#
# ChangeLog for src
#
# Generated by Trac 1.4.4
# Jan 15, 2025, 3:41:47 AM

Tue, 20 Oct 2009 08:54:51 GMT Frederik Heber <heber@…> [c75de1]
	* src/vector.hpp (modified)

	iostream was missing in vector includes.


Mon, 19 Oct 2009 13:09:29 GMT Frederik Heber <heber@…> [4455f4]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_template.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Huge Refactoring: class atom split up into several inherited classes. ...


Sun, 18 Oct 2009 19:58:38 GMT Frederik Heber <heber@…> [9eefda]
	* src/molecule_graph.cpp (modified)

	Added BFSAccounting and DFSAccounting structures and all functions ...


Sun, 18 Oct 2009 18:12:53 GMT Frederik Heber <heber@…> [43587e]
	* src/molecule_graph.cpp (modified)

	Refactored molecule::BuildInducedSubgraph()

	- new functions ...


Sun, 18 Oct 2009 17:52:47 GMT Frederik Heber <heber@…> [ce7cc5]
	* src/molecule_graph.cpp (modified)

	Refactored molecule::BreadthFirstSearchAdd()

	- new function: ...


Sun, 18 Oct 2009 17:07:33 GMT Frederik Heber <heber@…> [ba4170]
	* src/molecule_graph.cpp (modified)

	Refactored CheckAdjacencyFileAgainstMolecule().

	- new functions: ...


Sun, 18 Oct 2009 16:35:25 GMT Frederik Heber <heber@…> [df8b19]
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_template.hpp (modified)

	Removed ResetAllAtomNumbers(), replaced by templated ...


Sun, 18 Oct 2009 16:09:26 GMT Frederik Heber <heber@…> [2cc75c3]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Shifted molecuke::InitComponentNumbers() to atom::InitComponentNr.
 ...


Sun, 18 Oct 2009 16:01:57 GMT Frederik Heber <heber@…> [ef9aae]
	* src/molecule_graph.cpp (modified)

	Refactored molecule::CyclicStructureAnalysis()

	- new functions: ...


Sun, 18 Oct 2009 15:13:46 GMT Frederik Heber <heber@…> [174e0e]
	* src/molecule_graph.cpp (modified)

	Refactored molecule::DepthFirstSearchAnalysis()

	- new functions: ...


Sun, 18 Oct 2009 14:51:38 GMT Frederik Heber <heber@…> [266237]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/builder.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/lists.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/Makefile.am (modified)
	* src/unittests/listofbondsunittest.cpp (added)
	* src/unittests/listofbondsunittest.hpp (added)

	Huge refactoring: molecule::ListOfBondsPerAtom and ...


Sat, 17 Oct 2009 19:47:58 GMT Frederik Heber <heber@…> [b8b75d]
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Refactored CreateAdjacencyList().

	- new auxiliary functions: ...


Sat, 17 Oct 2009 19:46:28 GMT Frederik Heber <heber@…> [07051c]
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)

	Extended class LinkedCell to handle a relative offset to current ...


Sat, 17 Oct 2009 17:06:42 GMT Frederik Heber <heber@…> [44a59b]
	* src/builder.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Renamed and rewritten CreateAdjacencyList2().

	- rename ...


Sat, 17 Oct 2009 16:54:46 GMT Frederik Heber <heber@…> [09048c]
	* src/analysis_correlation.hpp (modified)
	* src/builder.cpp (modified)

	Added case 'C' to ParseCommandLineOptions with ...


Sat, 17 Oct 2009 16:49:59 GMT Frederik Heber <heber@…> [ad8b0d]
	* src/helpers.hpp (modified)
	* src/vector.cpp (modified)

	Templated version of flip now operates with references instead of ...


Sat, 17 Oct 2009 16:47:06 GMT Frederik Heber <heber@…> [3a9fe9]
	* src/config.cpp (modified)
	* src/config.hpp (modified)

	LoadMolecule externalized from Load()

	- new function ...


Sat, 17 Oct 2009 16:42:37 GMT Frederik Heber <heber@…> [b1f254]
	* src/analysis_correlation.cpp (modified)
	* src/analysis_correlation.hpp (modified)

	Functions to output correlations directly added.

	- new ...


Sat, 17 Oct 2009 05:49:05 GMT Frederik Heber <heber@…> [c144ed2]
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)

	flip() is now templated.
	Signed-off-by: Frederik Heber ...


Thu, 15 Oct 2009 08:10:10 GMT Frederik Heber <heber@…> [db6bf74]
	* src/builder.cpp (modified)
	* src/periodentafel.cpp (modified)

	Fixed two memory leaks.

	- FIX: if the element database could not be ...


Wed, 14 Oct 2009 11:18:14 GMT Frederik Heber <heber@…> [bbc338]
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)

	Unit tests AnalysisCorrelation is done.

	- four carbon atoms were ...


Wed, 14 Oct 2009 11:12:42 GMT Frederik Heber <heber@…> [6cd79d]
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)

	performCriticalExit() must not be defined static.

	Note that static ...


Wed, 14 Oct 2009 11:10:47 GMT Frederik Heber <heber@…> [a2028e]
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)

	UnitTest AnalysisCorrelationToSurface revealed two bugs:

	- BUGFIX: ...


Wed, 14 Oct 2009 11:01:47 GMT Frederik Heber <heber@…> [f74d08]
	* src/analysis_correlation.hpp (modified)

	Check whether map is not NULL in GetMinMax() and BinData(). ...


Tue, 13 Oct 2009 16:42:58 GMT Frederik Heber <heber@…> [c4d4df]
	* src/Makefile.am (modified)
	* src/analysis_correlation.cpp (added)
	* src/analysis_correlation.hpp (added)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/unittests/AnalysisCorrelationToPointUnitTest.cpp (added)
	* src/unittests/AnalysisCorrelationToPointUnitTest.hpp (added)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (added)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (added)
	* src/unittests/AnalysisPairCorrelationUnitTest.cpp (added)
	* src/unittests/AnalysisPairCorrelationUnitTest.hpp (added)
	* src/unittests/Makefile.am (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	Pair correlation analysis added.

	- new file ...


Tue, 13 Oct 2009 16:42:30 GMT Frederik Heber <heber@…> [93d120]
	* src/molecule_fragmentation.cpp (modified)

	Fixed broken test "Fragmentation - Fragmentation".

	- BUGFIX: Code ...


Mon, 12 Oct 2009 13:26:12 GMT Frederik Heber <heber@…> [407536]
	* src/molecule_fragmentation.cpp (modified)

	Refactored molecule::FragmentBOSSANOVA().

	- renamed functions: ...


Mon, 12 Oct 2009 13:05:46 GMT Frederik Heber <heber@…> [14e73a]
	* src/molecule_fragmentation.cpp (modified)

	Refactored molecule::PowerSetGenerator().

	- new functions are: ...


Mon, 12 Oct 2009 12:49:19 GMT Frederik Heber <heber@…> [d2943b]
	* src/molecule_fragmentation.cpp (modified)

	Rewritten molecule::molecule::SPFragmentGenerator()

	- new functions ...


Mon, 12 Oct 2009 12:10:43 GMT Frederik Heber <heber@…> [5034e1]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_template.hpp (modified)

	First half of molecule_fragmentation.cpp refactoring.

	- new ...


Mon, 12 Oct 2009 10:30:02 GMT Frederik Heber <heber@…> [4a7776a]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_template.hpp (modified)

	Complete refactoring of molecule_dynamics.cpp

	- new small ...


Fri, 09 Oct 2009 14:35:14 GMT Frederik Heber <heber@…> [ccd9f5]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)

	First half of molecule_dynamics.cpp is refactored into smaller parts. ...


Fri, 09 Oct 2009 12:30:54 GMT Frederik Heber <heber@…> [c111db]
	* Makefile.am (modified)
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/unittests/ActOnAllUnitTest.cpp (moved)
	* src/unittests/ActOnAllUnitTest.hpp (moved)
	* src/unittests/ActOnAlltest.hpp (moved)
	* src/unittests/Makefile.am (added)
	* src/unittests/memoryallocatorunittest.cpp (moved)
	* src/unittests/memoryallocatorunittest.hpp (moved)
	* src/unittests/memoryusageobserverunittest.cpp (moved)
	* src/unittests/memoryusageobserverunittest.hpp (moved)
	* src/unittests/tesselationunittest.cpp (moved)
	* src/unittests/tesselationunittest.hpp (moved)
	* src/unittests/vectorunittest.cpp (moved)
	* src/unittests/vectorunittest.hpp (moved)

	Merge branch 'new-delete-conversion' into CodeRefactoring
 ...


Fri, 09 Oct 2009 12:08:24 GMT Frederik Heber <heber@…> [87e2e39]
	* Makefile.am (modified)
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/unittests/Makefile.am (added)
	* src/unittests/memoryallocatorunittest.cpp (moved)
	* src/unittests/memoryallocatorunittest.hpp (moved)
	* src/unittests/memoryusageobserverunittest.cpp (moved)
	* src/unittests/memoryusageobserverunittest.hpp (moved)
	* src/unittests/tesselationunittest.cpp (moved)
	* src/unittests/tesselationunittest.hpp (moved)
	* src/unittests/vectorunittest.cpp (moved)
	* src/unittests/vectorunittest.hpp (moved)

	Merge branch 'new-delete-conversion' of ...


Fri, 09 Oct 2009 11:57:41 GMT Frederik Heber <heber@…> [49f802c]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_template.hpp (modified)

	Implementing templated iterators done for molecule.cpp

	- new ...


Fri, 09 Oct 2009 10:54:52 GMT Frederik Heber <heber@…> [f66195]
	* src/ActOnAllUnitTest.cpp (modified)
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/datacreator.cpp (modified)
	* src/datacreator.hpp (modified)
	* src/element.hpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/ellipsoid.hpp (modified)
	* src/graph.cpp (modified)
	* src/graph.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/leastsquaremin.cpp (modified)
	* src/leastsquaremin.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/lists.hpp (added)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/molecule_template.hpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)
	* src/periodentafel.cpp (modified)
	* src/periodentafel.hpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/tesselationunittest.hpp (modified)
	* src/vector.hpp (modified)
	* src/verbose.cpp (modified)
	* src/verbose.hpp (modified)

	forward declarations used to untangle interdependet classes.

	- ...


Wed, 07 Oct 2009 15:35:17 GMT metzler <metzler@…> [b9907c]
	* Makefile.am (modified)
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/unittests/Makefile.am (modified)

	Ticket 30: Put molecuilder unit tests in their own subfolder in src


Wed, 07 Oct 2009 15:04:23 GMT Saskia Metzler <metzler@…> [be90f1]
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/unittests/Makefile.am (added)
	* src/unittests/memoryallocatorunittest.cpp (moved)
	* src/unittests/memoryallocatorunittest.hpp (moved)
	* src/unittests/memoryusageobserverunittest.cpp (moved)
	* src/unittests/memoryusageobserverunittest.hpp (moved)
	* src/unittests/tesselationunittest.cpp (moved)
	* src/unittests/tesselationunittest.hpp (moved)
	* src/unittests/vectorunittest.cpp (moved)
	* src/unittests/vectorunittest.hpp (moved)

	temp commit


Wed, 07 Oct 2009 14:29:57 GMT Frederik Heber <heber@…> [e41951]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/molecule.cpp (modified)

	used forward declaration to untangle atom and bond declarations, ...


Wed, 07 Oct 2009 13:18:59 GMT Frederik Heber <heber@…> [23b830]
	* src/molecule.cpp (modified)

	molecule::CountElements() changed to use ...


Wed, 07 Oct 2009 13:16:13 GMT Frederik Heber <heber@…> [681a8a]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (modified)

	in molecule::OutputTrajectoriesXYZ() ActOnAllAtoms used by new ...


Wed, 07 Oct 2009 13:11:28 GMT Frederik Heber <heber@…> [fcd7b6]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_geometry.cpp (modified)

	In molecule::OutputTrajectories() ActOnAllAtoms() with new function ...


Tue, 06 Oct 2009 17:57:01 GMT Frederik Heber <heber@…> [e9f8f9]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_template.hpp (added)

	More functions of molecule now use templated iterators.

	- the ...


Tue, 06 Oct 2009 17:56:15 GMT Frederik Heber <heber@…> [ebcade]
	* src/builder.cpp (modified)
	* tests/Makefile.am (modified)
	* tests/regression/Fragmentation/1/pre/test.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment0.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment0.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragment1.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment1.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragment2.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment2.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragment3.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment3.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragment4.conf (added)
	* tests/regression/Fragmentation/2/post/BondFragment4.conf.xyz (added)
	* tests/regression/Fragmentation/2/post/BondFragmentAdjacency.dat (added)
	* tests/regression/Fragmentation/2/post/BondFragmentForces-Factors.dat (added)
	* tests/regression/Fragmentation/2/post/BondFragmentKeySets.dat (added)
	* tests/regression/Fragmentation/2/post/BondFragmentOrderAtSite.dat (added)
	* tests/regression/Fragmentation/2/post/BondFragmentTE-Factors.dat (added)
	* tests/regression/Fragmentation/2/post/test.conf (added)
	* tests/regression/Fragmentation/2/pre/test.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment0.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragment1.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragment2.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragment3.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragment4.conf (added)
	* tests/regression/Fragmentation/3/pre/BondFragment4.conf.xyz (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (added)
	* tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (added)
	* tests/regression/Fragmentation/3/pre/test.conf (added)
	* tests/regression/Graph/1/post/test.conf (added)
	* tests/regression/Graph/1/pre/test.conf (added)
	* tests/regression/Simple_configuration/1/post/test.xyz (added)
	* tests/regression/Simple_configuration/2/post/test.conf (added)
	* tests/regression/Simple_configuration/2/post/test.conf.xyz (added)
	* tests/regression/Simple_configuration/2/pre/test.xyz (added)
	* tests/regression/Simple_configuration/3/post/test.conf (added)
	* tests/regression/Simple_configuration/3/post/test.conf.xyz (added)
	* tests/regression/Simple_configuration/4/post/test.conf (added)
	* tests/regression/Simple_configuration/4/post/test.conf.xyz (added)
	* tests/regression/Simple_configuration/4/pre/test.conf (added)
	* tests/regression/Simple_configuration/5/post/test.conf (added)
	* tests/regression/Simple_configuration/5/post/test.conf.xyz (added)
	* tests/regression/Simple_configuration/5/pre/test.conf (added)
	* tests/regression/Simple_configuration/6/pre/empty.conf (added)
	* tests/regression/Simple_configuration/7/pre/test.conf (added)
	* tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (added)
	* tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/1/post/test.conf (added)
	* tests/regression/Tesselation/1/pre/test.conf (added)
	* tests/regression/Tesselation/2/post/ConvexEnvelope.dat (added)
	* tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (added)
	* tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/2/post/test.conf (added)
	* tests/regression/Tesselation/2/pre/test.conf (added)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (added)
	* tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/3/post/tecplot.phy (added)
	* tests/regression/Tesselation/3/post/test.conf (added)
	* tests/regression/Tesselation/3/pre/test.conf (added)
	* tests/regression/Tesselation/4/post/NonConvexEnvelope.dat (added)
	* tests/regression/Tesselation/4/post/NonConvexEnvelope.r3d (added)
	* tests/regression/Tesselation/4/post/test.conf (added)
	* tests/regression/Tesselation/4/pre/test.conf (added)
	* tests/testsuite.at (modified)

	Extended the testsuite to encompass the vital areas of molecuilder.
 ...


Tue, 06 Oct 2009 11:15:50 GMT metzler <metzler@…> [21b9c3]
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/memoryusageobserverunittest.cpp (modified)
	* src/memoryusageobserverunittest.hpp (modified)

	#22 Write a critical exit function


Mon, 05 Oct 2009 22:10:53 GMT Frederik Heber <heber@…> [cee0b57]
	* src/Makefile.am (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.hpp (modified)
	* src/graph.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (added)
	* src/molecule_fragmentation.cpp (added)
	* src/molecule_geometry.cpp (added)
	* src/molecule_graph.cpp (added)
	* src/molecule_pointcloud.cpp (added)
	* src/moleculelist.cpp (modified)
	* src/verbose.cpp (modified)

	class molecule implementation split up into six separate parts.

	- ...


Mon, 05 Oct 2009 22:09:51 GMT Frederik Heber <heber@…> [d09ff7]
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	new function Vector::WrapPeriodically() and ...


Mon, 05 Oct 2009 22:08:57 GMT Frederik Heber <heber@…> [e65246]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/molecule.cpp (moved)
	* src/molecule.hpp (moved)

	New function atom::CorrectFactor() and atom::EqualsFather().

	- are ...


Mon, 05 Oct 2009 21:14:28 GMT Frederik Heber <heber@…> [eaee7f]
	* src/ActOnAllUnitTest.cpp (modified)
	* src/ActOnAlltest.hpp (modified)

	even the class of the member function can be templated, see ...


Mon, 05 Oct 2009 20:51:24 GMT Frederik Heber <heber@…> [33f9f7]
	* src/ActOnAllUnitTest.cpp (modified)
	* src/ActOnAllUnitTest.hpp (modified)
	* src/ActOnAlltest.hpp (modified)
	* src/Makefile.am (modified)
	* src/molecules.hpp (modified)

	Member functions of Vector class may be called while going over an ...


Mon, 05 Oct 2009 18:45:06 GMT Frederik Heber <heber@…> [13a574]
	* configure.ac (modified)
	* m4/ax_boost_base.m4 (added)
	* m4/ax_boost_program_options.m4 (added)
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/defs.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/memoryallocator.hpp (added)
	* src/memoryallocatorunittest.cpp (added)
	* src/memoryallocatorunittest.hpp (added)
	* src/memoryusageobserver.cpp (added)
	* src/memoryusageobserver.hpp (added)
	* src/memoryusageobserverunittest.cpp (added)
	* src/memoryusageobserverunittest.hpp (added)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationunittest.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (modified)
	* src/vectorunittest.hpp (modified)
	* tests/testsuite.at (modified)

	Merge branch 'ConvexHull' into ActOnAll

	Conflicts:

	        ...


Mon, 05 Oct 2009 18:43:43 GMT Frederik Heber <heber@…> [fa861b]
	* configure.ac (modified)
	* m4/ax_boost_base.m4 (added)
	* m4/ax_boost_program_options.m4 (added)
	* src/Makefile.am (modified)

	Included BOOST library MPL into autoconf setup.


Mon, 05 Oct 2009 17:21:58 GMT Frederik Heber <heber@…> [c26f44]
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/builder.cpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/molecules.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationunittest.cpp (modified)
	* tests/testsuite.at (modified)

	Fixed testsuite, removed some minor bugs.

	- ...


Mon, 05 Oct 2009 16:05:53 GMT Frederik Heber <heber@…> [a33931]
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/defs.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/memoryallocator.hpp (added)
	* src/memoryallocatorunittest.cpp (added)
	* src/memoryallocatorunittest.hpp (added)
	* src/memoryusageobserver.cpp (added)
	* src/memoryusageobserver.hpp (added)
	* src/memoryusageobserverunittest.cpp (added)
	* src/memoryusageobserverunittest.hpp (added)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/parser.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (modified)
	* src/vectorunittest.hpp (modified)

	Merge branch 'ConcaveHull' into ConvexHull

	Conflicts:

	        ...


Mon, 05 Oct 2009 15:43:25 GMT Frederik Heber <heber@…> [d3dfe18]
	* src/atom.cpp (modified)
	* src/bond.cpp (modified)

	new/delete conversion.

	mode change only, nothing else.


Mon, 05 Oct 2009 15:42:20 GMT Frederik Heber <heber@…> [5417c5]
	* src/analyzer.cpp (modified)

	New/delete conversion.

	82: "main" missing in msg


Mon, 05 Oct 2009 14:59:11 GMT Frederik Heber <heber@…> [c0917c]
	* src/builder.cpp (modified)
	* src/memoryusageobserver.cpp (modified)
	* src/memoryusageobserver.hpp (modified)
	* src/memoryusageobserverunittest.cpp (modified)
	* src/memoryusageobserverunittest.hpp (modified)

	Merge branch 'ConcaveHull' of ...


Mon, 05 Oct 2009 14:50:43 GMT metzler <metzler@…> [b66c22]
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (added)
	* src/memoryusageobserver.hpp (added)
	* src/memoryusageobserverunittest.cpp (added)
	* src/memoryusageobserverunittest.hpp (added)

	#19 Observe memory usage


Mon, 05 Oct 2009 14:35:06 GMT Frederik Heber <heber@…> [41194a]
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/config.cpp (modified)
	* src/defs.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/memoryallocator.hpp (added)
	* src/memoryallocatorunittest.cpp (added)
	* src/memoryallocatorunittest.hpp (added)
	* src/memoryusageobserver.cpp (added)
	* src/memoryusageobserver.hpp (added)
	* src/memoryusageobserverunittest.cpp (added)
	* src/memoryusageobserverunittest.hpp (added)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/parser.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/vector.cpp (modified)

	Merge branch 'ConcaveHull' of ...


Mon, 05 Oct 2009 14:31:35 GMT Frederik Heber <heber@…> [aba92d]
	* src/ActOnAllUnitTest.cpp (added)
	* src/ActOnAllUnitTest.hpp (added)
	* src/ActOnAlltest.hpp (added)
	* src/Makefile.am (modified)

	ActOnAll is a test (not in the molecuilder source tree, but as a ...


Mon, 05 Oct 2009 14:12:18 GMT metzler <metzler@…> [c30180]
	* src/Makefile.am (modified)
	* src/builder.cpp (modified)
	* src/helpers.cpp (modified)
	* src/memoryallocator.hpp (modified)
	* src/memoryusageobserver.cpp (added)
	* src/memoryusageobserver.hpp (added)
	* src/memoryusageobserverunittest.cpp (added)
	* src/memoryusageobserverunittest.hpp (added)

	#19 Observe memory usage


Fri, 02 Oct 2009 15:19:51 GMT Frederik Heber <heber@…> [7dea7c]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)

	Fixes to the (Non)ConvexTesselation, working with ...


Fri, 02 Oct 2009 15:18:43 GMT Frederik Heber <heber@…> [e4a379]
	* src/vector.cpp (modified)

	FIX of Vector::GetIntersectionWithPlane()

	- Direction was not ...


Fri, 02 Oct 2009 13:02:26 GMT Frederik Heber <heber@…> [0227a9]
	* src/tesselationunittest.cpp (added)
	* src/tesselationunittest.hpp (added)

	new tesselation unit test

	- excluded some more files (mostly ecut ...


Mon, 28 Sep 2009 20:00:33 GMT Frederik Heber <heber@…> [57066a]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)

	Various fixes and attempt to get convex hull working.

	- ...


Mon, 28 Sep 2009 18:46:25 GMT Frederik Heber <heber@…> [91e7e4a]
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)

	new function CalculateVolumeofGeneralTetraeder().

	- is used when a ...


Mon, 28 Sep 2009 18:43:02 GMT Frederik Heber <heber@…> [d52e70c]
	* src/atom.cpp (modified)
	* src/config.cpp (modified)
	* src/vectorunittest.cpp (modified)

	Small fixes.

	- FIX: atom::~atom(): Name is free'd
	- ...


Mon, 28 Sep 2009 18:41:52 GMT Frederik Heber <heber@…> [f7f7a4]
	* src/builder.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Implemenation of embedding merge, untested. LinearInterpolation now ...


Mon, 28 Sep 2009 18:38:06 GMT Frederik Heber <heber@…> [8cd903]
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)

	LinkedCell has another constructor initialised from LinkedNodes (list ...


Mon, 28 Sep 2009 18:31:58 GMT Frederik Heber <heber@…> [d04966]
	* src/Makefile.am (modified)
	* src/tesselationunittest.cpp (added)
	* src/tesselationunittest.hpp (added)

	Added Tesselation unit test

	- new file tesselationunittest with ...


Mon, 21 Sep 2009 11:48:42 GMT Saskia Metzler <metzler@…> [29812d]
	* src/Makefile.am (modified)
	* src/analyzer.cpp (modified)
	* src/atom.cpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/defs.hpp (modified)
	* src/helpers.cpp (modified)
	* src/helpers.hpp (modified)
	* src/joiner.cpp (modified)
	* src/memoryallocator.hpp (added)
	* src/memoryallocatorunittest.cpp (added)
	* src/memoryallocatorunittest.hpp (added)
	* src/moleculelist.cpp (modified)
	* src/molecules.cpp (modified)
	* src/parser.cpp (modified)
	* src/stackclass.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/vector.cpp (modified)

	Ticket 11: use templates and/or traits to fix Malloc/ReAlloc-Free ...


Fri, 21 Aug 2009 12:19:08 GMT Frederik Heber <heber@…> [065e82]
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	FIX: Tesselation::RemovePointFromTesselatedSurface() is working ...


Fri, 21 Aug 2009 12:17:52 GMT Frederik Heber <heber@…> [d4fa23]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)

	New function RemoveAllBoundaryPoints() for sequentially removing all ...


Fri, 21 Aug 2009 12:17:25 GMT Frederik Heber <heber@…> [9ba9ee]
	* src/molecules.cpp (modified)

	formula typo in molecule::PrincipalAxisSystem() fixed


Thu, 20 Aug 2009 15:40:49 GMT Saskia Metzler <metzler@…> [89c8b2]
	* src/atom.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (modified)
	* src/vectorunittest.hpp (modified)

	Ticket 17: Write new function molecule::CopyMoleculeFromSubRegion()


Thu, 20 Aug 2009 11:35:19 GMT Saskia Metzler <metzler@…> [78b73c]
	* src/vector.cpp (modified)
	* src/vectorunittest.cpp (modified)
	* src/vectorunittest.hpp (modified)

	Ticket 16: Unit tests for Vector::RotateVector(), additionally fixing ...


Thu, 20 Aug 2009 07:48:07 GMT Frederik Heber <heber@…> [34e0592]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/config.hpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)

	Merge branch 'ConcaveHull' of ...


Wed, 19 Aug 2009 14:31:29 GMT Frederik Heber <heber@…> [1d9b7aa]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)

	Smaller fixes, but convex tesselation not working yet

	- ...


Wed, 19 Aug 2009 12:30:21 GMT Frederik Heber <heber@…> [99c484]
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/leastsquaremin.cpp (added)
	* src/leastsquaremin.hpp (added)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (added)
	* src/vectorunittest.hpp (added)

	Merge branch 'VectorUnitTest' into ConcaveHull


Wed, 19 Aug 2009 12:23:05 GMT Frederik Heber <heber@…> [ef9df36]
	* src/Makefile.am (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (modified)
	* src/vectorunittest.hpp (modified)

	VectorUnitTest extended to Projections and Line intersection, some ...


Wed, 19 Aug 2009 12:22:08 GMT Frederik Heber <heber@…> [658efb]
	* src/boundary.cpp (modified)
	* src/builder.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)

	Replaced Vector::Projection() by Vector::ScalarProduct()

	- ...


Tue, 18 Aug 2009 13:59:11 GMT Saskia Metzler <metzler@…> [7c14ec]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Ticket 15: new function RemoveDegeneratedTriangles()
	Added functions ...


Tue, 18 Aug 2009 08:48:06 GMT Frederik Heber <heber@…> [54a746]
	* configure.ac (modified)
	* src/Makefile.am (modified)
	* src/leastsquaremin.cpp (added)
	* src/leastsquaremin.hpp (added)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)
	* src/vectorunittest.cpp (added)
	* src/vectorunittest.hpp (added)

	Incorporation of Unit test on class Vector.

	- new file ...


Tue, 18 Aug 2009 08:42:39 GMT Frederik Heber <heber@…> [0077b5]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Further bugfixes to three-step-procedure in convex envelope, not yet ...


Mon, 17 Aug 2009 13:20:16 GMT Saskia Metzler <metzler@…> [f1cccd]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)

	Ticket 14: Rename .._.. functions in boundary.cpp


Mon, 17 Aug 2009 10:48:03 GMT Frederik Heber <heber@…> [093645]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)

	Rewrite of ConvexizeNonconvexEnvelope() with three steps: Remove ...


Mon, 17 Aug 2009 10:30:53 GMT Frederik Heber <heber@…> [16d866]
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	documentation, some renames (..Triangle.. -> ..Tesselation..) and a ...


Mon, 17 Aug 2009 10:29:03 GMT Frederik Heber <heber@…> [86381b]
	* src/builder.cpp (modified)

	Sorted the menu list in ParseCommandLineParamaters() and print volume ...


Mon, 10 Aug 2009 16:11:47 GMT Frederik Heber <heber@…> [08ef35]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	New function ConvexizeNonconvexEnvelope() to calculate the volume of ...


Sat, 08 Aug 2009 19:25:28 GMT Frederik Heber <heber@…> [5c7bf8]
	* src/boundary.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	BUGFIXes to Find_convex_... and Find_non_convex_... algorithms

	- ...


Sat, 08 Aug 2009 19:22:28 GMT Frederik Heber <heber@…> [8bb475f]
	* src/builder.cpp (modified)

	ParseCommandLineOptions(), NonConvex tesselation is now clocked.


Sat, 08 Aug 2009 19:19:23 GMT Frederik Heber <heber@…> [46670d]
	* src/vector.cpp (modified)
	* src/vector.hpp (modified)

	BUGFIXES to some vector functions.

	- Vector::MakeNormalVector() ... ...


Sat, 08 Aug 2009 19:17:51 GMT Frederik Heber <heber@…> [055861]
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)

	new stream operator with just one parameter and virtual destructor


Fri, 07 Aug 2009 12:50:27 GMT Frederik Heber <heber@…> [8d31ce]
	* src/TAGS (deleted)

	excluded unimportant stuff, depcomp and install-sh from util


Fri, 07 Aug 2009 12:48:06 GMT Frederik Heber <heber@…> [133d56]
	* src/boundary.cpp (modified)

	output of terminating special property comment in .r3d file had no ...


Fri, 07 Aug 2009 12:46:27 GMT Frederik Heber <heber@…> [1999d8]
	* src/linkedcell.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	BUGFIX: PointCloud implementation in molecule stopped one before ...


Fri, 07 Aug 2009 09:13:21 GMT Frederik Heber <heber@…> [f3278b]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/builder.cpp (modified)
	* src/molecules.cpp (modified)
	* src/molecules.hpp (modified)

	Test case of filling a simulation domain with water included.


Fri, 07 Aug 2009 09:12:19 GMT Frederik Heber <heber@…> [1953f9]
	* src/tesselation.cpp (modified)

	FIX: We have to check whether we create a degenerate triangle also on ...


Tue, 04 Aug 2009 13:55:11 GMT Frederik Heber <heber@…> [9f97c5]
	* src/builder.cpp (modified)

	FillWithMolecule() for testing built into ParseCommandLine()


Tue, 04 Aug 2009 13:53:55 GMT Frederik Heber <heber@…> [ef0e6d]
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)

	find_(non)_convex_border TesselStruct is not free'd anymore, ...