# # ChangeLog for molecuilder/src/atom.hpp # # Generated by Trac 1.6 # Sep 22, 2025, 7:59:04 AM 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, 04 Mar 2010 10:33:44 GMT Tillmann Crueger [f058ef] * molecuilder/src/Descriptors/MoleculeIdDescriptor.cpp (added) * molecuilder/src/Descriptors/MoleculeIdDescriptor.hpp (added) * molecuilder/src/Descriptors/MoleculeIdDescriptor_impl.hpp (added) * molecuilder/src/Makefile.am (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/unittests/AtomDescriptorTest.cpp (moved) * molecuilder/src/unittests/AtomDescriptorTest.hpp (moved) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/MoleculeDescriptorTest.cpp (added) * molecuilder/src/unittests/MoleculeDescriptorTest.hpp (added) * molecuilder/src/unittests/atomsCalculationTest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Added methods to query Molecules by ID Wed, 03 Mar 2010 17:47:40 GMT Tillmann Crueger [3746aeb] * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) Added mechanisms that allow reuse of IDs and changing Ids of Atoms Wed, 24 Feb 2010 16:21:12 GMT Tillmann Crueger [7bfc19] * molecuilder/src/Legacy/oldmenu.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/atom_particleinfo.cpp (modified) * molecuilder/src/atom_particleinfo.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/lists.cpp (added) * molecuilder/src/lists.hpp (modified) * molecuilder/src/molecule.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/DescriptorUnittest.cpp (modified) * molecuilder/src/unittests/DescriptorUnittest.hpp (modified) * molecuilder/src/unittests/Makefile.am (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) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/manipulateAtomsTest.cpp (modified) Made the world solely responsible for creating and destroying atoms. 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, 27 Oct 2009 08:54:44 GMT Frederik Heber [94d0ad] * 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_particleinfo.cpp (modified) * molecuilder/src/atom_particleinfo.hpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/atom_trajectoryparticle.hpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Begun with ticket #38 (make const what is const). - basically all ... Tue, 20 Oct 2009 08:55:17 GMT Frederik Heber [2e2a70] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/atom_atominfo.cpp (added) * molecuilder/src/atom_atominfo.hpp (added) * molecuilder/src/atom_bondedparticle.cpp (added) * molecuilder/src/atom_bondedparticle.hpp (added) * molecuilder/src/atom_bondedparticleinfo.cpp (added) * molecuilder/src/atom_bondedparticleinfo.hpp (added) * molecuilder/src/atom_graphnode.cpp (added) * molecuilder/src/atom_graphnode.hpp (added) * molecuilder/src/atom_graphnodeinfo.cpp (added) * molecuilder/src/atom_graphnodeinfo.hpp (added) * molecuilder/src/atom_particleinfo.cpp (added) * molecuilder/src/atom_particleinfo.hpp (added) * molecuilder/src/atom_trajectoryparticle.cpp (added) * molecuilder/src/atom_trajectoryparticle.hpp (added) * molecuilder/src/atom_trajectoryparticleinfo.cpp (added) * molecuilder/src/atom_trajectoryparticleinfo.hpp (added) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Refactored atom.cpp into multiple files. After the class atom was ... Mon, 19 Oct 2009 13:09:29 GMT Frederik Heber [6b937bd] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Huge Refactoring: class atom split up into several inherited classes. ... 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 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 ... Mon, 12 Oct 2009 12:10:43 GMT Frederik Heber [ff9879] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) First half of molecule_fragmentation.cpp refactoring. - new ... 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 11:57:41 GMT Frederik Heber [3efb4a] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_template.hpp (modified) Implementing templated iterators done for molecule.cpp - new ... 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 14:29:57 GMT Frederik Heber [70b7aa] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/molecule.cpp (modified) used forward declaration to untangle atom and bond declarations, ... Wed, 07 Oct 2009 13:16:13 GMT Frederik Heber [0cd3b2] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.cpp (modified) in molecule::OutputTrajectoriesXYZ() ActOnAllAtoms used by new ... 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 ... Tue, 06 Oct 2009 17:57:01 GMT Frederik Heber [8ffe32] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_template.hpp (added) More functions of molecule now use templated iterators. - the ... Mon, 05 Oct 2009 22:08:57 GMT Frederik Heber [dcbdf2] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/molecule.cpp (moved) * molecuilder/src/molecule.hpp (moved) New function atom::CorrectFactor() and atom::EqualsFather(). - are ... Sat, 08 Aug 2009 19:17:51 GMT Frederik Heber [e0521b] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) new stream operator with just one parameter and virtual destructor Mon, 03 Aug 2009 20:21:05 GMT Frederik Heber [f4a346] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (added) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (added) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (added) * molecuilder/src/element.cpp (modified) * molecuilder/src/element.hpp (added) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (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 (added) * molecuilder/src/tesselation.hpp (added) * molecuilder/src/tesselationhelpers.cpp (added) * molecuilder/src/tesselationhelpers.hpp (added) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.hpp (added) Merge branch 'TesselationRefactoring' into ConcaveHull Conflicts: ... Mon, 03 Aug 2009 15:09:12 GMT Frederik Heber [4dca8e] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/element.hpp (added) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/verbose.hpp (added) definitions for class element and verbose moved to their own header ... Mon, 03 Aug 2009 14:48:42 GMT Frederik Heber [834ff3] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (added) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (added) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (added) * molecuilder/src/tesselation.hpp (added) * molecuilder/src/tesselationhelpers.cpp (added) * molecuilder/src/tesselationhelpers.hpp (added) * molecuilder/src/vector.hpp (modified) Huge refactoring of Tesselation routines, but not finished yet. - ...