#
# ChangeLog for /
#
# Generated by Trac 1.6
# May 25, 2025, 11:17:27 PM

Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber <heber@…> [50eff3]
	* src/Parameters/Value_impl.hpp (modified)

	FIX: Value::getValidRange() and ::getValidValues() were broken.

	- ...


Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber <heber@…> [4e904b]
	* src/Atom/atom.cpp (modified)
	* src/Atom/atom.hpp (modified)
	* src/molecule.cpp (modified)

	Removed atom::IsInShape().

	- this makes libMolecuilderAtom not ...


Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber <heber@…> [a2f5e5]
	* src/Parser/MpqcParser_Parameters.cpp (modified)
	* src/Parser/MpqcParser_Parameters.hpp (modified)
	* src/Parser/Psi3Parser.hpp (modified)
	* src/Parser/Psi3Parser_Parameters.cpp (modified)
	* src/Parser/Psi3Parser_Parameters.hpp (modified)
	* src/Parser/unittests/ParserPsi3UnitTest.cpp (modified)

	FIX: Cleaned up includes in Psi3Parser_Parameters.


Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber <heber@…> [42f2f0]
	* src/Parser/MpqcParser_Parameters.cpp (modified)
	* src/Parser/MpqcParser_Parameters.hpp (modified)
	* src/Parser/Psi3Parser_Parameters.cpp (modified)
	* src/Parser/Psi3Parser_Parameters.hpp (modified)

	FIX: MpqcParser_Parameter now simply uses Parameter<string> instead ...


Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber <heber@…> [58fccca]
	* src/Parser/XyzParser.cpp (modified)

	FIX: XyzParser::load() stumbled if no empty line between timesteps.
 ...


Wed, 13 Feb 2013 15:47:45 GMT Frederik Heber <heber@…> [b4b364]
	* src/Parameters/unittests/Makefile.am (modified)
	* src/Parser/Parameters/unittests/Makefile.am (modified)

	FIX: Parameter unit tests all lacked CodePatterns lib.


Wed, 13 Feb 2013 15:47:38 GMT Frederik Heber <heber@…> [7d82a5]
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)
	* src/Atom/atom_bondedparticleinfo.hpp (modified)
	* src/Bond/bond.cpp (modified)
	* src/Bond/bond.hpp (modified)
	* src/Fragmentation/BondsPerShortestPath.cpp (modified)
	* src/Fragmentation/BondsPerShortestPath.hpp (modified)
	* src/Fragmentation/PowerSetGenerator.cpp (modified)
	* src/Graph/BreadthFirstSearchAdd.cpp (modified)
	* src/Graph/CyclicStructureAnalysis.cpp (modified)
	* src/Graph/DepthFirstSearchAnalysis.cpp (modified)
	* src/Tesselation/boundary.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified)
	* src/World.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)

	Changed bond::ptr into boost::shared_ptr.

	Changes:
	- refactored ...


Wed, 13 Feb 2013 14:29:35 GMT Frederik Heber <heber@…> [c8302f3]
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.hpp (modified)

	Removed molecule::RemoveBond(s) and ::removeAtom().

	- this ...


Thu, 17 Jan 2013 22:59:15 GMT Frederik Heber <heber@…> [88c8ec]
	* src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified)
	* src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified)
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)
	* src/Atom/atom_bondedparticleinfo.hpp (modified)
	* src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (modified)
	* src/Bond/BondInfo.cpp (modified)
	* src/Bond/BondInfo.hpp (modified)
	* src/Bond/bond.cpp (modified)
	* src/Bond/bond.hpp (modified)
	* src/Fragmentation/BondsPerShortestPath.cpp (modified)
	* src/Fragmentation/PowerSetGenerator.cpp (modified)
	* src/Fragmentation/PowerSetGenerator.hpp (modified)
	* src/Graph/BondGraph.hpp (modified)
	* src/Graph/BreadthFirstSearchAdd.cpp (modified)
	* src/Graph/BreadthFirstSearchAdd.hpp (modified)
	* src/Graph/CyclicStructureAnalysis.cpp (modified)
	* src/Graph/CyclicStructureAnalysis.hpp (modified)
	* src/Graph/DepthFirstSearchAnalysis.cpp (modified)
	* src/Graph/DepthFirstSearchAnalysis.hpp (modified)
	* src/Parser/Psi3Parser.cpp (modified)
	* src/Tesselation/boundary.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified)
	* src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)

	REFACTOR: Replaced all "bond *" appearances by bond::ptr.

	- this is ...


Thu, 20 Dec 2012 09:44:30 GMT Frederik Heber <heber@…> [d6b6ce]
	* configure.ac (modified)

	Set version to 1.3.9.

	- Molecuilder library is now 11:0:0.
	- ...


Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber <heber@…> [a30b7f]
	* src/LevMartester.cpp (modified)

	Added check on L2 sum and Lmax norms of fitted Tersoff with respect ...


Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber <heber@…> [17b3598]
	* src/LevMartester.cpp (modified)

	Starting parameters for Tersoff minimization in LevMartester are now ...


Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber <heber@…> [d03292]
	* src/FunctionApproximation/FunctionApproximation.cpp (modified)
	* src/FunctionApproximation/FunctionModel.hpp (modified)
	* src/LevMartester.cpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified)
	* src/Potentials/Specifics/PairPotential_Morse.hpp (modified)

	Implemented box constraints for FunctionModel, using a feature of ...


Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber <heber@…> [f48ad3]
	* src/LevMartester.cpp (modified)
	* src/Makefile.am (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified)
	* src/Potentials/Specifics/PairPotential_Morse.hpp (modified)

	LevMartester now uses FunctionModel::setParameter() to set initial ...


Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber <heber@…> [eb1efe]
	* src/FunctionApproximation/FunctionArgument.hpp (modified)
	* src/LevMartester.cpp (modified)
	* src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified)
	* src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp (modified)

	Extended LevMartester to fit a Tersoff potential to the first order ...


Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber <heber@…> [bc55c9]
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)

	Added NaN check to Tersoff's parameter_derivative().


Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber <heber@…> [56c5de4]
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)

	Added an offset to the Tersoff potential.


Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber <heber@…> [2e9486]
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)

	FIX: Tersoff must sum potential over every of the arguments.


Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber <heber@…> [ca8d82]
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)

	FIX: Corrected parameter derivatives of ManyBodyPotential_Tersoff.
 ...


Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber <heber@…> [f904d5]
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)

	Added complete parameter derivatives to ManyBodyPotential_Tersoff.
 ...


Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber <heber@…> [752dc7]
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)
	* src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified)

	FIX: Made R and S also fixed parameters, this is in accordance with ...


Wed, 19 Dec 2012 15:25:54 GMT Frederik Heber <heber@…> [990a62]
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)
	* src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified)

	FIX: Tersoff parameters lambda3, alpha, chi, and omega are now fixed. ...


Wed, 19 Dec 2012 15:25:53 GMT Frederik Heber <heber@…> [ffc368]
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)
	* src/Potentials/Specifics/unittests/Makefile.am (modified)
	* src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (added)
	* src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp (added)

	ManyBodyPotential_Tersoff is now correctly implemented.

	- changed ...


Wed, 19 Dec 2012 15:25:53 GMT Frederik Heber <heber@…> [e7579e]
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)

	Changed ManyBodyPotential_Tersoff to also have parameters_t instead ...


Wed, 19 Dec 2012 15:25:43 GMT Frederik Heber <heber@…> [76cbd0]
	* src/Potentials/Specifics/PairPotential_Morse.cpp (modified)
	* src/Potentials/Specifics/PairPotential_Morse.hpp (modified)
	* src/Potentials/Specifics/unittests/Makefile.am (modified)
	* src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (added)
	* src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.hpp (added)

	Added PairPotential_MorseUnitTest.

	- so far, added simple test on ...


Wed, 19 Dec 2012 15:25:43 GMT Frederik Heber <heber@…> [b70b53]
	* src/Potentials/Specifics/PairPotential_Morse.cpp (modified)

	FIX: Checked PairPotential_Morse::parameter_derivative with Maple.
 ...


Wed, 19 Dec 2012 15:25:43 GMT Frederik Heber <heber@…> [155cc2]
	* src/LevMartester.cpp (modified)
	* src/Potentials/Makefile.am (modified)
	* src/Potentials/Specifics/PairPotential_Morse.cpp (added)
	* src/Potentials/Specifics/PairPotential_Morse.hpp (added)

	Added PairPotential_Morse with derivatives, used by LevMartester.

	- ...


Wed, 19 Dec 2012 15:25:32 GMT Frederik Heber <heber@…> [9e903b]
	* src/FunctionApproximation/FunctionArgument.cpp (added)
	* src/FunctionApproximation/FunctionArgument.hpp (modified)
	* src/FunctionApproximation/Makefile.am (modified)

	Added operator<<() to FunctionArgument.


Wed, 19 Dec 2012 15:25:32 GMT Frederik Heber <heber@…> [371c8b]
	* src/FunctionApproximation/FunctionApproximation.cpp (modified)
	* src/FunctionApproximation/FunctionApproximation.hpp (modified)

	Added FunctionApproximation::checkParameterDerivatives().

	- ...


Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber <heber@…> [63b9f7]
	* src/FunctionApproximation/FunctionApproximation.cpp (modified)
	* src/FunctionApproximation/FunctionApproximation.hpp (modified)

	REFACTOR: Split off prepareModel() and prepareOutput() from ...


Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber <heber@…> [76e63d]
	* src/FunctionApproximation/FunctionApproximation.cpp (modified)
	* src/FunctionApproximation/FunctionApproximation.hpp (modified)

	Extended FunctionApproximation::operator() to receive JacobianMode ...


Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber <heber@…> [3c1465]
	* src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified)
	* src/Potentials/Specifics/unittests/Makefile.am (added)
	* src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (added)
	* src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.hpp (added)
	* src/unittests/Makefile.am (modified)

	Added PairPotential_HarmonicUnitTest.

	- so far, we test the ...


Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber <heber@…> [5b5724]
	* src/FunctionApproximation/FunctionApproximation.cpp (modified)
	* src/FunctionApproximation/FunctionApproximation.hpp (modified)
	* src/FunctionApproximation/FunctionArgument.hpp (modified)
	* src/LevMartester.cpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified)

	FunctionApproximation now uses levmar_der, i.e. additionally the ...


Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber <heber@…> [1dca9a]
	* src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified)

	Modified PairPotential_Harmonic to have an internal vector of ...


Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber <heber@…> [3ccea3]
	* src/FunctionApproximation/FunctionModel.hpp (modified)
	* src/Potentials/EmpiricalPotential.hpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified)

	EmpiricalPotential and FunctionModel are now inherited virtually, ...


Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber <heber@…> [dac89b1]
	* src/LevMartester.cpp (modified)

	Using FunctionModel and setTrainingData in LevMartester.


Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber <heber@…> [65c42c]
	* src/LevMartester.cpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified)

	PairPotential_Harmonic now has additional offset parameter.

	- do we ...


Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber <heber@…> [c62f96]
	* src/FunctionApproximation/FunctionApproximation.cpp (modified)
	* src/LevMartester.cpp (modified)
	* src/Makefile.am (modified)

	LevMartester uses now FunctionApproximation.


Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber <heber@…> [4f82f8]
	* src/Potentials/EmpiricalPotential.hpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified)
	* src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified)

	Rewrote EmpiricalPotentials and the specific implementations such ...


Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber <heber@…> [66cfc7]
	* src/FunctionApproximation/FunctionApproximation.cpp (added)
	* src/FunctionApproximation/FunctionApproximation.hpp (added)
	* src/FunctionApproximation/FunctionArgument.hpp (added)
	* src/FunctionApproximation/FunctionModel.hpp (added)
	* src/FunctionApproximation/Makefile.am (added)
	* src/Makefile.am (modified)

	Added new class FunctionApproximation that encapsulates the LevMar ...


Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber <heber@…> [dda3e8]
	* src/Potentials/helpers.hpp (modified)

	Added Helpers::isEqual() as equality operator taking numerical ...


Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber <heber@…> [bf12d1]
	* src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified)
	* src/Fragmentation/Summation/writeTable.hpp (modified)

	FIX: WriteTable might fail because of size_t difference.

	- ...


Wed, 19 Dec 2012 15:25:03 GMT Frederik Heber <heber@…> [f06d52]
	* configure.ac (modified)
	* m4/ax_blas.m4 (added)
	* m4/ax_lapack.m4 (added)
	* src/LevMartester.cpp (added)
	* src/Makefile.am (modified)

	Added LevMartester that employs levmar package for non-linear ...


Sun, 16 Dec 2012 19:47:28 GMT Frederik Heber <heber@…> [fe0355]
	* src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp (moved)
	* src/Fragmentation/Homology/unittests/Makefile.am (modified)
	* src/Fragmentation/Makefile.am (modified)
	* src/Makefile.am (modified)
	* src/UIElements/Makefile.am (modified)

	Split HomologyGraph_getFromKeyset module off from ...


Sun, 16 Dec 2012 19:47:28 GMT Frederik Heber <heber@…> [610c11]
	* src/Potentials/Makefile.am (modified)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (added)
	* src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (added)

	Added Tersoff potential as first many-body potential.


Sun, 16 Dec 2012 19:47:27 GMT Frederik Heber <heber@…> [6bb72a]
	* src/Makefile.am (modified)
	* src/Potentials/EmpiricalPotential.hpp (added)
	* src/Potentials/Makefile.am (added)
	* src/Potentials/Specifics/PairPotential_Harmonic.cpp (added)
	* src/Potentials/Specifics/PairPotential_Harmonic.hpp (added)
	* src/Potentials/helpers.hpp (added)

	Added general interface EmpiricalPotential and a first potential, the ...


Fri, 14 Dec 2012 17:40:29 GMT Frederik Heber <heber@…> [da5b82]
	* configure.ac (modified)

	Set version to 1.3.8.

	- Molecuilder library is now 10:3:0.
	- ...


Fri, 14 Dec 2012 17:40:29 GMT Frederik Heber <heber@…> [97a858]
	* utils/developer/CheckAllPossibleEnables.sh (added)
	* utils/developer/CheckMolecuilderCommitRanges.sh (added)
	* utils/developer/CheckMolecuilderEnables.sh (added)
	* utils/developer/CheckMolecuilderWithPrefetchedPackages.sh (added)
	* utils/developer/README (added)

	Added some developer scripts to check on commits and releases.


Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber <heber@…> [12098a]
	* src/Actions/ShapeAction/RemoveShapeAction.cpp (modified)
	* src/Actions/ShapeAction/RemoveShapeAction.def (modified)

	Refactoring: use vector<Shape> instead of vector<Shape*> in ...


Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber <heber@…> [29ea65]
	* src/Actions/GlobalListOfActions.hpp (modified)
	* src/Actions/Makefile.am (modified)
	* src/Actions/ShapeAction/StretchShapeAction.cpp (added)
	* src/Actions/ShapeAction/StretchShapeAction.def (added)
	* src/Actions/ShapeAction/StretchShapeAction.hpp (added)
	* src/UIElements/Views/Qt4/QtShapeController.cpp (modified)
	* tests/Python/AllActions/options.dat (modified)

	StretchShapeAction added


Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber <heber@…> [3ce0f1]
	* src/Actions/ShapeAction/RotateShapeAction.cpp (modified)
	* src/Actions/ShapeAction/RotateShapeAction.def (modified)

	RotateShapeAction now handles center!=0


Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber <heber@…> [216dad]
	* src/UIElements/Views/Qt4/QtShapeController.cpp (modified)

	added shape edit actions to QtShapeController


Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber <heber@…> [7e19060]
	* src/Actions/ShapeAction/CreateShapeAction.cpp (modified)
	* src/Actions/ShapeAction/RotateShapeAction.cpp (modified)

	use degrees as angle input in shape actions


Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber <heber@…> [a2bbb1]
	* src/Actions/GlobalListOfActions.hpp (modified)
	* src/Actions/Makefile.am (modified)
	* src/Actions/ShapeAction/RotateShapeAction.cpp (added)
	* src/Actions/ShapeAction/RotateShapeAction.def (added)
	* src/Actions/ShapeAction/RotateShapeAction.hpp (added)

	RotateShapeAction added


Fri, 14 Dec 2012 17:40:13 GMT Frederik Heber <heber@…> [0b5057]
	* src/Actions/GlobalListOfActions.hpp (modified)
	* src/Actions/Makefile.am (modified)
	* src/Actions/ShapeAction/TranslateShapeAction.cpp (added)
	* src/Actions/ShapeAction/TranslateShapeAction.def (added)
	* src/Actions/ShapeAction/TranslateShapeAction.hpp (added)
	* tests/Python/AllActions/options.dat (modified)

	TranslateShapeAction added


Fri, 14 Dec 2012 17:40:12 GMT Frederik Heber <heber@…> [467069]
	* src/Tesselation/tesselation.cpp (modified)

	"FIX": allow tesselation of points with negative coordinates


Fri, 14 Dec 2012 17:40:12 GMT Frederik Heber <heber@…> [2defa9]
	* src/Shapes/ShapeFactory.cpp (modified)

	FIX: (ShapeFactory) wrong test for trivial rotations


Fri, 14 Dec 2012 17:40:12 GMT Frederik Heber <heber@…> [13202c]
	* src/Shapes/BaseShapes.cpp (modified)
	* src/Shapes/unittests/ShapeOpsUnitTest.cpp (modified)
	* src/Shapes/unittests/ShapeOpsUnitTest.hpp (modified)

	FIX: made Cuboid.isOnSurface() robust enough for transformations


Fri, 14 Dec 2012 17:40:12 GMT Frederik Heber <heber@…> [148dde0]
	* src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified)

	FIX: missing map.erase() in GLWorldScene::removeShape()


Fri, 14 Dec 2012 17:39:52 GMT Frederik Heber <heber@…> [6d084a4]
	* src/Jobs/InterfaceVMGJob.cpp (modified)

	DEBUG: InterfaceVMGJob does not printGrids anymore.

	- output folder ...


Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber <heber@…> [91a565]
	* src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified)

	DEBUG: Added some debugging output for constructed HomologyGraphs in ...


Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber <heber@…> [28e203]
	* src/Fragmentation/Homology/HomologyGraph.cpp (modified)
	* src/Fragmentation/Homology/HomologyGraph.hpp (modified)
	* src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified)
	* src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified)
	* src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified)

	FIX: nodes_t and edges_t in HomologyGraph must be a map.

	- there ...


Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber <heber@…> [d058e6]
	* src/Fragmentation/Homology/HomologyContainer.hpp (modified)

	Exposed const begin,end of container in HomologyContainer to allow ...


Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber <heber@…> [79398d]
	* src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified)
	* src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified)
	* src/Fragmentation/Automation/FragmentationResults.hpp (modified)
	* src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified)
	* src/Fragmentation/Summation/AllLevelSummator.hpp (modified)
	* src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified)
	* src/Fragmentation/Summation/SumUpPerLevel.hpp (modified)

	Extended map<IndexSet, MapType> in FragmentResults to a pair of ...


Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber <heber@…> [2dd305]
	* src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified)
	* src/Fragmentation/Automation/FragmentationResults.cpp (modified)
	* src/Fragmentation/Automation/FragmentationResults.hpp (modified)

	Split FragmentResults functionality in cstor into cstor and ...


Fri, 14 Dec 2012 17:39:42 GMT Frederik Heber <heber@…> [bfbd4a]
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Fragmentation/Fragmentation.hpp (modified)
	* src/Fragmentation/Graph.cpp (modified)
	* src/Fragmentation/Graph.hpp (modified)

	Storing KeySet file with global ids now.

	- We now parse in key set ...


Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber <heber@…> [d1ba0d]
	* src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified)
	* src/moleculelist.cpp (modified)

	FIX: Forces-Factors are now written with global ids, ...


Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber <heber@…> [e71325]
	* src/Fragmentation/AdaptivityMap.cpp (modified)
	* src/Fragmentation/AdaptivityMap.hpp (modified)
	* src/Fragmentation/Fragmentation.cpp (modified)
	* src/Fragmentation/Fragmentation.hpp (modified)
	* src/Fragmentation/Graph.cpp (modified)
	* src/Fragmentation/Graph.hpp (modified)

	FIX: All functions in Fragmentation and related now use const string ...


Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber <heber@…> [17c03f]
	* src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified)
	* src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified)
	* src/Fragmentation/Automation/FragmentationResults.cpp (modified)
	* src/Fragmentation/Automation/Makefile.am (modified)
	* src/Fragmentation/Automation/parseKeySetFile.cpp (added)
	* src/Fragmentation/Automation/parseKeySetFile.hpp (added)

	Extracted parseKeySetFile from FragmentationResults, ...


Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber <heber@…> [766767]
	* src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified)

	appendToHomologyFile() now constructs the HomologyGraph and its ...


Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber <heber@…> [372c912]
	* src/Fragmentation/Homology/HomologyGraph.cpp (modified)
	* src/Fragmentation/Homology/HomologyGraph.hpp (modified)
	* src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified)
	* src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (modified)

	Extended HomologyGraph to also be constructable from IndexSet ...


Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber <heber@…> [b8f0b25]
	* src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified)
	* src/Fragmentation/Automation/FragmentationChargeDensity.cpp (modified)
	* src/Fragmentation/Automation/FragmentationChargeDensity.hpp (modified)
	* src/Fragmentation/Automation/FragmentationResults.cpp (modified)
	* src/Fragmentation/Automation/FragmentationResults.hpp (modified)
	* src/Fragmentation/Summation/AllLevelOrthogonalSummator.hpp (modified)
	* src/Fragmentation/Summation/AllLevelSummator.hpp (modified)
	* src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified)
	* src/Fragmentation/Summation/SumUpPerLevel.hpp (modified)

	Extended FragmentResults and FragmentationChargeDensity to contain ...


Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber <heber@…> [69e065]
	* src/Fragmentation/Summation/OrthogonalSummator.hpp (modified)
	* src/Fragmentation/Summation/Summator.hpp (modified)

	Added getContributionForIndexSet() and ...Value...() to ...


Fri, 14 Dec 2012 17:39:41 GMT Frederik Heber <heber@…> [07266b]
	* src/Fragmentation/Summation/SetValueMap.hpp (modified)

	Added SetValueMap::getConstValue() for getting const reference to ...


Fri, 14 Dec 2012 17:39:40 GMT Frederik Heber <heber@…> [240c3e]
	* src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified)
	* tests/Python/AllActions/options.dat (modified)

	FragmentationAutomationAction now uses a file containing a serialized ...


Fri, 14 Dec 2012 17:39:40 GMT Frederik Heber <heber@…> [37ce5d]
	* src/Makefile.am (modified)

	FIX: Switched SYSTEM and FILESYSTEM libs in LDADD in src/Makefile.am.


Fri, 14 Dec 2012 17:39:31 GMT Frederik Heber <heber@…> [f24af7]
	* src/Actions/FillAction/FillRegularGridAction.cpp (modified)
	* src/molecule.cpp (modified)

	FIX: FillRegularGridAction is now usable with random-atom- ...


Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber <heber@…> [55feea1]
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)

	molecule::getBoundingShape() can now be given an additional boundary ...


Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber <heber@…> [0e2e6c]
	* src/Filling/Inserter/RandomInserter.cpp (modified)

	DEBUG: Checked that RandomInserter does its job correctly (correct
	undo).


Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber <heber@…> [35ec9c]
	* src/Filling/ClusterInterface.cpp (added)
	* src/Filling/ClusterInterface.hpp (modified)
	* src/Filling/Makefile.am (modified)

	Added output operator to ClusterInterface.


Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber <heber@…> [5251af]
	* src/Thermostats/ThermoStatContainer.cpp (modified)

	FIX: ThermoStatContainer generated a default thermostat but did not ...


Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber <heber@…> [4882d5]
	* src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.def (modified)
	* src/Atom/atom_atominfo.cpp (modified)
	* src/Atom/atom_atominfo.hpp (modified)
	* src/Dynamics/VerletForceIntegration.hpp (modified)
	* src/Thermostats/ThermoStatContainer.hpp (modified)
	* tests/Python/AllActions/options.dat (modified)
	* tests/regression/Molecules/VerletIntegration/post/test.conf (modified)
	* tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified)

	Rewrote VerletIntegrationAction to diminish dependence on ...


Fri, 14 Dec 2012 17:38:49 GMT Frederik Heber <heber@…> [8b886f]
	* src/Actions/GlobalListOfActions.hpp (modified)
	* src/Actions/Makefile.am (modified)
	* src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (added)
	* src/Actions/MoleculeAction/ChangeBondAngleAction.def (added)
	* src/Actions/MoleculeAction/ChangeBondAngleAction.hpp (added)
	* tests/Python/AllActions/options.dat (modified)
	* tests/regression/Makefile.am (modified)
	* tests/regression/Molecules/ChangeBondAngle/post/water.pdb (added)
	* tests/regression/Molecules/ChangeBondAngle/pre/water.pdb (added)
	* tests/regression/Molecules/ChangeBondAngle/testsuite-molecules-change-bond-angle.at (added)
	* tests/regression/Molecules/testsuite-molecules.at (modified)

	Added ChangeBondAngleAction that changes the bond angle while keeping ...


Fri, 14 Dec 2012 14:30:23 GMT Frederik Heber <heber@…> [f63e41]
	* src/Actions/BondAction/BondAddAction.cpp (added)
	* src/Actions/BondAction/BondAddAction.def (added)
	* src/Actions/BondAction/BondAddAction.hpp (added)
	* src/Actions/BondAction/BondRemoveAction.cpp (added)
	* src/Actions/BondAction/BondRemoveAction.def (added)
	* src/Actions/BondAction/BondRemoveAction.hpp (added)
	* src/Actions/GlobalListOfActions.hpp (modified)
	* src/Actions/Makefile.am (modified)
	* src/Atom/atom_bondedparticle.cpp (modified)
	* src/Atom/atom_bondedparticle.hpp (modified)
	* src/Atom/atom_bondedparticleinfo.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.cpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser.hpp (modified)
	* src/UIElements/Menu/MenuDescription.cpp (modified)
	* tests/regression/Bond/Add/post/test.pdb (added)
	* tests/regression/Bond/Add/pre/test.pdb (added)
	* tests/regression/Bond/Add/testsuite-bond-add.at (added)
	* tests/regression/Bond/Remove/post/test.pdb (added)
	* tests/regression/Bond/Remove/pre/test.pdb (added)
	* tests/regression/Bond/Remove/testsuite-bond-remove.at (added)
	* tests/regression/Bond/testsuite-bond.at (added)
	* tests/regression/Makefile.am (modified)
	* tests/regression/testsuite.at (modified)

	Added Actions to add and remove a bond in between two atoms.

	- ...


Fri, 14 Dec 2012 14:30:22 GMT Frederik Heber <heber@…> [cb2465]
	* src/Actions/AtomAction/AddAction.hpp (modified)
	* src/Actions/AtomAction/RemoveAction.hpp (modified)

	FIX: Changed Atom's AddAction and RemoveAction header inclusion ...


Fri, 14 Dec 2012 14:29:54 GMT Frederik Heber <heber@…> [e85169]
	* src/Fragmentation/BondsPerShortestPath.cpp (modified)

	FIX: Prevented errors message occured due to clearing BondsPerSPList. ...


Fri, 14 Dec 2012 14:29:45 GMT Frederik Heber <heber@…> [0cfc27]
	* LinearAlgebra/configure.ac (modified)
	* LinearAlgebra/src/unittests/Makefile.am (modified)
	* configure.ac (modified)
	* src/unittests/Makefile.am (modified)

	If no CPPUNIT is found, compilation of unit tests is disabled.

	- ...


Fri, 14 Dec 2012 14:29:34 GMT Frederik Heber <heber@…> [7ace68]
	* src/Parser/Psi3Parser.cpp (modified)
	* src/Parser/Psi3Parser.hpp (modified)
	* src/Parser/unittests/ParserPsi3UnitTest.cpp (modified)
	* tests/regression/Parser/Psi3/pre/testtwocon.psi (modified)
	* tests/regression/Parser/Psi3/pre/testuhf.psi (modified)

	Added multiplicity guesser for Psi3Parser's UHF.

	- TESTFIX: changed ...


Fri, 14 Dec 2012 14:29:09 GMT Frederik Heber <heber@…> [14de8e1]
	* src/Makefile.am (modified)
	* src/PythonScripting.hpp (added)
	* src/builder_init.cpp (modified)

	Molecuilder parses and executes python script 'molecuilder.py' prior ...


Fri, 14 Dec 2012 13:03:36 GMT Frederik Heber <heber@…> [7ef5b9a]
	* src/UIElements/Dialog.hpp (modified)
	* src/documentation/constructs/actions.dox (modified)

	DOCU: Extended documentation on how values from the user are ...


Fri, 14 Dec 2012 13:03:12 GMT Frederik Heber <heber@…> [6ffc0b]
	* src/documentation/tests/regression-tests.dox (modified)
	* src/documentation/tests/unit-tests.dox (modified)

	DOCU: Enhanced documentation of tests with information from TRAC.


Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber <heber@…> [3b75c2]
	* src/Parser/FormatParserStorage.cpp (modified)
	* src/Parser/FormatParser_common.cpp (modified)

	FIX: FormatParserStorage now first deletes the parser, that flushes ...


Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber <heber@…> [fc41df]
	* src/Parser/TremoloParser.cpp (modified)

	FIX: TremoloParser::readAtomDataLine now uses const ref word and ...


Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber <heber@…> [05e2ed]
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/TremoloParser.hpp (modified)
	* src/Parser/unittests/ParserTremoloUnitTest.cpp (modified)
	* tests/regression/Makefile.am (modified)
	* tests/regression/Parser/Tremolo/pre/bio.data (added)
	* tests/regression/Parser/Tremolo/pre/bio.potentials (added)
	* tests/regression/Parser/Tremolo/testsuite-parser-tremolo-improper.at (added)
	* tests/regression/Parser/testsuite-parser.at (modified)

	FIX: TremoloParser did not load/save imprData or torsion correctly.
 ...


Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber <heber@…> [67ab71]
	* src/Parser/TremoloParser.cpp (modified)
	* tests/regression/Parser/Tremolo-Potentials/post/test.data (modified)
	* tests/regression/Parser/Tremolo/post/test.data (modified)
	* tests/regression/Parser/Tremolo/post/test_xyz.data (added)
	* tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save.at (modified)

	FIX: default's resSeq in TremoloParser written inconsistently.

	- ...


Fri, 14 Dec 2012 13:02:49 GMT Frederik Heber <heber@…> [a86cda]
	* src/Parser/TremoloParser.cpp (modified)

	FIX: TremoloParser tripped over following tab in ATOMDATA line.

	- ...


Fri, 14 Dec 2012 13:02:14 GMT Frederik Heber <heber@…> [0d97b4]
	* tests/regression/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at (modified)
	* tests/regression/Analysis/CalculateCellVolume/testsuite-analysis-calculate-cell-volume.at (modified)
	* tests/regression/Analysis/CalculateMolarMass/testsuite-analysis-calculate-molar-mass.at (modified)
	* tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/testsuite-analysis-dipole-angular-correlation-periodic-boundaries.at (modified)
	* tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified)
	* tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified)
	* tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (modified)
	* tests/regression/Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at (modified)
	* tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified)
	* tests/regression/Analysis/PointCorrelation/testsuite-analysis-point-correlation.at (modified)
	* tests/regression/Analysis/PrincipalAxisSystem/testsuite-analysis-principal-axis-system.at (modified)
	* tests/regression/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified)
	* tests/regression/Analysis/testsuite-analysis.at (modified)
	* tests/regression/Atoms/Add/testsuite-atoms-add.at (modified)
	* tests/regression/Atoms/ChangeElement/testsuite-atoms-change-element.at (modified)
	* tests/regression/Atoms/Remove/testsuite-atoms-remove.at (modified)
	* tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified)
	* tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified)
	* tests/regression/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at (modified)
	* tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified)
	* tests/regression/Atoms/testsuite-atoms.at (modified)
	* tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified)
	* tests/regression/Domain/BoundInBox/testsuite-domain-bound-in-box.at (modified)
	* tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified)
	* tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified)
	* tests/regression/Domain/ChangeBox/testsuite-domain-change-box.at (modified)
	* tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified)
	* tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified)
	* tests/regression/Domain/SetBoundaryConditions/testsuite-domain-set-boundary-conditions.at (modified)
	* tests/regression/Domain/testsuite-domain.at (modified)
	* tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (modified)
	* tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (modified)
	* tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (modified)
	* tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid-with-surface.at (modified)
	* tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid.at (modified)
	* tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified)
	* tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified)
	* tests/regression/Filling/testsuite-filling.at (modified)
	* tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified)
	* tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified)
	* tests/regression/Fragmentation/testsuite-fragmentation.at (modified)
	* tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified)
	* tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (modified)
	* tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified)
	* tests/regression/Graph/testsuite-graph.at (modified)
	* tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified)
	* tests/regression/Molecules/BondFile/testsuite-molecules-tremolo-dbond-file.at (modified)
	* tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified)
	* tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at (modified)
	* tests/regression/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at (modified)
	* tests/regression/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at (modified)
	* tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified)
	* tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified)
	* tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified)
	* tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (modified)
	* tests/regression/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at (modified)
	* tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond.at (modified)
	* tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified)
	* tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified)
	* tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified)
	* tests/regression/Molecules/testsuite-molecules.at (modified)
	* tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified)
	* tests/regression/Options/ElementsDb/testsuite-options-elements-db.at (modified)
	* tests/regression/Options/ElementsDb/testsuite-options-no-elements-db.at (modified)
	* tests/regression/Options/Empty/testsuite-options-empty-configs.at (modified)
	* tests/regression/Options/FastParsing/testsuite-options-fast-parsing.at (modified)
	* tests/regression/Options/Help/testsuite-options-help.at (modified)
	* tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified)
	* tests/regression/Options/SetDefaultName/testsuite-options-set-default-name.at (modified)
	* tests/regression/Options/SetWorldTime/testsuite-options-set-world-time.at (modified)
	* tests/regression/Options/Verbosity/testsuite-options-verbosity.at (modified)
	* tests/regression/Options/Warranty/testsuite-options-warranty.at (modified)
	* tests/regression/Options/testsuite-options.at (modified)
	* tests/regression/Parser/Mpqc/testsuite-parser-mpqc-empty.at (modified)
	* tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at (modified)
	* tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified)
	* tests/regression/Parser/Mpqc/testsuite-parser-mpqc-save.at (modified)
	* tests/regression/Parser/Pcp/testsuite-parser-pcp-empty.at (modified)
	* tests/regression/Parser/Pcp/testsuite-parser-pcp-load-multiply.at (modified)
	* tests/regression/Parser/Pcp/testsuite-parser-pcp-load.at (modified)
	* tests/regression/Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at (modified)
	* tests/regression/Parser/Pcp/testsuite-parser-pcp-save.at (modified)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb-CONECTs_empty_space.at (modified)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb-capital_letters_element.at (modified)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb-empty.at (modified)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb-load-multiply.at (modified)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb-load-various.at (modified)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb-load.at (modified)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at (modified)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb-save.at (modified)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb-with-conects.at (modified)
	* tests/regression/Parser/Psi3/testsuite-parser-psi3-empty.at (modified)
	* tests/regression/Parser/Psi3/testsuite-parser-psi3-load-multiply.at (modified)
	* tests/regression/Parser/Psi3/testsuite-parser-psi3-load.at (modified)
	* tests/regression/Parser/Psi3/testsuite-parser-psi3-save.at (modified)
	* tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (modified)
	* tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (modified)
	* tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-none.at (modified)
	* tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-theory.at (modified)
	* tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at (modified)
	* tests/regression/Parser/SetParameters/Psi3/testsuite-parser-set-parameters-psi3-reference.at (modified)
	* tests/regression/Parser/SetParameters/Psi3/testsuite-parser-set-parameters-psi3-wavefunction.at (modified)
	* tests/regression/Parser/Tremolo-Exttypes/testsuite-parser-tremolo-save-selected-atoms-as-exttypes.at (modified)
	* tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-load.at (modified)
	* tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-save.at (modified)
	* tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials.at (modified)
	* tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at (modified)
	* tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (modified)
	* tests/regression/Parser/Tremolo/testsuite-parser-tremolo-empty.at (modified)
	* tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at (modified)
	* tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load.at (modified)
	* tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save-unique_usedfields.at (modified)
	* tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save.at (modified)
	* tests/regression/Parser/Xyz/testsuite-parser-xyz-empty.at (modified)
	* tests/regression/Parser/Xyz/testsuite-parser-xyz-load-multiply.at (modified)
	* tests/regression/Parser/Xyz/testsuite-parser-xyz-load-various.at (modified)
	* tests/regression/Parser/Xyz/testsuite-parser-xyz-load.at (modified)
	* tests/regression/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at (modified)
	* tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified)
	* tests/regression/Parser/testsuite-parser.at (modified)
	* tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified)
	* tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified)
	* tests/regression/RandomNumbers/testsuite-randomnumbers.at (modified)
	* tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-select-all-atoms.at (modified)
	* tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-unselect-all-atoms.at (modified)
	* tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-select-all-atoms-of-molecule.at (modified)
	* tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-unselect-all-atoms-of-molecule.at (modified)
	* tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-select-atoms-by-element.at (modified)
	* tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-unselect-atoms-by-element.at (modified)
	* tests/regression/Selection/Atoms/AtomById/testsuite-selection-select-atom-by-id-multiple.at (modified)
	* tests/regression/Selection/Atoms/AtomById/testsuite-selection-select-atom-by-id.at (modified)
	* tests/regression/Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id-multiple.at (modified)
	* tests/regression/Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id.at (modified)
	* tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-select-atom-by-order.at (modified)
	* tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-unselect-atom-by-order.at (modified)
	* tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified)
	* tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified)
	* tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified)
	* tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified)
	* tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified)
	* tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified)
	* tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified)
	* tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at (modified)
	* tests/regression/Selection/Atoms/InvertAtoms/testsuite-selection-invert-atoms.at (modified)
	* tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified)
	* tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-select-all-molecules.at (modified)
	* tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-unselect-all-molecules.at (modified)
	* tests/regression/Selection/Molecules/ClearMolecules/testsuite-selection-clear-molecules.at (modified)
	* tests/regression/Selection/Molecules/InvertMolecules/testsuite-selection-invert-molecules.at (modified)
	* tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-select-molecules-by-formula.at (modified)
	* tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-unselect-molecules-by-formula.at (modified)
	* tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at (modified)
	* tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at (modified)
	* tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-select-molecules-by-name.at (modified)
	* tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-unselect-molecules-by-name.at (modified)
	* tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-backward.at (modified)
	* tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-forward.at (modified)
	* tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-backward.at (modified)
	* tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-forward.at (modified)
	* tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-select-atoms-molecules.at (modified)
	* tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-unselect-atoms-molecules.at (modified)
	* tests/regression/Selection/Molecules/testsuite-selection-molecules.at (modified)
	* tests/regression/Selection/testsuite-selection.at (modified)
	* tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified)
	* tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified)
	* tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified)
	* tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified)
	* tests/regression/Tesselation/testsuite-tesselation.at (modified)
	* tests/regression/testsuite.at (modified)

	FIX: Disclaimer appeared twice in each testsuite. Second time
	removed.


Fri, 14 Dec 2012 13:01:57 GMT Frederik Heber <heber@…> [1d02c2d]
	* src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified)

	FIX: GLWorldView lacked molecule include.


Fri, 14 Dec 2012 13:01:56 GMT Frederik Heber <heber@…> [8ce730]
	* src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified)

	FIX: Issue related to LOG_OBSERVER in ...


Fri, 14 Dec 2012 11:03:46 GMT Frederik Heber <heber@…> [c8f12e]
	* configure.ac (modified)

	Set version to 1.3.7

	- Codename "Fine structure constant" (the fine ...