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) New function BondGraph::getMinMaxDistance(). - Covalent and ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [f71baf] * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/builder_init.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule_graph.cpp (modified) Made BondGraph an instance of World, removed from config. - ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [5309ba] * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPointSet.hpp (modified) * src/Helpers/helpers.hpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) Renamed ParticleInfo_nr back to Nr. - Note that this mostly ... Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber [735b1c] * src/BoundaryPointSet.cpp (modified) * src/BoundaryPointSet.hpp (modified) * src/analysis_bonds.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) ParticleInfo::ParticleInfo_nr is protected and accessed via ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [a479fa] * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/BoundaryPointSet.cpp (modified) * src/BoundaryPointSet.hpp (modified) * src/Helpers/helpers.hpp (modified) * src/analysis_bonds.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/bond.cpp (modified) * src/boundary.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) Renamed ParticleInfo::nr to ParticleInfo::ParticleInfo_nr for easier ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [5702cdb] * src/Makefile.am (modified) * src/molecule.hpp (modified) * src/molecule_pointcloud.cpp (deleted) Removed molecule_pointcloud.cpp. Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [caa06ef] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/IPointCloud.hpp (modified) * src/PointCloudAdaptor.hpp (modified) * src/boundary.cpp (modified) * src/molecule_graph.cpp (modified) * src/tesselation.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) Added name to PointCloudAdaptor, set by constructor. - name is used ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [34c43a] * configure.ac (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/IPointCloud.hpp (added) * src/Makefile.am (modified) * src/PointCloud.cpp (deleted) * src/PointCloud.hpp (deleted) * src/PointCloudAdaptor.hpp (added) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/ellipsoid.cpp (modified) * src/linkedcell.cpp (modified) * src/linkedcell.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/TesselationUnitTest.cpp (modified) * src/unittests/TesselationUnitTest.hpp (modified) * src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) Bigger change: Replaced PointCloud by PointCloudAdaptor. - ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [ba5215] * src/BoundaryPointSet.cpp (modified) * src/BoundaryPointSet.hpp (modified) * src/TesselPoint.cpp (modified) * src/TesselPoint.hpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) Extended BoundaryPointSet by functions to directly access TesselPoint ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [fa60dd] * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) Removed molecule::GetName() usage in QtMoleculeView. - in ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [fff733] * src/PointCloud.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) Fixed PointCloud implementation in class Tesselation. - removed ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [e34254] * src/atom_atominfo.cpp (modified) Changed operator<< (AtomInfo), less verbose for single time step. Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [4d5553] * src/config.cpp (modified) Changed verbosity for LoadMolecule(). Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [b23e26] * src/parser.cpp (modified) * src/parser.hpp (modified) Added operator<< for MatrixContainer class. Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [1bfc8e] * src/Parser/PcpParser.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule_dynamics.cpp (modified) Removed ThermostatContainer instance from config, instance from World ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [9b8387] * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified) DOCUFIX: enhanced description of RotateAroundSelfByAngleAction's ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [9d37ac] * src/molecule_graph.cpp (modified) DOCUFIX: Removed *out as parameter from waaay back ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [4afa46] * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) Added call to molecule::getAtomCount() to end of each parser's ... Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber [637358] * src/Parser/XyzParser.cpp (modified) Changed slightly XyzParser::load(). - AddedAtoms is now a vector.