#
# ChangeLog for molecuilder/src/atom.hpp
#
# Generated by Trac 1.6
# Sep 22, 2025, 12:19:12 PM

Wed, 04 Nov 2009 19:56:04 GMT Frederik Heber <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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.

	- ...