# # ChangeLog for molecuilder/src/molecule_dynamics.cpp # # Generated by Trac 1.6 # Sep 22, 2025, 1:27:30 PM 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 ... 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 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 11:33:54 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, 10 Mar 2010 17:51:48 GMT Tillmann Crueger [4c60ef] * molecuilder/src/Actions/AtomsCalculation_impl.hpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.cpp (modified) * molecuilder/src/Descriptors/AtomDescriptor.cpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor.cpp (modified) * molecuilder/src/Descriptors/MoleculeDescriptor.cpp (modified) * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Patterns/Singleton.hpp (added) * molecuilder/src/Patterns/Singleton_impl.hpp (added) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/WorldIterators.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom_atominfo.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.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/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/MoleculeDescriptorTest.cpp (modified) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Added generic singleton Pattern that can be inherited to any class ... Fri, 26 Feb 2010 13:57:01 GMT Tillmann Crueger [dc5413] * molecuilder/configure.ac (modified) * molecuilder/src/Actions/small_actions.hpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/Patterns/Observer.cpp (modified) * molecuilder/src/Patterns/Observer.hpp (modified) * molecuilder/src/UIElements/TextStatusIndicator.cpp (added) * molecuilder/src/UIElements/TextStatusIndicator.hpp (added) * molecuilder/src/UIElements/TextWindow.cpp (modified) * molecuilder/src/UIElements/TextWindow.hpp (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/gslmatrix.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * 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/CacheableTest.cpp (modified) * molecuilder/src/unittests/DescriptorUnittest.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/ObserverTest.cpp (modified) * molecuilder/src/unittests/TestRunnerMain.cpp (added) * molecuilder/src/unittests/UnitTestMain.cpp (added) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/gslmatrixsymmetricunittest.cpp (modified) * molecuilder/src/unittests/gslmatrixunittest.cpp (modified) * molecuilder/src/unittests/gslvectorunittest.cpp (modified) * molecuilder/src/unittests/infounittest.cpp (modified) * molecuilder/src/unittests/linearsystemofequationsunittest.cpp (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/logunittest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) * molecuilder/src/unittests/memoryallocatorunittest.cpp (modified) * molecuilder/src/unittests/memoryusageobserverunittest.cpp (modified) * molecuilder/src/unittests/stackclassunittest.cpp (modified) * molecuilder/src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp (modified) * molecuilder/src/unittests/tesselation_insideoutsideunittest.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/tests/Tesselations/defs.in (modified) Merge branch 'FreddiesRefactoring' into StructureRefactoring ... Fri, 26 Feb 2010 12:40:52 GMT Tillmann Crueger [98a2987] * molecuilder/src/Actions/MakroAction.cpp (modified) * molecuilder/src/Actions/ManipulateAtomsProcess.cpp (modified) * molecuilder/src/Actions/Process.cpp (modified) * molecuilder/src/Descriptors/AtomDescriptor.cpp (modified) * molecuilder/src/Descriptors/AtomDescriptor_impl.hpp (modified) * molecuilder/src/Descriptors/AtomIdDescriptor.cpp (modified) * molecuilder/src/Descriptors/AtomIdDescriptor_impl.hpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor.cpp (modified) * molecuilder/src/Descriptors/AtomTypeDescriptor_impl.hpp (modified) * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/Menu/DisplayMenuItem.cpp (modified) * molecuilder/src/Menu/TextMenu.cpp (modified) * molecuilder/src/Patterns/Cacheable.hpp (modified) * molecuilder/src/UIElements/Dialog.cpp (modified) * molecuilder/src/UIElements/TextDialog.cpp (modified) * molecuilder/src/Views/MethodStringView.cpp (modified) * molecuilder/src/Views/MethodStringView.hpp (modified) * molecuilder/src/Views/StreamStringView.cpp (modified) * molecuilder/src/Views/StreamStringView.hpp (modified) * molecuilder/src/Views/StringView.hpp (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/WorldIterators.cpp (modified) * molecuilder/src/atom_particleinfo.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) Added -Wall flag and fixed several small hickups Fri, 26 Feb 2010 09:54:46 GMT Frederik Heber [81c129] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) FIX: Values in FindNonConvexBorder() and ... Thu, 25 Feb 2010 16:43:02 GMT Tillmann Crueger [8d9d38] * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.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/moleculelist.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/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) Made the world solely responsible for creating and erasing molecules. Sun, 10 Jan 2010 19:10:52 GMT Frederik Heber [00b5802] * molecuilder/src/molecule_dynamics.cpp (modified) BUGFIX - molecule::MinimiseConstrainedPotential() OldPotential was ... 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 ... Mon, 23 Nov 2009 18:22:33 GMT Frederik Heber [418117a] * 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/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/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/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/vector.cpp (modified) Verbosity corrected for ERROR and WARNING - present ERROR and ... 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 ... 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, 12 Oct 2009 10:30:02 GMT Frederik Heber [7c2f6b] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) Complete refactoring of molecule_dynamics.cpp - new small ... Fri, 09 Oct 2009 14:35:14 GMT Frederik Heber [104cf4] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) First half of molecule_dynamics.cpp is refactored into smaller parts. ... 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. - ... Wed, 07 Oct 2009 13:11:28 GMT Frederik Heber [567b7f] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) In molecule::OutputTrajectories() ActOnAllAtoms() with new function ... 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. - ...