#
# ChangeLog for /
#
# Generated by Trac 1.4.4
# Dec 29, 2024, 4:04:59 PM

Wed, 02 Mar 2011 21:48:20 GMT Frederik Heber <heber@…> [435065]
	* src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified)
	* src/Actions/MoleculeAction/VerletIntegrationAction.def (modified)
	* src/Dynamics/VerletForceIntegration.hpp (added)
	* src/Makefile.am (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* tests/regression/Molecules/VerletIntegration/post/test.conf (moved)
	* tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified)

	Rewrote VerletForceIntegration into a functor in Dynamics/.

	- we ...


Wed, 02 Mar 2011 21:40:51 GMT Frederik Heber <heber@…> [eb33c4]
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified)
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified)
	* src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified)
	* tests/regression/Molecules/LinearInterpolationofTrajectories/post/teststep.conf (added)
	* tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at (modified)

	LinearInterpolationofTrajectoriesAction only interpolates, does not ...


Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber <heber@…> [e355762]
	* src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified)
	* src/Dynamics/MinimiseConstrainedPotential.cpp (modified)
	* src/Dynamics/MinimiseConstrainedPotential.hpp (modified)
	* src/molecule_dynamics.cpp (modified)

	Rewrote MinimiseConstrainedPotential to just use std::map instead of ...


Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber <heber@…> [fe6f20]
	* src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (added)
	* src/Actions/AtomAction/SaveSelectedAtomsAction.def (added)
	* src/Actions/AtomAction/SaveSelectedAtomsAction.hpp (moved)
	* src/Actions/Makefile.am (modified)
	* src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (moved)
	* src/Actions/MoleculeAction/SaveSelectedMoleculesAction.def (moved)
	* src/Actions/MoleculeAction/SaveSelectedMoleculesAction.hpp (added)
	* tests/regression/Atoms/SaveSelectedAtoms/post/testsave.xyz (added)
	* tests/regression/Atoms/SaveSelectedAtoms/pre/test.xyz (added)
	* tests/regression/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at (added)
	* tests/regression/Atoms/testsuite-atoms.at (modified)
	* tests/regression/Makefile.am (modified)
	* tests/regression/Molecules/SaveSelectedMolecules/post/testsave.xyz (added)
	* tests/regression/Molecules/SaveSelectedMolecules/pre/test.xyz (added)
	* tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (added)
	* tests/regression/Molecules/testsuite-molecules.at (modified)

	New Action SaveSelectedAtoms and renamed SaveAction -> ...


Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber <heber@…> [8009ce]
	* src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveTemperatureAction.def (modified)
	* src/AtomSet.hpp (modified)
	* src/Dynamics/OutputTemperature.hpp (added)
	* src/Makefile.am (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* tests/regression/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at (modified)

	Rewrote OutputTemperature into a functor in Dynamics/

	- formerly ...


Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber <heber@…> [20943b]
	* src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified)
	* src/Dynamics/LinearInterpolationBetweenSteps.hpp (added)
	* src/Makefile.am (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)

	Rewrote LinearInterpolationBetweenSteps into a functor in Dynamics/
 ...


Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber <heber@…> [9e23a3]
	* src/Dynamics/MinimiseConstrainedPotential.cpp (added)
	* src/Dynamics/MinimiseConstrainedPotential.hpp (added)
	* src/Makefile.am (modified)
	* src/molecule.hpp (modified)
	* src/molecule_dynamics.cpp (modified)

	Rewrote MinimiseConstrainedPotential into a functor in Dynamics/.

	- ...


Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber <heber@…> [632508]
	* src/Actions/CommandAction/BondLengthTableAction.cpp (modified)
	* src/Actions/CommandAction/BondLengthTableAction.def (modified)
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/Graph/BondGraph.cpp (moved)
	* src/Graph/BondGraph.hpp (moved)
	* src/Makefile.am (modified)
	* src/World.cpp (modified)
	* src/builder_init.cpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)

	Moved files bondgraph.?pp -> Graph/BondGraph.?pp.


Tue, 01 Mar 2011 13:17:09 GMT Frederik Heber <heber@…> [607eab]
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)

	BondGraph::...MinMaxDistance() now return range<double> instead of ...


Tue, 01 Mar 2011 13:17:08 GMT Frederik Heber <heber@…> [cff66c]
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)

	Removed bool is Angstroem from all BondGraph::...() member functions. ...


Tue, 01 Mar 2011 13:17:08 GMT Frederik Heber <heber@…> [111f4a]
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)

	Const-ness and cosmetic fixes to class BondGraph.

	- made ...


Tue, 01 Mar 2011 13:17:08 GMT Frederik Heber <heber@…> [0ec7fe]
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)

	Removed BondGraph::max_distance along with getter and setter.

	- ...


Tue, 01 Mar 2011 13:17:08 GMT Frederik Heber <heber@…> [300220]
	* configure.ac (modified)
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)

	BondGraph::..MinMaxDistance() changed to use range<double>.

	- ...


Tue, 01 Mar 2011 13:17:07 GMT Frederik Heber <heber@…> [0cbad2]
	* src/Actions/MoleculeAction/BondFileAction.cpp (modified)
	* src/Actions/MoleculeAction/BondFileAction.def (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* tests/regression/Molecules/BondFile/post/test.pdb (added)
	* tests/regression/Molecules/BondFile/pre/silica.dbond.0000 (added)
	* tests/regression/Molecules/BondFile/pre/silica.pov1.0000.pdb (added)
	* tests/regression/Molecules/BondFile/pre/test.dbond (modified)
	* tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at (modified)

	Moved molecule::CreateAdjacencyListFromDbondFile() over to BondGraph ...


Tue, 01 Mar 2011 12:49:28 GMT Frederik Heber <heber@…> [3738f0]
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/AtomSet.hpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)
	* tests/Fragmentations/defs.in (modified)
	* tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified)
	* tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified)
	* tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified)
	* tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified)

	Moved molecule::CreateAdjacencyList over to class BondGraph.

	to ...


Tue, 01 Mar 2011 10:16:46 GMT Frederik Heber <heber@…> [ce5f05]
	* src/Helpers/defs.hpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)

	Moved Shading and EdgeType from defs.hpp to bond.hpp, getColor from ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [4092c5]
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Changed BondGraph::...MinMaxDistance()'s parameters to const ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [b9772a]
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Renamed function pointer in molecule::CreateAdjacencyList to ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [4b5cf8]
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)

	BondedParticle::OutputBondOfAtom() now takes stream to print to.


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [458c31]
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)

	molecule::BondCount is now Cachable and private.

	- renamed ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [d4a44c]
	* src/Actions/FragmentationAction/CreateAdjacencyAction.cpp (moved)
	* src/Actions/FragmentationAction/CreateAdjacencyAction.def (moved)
	* src/Actions/FragmentationAction/CreateAdjacencyAction.hpp (moved)
	* src/Actions/Makefile.am (modified)
	* tests/regression/Graph/1/pre/test2.conf (deleted)

	Renamed ConstructBondGraphAction -> CreateAdjacencyAction.


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [715b67]
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)
	* src/unittests/AnalysisBondsUnitTest.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)
	* src/unittests/CountBondsUnitTest.cpp (modified)

	Renamed BondGraph::ConstructBondGraph -> CreateAdjacencyForMolecule.
 ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [7adf0f]
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)

	Removed molecule::BondDistance, replaced by ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [e7350d4]
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)

	DOCUFIX: BondGraph - moved doxygen comments from cpp to header.


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [72d90e]
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/FragmentationAction.cpp (modified)
	* src/bondgraph.cpp (modified)
	* src/bondgraph.hpp (modified)

	New function BondGraph::getMinMaxDistance().

	- Covalent and ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [f71baf]
	* src/Actions/CommandAction/BondLengthTableAction.cpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified)
	* src/Actions/MoleculeAction/SaveBondsAction.cpp (modified)
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/builder_init.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/molecule_graph.cpp (modified)

	Made BondGraph an instance of World, removed from config.

	- ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [5309ba]
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/BoundaryPointSet.cpp (modified)
	* src/BoundaryPointSet.hpp (modified)
	* src/Helpers/helpers.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/tesselation.cpp (modified)

	Renamed ParticleInfo_nr back to Nr.

	- Note that this mostly ...


Tue, 01 Mar 2011 10:16:39 GMT Frederik Heber <heber@…> [735b1c]
	* src/BoundaryPointSet.cpp (modified)
	* src/BoundaryPointSet.hpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)

	ParticleInfo::ParticleInfo_nr is protected and accessed via ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [a479fa]
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/BoundaryPointSet.cpp (modified)
	* src/BoundaryPointSet.hpp (modified)
	* src/Helpers/helpers.hpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_particleinfo.hpp (modified)
	* src/bond.cpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/parser.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/unittests/TesselationUnitTest.cpp (modified)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified)

	Renamed ParticleInfo::nr to ParticleInfo::ParticleInfo_nr for easier ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [5702cdb]
	* src/Makefile.am (modified)
	* src/molecule.hpp (modified)
	* src/molecule_pointcloud.cpp (deleted)

	Removed molecule_pointcloud.cpp.


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [caa06ef]
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/IPointCloud.hpp (modified)
	* src/PointCloudAdaptor.hpp (modified)
	* src/boundary.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/TesselationUnitTest.cpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (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)

	Added name to PointCloudAdaptor, set by constructor.

	- name is used ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [34c43a]
	* configure.ac (modified)
	* src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified)
	* src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified)
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified)
	* src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified)
	* src/IPointCloud.hpp (added)
	* src/Makefile.am (modified)
	* src/PointCloud.cpp (deleted)
	* src/PointCloud.hpp (deleted)
	* src/PointCloudAdaptor.hpp (added)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* src/ellipsoid.cpp (modified)
	* src/linkedcell.cpp (modified)
	* src/linkedcell.hpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/molecule_pointcloud.cpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)
	* src/tesselationhelpers.cpp (modified)
	* src/tesselationhelpers.hpp (modified)
	* src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified)
	* src/unittests/LinkedCellUnitTest.cpp (modified)
	* src/unittests/TesselationUnitTest.cpp (modified)
	* src/unittests/TesselationUnitTest.hpp (modified)
	* src/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified)
	* src/unittests/Tesselation_InsideOutsideUnitTest.hpp (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)

	Bigger change: Replaced PointCloud by PointCloudAdaptor.

	- ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [ba5215]
	* src/BoundaryPointSet.cpp (modified)
	* src/BoundaryPointSet.hpp (modified)
	* src/TesselPoint.cpp (modified)
	* src/TesselPoint.hpp (modified)
	* src/atom_particleinfo.cpp (modified)
	* src/atom_particleinfo.hpp (modified)

	Extended BoundaryPointSet by functions to directly access TesselPoint ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [fa60dd]
	* src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified)

	Removed molecule::GetName() usage in QtMoleculeView.

	- in ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [fff733]
	* src/PointCloud.hpp (modified)
	* src/tesselation.cpp (modified)
	* src/tesselation.hpp (modified)

	Fixed PointCloud implementation in class Tesselation.

	- removed ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [e34254]
	* src/atom_atominfo.cpp (modified)

	Changed operator<< (AtomInfo), less verbose for single time step.


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [4d5553]
	* src/config.cpp (modified)

	Changed verbosity for LoadMolecule().


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [b23e26]
	* src/parser.cpp (modified)
	* src/parser.hpp (modified)

	Added operator<< for MatrixContainer class.


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [1bfc8e]
	* src/Parser/PcpParser.cpp (modified)
	* src/config.cpp (modified)
	* src/config.hpp (modified)
	* src/molecule_dynamics.cpp (modified)

	Removed ThermostatContainer instance from config, instance from World ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [9b8387]
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified)
	* src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified)

	DOCUFIX: enhanced description of RotateAroundSelfByAngleAction's ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [9d37ac]
	* src/molecule_graph.cpp (modified)

	DOCUFIX: Removed *out as parameter from waaay back ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [4afa46]
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/XyzParser.cpp (modified)

	Added call to molecule::getAtomCount() to end of each parser's ...


Tue, 01 Mar 2011 10:16:38 GMT Frederik Heber <heber@…> [637358]
	* src/Parser/XyzParser.cpp (modified)

	Changed slightly XyzParser::load().

	- AddedAtoms is now a vector.


Tue, 01 Mar 2011 10:16:37 GMT Frederik Heber <heber@…> [0180d6]
	* src/Parser/XyzParser.cpp (modified)
	* src/Parser/unittests/ParserXyzUnitTest.cpp (modified)
	* src/Parser/unittests/ParserXyzUnitTest.hpp (modified)
	* tests/regression/Parser/Xyz/post/testmulti.xyz (added)
	* tests/regression/Parser/Xyz/pre/testmulti.xyz (added)
	* tests/regression/Parser/Xyz/testsuite-parser-xyz.at (modified)

	Enhanced XyzParser to load and save multiple time steps.

	- Extended ...


Thu, 24 Feb 2011 20:22:51 GMT Frederik Heber <heber@…> [c6aeb1]
	* tests/regression/Parser/Pdb/post/test_conect.pdb (added)
	* tests/regression/Parser/Pdb/pre/test_conect.pdb (added)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb.at (modified)

	Added regression test for Parser/Pdb for PDB files with CONECT
	entries.


Thu, 24 Feb 2011 20:22:02 GMT Frederik Heber <heber@…> [48801a]
	* src/Parser/PdbParser.cpp (modified)

	Decreased verbosity of PdbParser for multiple time steps.

	- using ...


Thu, 24 Feb 2011 20:20:57 GMT Frederik Heber <heber@…> [3e383d]
	* src/Parser/PdbAtomInfoContainer.cpp (modified)
	* src/Parser/PdbAtomInfoContainer.hpp (modified)
	* src/Parser/PdbKey.hpp (modified)

	Removed PdbKey::timestep from PdbAtomInfoContainer as ...


Thu, 24 Feb 2011 20:18:39 GMT Frederik Heber <heber@…> [b0a2e3]
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/PdbParser.hpp (modified)

	Removed use of PdbKey::timestep, steps are parsed sequentially.

	- ...


Thu, 24 Feb 2011 20:09:50 GMT Frederik Heber <heber@…> [09c7a9]
	* src/Parser/PdbParser.cpp (modified)

	VERBOSE: PdbParser::save() print parsed trajectories.


Thu, 24 Feb 2011 19:55:33 GMT Frederik Heber <heber@…> [873037]
	* src/Parser/PdbAtomInfoContainer.cpp (modified)
	* src/Parser/PdbAtomInfoContainer.hpp (modified)
	* src/Parser/PdbParser.cpp (modified)

	Refined static filling of PdbAtomInfoContainer::knownDataKeys.

	- ...


Thu, 24 Feb 2011 19:55:15 GMT Frederik Heber <heber@…> [9dba5f]
	* src/Parser/PdbAtomInfoContainer.cpp (modified)
	* src/Parser/PdbAtomInfoContainer.hpp (modified)
	* src/Parser/PdbKey.hpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/PdbParser.hpp (modified)
	* tests/regression/Parser/Pdb/post/testmulti.pdb (added)
	* tests/regression/Parser/Pdb/post/testmulti2.pdb (added)
	* tests/regression/Parser/Pdb/pre/testmulti.pdb (added)
	* tests/regression/Parser/Pdb/pre/testmulti2.pdb (added)
	* tests/regression/Parser/Pdb/testsuite-parser-pdb.at (modified)

	PdbParser can now load and save multiple time steps.

	- WARNING: ...


Thu, 24 Feb 2011 19:48:13 GMT Frederik Heber <heber@…> [fcac72]
	* src/Parser/PcpParser.cpp (modified)
	* src/config.cpp (modified)
	* tests/regression/Parser/Pcp/post/testmulti.conf (added)
	* tests/regression/Parser/Pcp/pre/testmulti.conf (added)
	* tests/regression/Parser/Pcp/testsuite-parser-pcp.at (modified)

	Added multiple time steps to PcpParser::OutputAtoms().

	- removed ...


Thu, 24 Feb 2011 19:47:41 GMT Frederik Heber <heber@…> [6a465e]
	* src/ConfigFileBuffer.cpp (modified)
	* src/Parser/unittests/ParserPcpUnitTest.cpp (modified)
	* src/config.cpp (modified)
	* tests/regression/Molecules/SaveTemperature/post/test.ekin (modified)

	Rewrote LoadMolecule() for PcpParser.

	- LoadMolecule() rewritten as ...


Thu, 24 Feb 2011 19:43:03 GMT Frederik Heber <heber@…> [03c77c]
	* src/ConfigFileBuffer.cpp (modified)
	* src/Makefile.am (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/bond.cpp (modified)
	* src/bond.hpp (modified)
	* src/config.cpp (modified)
	* src/graph.hpp (modified)
	* src/lists.hpp (deleted)
	* src/molecule.cpp (modified)
	* src/molecule.hpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/periodentafel.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)

	bonds::previous and ::next removed, lists.hpp deleted.

	- the last ...


Thu, 24 Feb 2011 19:39:42 GMT Frederik Heber <heber@…> [8aba3c]
	* src/unittests/ListOfBondsUnitTest.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.hpp (modified)

	TEST: Extended ListOfBondsUnitTest for multiple time steps ...


Thu, 24 Feb 2011 19:36:56 GMT Frederik Heber <heber@…> [af897f]
	* src/atom_bondedparticle.cpp (modified)

	Small change to BondedParticle::UnregisterAllBond().

	- As ...


Thu, 24 Feb 2011 19:33:17 GMT Frederik Heber <heber@…> [583081]
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/moleculelist.cpp (modified)

	New function BondedParticle::ClearBondsAtStep(), used by ...


Thu, 24 Feb 2011 19:32:28 GMT Frederik Heber <heber@…> [38c44b]
	* src/atom_bondedparticleinfo.cpp (modified)

	Added verbosity to AppendTrajectoryStep() of BondedParticle.


Thu, 24 Feb 2011 19:32:10 GMT Frederik Heber <heber@…> [1e6249]
	* src/atom.cpp (modified)
	* src/atom_bondedparticleinfo.cpp (modified)
	* src/atom_bondedparticleinfo.hpp (modified)

	BondedParticle has virtual UpdateSteps() to allow consistent ...


Thu, 24 Feb 2011 19:26:14 GMT Frederik Heber <heber@…> [073a9e4]
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/unittests/ParserTremoloUnitTest.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)
	* src/molecule.cpp (modified)
	* src/unittests/BondGraphUnitTest.cpp (modified)

	BondedParticle::(Un)RegisterBond,AddBond,IsBondedTo with step.

	- ...


Thu, 24 Feb 2011 19:09:31 GMT Frederik Heber <heber@…> [d557374]
	* src/atom_bondedparticle.cpp (modified)
	* src/bond.cpp (modified)

	Cosmetic changes to class bond::~bond and
	BondedParticle::UnregisterBond.


Thu, 24 Feb 2011 19:06:37 GMT Frederik Heber <heber@…> [93c6e9]
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)

	BondedParticle::UnregisterBond() uses ...


Thu, 24 Feb 2011 18:59:11 GMT Frederik Heber <heber@…> [9a3a53]
	* src/atom_bondedparticleinfo.hpp (modified)

	BondedParticleInfo::ListOfBonds is (just) protected to allow ...


Thu, 24 Feb 2011 18:56:45 GMT Frederik Heber <heber@…> [a2bdbe]
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticle.hpp (modified)

	BondedParticle::UnregisterAllBond with new parameter step.

	- cleans ...


Thu, 24 Feb 2011 18:51:32 GMT Frederik Heber <heber@…> [9d83b6]
	* src/Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified)
	* src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (modified)
	* src/Actions/MoleculeAction/CopyAction.cpp (modified)
	* src/Parser/PdbParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/WorldTime.hpp (modified)
	* src/analysis_bonds.cpp (modified)
	* src/analysis_correlation.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)
	* src/atom_bondedparticleinfo.cpp (modified)
	* src/atom_bondedparticleinfo.hpp (modified)
	* src/boundary.cpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_fragmentation.cpp (modified)
	* src/molecule_geometry.cpp (modified)
	* src/molecule_graph.cpp (modified)
	* src/moleculelist.cpp (modified)
	* src/unittests/ListOfBondsUnitTest.cpp (modified)

	BondedParticleInfo now has vector<BondList>

	- vector<BondList> ...


Thu, 24 Feb 2011 18:40:16 GMT Frederik Heber <heber@…> [c0d9eb]
	* src/atom.cpp (modified)
	* src/atom_bondedparticle.cpp (modified)

	FIX: Moved BondedParticle::CountBonds() from atom.cpp to ...


Thu, 24 Feb 2011 18:36:50 GMT Frederik Heber <heber@…> [fb9eba]
	* src/atom_atominfo.cpp (modified)

	Added verbosity to AppendTrajectoryStep() of AtomInfo.


Thu, 24 Feb 2011 18:36:33 GMT Frederik Heber <heber@…> [e2373df]
	* src/TesselPoint.cpp (modified)
	* src/TesselPoint.hpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)

	TesselPoint, Atom and AtomInfo have virtual UpdateSteps() to allow ...


Thu, 24 Feb 2011 18:31:34 GMT Frederik Heber <heber@…> [fb0b62]
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)

	AtomInfo: Commented-out operator* and *= with double.

	- this is ...


Thu, 24 Feb 2011 18:21:47 GMT Frederik Heber <heber@…> [443547]
	* src/atom.cpp (modified)
	* src/atom_atominfo.hpp (modified)

	AtomInfo: AtomicPosition, ..Velocity, ..Force are protected to allow ...


Thu, 24 Feb 2011 18:20:58 GMT Frederik Heber <heber@…> [b1a5d9]
	* src/atom_atominfo.cpp (modified)

	operator<< for AtomInfo now prints just start and end of timestep.


Thu, 24 Feb 2011 18:20:40 GMT Frederik Heber <heber@…> [1b558c]
	* src/atom_atominfo.cpp (modified)

	All Accessor to position, velocity or force use
	WorldTime::CurrentTime.


Thu, 24 Feb 2011 18:15:00 GMT Frederik Heber <heber@…> [6b020f]
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)

	AtomInfo::getter and setter's step is now unsigned int.


Thu, 24 Feb 2011 17:56:03 GMT Frederik Heber <heber@…> [056e70]
	* src/AtomSet.hpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Thermostats/Berendsen.cpp (modified)
	* src/Thermostats/GaussianThermostat.cpp (modified)
	* src/Thermostats/Langevin.cpp (modified)
	* src/Thermostats/NoseHoover.cpp (modified)
	* src/Thermostats/Woodcock.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_geometry.cpp (modified)

	Suffixed getters and setters for AtomInfo trajecories with AtStep.
 ...


Thu, 24 Feb 2011 17:46:46 GMT Frederik Heber <heber@…> [6625c3]
	* src/AtomSet.hpp (modified)
	* src/Makefile.am (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Thermostats/Berendsen.cpp (modified)
	* src/Thermostats/GaussianThermostat.cpp (modified)
	* src/Thermostats/Langevin.cpp (modified)
	* src/Thermostats/Langevin.hpp (modified)
	* src/Thermostats/NoseHoover.cpp (modified)
	* src/Thermostats/Woodcock.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom.hpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/atom_trajectoryparticle.cpp (deleted)
	* src/atom_trajectoryparticle.hpp (deleted)
	* src/atom_trajectoryparticleinfo.cpp (deleted)
	* src/atom_trajectoryparticleinfo.hpp (deleted)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)
	* src/molecule_dynamics.cpp (modified)
	* src/molecule_geometry.cpp (modified)

	Removed atom_trajectoryparticle*, replaced by AtomInfo class now ...


Thu, 24 Feb 2011 16:35:59 GMT Frederik Heber <heber@…> [54b42e]
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)

	AtomInfo::AtomicPosition, ::AtomicVelocity, ::AtomicForce are now a ...


Thu, 24 Feb 2011 16:30:56 GMT Frederik Heber <heber@…> [bce72c]
	* src/AtomicInfo.cpp (modified)
	* src/Parser/PcpParser.cpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/unittests/ParserTremoloUnitTest.cpp (modified)
	* src/atom.cpp (modified)
	* src/atom_atominfo.cpp (modified)
	* src/atom_atominfo.hpp (modified)
	* src/config.cpp (modified)
	* src/molecule.cpp (modified)

	AtomicInfo::AtomicVelocity and ::AtomicForce are now private.

	- ...


Thu, 24 Feb 2011 16:27:00 GMT Frederik Heber <heber@…> [c864a8]
	* src/atom_trajectoryparticle.cpp (modified)
	* src/atom_trajectoryparticle.hpp (modified)
	* src/molecule_dynamics.cpp (modified)

	Moved TrajectoryParticle::EvaluateConstrainedForce() into ...


Thu, 24 Feb 2011 16:26:28 GMT Frederik Heber <heber@…> [76163d]
	* src/World.cpp (modified)

	World::setTime() now checks whether CurrentTime changes at all.

	- ...


Thu, 24 Feb 2011 16:06:21 GMT Frederik Heber <heber@…> [d297a3]
	* src/World.cpp (modified)
	* src/World.hpp (modified)
	* src/WorldTime.hpp (modified)

	World::setTime() is single access point to modifying ...


Thu, 24 Feb 2011 16:05:50 GMT Frederik Heber <heber@…> [6bb605]
	* src/Actions/WorldAction/SetWorldTimeAction.cpp (modified)
	* src/Makefile.am (modified)
	* src/WorldTime.cpp (modified)
	* src/WorldTime.hpp (modified)
	* src/unittests/WorldTimeUnitTest.cpp (modified)

	Worldtime now has static CurrentTime and static (inline) ...


Thu, 24 Feb 2011 16:01:50 GMT Frederik Heber <heber@…> [aa04ae]
	* src/Actions/Makefile.am (modified)
	* src/Actions/WorldAction/SetWorldTimeAction.cpp (added)
	* src/Actions/WorldAction/SetWorldTimeAction.def (added)
	* src/Actions/WorldAction/SetWorldTimeAction.hpp (added)
	* tests/regression/Makefile.am (modified)
	* tests/regression/Options/SetWorldTime/testsuite-options-set-world-time.at (added)
	* tests/regression/Options/testsuite-options.at (modified)

	Implemented SetWorldTimeAction and regression test on that.

	- ...


Thu, 24 Feb 2011 15:54:52 GMT Frederik Heber <heber@…> [f649de]
	* src/Makefile.am (modified)
	* src/WorldTime.cpp (added)
	* src/WorldTime.hpp (added)
	* src/unittests/Makefile.am (modified)
	* src/unittests/WorldTimeUnitTest.cpp (added)
	* src/unittests/WorldTimeUnitTest.hpp (added)

	Implemented class WorldTime.

	- WorldTime contains the current, ...


Fri, 11 Feb 2011 21:37:26 GMT Frederik Heber <heber@…> [7a51be]
	* src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified)
	* src/Actions/MoleculeAction/FillWithMoleculeAction.def (modified)
	* src/Parser/FormatParserStorage.cpp (modified)
	* src/Parser/FormatParserStorage.hpp (modified)
	* src/boundary.cpp (modified)
	* src/boundary.hpp (modified)
	* tests/regression/Filling/FillVoidWithMolecule/pre/water.data (modified)
	* tests/regression/Filling/FillWithMolecule/post/empty.xyz (added)
	* tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (modified)

	new function FormatParserStorage::get to obtain specialized ...


Fri, 11 Feb 2011 20:55:44 GMT Frederik Heber <heber@…> [170ba6]
	* configure.ac (modified)
	* src/Descriptors/MoleculeOrderDescriptor.cpp (modified)
	* tests/regression/Makefile.am (modified)
	* tests/regression/Selection/Atoms/testsuite-selection-atoms.at (added)
	* tests/regression/Selection/Molecules/MoleculeByOrder/post/empty.xyz (added)
	* tests/regression/Selection/Molecules/MoleculeByOrder/post/twowater.xyz (added)
	* tests/regression/Selection/Molecules/MoleculeByOrder/post/water_id0.xyz (added)
	* tests/regression/Selection/Molecules/MoleculeByOrder/post/water_id1.xyz (added)
	* tests/regression/Selection/Molecules/MoleculeByOrder/pre/twowater.xyz (added)
	* tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-molecule-by-order.at (added)
	* tests/regression/Selection/Molecules/testsuite-selection-molecules.at (added)
	* tests/regression/Selection/testsuite-selection.at (modified)

	BUGFIX: MoleculeOrderDescription was not working in reverse because ...


Fri, 11 Feb 2011 17:55:25 GMT Frederik Heber <heber@…> [69948e]
	* src/boundary.cpp (modified)

	BUGFIX: FillVoidWithMolecule() crashed when filling molecule is ...


Thu, 10 Feb 2011 19:09:31 GMT Frederik Heber <heber@…> [844b2e]
	* configure.ac (modified)

	We now require CodePatterns v1.0.8 for LOG() shorthand to logger and ...


Thu, 10 Feb 2011 19:09:31 GMT Frederik Heber <heber@…> [23d7ff]
	* src/Actions/Action.cpp (modified)
	* src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.def (modified)
	* src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.def (modified)
	* tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-atoms-inside-cuboid.at (modified)

	Added default rotation angles to (Not)AllAtomsInsideCuboidAction.

	- ...


Thu, 10 Feb 2011 19:09:30 GMT Frederik Heber <heber@…> [528b3e]
	* src/Actions/Makefile.am (modified)
	* src/Actions/Values.cpp (added)
	* src/Actions/Values.hpp (modified)
	* src/Box.cpp (modified)
	* src/Box.hpp (modified)
	* src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified)
	* src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified)
	* src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified)

	Added conversion functions to VectorValue and BoxValue and changed ...


Thu, 10 Feb 2011 19:08:22 GMT Frederik Heber <heber@…> [b6b3b2]
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/MpqcParser_Parameters.cpp (modified)
	* src/Parser/unittests/ParserMpqcUnitTest.cpp (modified)

	Merge branch 'MpqcParser_fixes' into stable


Thu, 10 Feb 2011 19:07:17 GMT Frederik Heber <heber@…> [0bfe73]
	* src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified)
	* src/RandomNumbers/RandomNumberDistributionFactory.hpp (modified)
	* src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified)
	* src/RandomNumbers/RandomNumberEngineFactory.hpp (modified)
	* src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified)
	* src/RandomNumbers/RandomNumberGeneratorFactory.hpp (modified)
	* src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified)

	Merge branch 'RandomNumber_fixes' into stable


Thu, 10 Feb 2011 18:58:48 GMT Frederik Heber <heber@…> [311da7b]
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/MpqcParser_Parameters.cpp (modified)
	* src/Parser/unittests/ParserMpqcUnitTest.cpp (modified)

	FIX: Changed MpqcParser.

	- some ASSERTs were missing and showed up ...


Thu, 10 Feb 2011 18:50:14 GMT Frederik Heber <heber@…> [c14c78]
	* src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified)
	* src/RandomNumbers/RandomNumberDistributionFactory.hpp (modified)
	* src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified)
	* src/RandomNumbers/RandomNumberEngineFactory.hpp (modified)
	* src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified)
	* src/RandomNumbers/RandomNumberGeneratorFactory.hpp (modified)
	* src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified)

	Some bugfixes for RandomNumber... stuff.

	- BUGFIX: Asserts ...


Wed, 09 Feb 2011 20:04:56 GMT Frederik Heber <heber@…> [acd638]
	* src/Parser/TremoloParser.cpp (modified)
	* tests/regression/Molecules/Copy/post/tensid.data (added)
	* tests/regression/Molecules/Copy/pre/tensid.data (added)
	* tests/regression/Molecules/Copy/pre/tensid.potentials (added)
	* tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified)

	BUGFIX: copied atoms were not correctly stored with respect to Type, ...


Wed, 09 Feb 2011 17:25:13 GMT Frederik Heber <heber@…> [4d4d33]
	* src/Actions/Makefile.am (modified)
	* src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (added)
	* src/Actions/ParserAction/ParseTremoloPotentialsAction.def (added)
	* src/Actions/ParserAction/ParseTremoloPotentialsAction.hpp (added)
	* src/Parser/TremoloAtomInfoContainer.cpp (modified)
	* src/Parser/TremoloAtomInfoContainer.hpp (modified)
	* src/Parser/TremoloParser.cpp (modified)
	* src/Parser/TremoloParser.hpp (modified)
	* src/Parser/unittests/ParserTremoloUnitTest.cpp (modified)

	Added tremolo's potential file parsing, reported by Daniel Dueck.
 ...


Mon, 07 Feb 2011 10:45:57 GMT Frederik Heber <heber@…> [1a6bda]
	* src/config.cpp (modified)
	* src/config.hpp (modified)

	Removed basis from config, which now resides in
	MpqcParser_Parameters.


Mon, 07 Feb 2011 10:45:43 GMT Frederik Heber <heber@…> [4cbca0]
	* src/Parser/MpqcParser.cpp (modified)
	* tests/regression/Parser/Mpqc-SetParameters/post/testCLHF.in (added)
	* tests/regression/Parser/Mpqc-SetParameters/pre/testCLHF.in (added)
	* tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters.at (modified)
	* tests/regression/Parser/Mpqc/post/testCLHF.in (added)
	* tests/regression/Parser/Mpqc/post/testCLKS.in (added)
	* tests/regression/Parser/Mpqc/post/testMBPT2.in (moved)
	* tests/regression/Parser/Mpqc/post/testMBPT2_R12.in (added)
	* tests/regression/Parser/Mpqc/pre/testCLHF.in (added)
	* tests/regression/Parser/Mpqc/pre/testCLKS.in (added)
	* tests/regression/Parser/Mpqc/pre/testMBPT2.in (added)
	* tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in (added)
	* tests/regression/Parser/Mpqc/testsuite-parser-mpqc.at (modified)

	Implemented full MpqcParser::load().

	- regression tests for four ...


Mon, 07 Feb 2011 10:43:50 GMT Frederik Heber <heber@…> [963321a]
	* src/Actions/Makefile.am (modified)
	* src/Actions/ParserAction/SetGaussianBasisAction.cpp (deleted)
	* src/Actions/ParserAction/SetMpqcParametersAction.cpp (added)
	* src/Actions/ParserAction/SetMpqcParametersAction.def (moved)
	* src/Actions/ParserAction/SetMpqcParametersAction.hpp (moved)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/MpqcParser.hpp (modified)
	* src/Parser/MpqcParser_Parameters.cpp (modified)
	* tests/regression/Makefile.am (modified)
	* tests/regression/Parser/Mpqc-SetBasis/testsuite-parser-mpqc-set-basis.at (deleted)
	* tests/regression/Parser/Mpqc-SetParameters/pre/test.xyz (added)
	* tests/regression/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters.at (added)
	* tests/regression/Parser/testsuite-parser.at (modified)

	Converted SetGaussianBasisAction into SetMpqcParametersAction.

	- ...


Mon, 07 Feb 2011 10:43:41 GMT Frederik Heber <heber@…> [44fce5]
	* src/Parser/Makefile.am (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/MpqcParser_Parameters.cpp (modified)
	* src/Parser/MpqcParser_Parameters.hpp (modified)
	* src/Parser/MpqcParser_Parameters_initBasis.cpp (added)
	* src/Parser/unittests/ParserMpqcUnitTest.cpp (modified)
	* src/Parser/unittests/ParserMpqcUnitTest.hpp (modified)

	Extended MpqcParser_Parameters, can set and get all values.

	- new ...


Mon, 07 Feb 2011 10:43:35 GMT Frederik Heber <heber@…> [61d69a4]
	* src/Parser/Makefile.am (modified)
	* src/Parser/MpqcParser.cpp (modified)
	* src/Parser/MpqcParser.hpp (modified)
	* src/Parser/MpqcParser_Parameters.cpp (added)
	* src/Parser/MpqcParser_Parameters.hpp (added)
	* src/Parser/unittests/ParserMpqcUnitTest.cpp (modified)
	* src/Parser/unittests/ParserMpqcUnitTest.hpp (modified)
	* tests/regression/Atoms/Add/post/test.in (modified)
	* tests/regression/Atoms/Remove/post/test.in (modified)
	* tests/regression/Parser/Mpqc/post/test.in (modified)

	Added MpqcParser_Parameter class to MpqcParser.

	- contains all ...