# # ChangeLog for molecuilder # # Generated by Trac 1.6 # Sep 25, 2025, 6:32:49 PM Fri, 30 Apr 2010 09:32:59 GMT Tillmann Crueger [aab470] * molecuilder/src/Plane.cpp (modified) * molecuilder/src/Plane.hpp (modified) Added exception specifiers to plane class Fri, 30 Apr 2010 09:23:37 GMT Tillmann Crueger [7a8319] * molecuilder/src/Exceptions/LinearDependenceException.cpp (modified) * molecuilder/src/Exceptions/LinearDependenceException.hpp (modified) * molecuilder/src/Exceptions/MathException.cpp (added) * molecuilder/src/Exceptions/MathException.hpp (added) * molecuilder/src/Exceptions/ZeroVectorException.cpp (added) * molecuilder/src/Exceptions/ZeroVectorException.hpp (added) * molecuilder/src/Makefile.am (modified) * molecuilder/src/Plane.cpp (modified) Added more Exceptions to the project to signal differen Math erorrs Fri, 30 Apr 2010 09:03:57 GMT Tillmann Crueger [0e9394] * molecuilder/src/Makefile.am (modified) * molecuilder/src/Plane.cpp (modified) * molecuilder/src/Plane.hpp (modified) * molecuilder/src/Space.cpp (added) * molecuilder/src/Space.hpp (added) Added a class Space to represent general subspaces of R^3 (planes and ... Thu, 29 Apr 2010 21:25:44 GMT Frederik Heber [c53e0b] * molecuilder/src/Helpers/MemDebug.cpp (modified) Merge branch 'FixMemDebug_strncpy' into StructureRefactoring Thu, 29 Apr 2010 21:25:09 GMT Frederik Heber [93b12d] * molecuilder/src/Helpers/MemDebug.cpp (modified) FIX: strncpy was lacking cstring include. Thu, 29 Apr 2010 16:11:43 GMT Tillmann Crueger [465abf] * molecuilder/src/Plane.cpp (modified) * molecuilder/src/Plane.hpp (modified) Added a method that allows construction of three arbitrary points on ... Thu, 29 Apr 2010 16:03:30 GMT Tillmann Crueger [6a314f] * molecuilder/src/Plane.cpp (modified) * molecuilder/src/unittests/vectorunittest.cpp (modified) * molecuilder/src/unittests/vectorunittest.hpp (modified) * molecuilder/src/vector.cpp (modified) FIX: Bug that caused memory corruption in ... Thu, 29 Apr 2010 15:30:55 GMT Tillmann Crueger [16eb32] * molecuilder/src/Helpers/MemDebug.cpp (modified) FIX: Stupid bug in the Debug-new that destroyed some memory Thu, 29 Apr 2010 14:38:29 GMT Tillmann Crueger [5d1a94] * molecuilder/src/Helpers/MemDebug.cpp (modified) * molecuilder/src/Helpers/MemDebug.hpp (modified) Improved comments for the memory tracker Thu, 29 Apr 2010 13:55:21 GMT Tillmann Crueger [0d111b] * molecuilder/src/Exceptions/CustomException.cpp (added) * molecuilder/src/Exceptions/CustomException.hpp (added) * molecuilder/src/Exceptions/LinearDependenceException.cpp (added) * molecuilder/src/Exceptions/LinearDependenceException.hpp (added) * molecuilder/src/Helpers/fast_functions.hpp (added) * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/Plane.cpp (added) * molecuilder/src/Plane.hpp (added) * molecuilder/src/UIElements/TextDialog.cpp (modified) * molecuilder/src/analysis_bonds.cpp (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/gslmatrix.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/leastsquaremin.cpp (modified) * molecuilder/src/linearsystemofequations.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/test/ActOnAlltest.hpp (modified) * molecuilder/src/triangleintersectionlist.cpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.hpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/CountBondsUnitTest.cpp (modified) * molecuilder/src/unittests/LinkedCellUnitTest.cpp (modified) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * molecuilder/src/unittests/vectorunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vector_ops.cpp (added) * molecuilder/src/vector_ops.hpp (added) Merge branch 'VectorRefactoring' into StructureRefactoring ... Wed, 28 Apr 2010 14:52:56 GMT Tillmann Crueger [32842d8] * molecuilder/src/Helpers/fast_functions.hpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/SingleVector.cpp (deleted) * molecuilder/src/SingleVector.hpp (deleted) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Removed Algebraic Hierachy from vector. Wed, 28 Apr 2010 13:31:57 GMT Tillmann Crueger [90c4460] * molecuilder/src/Actions/Action.cpp (modified) * molecuilder/src/Actions/ActionHistory.cpp (modified) * molecuilder/src/Helpers/MemDebug.cpp (added) * molecuilder/src/Helpers/MemDebug.hpp (added) * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) Added a small memory tracker to the programm. Tue, 27 Apr 2010 14:25:42 GMT Frederik Heber [075729] * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/analysis_bonds.cpp (modified) * molecuilder/src/analysis_bonds.hpp (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_graphnode.cpp (modified) * molecuilder/src/atom_particleinfo.cpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/errorlogger.cpp (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/gslvector.cpp (modified) * molecuilder/src/gslvector.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/info.cpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/log.cpp (modified) * molecuilder/src/log.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/triangleintersectionlist.cpp (added) * molecuilder/src/triangleintersectionlist.hpp (added) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * molecuilder/src/unittests/CountBondsUnitTest.cpp (added) * molecuilder/src/unittests/CountBondsUnitTest.hpp (added) * molecuilder/src/unittests/LinkedCellUnitTest.cpp (added) * molecuilder/src/unittests/LinkedCellUnitTest.hpp (added) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.hpp (modified) * molecuilder/src/unittests/gslvectorunittest.cpp (modified) * molecuilder/src/unittests/gslvectorunittest.hpp (modified) * molecuilder/src/unittests/logunittest.cpp (modified) * molecuilder/src/unittests/memoryallocatorunittest.cpp (modified) * molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (modified) * molecuilder/src/unittests/tesselation_insideoutsideunittest.hpp (modified) * molecuilder/src/unittests/tesselationunittest.cpp (modified) * molecuilder/src/unittests/tesselationunittest.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/src/verbose.hpp (modified) * molecuilder/tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (deleted) * molecuilder/tests/Tesselations/defs.in (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) * util/Makefile.am (modified) * util/configure.ac (modified) * util/src/Makefile.am (modified) * util/src/NanoCreator.c (modified) * util/src/average.cpp (modified) * util/src/average.hpp (added) * util/src/averager.cpp (added) * util/src/unittests/AverageColumnsUnitTest.cpp (added) * util/src/unittests/AverageColumnsUnitTest.hpp (added) * util/src/unittests/Makefile.am (added) Merge branch 'Analysis_PairCorrelation' into StructureRefactoring ... Mon, 26 Apr 2010 18:19:38 GMT Frederik Heber [2bc713] * molecuilder/tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (deleted) * molecuilder/tests/Tesselations/defs.in (modified) Merge branch 'FixMolecuilderTestsTesselations_defs' into ... Mon, 26 Apr 2010 18:19:03 GMT Frederik Heber [9600a7] * molecuilder/tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (deleted) * molecuilder/tests/Tesselations/defs.in (modified) FIX: Tesselation does not work in first run due to still present ... Mon, 26 Apr 2010 17:25:44 GMT Frederik Heber [3d1097] * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) Regression test of Tesselation for test case 15 "Big non-convex ... Mon, 26 Apr 2010 16:38:47 GMT Frederik Heber [326a42d] * molecuilder/src/World.cpp (modified) Merge branch 'FixWorld_wrongauthor' into Analysis_PairCorrelation Mon, 26 Apr 2010 16:38:14 GMT Frederik Heber [5a40b8] * molecuilder/src/World.cpp (modified) FIX: Author of World.cpp has been wrongly set (by eclipse) to heber ... Mon, 26 Apr 2010 16:35:42 GMT Frederik Heber [caab20] * molecuilder/src/World.cpp (modified) Merge branch 'FixWorld_differentdefaultcell_size' into ... Mon, 26 Apr 2010 16:34:22 GMT Frederik Heber [8758eb] * molecuilder/src/World.cpp (modified) FIX: cell_size in World has not been set to a default size, i.e. has ... Mon, 26 Apr 2010 16:22:17 GMT Frederik Heber [732da7] * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) Merge branch 'FixAnalysisBonds_carbonwrongZ' into ... Mon, 26 Apr 2010 16:19:32 GMT Frederik Heber [da09739] * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) FIX: AnalysisBondsUnitTests has been broken due to Z of carbon same ... Mon, 26 Apr 2010 16:13:02 GMT Frederik Heber [5a2599] * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) Merge branch 'FixAnalysisCorrelation_zeroinitallbins' into ... Mon, 26 Apr 2010 16:11:23 GMT Frederik Heber [424890] * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) FIX: AnalysisCorrelationToPointUnitTest has been broken due to init ... Mon, 26 Apr 2010 16:04:41 GMT Frederik Heber [bb50e0] * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) Merge branch 'FixAnalysisCorrelation_zeroinitallbins' into ... Mon, 26 Apr 2010 16:00:24 GMT Frederik Heber [a3c47c] * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) FIX: AnalysisCorrelationToSurfaceUnitTest has been broken since ... Mon, 26 Apr 2010 15:47:54 GMT Frederik Heber [d1829c] * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.hpp (modified) Merge branch 'FixBondGraphUnitTest_hydrogencarbon' into ... Mon, 26 Apr 2010 15:42:45 GMT Frederik Heber [aa8542] * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.hpp (modified) BUGFIX: BondGraphUnitTest was not working. Changes: - atoms are ... Mon, 26 Apr 2010 13:49:59 GMT Tillmann Crueger [1561e2] * molecuilder/src/Actions/small_actions.cpp (modified) * molecuilder/src/Helpers/Assert.cpp (modified) * molecuilder/src/Helpers/Assert.hpp (modified) Added macros that allow type safe casting using the Assert mechanism Sun, 25 Apr 2010 13:36:17 GMT Tillmann Crueger [0707dd] * molecuilder/src/Helpers/Assert.hpp (modified) FIX: Repaired some of the NDEBUG macros for ASSERT Sun, 25 Apr 2010 13:16:09 GMT Tillmann Crueger [dd43a7] * molecuilder/src/UIElements/TextDialog.cpp (modified) Made the input methods more robust to invalid inputs. Sun, 25 Apr 2010 12:48:24 GMT Tillmann Crueger [65b413] * molecuilder/src/Helpers/Assert.hpp (modified) * molecuilder/src/Patterns/Observer.cpp (modified) * molecuilder/src/Patterns/Observer.hpp (modified) * molecuilder/src/unittests/ObserverTest.cpp (modified) Small improvements to Observer code Sat, 24 Apr 2010 15:27:00 GMT Tillmann Crueger [c0332d] * molecuilder/src/Helpers/Assert.hpp (modified) * molecuilder/src/Patterns/Observer.cpp (modified) * molecuilder/src/Patterns/Observer.hpp (modified) * molecuilder/src/unittests/ObserverTest.cpp (modified) * molecuilder/src/unittests/ObserverTest.hpp (modified) Added methods for specialized Notifications from the Observer Framework Fri, 23 Apr 2010 08:09:40 GMT Frederik Heber [d2390d] * molecuilder/src/boundary.cpp (modified) Don't exit when no starting triangle has been found. - The issue is ... Thu, 22 Apr 2010 20:09:48 GMT Frederik Heber [af20f3] * molecuilder/src/tesselation.cpp (modified) BUGFIX in Tesselation::FindThirdPointForTesselation() - ThirdPoint of ... Thu, 22 Apr 2010 15:47:22 GMT Frederik Heber [f07455] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) FIX: Tesselation::FindStartingTriangle() returns false when no ... Thu, 22 Apr 2010 15:03:42 GMT Frederik Heber [424d3fe] * molecuilder/src/tesselation.cpp (modified) BUGFIX of Tesselation::FindStartingTriangle() - second Point ... Thu, 22 Apr 2010 14:13:32 GMT Frederik Heber [447896] * molecuilder/src/tesselation.cpp (modified) BUGFIX of Tesselation::AddTesselationLine() - comparing Vector ... Thu, 22 Apr 2010 14:10:08 GMT Frederik Heber [fda112] * molecuilder/src/tesselation.cpp (modified) BUGFIX in Tesselation::FindThirdPointForTesselation() - regarding ... Thu, 22 Apr 2010 14:07:14 GMT Frederik Heber [d22a30] * molecuilder/src/tesselation.cpp (modified) small changes to tesselation. - ... Thu, 22 Apr 2010 14:05:32 GMT Frederik Heber [2cd534] * molecuilder/src/boundary.cpp (modified) FindNonConvexBorder(): Instead of listing all open lines, just list ... Thu, 22 Apr 2010 14:02:09 GMT Frederik Heber [423c7b] * molecuilder/src/tesselationhelpers.cpp (modified) Changed verbosity of "sum of angle"-warning in ... Thu, 22 Apr 2010 14:00:03 GMT Frederik Heber [1f2e46] * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_graphnode.cpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/info.cpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/unittests/logunittest.cpp (modified) * molecuilder/src/unittests/memoryallocatorunittest.cpp (modified) * molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) Huge change: Log() << Verbose(.) --> DoLog(.) && (Log() << Verbose(.) ... Wed, 21 Apr 2010 12:07:01 GMT Frederik Heber [c43766] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Rewrite of tesselation: treatment of degenerated triangles and ... Wed, 21 Apr 2010 11:46:40 GMT Frederik Heber [7d1633] * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/triangleintersectionlist.cpp (modified) * molecuilder/src/vector.cpp (modified) Made some remaining cout's "info Log() << Verbose(.)"'s ... - ... Wed, 21 Apr 2010 11:42:54 GMT Frederik Heber [ad98d4] * molecuilder/src/errorlogger.cpp (modified) * molecuilder/src/log.cpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/src/verbose.hpp (modified) FIX: errorLogger now has absolute verbosity (i.e. CRITIAL is whatever ... Tue, 20 Apr 2010 12:20:10 GMT Frederik Heber [60612f] * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Memory leak fixes and code cleanup after tesselation rewrite. - ... Tue, 20 Apr 2010 12:19:24 GMT Frederik Heber [0161a3] * molecuilder/src/bondgraph.cpp (modified) Fixed a warning in BondGraph::LoadBondLengthTable() due to missing ... Tue, 20 Apr 2010 10:35:15 GMT Frederik Heber [39f41d5] * molecuilder/src/tesselationhelpers.cpp (modified) WriteTecplotFile() checked whether Tesselation::LastTriangle is not NULL. Tue, 20 Apr 2010 10:34:43 GMT Frederik Heber [086db0] * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Rewrite of tesselation procedure: treatment of degenerated triangles. ... Tue, 20 Apr 2010 09:21:51 GMT Frederik Heber [342fbc9] * molecuilder/src/linkedcell.cpp (modified) BUGFIXES: LinkedCell::SetIndexToNode() had wrong boundaries in zero ... Fri, 16 Apr 2010 13:52:20 GMT Frederik Heber [adff53] * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) FIX: If multiple open lines can be chosen in AddTesselationLine(), ... Fri, 16 Apr 2010 12:26:16 GMT Frederik Heber [7c2ebb] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (modified) * molecuilder/src/unittests/tesselationunittest.cpp (modified) New approach to degenerated triangles: Recognize on creation and add ... Thu, 15 Apr 2010 15:22:51 GMT Frederik Heber [ce0de8] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (modified) * molecuilder/src/unittests/tesselationunittest.cpp (modified) Renamed AddCandidateTriangle() -> AddCandidatePolygon() - ... Thu, 15 Apr 2010 15:01:27 GMT Frederik Heber [e34098] * molecuilder/src/World.cpp (modified) FIX: string instead of string.h was included for strcpy() Thu, 15 Apr 2010 13:17:15 GMT Tillmann Crueger [298621] * molecuilder/src/Actions/Action.hpp (modified) Improved documentation for the Action pattern Thu, 15 Apr 2010 10:54:26 GMT Tillmann Crueger [e7ea64] * molecuilder/src/Makefile.am (modified) * molecuilder/src/SingleVector.cpp (modified) * molecuilder/src/SingleVector.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * molecuilder/src/unittests/vectorunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vector_ops.cpp (modified) Changed implementation of Vector to forward operations to contained ... Tue, 13 Apr 2010 13:22:42 GMT Tillmann Crueger [1f591b] * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Plane.cpp (modified) * molecuilder/src/SingleVector.cpp (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/test/ActOnAlltest.hpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/vectorunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vector_ops.cpp (modified) Prepared interface of Vector Class for transition to VectorComposites Mon, 12 Apr 2010 16:45:07 GMT Frederik Heber [4283d0] * molecuilder/src/boundary.cpp (modified) FIX: changed the order in which triangles are picked next during ... Mon, 12 Apr 2010 16:44:29 GMT Frederik Heber [a732ff] * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Changes to BoundaryTriangleSet and CandidateForTesselation. - ... Mon, 12 Apr 2010 16:25:50 GMT Frederik Heber [41c00d] * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) BUGFIX: LinkedCell::GetPointsInsideSphere() did not work if center of ... Fri, 09 Apr 2010 14:45:49 GMT Tillmann Crueger [0f55b2] * molecuilder/src/Makefile.am (modified) * molecuilder/src/Plane.cpp (modified) * molecuilder/src/Plane.hpp (modified) * molecuilder/src/SingleVector.cpp (added) * molecuilder/src/SingleVector.hpp (added) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Started work on the VectorComposites Fri, 09 Apr 2010 13:41:52 GMT Frederik Heber [f7e187] * molecuilder/src/unittests/LinkedCellUnitTest.cpp (modified) * molecuilder/src/unittests/LinkedCellUnitTest.hpp (modified) Full-working LinkedCellUnitTest. - new unit test for class ... Fri, 09 Apr 2010 13:41:26 GMT Frederik Heber [e760c1] * molecuilder/src/atom_particleinfo.cpp (modified) ofstream operators now check for Name being NULL and print NULL in ... Fri, 09 Apr 2010 13:39:03 GMT Frederik Heber [ef016c] * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) changes to LinkedCell::GetNeighbourBounds(), ... Fri, 09 Apr 2010 10:14:20 GMT heber [bd8561] * molecuilder/src/unittests/LinkedCellUnitTest.cpp (added) * molecuilder/src/unittests/LinkedCellUnitTest.hpp (added) * molecuilder/src/unittests/Makefile.am (modified) New Unit test for class LinkedCell. - this is just the skeleton, so ... Fri, 09 Apr 2010 09:55:39 GMT heber [6dd8d3] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (modified) * molecuilder/src/unittests/tesselation_insideoutsideunittest.hpp (modified) * molecuilder/src/unittests/tesselationunittest.cpp (modified) * molecuilder/src/unittests/tesselationunittest.hpp (modified) LinkedNodes is now declared inside LinkedCell and some new functions. ... Thu, 08 Apr 2010 14:28:21 GMT Tillmann Crueger [91b18cd] * molecuilder/src/Actions/Action.hpp (modified) More documentation for Action class added Thu, 08 Apr 2010 14:00:11 GMT Tillmann Crueger [abd4a1] * molecuilder/src/Actions/Action.cpp (modified) * molecuilder/src/Actions/Action.hpp (modified) * molecuilder/src/Actions/ActionHistory.cpp (modified) * molecuilder/src/Actions/ActionSequence.cpp (modified) * molecuilder/src/Actions/ActionSequence.hpp (modified) * molecuilder/src/Actions/MakroAction.cpp (modified) * molecuilder/src/Actions/Process.cpp (modified) * molecuilder/src/Actions/Process.hpp (modified) * molecuilder/src/unittests/ActionSequenceTest.cpp (modified) Added detailed documentation for the Action class Wed, 07 Apr 2010 15:45:38 GMT Tillmann Crueger [71910a] * molecuilder/src/Exceptions/CustomException.cpp (added) * molecuilder/src/Exceptions/CustomException.hpp (added) * molecuilder/src/Exceptions/LinearDependenceException.cpp (added) * molecuilder/src/Exceptions/LinearDependenceException.hpp (added) * molecuilder/src/Helpers/fast_functions.hpp (added) * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/Plane.cpp (added) * molecuilder/src/Plane.hpp (added) * molecuilder/src/UIElements/TextDialog.cpp (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/gslmatrix.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/leastsquaremin.cpp (modified) * molecuilder/src/linearsystemofequations.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.hpp (modified) * molecuilder/src/unittests/vectorunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vector_ops.cpp (added) * molecuilder/src/vector_ops.hpp (added) Made data internal data-structure of vector class private - ... Thu, 01 Apr 2010 18:52:09 GMT Frederik Heber [6250e5] * molecuilder/src/analysis_bonds.cpp (modified) * molecuilder/src/unittests/CountBondsUnitTest.cpp (modified) Enhanced CountHydrogenBridgeBonds() a bit. - new functions ... Thu, 01 Apr 2010 13:49:25 GMT Frederik Heber [794482] * molecuilder/src/analysis_bonds.cpp (modified) * molecuilder/src/analysis_bonds.hpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/unittests/CountBondsUnitTest.cpp (modified) Moved functions CountBondsOfTwo(), CountBondsOfThree() and ... Thu, 01 Apr 2010 09:35:42 GMT Frederik Heber [768125] * molecuilder/src/unittests/CountBondsUnitTest.cpp (modified) Added output of test cases for visualization. Is commented out ... Tue, 30 Mar 2010 18:52:14 GMT Frederik Heber [32526c] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/unittests/CountBondsUnitTest.cpp (added) * molecuilder/src/unittests/CountBondsUnitTest.hpp (added) * molecuilder/src/unittests/Makefile.am (modified) BUGFIX: CountHydrogenBridgeBonds() was half-broken, ... Fri, 26 Mar 2010 15:13:31 GMT Tillmann Crueger [770138] * molecuilder/src/Actions/Action.cpp (modified) * molecuilder/src/Actions/Action.hpp (modified) * molecuilder/src/Actions/ActionHistory.cpp (modified) * molecuilder/src/Actions/ActionHistory.hpp (modified) * molecuilder/src/Menu/ActionMenuItem.cpp (modified) * molecuilder/src/Menu/ActionMenuItem.hpp (modified) * molecuilder/src/Menu/MenuItem.cpp (modified) * molecuilder/src/Menu/MenuItem.hpp (modified) * molecuilder/src/Menu/TextMenu.cpp (modified) Added mechanism that deactivates undo and redo menupoint if not ... Thu, 25 Mar 2010 13:08:39 GMT Tillmann Crueger [cbc639] * molecuilder/src/UIElements/TextWindow.cpp (modified) Added undo and redo menupoints TODO: make it possible to disable ... Thu, 25 Mar 2010 13:01:35 GMT Tillmann Crueger [b787af] * molecuilder/src/UIElements/Dialog.cpp (modified) * molecuilder/src/UIElements/Dialog.hpp (modified) * molecuilder/src/UIElements/TextDialog.cpp (modified) * molecuilder/src/UIElements/TextDialog.hpp (modified) Repaired code that was broken by merge Thu, 25 Mar 2010 13:00:29 GMT Tillmann Crueger [eb129c] * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Merge branch 'StructureRefactoring' into MenuRefactoring Thu, 25 Mar 2010 12:59:20 GMT Tillmann Crueger [c3294f] * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Repaired broken unittest Thu, 25 Mar 2010 12:01:58 GMT Tillmann Crueger [fe3540] * molecuilder/src/Actions/Action.cpp (modified) * molecuilder/src/Actions/Action.hpp (modified) * molecuilder/src/Actions/ActionHistory.cpp (added) * molecuilder/src/Actions/ActionHistory.hpp (added) * molecuilder/src/Actions/ActionRegistry.cpp (modified) * molecuilder/src/Actions/ActionRegistry.hpp (modified) * molecuilder/src/Actions/ActionSequence.cpp (modified) * molecuilder/src/Actions/ActionSequence.hpp (modified) * molecuilder/src/Actions/AtomsCalculation_impl.hpp (modified) * molecuilder/src/Actions/Calculation.hpp (modified) * molecuilder/src/Actions/Calculation_impl.hpp (modified) * molecuilder/src/Actions/ErrorAction.cpp (modified) * molecuilder/src/Actions/ErrorAction.hpp (modified) * molecuilder/src/Actions/MakroAction.cpp (modified) * molecuilder/src/Actions/MakroAction.hpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.cpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.hpp (modified) * molecuilder/src/Actions/MethodAction.cpp (modified) * molecuilder/src/Actions/MethodAction.hpp (modified) * molecuilder/src/Actions/small_actions.cpp (modified) * molecuilder/src/Actions/small_actions.hpp (modified) * molecuilder/src/Descriptors/AtomDescriptor.cpp (modified) * molecuilder/src/Descriptors/AtomDescriptor.hpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor.cpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor.hpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * molecuilder/src/Descriptors/DescriptorBase.hpp (added) * molecuilder/src/Descriptors/DescriptorBase_impl.hpp (added) * molecuilder/src/Descriptors/MoleculeDescriptor.cpp (modified) * molecuilder/src/Descriptors/MoleculeDescriptor.hpp (modified) * molecuilder/src/Descriptors/SelectiveIterator.hpp (added) * molecuilder/src/Descriptors/SelectiveIterator_impl.hpp (added) * molecuilder/src/Helpers/Assert.cpp (added) * molecuilder/src/Helpers/Assert.hpp (added) * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/Menu/TextMenu.cpp (modified) * molecuilder/src/Menu/TextMenu.hpp (modified) * molecuilder/src/Patterns/Cacheable.hpp (modified) * molecuilder/src/Patterns/Observer.cpp (modified) * molecuilder/src/Patterns/Observer.hpp (modified) * molecuilder/src/Patterns/Singleton.hpp (added) * molecuilder/src/Patterns/Singleton_impl.hpp (added) * molecuilder/src/UIElements/TextWindow.cpp (modified) * molecuilder/src/UIElements/TextWindow.hpp (modified) * molecuilder/src/UIElements/UIFactory.cpp (modified) * molecuilder/src/UIElements/UIFactory.hpp (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/WorldIterators.cpp (deleted) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/atom_atominfo.cpp (modified) * molecuilder/src/atom_atominfo.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/element.hpp (modified) * molecuilder/src/errorlogger.cpp (modified) * molecuilder/src/errorlogger.hpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/leastsquaremin.hpp (modified) * molecuilder/src/log.cpp (modified) * molecuilder/src/logger.cpp (modified) * molecuilder/src/logger.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/types.hpp (added) * molecuilder/src/unittests/ActionSequenceTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/AtomDescriptorTest.cpp (modified) * molecuilder/src/unittests/AtomDescriptorTest.hpp (modified) * molecuilder/src/unittests/CacheableTest.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/MoleculeDescriptorTest.cpp (modified) * molecuilder/src/unittests/MoleculeDescriptorTest.hpp (modified) * molecuilder/src/unittests/ObserverTest.cpp (modified) * molecuilder/src/unittests/ObserverTest.hpp (modified) * molecuilder/src/unittests/SingletonTest.cpp (added) * molecuilder/src/unittests/SingletonTest.hpp (added) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.hpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/logunittest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Merge branch 'StructureRefactoring' into MenuRefactoring Thu, 25 Mar 2010 12:01:27 GMT Tillmann Crueger [8d9984] * molecuilder/src/Actions/Action.cpp (modified) * molecuilder/src/Actions/ActionHistory.cpp (added) * molecuilder/src/Actions/ActionHistory.hpp (added) * molecuilder/src/Actions/ActionRegistry.cpp (modified) * molecuilder/src/Actions/small_actions.cpp (modified) * molecuilder/src/Actions/small_actions.hpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/Menu/TextMenu.cpp (modified) * molecuilder/src/Menu/TextMenu.hpp (modified) * molecuilder/src/UIElements/TextDialog.cpp (modified) * molecuilder/src/UIElements/TextWindow.cpp (modified) * molecuilder/src/UIElements/TextWindow.hpp (modified) * molecuilder/src/builder.cpp (modified) Added full undo functioniality Thu, 25 Mar 2010 10:06:49 GMT Tillmann Crueger [521e29] * molecuilder/src/Actions/Action.cpp (modified) * molecuilder/src/Actions/Action.hpp (modified) * molecuilder/src/Actions/ActionSequence.cpp (modified) * molecuilder/src/Actions/ActionSequence.hpp (modified) * molecuilder/src/Actions/Calculation.hpp (modified) * molecuilder/src/Actions/Calculation_impl.hpp (modified) * molecuilder/src/Actions/ErrorAction.cpp (modified) * molecuilder/src/Actions/ErrorAction.hpp (modified) * molecuilder/src/Actions/MakroAction.cpp (modified) * molecuilder/src/Actions/MakroAction.hpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.cpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.hpp (modified) * molecuilder/src/Actions/MethodAction.cpp (modified) * molecuilder/src/Actions/MethodAction.hpp (modified) * molecuilder/src/Actions/small_actions.cpp (modified) * molecuilder/src/Actions/small_actions.hpp (modified) * molecuilder/src/UIElements/TextDialog.cpp (modified) * molecuilder/src/unittests/ActionSequenceTest.cpp (modified) Switched type of pointer used for ActionStates Wed, 24 Mar 2010 16:26:21 GMT Tillmann Crueger [0012e6] * molecuilder/src/Actions/Action.cpp (modified) * molecuilder/src/Actions/Action.hpp (modified) * molecuilder/src/Actions/ActionSequence.cpp (modified) * molecuilder/src/Actions/ActionSequence.hpp (modified) * molecuilder/src/Actions/Calculation.hpp (modified) * molecuilder/src/Actions/Calculation_impl.hpp (modified) * molecuilder/src/Actions/ErrorAction.cpp (modified) * molecuilder/src/Actions/ErrorAction.hpp (modified) * molecuilder/src/Actions/MakroAction.cpp (modified) * molecuilder/src/Actions/MakroAction.hpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.cpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.hpp (modified) * molecuilder/src/Actions/MethodAction.cpp (modified) * molecuilder/src/Actions/MethodAction.hpp (modified) * molecuilder/src/Actions/small_actions.cpp (modified) * molecuilder/src/Actions/small_actions.hpp (modified) * molecuilder/src/unittests/ActionSequenceTest.cpp (modified) Added methods that allow bookkeeping of actions for undo/redo methods Wed, 24 Mar 2010 10:27:37 GMT Tillmann Crueger [91379c] * molecuilder/src/Helpers/Assert.hpp (modified) Added detailed instruction on how to use ASSERT() Fri, 19 Mar 2010 16:55:28 GMT Tillmann Crueger [c8d1952] * molecuilder/src/Patterns/Cacheable.hpp (modified) Made the cacheable always recalculate when the owner is in the ... Fri, 19 Mar 2010 16:44:08 GMT Tillmann Crueger [239987d] * molecuilder/src/Patterns/Observer.cpp (modified) * molecuilder/src/Patterns/Observer.hpp (modified) * molecuilder/src/unittests/ObserverTest.cpp (modified) * molecuilder/src/unittests/ObserverTest.hpp (modified) Improved Observer Framework to include methods to report the state ... Fri, 19 Mar 2010 16:40:04 GMT Tillmann Crueger [9f3025] * molecuilder/src/Patterns/Cacheable.hpp (modified) Rebuilt Cacheables using the state pattern Fri, 19 Mar 2010 16:30:57 GMT Tillmann Crueger [36b8d8] * molecuilder/src/Helpers/Assert.cpp (modified) * molecuilder/src/Helpers/Assert.hpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) Added more functionality to custom asserts. - Asserts allow now ... Fri, 19 Mar 2010 15:42:58 GMT Frederik Heber [7e4dc3f] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (modified) * molecuilder/src/builder.cpp (modified) Implemented counting of bonds over all atoms. - new functions in ... Thu, 18 Mar 2010 15:38:56 GMT Frederik Heber [ac86192] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (modified) * molecuilder/src/builder.cpp (modified) Introduced CountHydrogenBridgeBonds() function. - ... Thu, 18 Mar 2010 14:48:20 GMT Tillmann Crueger [43ed42] * molecuilder/src/Helpers/Assert.cpp (added) * molecuilder/src/Helpers/Assert.hpp (added) * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/unittests/AtomDescriptorTest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Added custom Assert makro that allows ignoring asserts Thu, 18 Mar 2010 11:39:57 GMT Frederik Heber [800dc3] * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) Merge branch 'FixGeneralizeStoreAdjacencyToFile' into ... Thu, 18 Mar 2010 11:39:21 GMT Frederik Heber [6acc8e4] * molecuilder/src/bondgraph.hpp (modified) * molecuilder/src/defs.hpp (modified) Shifted BONDTHRESHOLD from defs.hpp over to bondgraph.hpp and lowered ... Thu, 18 Mar 2010 11:37:26 GMT Frederik Heber [31ccb6] * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) molecule::StoreAdjacencyToFile() and molecule::StoreBondsToFile() now ... Thu, 18 Mar 2010 11:33:54 GMT Frederik Heber [12f57b] * molecuilder/src/analysis_bonds.cpp (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/log.cpp (modified) * molecuilder/src/log.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/triangleintersectionlist.cpp (modified) * molecuilder/src/unittests/logunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) Log() and eLog() are prepended by a DoLog()/DoeLog() construct. - ... Thu, 18 Mar 2010 10:21:13 GMT Frederik Heber [f87c2a] * molecuilder/src/World.cpp (modified) BUGFIX: DefaultName of molecule was too small an array. - We saw ... Wed, 17 Mar 2010 15:19:56 GMT Tillmann Crueger [5738177] * molecuilder/src/Actions/AtomsCalculation_impl.hpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.cpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.hpp (modified) * molecuilder/src/Descriptors/AtomDescriptor.hpp (modified) * molecuilder/src/Descriptors/DescriptorBase.hpp (added) * molecuilder/src/Descriptors/DescriptorBase_impl.hpp (added) * molecuilder/src/Descriptors/MoleculeDescriptor.hpp (modified) * molecuilder/src/Descriptors/SelectiveIterator.hpp (added) * molecuilder/src/Descriptors/SelectiveIterator_impl.hpp (added) * molecuilder/src/Makefile.am (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/WorldIterators.cpp (deleted) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/unittests/AtomDescriptorTest.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Added a generic Iterator that can be used to iterate only over ... Fri, 12 Mar 2010 14:20:15 GMT Tillmann Crueger [d639c7] * molecuilder/src/periodentafel.cpp (modified) Fixed memory leak in periodentafel Fri, 12 Mar 2010 13:16:01 GMT Tillmann Crueger [5dba7a] * molecuilder/src/Actions/AtomsCalculation_impl.hpp (modified) * molecuilder/src/Actions/Calculation_impl.hpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor.cpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor.hpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/atom_atominfo.cpp (modified) * molecuilder/src/atom_atominfo.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/element.hpp (modified) * molecuilder/src/leastsquaremin.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/types.hpp (added) * molecuilder/src/unittests/AtomDescriptorTest.hpp (modified) * molecuilder/src/unittests/CacheableTest.cpp (modified) * molecuilder/src/unittests/MoleculeDescriptorTest.hpp (modified) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.hpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) Made the periodentafel use STL-containers instead of custom llists Thu, 11 Mar 2010 16:53:08 GMT Tillmann Crueger [1e0785] * molecuilder/src/Patterns/Singleton.hpp (modified) Improved documentation for Singleton