# # ChangeLog for molecuilder/src/molecule_graph.cpp # # Generated by Trac 1.6 # Sep 21, 2025, 4:45:48 AM 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 ... 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 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 ... 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(.) ... 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 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. ... 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, 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 11:37:26 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. - ... Wed, 03 Mar 2010 14:53:07 GMT Frederik Heber [a83171] * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) Default molecule name can be set via command line, BUGFIX: ... Wed, 03 Mar 2010 10:13:19 GMT Frederik Heber [9565ec] * molecuilder/src/Makefile.am (modified) * molecuilder/src/World.cpp (added) * molecuilder/src/World.hpp (added) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (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/vector.cpp (modified) singleton class World introduced, contains only cell_size from class ... Tue, 02 Feb 2010 09:43:52 GMT Frederik Heber [6d0fcaa] * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_bondedparticle.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) Possibility to store all bonds to file added. So far we only could ... Wed, 16 Dec 2009 16:17:50 GMT Frederik Heber [16f34d] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/testsuite.at (modified) Fixing the testsuite. - Putting performCriticalExit() everywhere ... Mon, 23 Nov 2009 18:51:50 GMT Frederik Heber [3d4969] * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/helpers.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/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) Fixing ticket #18. - each eLog() << Verbose(0) is now followed by ... Wed, 04 Nov 2009 19:56:04 GMT Frederik Heber [543ce4] * molecuilder/src/Makefile.am (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.hpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_bondedparticle.hpp (modified) * molecuilder/src/atom_graphnode.cpp (modified) * molecuilder/src/atom_graphnode.hpp (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/element.cpp (modified) * molecuilder/src/element.hpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/errorlogger.cpp (moved) * molecuilder/src/errorlogger.hpp (moved) * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/log.cpp (modified) * molecuilder/src/log.hpp (modified) * molecuilder/src/logger.cpp (modified) * molecuilder/src/memoryallocator.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/molecule_pointcloud.cpp (modified) * molecuilder/src/molecule_template.hpp (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/tesselationhelpers.hpp (modified) * molecuilder/src/test/ActOnAlltest.hpp (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/Makefile.am (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/logunittest.cpp (modified) * molecuilder/src/unittests/memoryallocatorunittest.cpp (modified) * molecuilder/src/unittests/stackclassunittest.cpp (modified) * molecuilder/src/unittests/tesselationunittest.cpp (modified) * molecuilder/src/unittests/vectorunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) Huge change from ofstream * (const) out --> Log(). - first shift ... Wed, 04 Nov 2009 17:34:05 GMT Frederik Heber [20895b] * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Extension to the periodic boundary case for analysis_correlation.cpp ... Tue, 03 Nov 2009 16:34:31 GMT Frederik Heber [c1b4a4] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) "not working parsed molecule into subgraph splitting"-BUG fixed, ... Tue, 03 Nov 2009 14:34:02 GMT Frederik Heber [08b88b] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) Fixing not created adjacency list, partially fixing subgraph ... Tue, 03 Nov 2009 12:37:55 GMT Frederik Heber [8bc524] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/memoryallocator.hpp (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_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/unittests/memoryallocatorunittest.cpp (modified) Several memory bugfixes (thx valgrind). - main() - shortened case ... Mon, 02 Nov 2009 12:50:57 GMT Frederik Heber [df0520] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) Small changes. - VolumeOfConvexEnvelope() - setprecision corrected ... Fri, 30 Oct 2009 16:09:29 GMT Frederik Heber [245826] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) BondGraph is initialized within config::Load(), as it has to happen ... Fri, 30 Oct 2009 09:05:30 GMT Frederik Heber [5f697c] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_bondedparticle.hpp (modified) * molecuilder/src/bondgraph.cpp (added) * molecuilder/src/bondgraph.hpp (added) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (added) * molecuilder/src/unittests/bondgraphunittest.hpp (added) New class BondGraph. - BondGraph parses a file containing bond ... Tue, 27 Oct 2009 16:11:22 GMT Frederik Heber [a9b2a0a] * molecuilder/configure.ac (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/leastsquaremin.cpp (modified) * molecuilder/src/leastsquaremin.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Huge refactoring to make const what is const (ticket #38), continued. ... Sun, 18 Oct 2009 19:58:38 GMT Frederik Heber [99bed3] * molecuilder/src/molecule_graph.cpp (modified) Added BFSAccounting and DFSAccounting structures and all functions ... Sun, 18 Oct 2009 18:12:53 GMT Frederik Heber [e60069] * molecuilder/src/molecule_graph.cpp (modified) Refactored molecule::BuildInducedSubgraph() - new functions ... Sun, 18 Oct 2009 17:52:47 GMT Frederik Heber [9897787] * molecuilder/src/molecule_graph.cpp (modified) Refactored molecule::BreadthFirstSearchAdd() - new function: ... Sun, 18 Oct 2009 17:07:33 GMT Frederik Heber [312ba2] * molecuilder/src/molecule_graph.cpp (modified) Refactored CheckAdjacencyFileAgainstMolecule(). - new functions: ... Sun, 18 Oct 2009 16:35:25 GMT Frederik Heber [6e250f] * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) Removed ResetAllAtomNumbers(), replaced by templated ... Sun, 18 Oct 2009 16:09:26 GMT Frederik Heber [f444ce] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) Shifted molecuke::InitComponentNumbers() to atom::InitComponentNr. ... Sun, 18 Oct 2009 16:01:57 GMT Frederik Heber [c9f639] * molecuilder/src/molecule_graph.cpp (modified) Refactored molecule::CyclicStructureAnalysis() - new functions: ... Sun, 18 Oct 2009 15:13:46 GMT Frederik Heber [77894f] * molecuilder/src/molecule_graph.cpp (modified) Refactored molecule::DepthFirstSearchAnalysis() - new functions: ... Sun, 18 Oct 2009 14:51:38 GMT Frederik Heber [872b51] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/lists.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (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/unittests/Makefile.am (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (added) * molecuilder/src/unittests/listofbondsunittest.hpp (added) Huge refactoring: molecule::ListOfBondsPerAtom and ... Sat, 17 Oct 2009 19:47:58 GMT Frederik Heber [b0ee98] * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) Refactored CreateAdjacencyList(). - new auxiliary functions: ... Sat, 17 Oct 2009 17:06:42 GMT Frederik Heber [bee48d] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) Renamed and rewritten CreateAdjacencyList2(). - rename ... Fri, 09 Oct 2009 10:54:52 GMT Frederik Heber [17b3a5c] * molecuilder/src/ActOnAllUnitTest.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/element.hpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/leastsquaremin.cpp (modified) * molecuilder/src/leastsquaremin.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/lists.hpp (added) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.hpp (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_pointcloud.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) * molecuilder/src/tesselationunittest.hpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/src/verbose.hpp (modified) forward declarations used to untangle interdependet classes. - ... Mon, 05 Oct 2009 22:10:53 GMT Frederik Heber [f92d00] * molecuilder/src/Makefile.am (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/graph.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (added) * molecuilder/src/molecule_fragmentation.cpp (added) * molecuilder/src/molecule_geometry.cpp (added) * molecuilder/src/molecule_graph.cpp (added) * molecuilder/src/molecule_pointcloud.cpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/verbose.cpp (modified) class molecule implementation split up into six separate parts. - ...