#
# ChangeLog for /
#
# Generated by Trac 1.6
# Dec 7, 2025, 2:53:49 PM

Sun, 10 Jan 2010 19:15:01 GMT Frederik Heber <heber@…> [901774]
	* molecuilder/src/unittests/Makefile.am (modified)

	libgslwrapper.a added to LDADD of most tests.

	Since Vector class ...


Sun, 10 Jan 2010 19:12:40 GMT Frederik Heber <heber@…> [51a8a1]
	* molecuilder/src/tesselationhelpers.cpp (modified)

	BUGFIX - GetCenterOfSphere(): condition were not put correctly in ...


Sun, 10 Jan 2010 19:10:52 GMT Frederik Heber <heber@…> [00b5802]
	* molecuilder/src/molecule_dynamics.cpp (modified)

	BUGFIX - molecule::MinimiseConstrainedPotential() OldPotential was ...


Sun, 10 Jan 2010 19:09:56 GMT Frederik Heber <heber@…> [70e11d]
	* molecuilder/src/gslmatrix.hpp (modified)
	* molecuilder/src/gslvector.hpp (modified)
	* molecuilder/src/linearsystemofequations.hpp (modified)

	Inclusion of config.h was missing.

	This caused a bug with GSL's ...


Sun, 10 Jan 2010 19:09:14 GMT Frederik Heber <heber@…> [2c69a9]
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (modified)

	cstdlib header was missing, necessary for free, malloc and calloc
 ...


Sun, 10 Jan 2010 19:05:34 GMT Frederik Heber <heber@…> [e6fe8a]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/joiner.cpp (modified)
	* molecuilder/src/molecule.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/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* molecuilder/src/unittests/analysisbondsunittest.cpp (modified)
	* molecuilder/src/unittests/bondgraphunittest.cpp (modified)
	* molecuilder/src/unittests/listofbondsunittest.cpp (modified)
	* molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* molecuilder/src/unittests/tesselationunittest.cpp (modified)

	cstring header was missing in files, supplying definition of strlen, ...


Fri, 08 Jan 2010 17:48:35 GMT Frederik Heber <heber@…> [247d49]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/linearsystemofequations.cpp (added)
	* molecuilder/src/linearsystemofequations.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/linearsystemofequationsunittest.cpp (added)
	* molecuilder/src/unittests/linearsystemofequationsunittest.hpp (added)

	Wrapper class for gsl_linalg along with working Unit test.

	- new ...


Fri, 08 Jan 2010 17:46:51 GMT Frederik Heber <heber@…> [e651e7]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/gslmatrix.cpp (added)
	* molecuilder/src/gslmatrix.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/gslmatrixsymmetricunittest.cpp (added)
	* molecuilder/src/unittests/gslmatrixsymmetricunittest.hpp (added)
	* molecuilder/src/unittests/gslmatrixunittest.cpp (added)
	* molecuilder/src/unittests/gslmatrixunittest.hpp (added)

	Wrapper class for gsl_matrix along with working Unit test.

	- new ...


Fri, 08 Jan 2010 17:44:51 GMT Frederik Heber <heber@…> [22b47e]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/gslvector.cpp (added)
	* molecuilder/src/gslvector.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/gslvectorunittest.cpp (added)
	* molecuilder/src/unittests/gslvectorunittest.hpp (added)

	Wrapper class for gsl_vector along with working Unit test.

	- new ...


Fri, 08 Jan 2010 14:04:22 GMT Frederik Heber <heber@…> [a1acc5]
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (modified)
	* molecuilder/src/vector.cpp (modified)

	Attempt to fix the tesselation::IsInnerPoint().

	We try the ...


Tue, 29 Dec 2009 14:48:49 GMT Frederik Heber <heber@…> [eda56a]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (added)
	* molecuilder/src/unittests/tesselation_insideoutsideunittest.hpp (added)
	* molecuilder/src/unittests/tesselationunittest.cpp (modified)
	* molecuilder/src/unittests/tesselationunittest.hpp (modified)

	Changes to FindClosest...ToVector() and use of ..Map,..Set,..List ...


Sat, 19 Dec 2009 19:32:24 GMT Frederik Heber <heber@…> [ff4611]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_pointcloud.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)

	Attempt to fix the embedding.

	Basically it would be working, but ...


Sat, 19 Dec 2009 19:31:34 GMT Frederik Heber <heber@…> [f78203]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecule_geometry.cpp (modified)

	Smaller fixes.

	- analysis_correlation.cpp: Info objects created at ...


Thu, 17 Dec 2009 17:52:45 GMT Frederik Heber <heber@…> [16807e]
	* .gitignore (modified)
	* Makefile.am (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/info.cpp (added)
	* molecuilder/src/info.hpp (added)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/parser.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/infounittest.cpp (added)
	* molecuilder/src/unittests/infounittest.hpp (added)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/src/verbose.cpp (modified)
	* molecuilder/tests/Tesselations/defs.in (modified)
	* molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/testsuite.at (modified)
	* pcp/src/Makefile.am (modified)
	* pcp/src/pcp.c (modified)
	* util/src/CreateGaAs.c (modified)
	* util/src/CreateH2.c (modified)
	* util/src/GetPdb.c (modified)
	* util/src/Makefile.am (modified)
	* util/src/NanoCreator.c (modified)
	* util/src/ReadSrcIon.c (modified)
	* util/src/VibrAlyzer.c (modified)
	* util/src/average.cpp (modified)
	* util/src/diagonalize.c (modified)
	* util/src/stochastik.cpp (modified)

	Merge branch 'CorrectDegeneratedPolygons' into
	Analysis_PairCorrelation


Thu, 17 Dec 2009 17:50:04 GMT Frederik Heber <heber@…> [f4df97]
	* .gitignore (modified)
	* Makefile.am (modified)
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.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/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)
	* molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/testsuite.at (modified)
	* pcp/src/Makefile.am (modified)
	* pcp/src/pcp.c (modified)
	* util/src/CreateGaAs.c (modified)
	* util/src/CreateH2.c (modified)
	* util/src/GetPdb.c (modified)
	* util/src/Makefile.am (modified)
	* util/src/NanoCreator.c (modified)
	* util/src/ReadSrcIon.c (modified)
	* util/src/VibrAlyzer.c (modified)
	* util/src/average.cpp (modified)
	* util/src/diagonalize.c (modified)
	* util/src/stochastik.cpp (modified)

	Merge branch 'FixDegeneratedTesselation' into
	CorrectDegeneratedPolygons


Thu, 17 Dec 2009 17:45:35 GMT Frederik Heber <heber@…> [0310b8]
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

	Non-convex tesselation seems to be working.

	Seems like it has been ...


Wed, 16 Dec 2009 16:18:46 GMT Frederik Heber <heber@…> [281324]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/testsuite.at (modified)

	Merge branch 'FixTestSuite' into FixDegeneratedTesselation


Wed, 16 Dec 2009 16:18:41 GMT Frederik Heber <heber@…> [230b16]
	* molecuilder/src/Makefile.am (modified)
	* pcp/src/Makefile.am (modified)
	* util/src/Makefile.am (modified)

	Merge branch 'FixVersioning2' into FixDegeneratedTesselation


Wed, 16 Dec 2009 16:17:50 GMT Frederik Heber <heber@…> [16f34d]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified)
	* molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified)
	* molecuilder/tests/testsuite.at (modified)

	Fixing the testsuite.

	- Putting performCriticalExit() everywhere ...


Wed, 16 Dec 2009 16:01:11 GMT Frederik Heber <heber@…> [b7f3f3]
	* molecuilder/src/Makefile.am (modified)
	* pcp/src/Makefile.am (modified)
	* util/src/Makefile.am (modified)

	Removed --tags as we have signed the "initial_commit" tag.

	- git ...


Wed, 16 Dec 2009 12:05:41 GMT Frederik Heber <heber@…> [20a828]
	* .gitignore (modified)

	Merge branch 'Fixversioning' into FixDegeneratedTesselation


Wed, 16 Dec 2009 12:04:05 GMT Frederik Heber <heber@…> [59b9dd]
	* .gitignore (modified)

	Added versioning to each executable.

	 - credits to Ralf Wildenhues ...


Wed, 16 Dec 2009 11:53:06 GMT Frederik Heber <heber@…> [65f1dba]
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)

	Fix attempts of the Tesselation.

	One problem still remains:
	 - ...


Wed, 16 Dec 2009 11:51:17 GMT Frederik Heber <heber@…> [59b70a]
	* molecuilder/src/parser.cpp (modified)

	FIX: MatrixContainer::ParseMatrix() should not call ...


Wed, 16 Dec 2009 11:49:40 GMT Frederik Heber <heber@…> [35f733]
	* molecuilder/src/config.cpp (modified)

	BUGFIX: delete(mol) belongs to the commented-out ...


Wed, 16 Dec 2009 11:47:47 GMT Frederik Heber <heber@…> [ef87ee]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/builder.cpp (modified)
	* pcp/src/Makefile.am (modified)
	* pcp/src/pcp.c (modified)
	* util/src/CreateGaAs.c (modified)
	* util/src/CreateH2.c (modified)
	* util/src/GetPdb.c (modified)
	* util/src/Makefile.am (modified)
	* util/src/NanoCreator.c (modified)
	* util/src/ReadSrcIon.c (modified)
	* util/src/VibrAlyzer.c (modified)
	* util/src/average.cpp (modified)
	* util/src/diagonalize.c (modified)
	* util/src/stochastik.cpp (modified)

	Added versioning to each executable.

	- credits to Ralf Wildenhues ...


Wed, 16 Dec 2009 10:12:03 GMT Frederik Heber <heber@…> [02911f]
	* Makefile.am (modified)

	'make doc' target added (credits to Till Crueger for the patch)

	- ...


Sat, 28 Nov 2009 18:01:00 GMT Frederik Heber <heber@…> [246a3c]
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

	The finding of the degenerated polygons' endpoints was not yet ...


Sat, 28 Nov 2009 15:48:41 GMT Frederik Heber <heber@…> [1db34af]
	* molecuilder/src/tesselation.cpp (modified)

	Merge branch 'FixDegeneratedTesselation' into ...


Sat, 28 Nov 2009 15:45:59 GMT Frederik Heber <heber@…> [ea3627]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)

	Correction of degenerated polygons is working.

	- Correction of ...


Sat, 28 Nov 2009 15:07:42 GMT Frederik Heber <heber@…> [2dff2d]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)

	Correction of degenerated polygons is working.

	- Correction of ...


Fri, 27 Nov 2009 14:39:06 GMT Frederik Heber <heber@…> [f7490d]
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)

	First compiling version of CorrectDegeneratedPolygons.

	- several ...


Fri, 27 Nov 2009 14:38:33 GMT Frederik Heber <heber@…> [65d6b3]
	* molecuilder/src/config.cpp (modified)

	Rename of internal variable due to upcoming name-conflict with ...


Thu, 26 Nov 2009 11:46:58 GMT Frederik Heber <heber@…> [2c0e4e]

	Merge branch 'Forgotten_Tesselations_defs_in' into ...


Thu, 26 Nov 2009 11:45:45 GMT Frederik Heber <heber@…> [40b3f7]
	* molecuilder/tests/Tesselations/defs.in (added)

	Merge branch 'Forgotten_Tesselations_defs_in' into ...


Thu, 26 Nov 2009 11:45:04 GMT Frederik Heber <heber@…> [b61c30]
	* molecuilder/tests/Tesselations/defs.in (added)

	Forgot to add molecuilder/tests/Tesselations/defs.in


Thu, 26 Nov 2009 11:40:01 GMT Frederik Heber <heber@…> [a68d44]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/tests/Tesselations/defs.in (added)

	removing automatic dissection on loading, Tesselations test now ...


Thu, 26 Nov 2009 11:36:44 GMT Frederik Heber <heber@…> [013ad57]
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

	BUGFIX: testcase heptan was not correctly tesselated, as edges of a ...


Wed, 25 Nov 2009 15:52:27 GMT Frederik Heber <heber@…> [3aa635]
	* molecuilder/src/tesselation.cpp (modified)

	Tesselation::FindStartingTriangle() now also uses ...


Wed, 25 Nov 2009 15:29:18 GMT Frederik Heber <heber@…> [be2997]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)

	Multi-Candidate-Add included and incorporated class Info into ...


Wed, 25 Nov 2009 15:28:39 GMT Frederik Heber <heber@…> [edf611]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/info.cpp (added)
	* molecuilder/src/info.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/infounittest.cpp (added)
	* molecuilder/src/unittests/infounittest.hpp (added)
	* molecuilder/src/verbose.cpp (modified)

	New Info class that contains a global verbosity level, increased per ...


Wed, 25 Nov 2009 12:18:18 GMT Frederik Heber <heber@…> [4af89b]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)

	Now the best (in terms of ShortestAngle) baseline is picked among all ...


Tue, 24 Nov 2009 15:48:36 GMT Frederik Heber <heber@…> [1a3354]
	* molecuilder/src/atom_bondedparticle.cpp (modified)

	BUGFIX atom::CorrectBonDegree() wrongly increased bond degrees.

	- ...


Tue, 24 Nov 2009 15:34:49 GMT Frederik Heber <heber@…> [cc9225]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_pointcloud.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (modified)
	* molecuilder/tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (modified)
	* molecuilder/tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (modified)
	* molecuilder/tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (modified)
	* molecuilder/tests/Tesselations/Makefile.am (modified)
	* molecuilder/tests/Tesselations/N_N-dimethylacetamide/NonConvexEnvelope-N_N-dimethylacetamide.dat (modified)
	* molecuilder/tests/Tesselations/benzene.test (added)
	* molecuilder/tests/Tesselations/benzene/NonConvexEnvelope-benzene.dat (added)
	* molecuilder/tests/Tesselations/benzene/benzene.xyz (added)
	* molecuilder/tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (modified)
	* molecuilder/tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (modified)
	* molecuilder/tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (modified)
	* molecuilder/tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (modified)
	* molecuilder/tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (modified)
	* molecuilder/tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (modified)
	* molecuilder/tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (modified)
	* molecuilder/tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (modified)
	* molecuilder/tests/Tesselations/proline/NonConvexEnvelope-proline.dat (modified)
	* molecuilder/tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (modified)
	* molecuilder/tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (modified)
	* molecuilder/tests/Tesselations/tartaric_acid/NonConvexEnvelope-tartaric_acid.dat (modified)

	Fixes and naming of final Tecplot output file is now molecule name.
 ...


Mon, 23 Nov 2009 19:09:42 GMT Frederik Heber <heber@…> [7d1ad9]
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/errorlogger.cpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)

	bugfix to errorLogger and some error verbosity changes.

	- BUGFIX: ...


Mon, 23 Nov 2009 18:51:50 GMT Frederik Heber <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 <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 ...


Tue, 10 Nov 2009 20:59:00 GMT Frederik Heber <heber@…> [09d3b8]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)

	Attempt to fix tesselation for case 1_2-dimethylbenzene.

	- The ...


Tue, 10 Nov 2009 20:58:31 GMT Frederik Heber <heber@…> [2fbbc96]
	* molecuilder/src/builder.cpp (modified)

	Only biggest molecule is tesselated for now in ...


Tue, 10 Nov 2009 20:57:58 GMT Frederik Heber <heber@…> [f28e0c]
	* molecuilder/configure.ac (modified)
	* molecuilder/tests/Makefile.am (modified)
	* molecuilder/tests/Tesselations/1_2-dimethoxyethane.test (added)
	* molecuilder/tests/Tesselations/1_2-dimethoxyethane/1_2-dimethoxyethane.xyz (added)
	* molecuilder/tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (added)
	* molecuilder/tests/Tesselations/1_2-dimethylbenzene.test (added)
	* molecuilder/tests/Tesselations/1_2-dimethylbenzene/1_2-dimethylbenzene.xyz (added)
	* molecuilder/tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (added)
	* molecuilder/tests/Tesselations/1_2-dimethylbenzene/tecplot.phy (added)
	* molecuilder/tests/Tesselations/2-methylcyclohexanone.test (added)
	* molecuilder/tests/Tesselations/2-methylcyclohexanone/2-methylcyclohexanone.xyz (added)
	* molecuilder/tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (added)
	* molecuilder/tests/Tesselations/C16_0-Torus.test (added)
	* molecuilder/tests/Tesselations/C16_0-Torus/C16_0-Torus.xyz (added)
	* molecuilder/tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (added)
	* molecuilder/tests/Tesselations/Makefile.am (added)
	* molecuilder/tests/Tesselations/N_N-dimethylacetamide.test (added)
	* molecuilder/tests/Tesselations/N_N-dimethylacetamide/N_N-dimethylacetamide.xyz (added)
	* molecuilder/tests/Tesselations/N_N-dimethylacetamide/NonConvexEnvelope-N_N-dimethylacetamide.dat (added)
	* molecuilder/tests/Tesselations/cholesterol.test (added)
	* molecuilder/tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (added)
	* molecuilder/tests/Tesselations/cholesterol/cholesterol.xyz (added)
	* molecuilder/tests/Tesselations/cluster.test (added)
	* molecuilder/tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (added)
	* molecuilder/tests/Tesselations/cluster/cluster.dbond (added)
	* molecuilder/tests/Tesselations/cluster/cluster.xyz (added)
	* molecuilder/tests/Tesselations/cycloheptane.test (added)
	* molecuilder/tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (added)
	* molecuilder/tests/Tesselations/cycloheptane/cycloheptane.xyz (added)
	* molecuilder/tests/Tesselations/dimethyl_bromomalonate.test (added)
	* molecuilder/tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (added)
	* molecuilder/tests/Tesselations/dimethyl_bromomalonate/dimethyl_bromomalonate.xyz (added)
	* molecuilder/tests/Tesselations/glucose.test (added)
	* molecuilder/tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (added)
	* molecuilder/tests/Tesselations/glucose/glucose.xyz (added)
	* molecuilder/tests/Tesselations/heptan.test (added)
	* molecuilder/tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (added)
	* molecuilder/tests/Tesselations/heptan/heptan.xyz (added)
	* molecuilder/tests/Tesselations/isoleucine.test (added)
	* molecuilder/tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (added)
	* molecuilder/tests/Tesselations/isoleucine/isoleucine.xyz (added)
	* molecuilder/tests/Tesselations/neohexane.test (added)
	* molecuilder/tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (added)
	* molecuilder/tests/Tesselations/neohexane/neohexane.xyz (added)
	* molecuilder/tests/Tesselations/proline.test (added)
	* molecuilder/tests/Tesselations/proline/NonConvexEnvelope-proline.dat (added)
	* molecuilder/tests/Tesselations/proline/proline.xyz (added)
	* molecuilder/tests/Tesselations/putrescine.test (added)
	* molecuilder/tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (added)
	* molecuilder/tests/Tesselations/putrescine/putrescine.xyz (added)
	* molecuilder/tests/Tesselations/round_cluster.test (added)
	* molecuilder/tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (added)
	* molecuilder/tests/Tesselations/round_cluster/round_cluster.dbond (added)
	* molecuilder/tests/Tesselations/round_cluster/round_cluster.xyz (added)
	* molecuilder/tests/Tesselations/tartaric_acid.test (added)
	* molecuilder/tests/Tesselations/tartaric_acid/NonConvexEnvelope-tartaric_acid.dat (added)
	* molecuilder/tests/Tesselations/tartaric_acid/tartaric_acid.xyz (added)

	Added Tesselation testsets as TESTS to molecuilder.

	- defs.in with ...


Tue, 10 Nov 2009 20:53:33 GMT Frederik Heber <heber@…> [548cbf]
	* molecuilder/src/errorlogger.cpp (modified)
	* molecuilder/src/logger.cpp (modified)
	* molecuilder/src/verbose.hpp (modified)

	BUGFIX: Output is again indented, errorLogger prefixes according to ...


Sat, 07 Nov 2009 12:27:15 GMT Frederik Heber <heber@…> [e960b1]
	* molecuilder/src/unittests/bondgraphunittest.cpp (modified)
	* molecuilder/src/unittests/bondgraphunittest.hpp (modified)

	BUGFIX: unnecessary include in header, file not closed in definition ...


Sat, 07 Nov 2009 12:25:32 GMT Frederik Heber <heber@…> [e462b3]
	* molecuilder/src/analysis_bonds.cpp (modified)
	* molecuilder/src/analysis_bonds.hpp (modified)
	* molecuilder/src/unittests/analysisbondsunittest.cpp (modified)
	* molecuilder/src/unittests/analysisbondsunittest.hpp (modified)

	Two new bond analysis functions.

	- GetMaxMinMeanBondCount() - ...


Sat, 07 Nov 2009 12:17:55 GMT Frederik Heber <heber@…> [1fcedd]
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (modified)

	New function bond::GetDistance...()

	- bond::GetDistance() and ...


Sat, 07 Nov 2009 12:16:57 GMT Frederik Heber <heber@…> [486aa5]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Added config::SavePDB() and config::SaveMPQC().

	- note: for CODICE ...


Sat, 07 Nov 2009 09:46:08 GMT Frederik Heber <heber@…> [341850]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/analysis_bonds.cpp (added)
	* molecuilder/src/analysis_bonds.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/analysisbondsunittest.cpp (added)
	* molecuilder/src/unittests/analysisbondsunittest.hpp (added)

	Added initial analysis_bonds.cpp and unit test for Analysis of bonds. ...


Sat, 07 Nov 2009 09:44:11 GMT Frederik Heber <heber@…> [fc420f]
	* molecuilder/src/boundary.cpp (modified)

	LEAKFIX: FillBoxWithMolecule() had mismatch delete/delete[]

	- ...


Thu, 05 Nov 2009 18:14:08 GMT Frederik Heber <heber@…> [4ef101]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule_geometry.cpp (modified)

	LEAKFIX: ReturnFullMatrixForSymmetric() and InverseMatrix() have ...


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 ...


Wed, 04 Nov 2009 18:25:42 GMT Frederik Heber <heber@…> [ec70ec]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/errorLogger.cpp (added)
	* molecuilder/src/errorLogger.hpp (added)
	* molecuilder/src/log.cpp (added)
	* molecuilder/src/log.hpp (added)
	* molecuilder/src/logger.cpp (added)
	* molecuilder/src/logger.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/logunittest.cpp (added)
	* molecuilder/src/unittests/logunittest.hpp (added)
	* molecuilder/src/verbose.cpp (modified)
	* molecuilder/src/verbose.hpp (modified)

	Merge branch 'CodeRefactoring' of ...


Wed, 04 Nov 2009 18:15:10 GMT Frederik Heber <heber@…> [5f1d021]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/analysis_correlation.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* molecuilder/src/vector.cpp (modified)

	Periodic variants of AnalysisPair...() implemented.

	- BUGFIX: ...


Wed, 04 Nov 2009 17:34:05 GMT Frederik Heber <heber@…> [20895b]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/helpers.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/molecule_geometry.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)

	Extension to the periodic boundary case for analysis_correlation.cpp
 ...


Wed, 04 Nov 2009 15:08:11 GMT Frederik Heber <heber@…> [c1b76e]
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	config::Load() refactored: Dissection into connected subgraphs -> ...


Wed, 04 Nov 2009 14:54:31 GMT Frederik Heber <heber@…> [e1900f]
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/analysis_correlation.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified)
	* molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified)

	Closed ticket #48 (AnalysisCorrelation...() take MoleculeListClass ...


Wed, 04 Nov 2009 14:51:02 GMT Frederik Heber <heber@…> [4efdad]
	* molecuilder/src/config.cpp (modified)

	BUGFIX: Allocated one molecule too much in config::Load().

	- ...


Wed, 04 Nov 2009 12:57:24 GMT Frederik Heber <heber@…> [a3ffb44]
	* molecuilder/src/builder.cpp (modified)

	Closing ticket #47, case 'C' uses biggest molecule as surface for ...


Tue, 03 Nov 2009 16:34:31 GMT Frederik Heber <heber@…> [c1b4a4]
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/bondgraph.hpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/molecule_fragmentation.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)

	"not working parsed molecule into subgraph splitting"-BUG fixed, ...


Tue, 03 Nov 2009 14:34:02 GMT Frederik Heber <heber@…> [08b88b]
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/bondgraph.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Fixing not created adjacency list, partially fixing subgraph ...


Tue, 03 Nov 2009 12:38:08 GMT Frederik Heber <heber@…> [5f9f8b]
	* molecuilder/src/unittests/Makefile.am (modified)

	Removed libmolecuilder linking from unit tests where only some few ...


Tue, 03 Nov 2009 12:37:55 GMT Frederik Heber <heber@…> [8bc524]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/helpers.hpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/memoryusageobserver.cpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule_dynamics.cpp (modified)
	* molecuilder/src/molecule_fragmentation.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/unittests/memoryallocatorunittest.cpp (modified)

	Several memory bugfixes (thx valgrind).

	- main() - shortened case ...


Mon, 02 Nov 2009 12:50:57 GMT Frederik Heber <heber@…> [df0520]
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)

	Small changes.

	- VolumeOfConvexEnvelope() - setprecision corrected ...


Fri, 30 Oct 2009 16:09:29 GMT Frederik Heber <heber@…> [245826]
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)

	BondGraph is initialized within config::Load(), as it has to happen ...


Fri, 30 Oct 2009 15:49:38 GMT Frederik Heber <heber@…> [b84ab4]
	* molecuilder/src/bondgraph.cpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/unittests/bondgraphunittest.cpp (modified)

	BondGraph is parsed if command line switch '-g' is given.

	- ...


Fri, 30 Oct 2009 11:04:50 GMT Saskia Metzler <metzler@…> [96d8dc]
	* molecuilder/src/errorLogger.cpp (added)
	* molecuilder/src/errorLogger.hpp (added)
	* molecuilder/src/log.cpp (added)
	* molecuilder/src/log.hpp (added)
	* molecuilder/src/logger.cpp (added)
	* molecuilder/src/logger.hpp (added)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/logunittest.cpp (added)
	* molecuilder/src/unittests/logunittest.hpp (added)
	* molecuilder/src/verbose.cpp (modified)
	* molecuilder/src/verbose.hpp (modified)

	Ticket 43 Create a logging class

	The verbosity level can now be ...


Fri, 30 Oct 2009 09:05:30 GMT Frederik Heber <heber@…> [5f697c]
	* molecuilder/src/Makefile.am (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/atom_bondedparticle.hpp (modified)
	* molecuilder/src/bondgraph.cpp (added)
	* molecuilder/src/bondgraph.hpp (added)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)
	* molecuilder/src/unittests/bondgraphunittest.cpp (added)
	* molecuilder/src/unittests/bondgraphunittest.hpp (added)

	New class BondGraph.

	- BondGraph parses a file containing bond ...


Fri, 30 Oct 2009 08:29:31 GMT Frederik Heber <heber@…> [bc8155]
	* molecuilder/src/test/ActOnAlltest.hpp (modified)
	* molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified)
	* molecuilder/src/unittests/ActOnAllUnitTest.hpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)

	Test code is moved to its own source subdirectory: test.

	- ...


Fri, 30 Oct 2009 08:29:07 GMT Frederik Heber <heber@…> [92fc40]
	* molecuilder/src/test/ActOnAlltest.hpp (moved)
	* molecuilder/src/unittests/stackclassunittest.cpp (added)
	* molecuilder/src/unittests/stackclassunittest.hpp (added)

	Added Unit test for StackClass.

	- was former ...


Thu, 29 Oct 2009 10:09:05 GMT Frederik Heber <heber@…> [dbc152]
	* molecuilder/src/stackclass.hpp (modified)
	* molecuilder/src/unittests/Makefile.am (modified)

	Refactored StackClass with respect to tickets #38, #4.

	- #38 make ...


Tue, 27 Oct 2009 17:41:12 GMT Frederik Heber <heber@…> [6d7651]
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)

	Refactored tesselationhelpers.cpp with respect to ticket #38 (make ...


Tue, 27 Oct 2009 17:16:31 GMT Frederik Heber <heber@…> [069034]
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (modified)
	* molecuilder/src/config.cpp (modified)
	* molecuilder/src/config.hpp (modified)
	* molecuilder/src/memoryallocator.hpp (modified)
	* molecuilder/src/periodentafel.cpp (modified)
	* molecuilder/src/periodentafel.hpp (modified)
	* molecuilder/src/vector.hpp (modified)

	class config, ConfigFileBuffer, periodentafel and Vector are ...


Tue, 27 Oct 2009 16:11:22 GMT Frederik Heber <heber@…> [a9b2a0a]
	* molecuilder/configure.ac (modified)
	* molecuilder/src/analysis_correlation.cpp (modified)
	* molecuilder/src/analysis_correlation.hpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/ellipsoid.cpp (modified)
	* molecuilder/src/leastsquaremin.cpp (modified)
	* molecuilder/src/leastsquaremin.hpp (modified)
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/src/linkedcell.hpp (modified)
	* molecuilder/src/molecule.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_geometry.cpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/molecule_pointcloud.cpp (modified)
	* molecuilder/src/moleculelist.cpp (modified)
	* molecuilder/src/tesselation.cpp (modified)
	* molecuilder/src/tesselation.hpp (modified)
	* molecuilder/src/tesselationhelpers.cpp (modified)
	* molecuilder/src/tesselationhelpers.hpp (modified)
	* molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified)
	* molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* molecuilder/src/vector.cpp (modified)
	* molecuilder/src/vector.hpp (modified)

	Huge refactoring to make const what is const (ticket #38), continued. ...


Tue, 27 Oct 2009 11:51:52 GMT Frederik Heber <heber@…> [55a71b]
	* molecuilder/src/analyzer.cpp (modified)
	* molecuilder/src/boundary.cpp (modified)
	* molecuilder/src/boundary.hpp (modified)
	* molecuilder/src/molecule.hpp (modified)

	analyzer.cpp and boundary.cpp refactored.

	- ticket #39 is done with ...


Tue, 27 Oct 2009 11:45:23 GMT Frederik Heber <heber@…> [8b6ee4]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom_bondedparticle.cpp (modified)
	* molecuilder/src/bond.cpp (modified)
	* molecuilder/src/bond.hpp (modified)

	Begun with ticket #4 (shorten constructors) on class atom and class ...


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, 27 Oct 2009 08:53:25 GMT Frederik Heber <heber@…> [2e6aa1]
	* molecuilder/src/unittests/Makefile.am (modified)

	..._CPPFLAGS and ..._LDFLAGS in unittests/Makefile.am put into global ...


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 ...


Tue, 20 Oct 2009 08:54:51 GMT Frederik Heber <heber@…> [3b0ba2]
	* molecuilder/src/vector.hpp (modified)

	iostream was missing in vector includes.


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 19:58:38 GMT Frederik Heber <heber@…> [99bed3]
	* molecuilder/src/molecule_graph.cpp (modified)

	Added BFSAccounting and DFSAccounting structures and all functions ...


Sun, 18 Oct 2009 18:12:53 GMT Frederik Heber <heber@…> [e60069]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored molecule::BuildInducedSubgraph()

	- new functions ...


Sun, 18 Oct 2009 17:52:47 GMT Frederik Heber <heber@…> [9897787]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored molecule::BreadthFirstSearchAdd()

	- new function: ...


Sun, 18 Oct 2009 17:07:33 GMT Frederik Heber <heber@…> [312ba2]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored CheckAdjacencyFileAgainstMolecule().

	- new functions: ...


Sun, 18 Oct 2009 16:35:25 GMT Frederik Heber <heber@…> [6e250f]
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)
	* molecuilder/src/molecule_template.hpp (modified)

	Removed ResetAllAtomNumbers(), replaced by templated ...


Sun, 18 Oct 2009 16:09:26 GMT Frederik Heber <heber@…> [f444ce]
	* molecuilder/src/atom.cpp (modified)
	* molecuilder/src/atom.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)

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


Sun, 18 Oct 2009 16:01:57 GMT Frederik Heber <heber@…> [c9f639]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored molecule::CyclicStructureAnalysis()

	- new functions: ...


Sun, 18 Oct 2009 15:13:46 GMT Frederik Heber <heber@…> [77894f]
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored molecule::DepthFirstSearchAnalysis()

	- new functions: ...


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 ...


Sat, 17 Oct 2009 19:47:58 GMT Frederik Heber <heber@…> [b0ee98]
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)

	Refactored CreateAdjacencyList().

	- new auxiliary functions: ...


Sat, 17 Oct 2009 19:46:28 GMT Frederik Heber <heber@…> [aec775]
	* molecuilder/src/linkedcell.cpp (modified)
	* molecuilder/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@…> [bee48d]
	* molecuilder/src/builder.cpp (modified)
	* molecuilder/src/molecule.hpp (modified)
	* molecuilder/src/molecule_graph.cpp (modified)

	Renamed and rewritten CreateAdjacencyList2().

	- rename ...