# # ChangeLog for src # # Generated by Trac 1.6 # May 25, 2025, 6:04:09 AM Wed, 28 Mar 2012 12:10:43 GMT Frederik Heber [53bc04] * src/Tesselation/unittests/Makefile.am (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) * src/unittests/Makefile.am (modified) BUG: Added spherical and non-convex test cases to ... Tue, 27 Mar 2012 15:53:36 GMT Frederik Heber [418b5e] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) Added verbosity to some tesselation functions. - added exception ... Tue, 27 Mar 2012 15:53:36 GMT Frederik Heber [cc21cd] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.hpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) Added Tesselation::operator() that performs a tesselation on a given ... Tue, 27 Mar 2012 15:53:36 GMT Frederik Heber [bdf6c8] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) Added getter for surface area to class Tesselation. Tue, 27 Mar 2012 15:53:36 GMT Frederik Heber [ee0032] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/boundary.hpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) Extracted VolumeOfConvexEnvelope() from boundary and placed into ... Tue, 27 Mar 2012 15:53:36 GMT Frederik Heber [64b197] * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.hpp (modified) Added getArea() function to BoundaryTriangleSet. - this is taken ... Tue, 27 Mar 2012 15:53:36 GMT Frederik Heber [12c4cb] * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.hpp (modified) FIX: MoleculeOrderDescriptor was not working correctly. - added ... Tue, 27 Mar 2012 15:53:36 GMT Frederik Heber [4824045] * src/Descriptors/AtomDescriptor.hpp (modified) FIX: forward declaration of World is unnecessary in AtomDescriptor. Tue, 27 Mar 2012 15:53:36 GMT Frederik Heber [05a885] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) FIX: BondedParticle::addBond returns * const not const *. - return ... Tue, 27 Mar 2012 15:53:35 GMT Frederik Heber [46c832] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) FIX: PairCorrelation calculated max_distance in Box wrongly. - ... Tue, 27 Mar 2012 15:53:35 GMT Frederik Heber [4d2b33] * src/MoleculeListClass.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) FIX: molecule does not need a periodentafel. - removed ... Tue, 27 Mar 2012 15:53:35 GMT Frederik Heber [955b91] * LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (modified) * LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (modified) * LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Vector.hpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/triangleintersectionlist.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Query/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/unittests/BoxUnitTest.cpp (modified) FIX: Removed using namespace std in Vector.hpp. - this caused some ... Tue, 27 Mar 2012 15:53:35 GMT Frederik Heber [912c40] * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) FIX: AddEmptyBoundaryAction just returns Action::failure if there are ... Tue, 27 Mar 2012 15:53:35 GMT Frederik Heber [b49de6] * src/Actions/GraphAction/DepthFirstSearchAction.def (modified) FIX: DepthFirstSearchAction still expected parameter for maximum ... Tue, 27 Mar 2012 15:53:35 GMT Frederik Heber [ea0c8b] * src/Atom/atom.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/Atom/atom_particleinfo.hpp (modified) FIX: ParticleInfo did use ptr instead of const ref in copy cstor. - ... Tue, 27 Mar 2012 15:53:35 GMT Frederik Heber [c742fe] * src/Atom/atom.cpp (modified) FIX: atom's copy cstor does not use Observer mechanism on the newly ... Wed, 22 Feb 2012 11:29:59 GMT Frederik Heber [a292f6] * src/Makefile.am (modified) DISTCHECKFIX: Forgot to add IdPool_policy.hpp to Makefile.am. Wed, 22 Feb 2012 11:29:22 GMT Frederik Heber [2a0271] * src/Actions/Values.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) New function Box::isValid() to be discerned from ::isInside(). - ... Wed, 22 Feb 2012 11:29:22 GMT Frederik Heber [c96423] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) BUGFIX: LinkedCell_Model should use ceil, not floor for calculating ... Wed, 22 Feb 2012 11:29:05 GMT Frederik Heber [c1a9d6] * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * tests/regression/Analysis/PairCorrelation-RangeTest/post/bin_output-10.csv (modified) * tests/regression/Analysis/PairCorrelation-RangeTest/post/bin_output-20.csv (modified) * tests/regression/Analysis/PairCorrelation-RangeTest/post/bin_output-5.csv (modified) Rewrote PairCorrelation() to make use of new LinkedCell construct. ... Wed, 22 Feb 2012 11:29:05 GMT Frederik Heber [8fc1a6] * src/Analysis/analysis_correlation.cpp (modified) FIX: getDipole() was broken under periodic boundary conditions. - ... Wed, 22 Feb 2012 11:29:04 GMT Frederik Heber [a19b4f] * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) Removed parameter periodic from DipoleAngularCorrelationAction. - ... Wed, 22 Feb 2012 11:29:04 GMT Frederik Heber [153985] * src/Analysis/analysis_bonds.cpp (modified) Rewrote CountHydrogenBridgeBonds() to use new LinkedCell construct. ... Wed, 22 Feb 2012 11:29:04 GMT Frederik Heber [826e8c] * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (modified) * tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) Introduced new LinkedCell into BondGraph. - new convenience ... Wed, 22 Feb 2012 11:28:52 GMT Frederik Heber [cbcda6] * src/LinkedCell/LinkedCell_Model.hpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) BUGFIX: LinkedCell_View::getPointsInsideSphere() did not adhere to ... Wed, 22 Feb 2012 11:28:52 GMT Frederik Heber [5d41b3f] * src/LinkedCell/LinkedCell_Model.cpp (modified) FIX: LinkedCell_Model::getStep() uses Box::WrapPeriodically() on ... Wed, 22 Feb 2012 11:28:52 GMT Frederik Heber [ce81e76] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Controller.hpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (added) LinkedCell_Controller now signs on to Channel WorldTime::TimeChanged. ... Wed, 22 Feb 2012 11:28:52 GMT Frederik Heber [5e2864] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) FIX: LinkedCell_Controller now signs on to Channel ... Wed, 22 Feb 2012 11:28:52 GMT Frederik Heber [429069] * src/LinkedCell/LinkedCell_Controller.cpp (modified) FIX: Forgot that LinkedCell_Controller::updateModels() should also ... Wed, 22 Feb 2012 11:28:52 GMT Frederik Heber [040a5c] * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/WorldTime.hpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) WorldTime is now Observable. - this is required for the ... Wed, 22 Feb 2012 11:28:52 GMT Frederik Heber [38c5d1] * src/documentation/constructs/linkedcell.dox (modified) Documentation update on how to use the new linked cell construct. Wed, 22 Feb 2012 11:28:42 GMT Frederik Heber [712886] * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/molecule_geometry.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) Renamed Box::WrapPeriodically -> ::enforceBoundaryConditions. Wed, 22 Feb 2012 11:28:42 GMT Frederik Heber [7b9fe0] * src/Box.cpp (modified) * src/Box.hpp (modified) New function Box::periodicDistanceVector(), using ... Wed, 22 Feb 2012 11:28:42 GMT Frederik Heber [c52e08] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (added) * src/Actions/WorldAction/SetBoundaryConditionsAction.def (added) * src/Actions/WorldAction/SetBoundaryConditionsAction.hpp (added) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Box_BoundaryConditions.cpp (modified) * src/Box_BoundaryConditions.hpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Domain/SetBoundaryConditions/testsuite-domain-set-boundary-conditions.at (added) * tests/regression/Domain/testsuite-domain.at (modified) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/water-bounced.xyz (added) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/water-wrapped.xyz (added) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/pre/water.xyz (added) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added new action SetBoundaryConditionsAction. - Added new ... Wed, 22 Feb 2012 11:28:41 GMT Frederik Heber [d66cb7] * src/Box.cpp (modified) * src/Box.hpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) Replaced Conditions_t by BoundaryConditions::BCContainer in class Box. Wed, 22 Feb 2012 11:28:41 GMT Frederik Heber [dd067a] * src/Box_BoundaryConditions.cpp (added) * src/Box_BoundaryConditions.hpp (added) * src/Makefile.am (modified) * src/unittests/Box_BoundaryConditionsUnitTest.cpp (added) * src/unittests/Box_BoundaryConditionsUnitTest.hpp (added) * src/unittests/Makefile.am (modified) Add new namespace BoundaryConditions with class BCContainer. - ... Wed, 22 Feb 2012 11:28:28 GMT Frederik Heber [44f53e] * src/Analysis/analysis_correlation.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/WorldTime.cpp (modified) Made various verbosities a lot less annoying. - LinkedCell_Model ... Wed, 22 Feb 2012 11:27:55 GMT Frederik Heber [98c428] * 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) FormatParserStorage has now two convenience functions ::load(). - ... Wed, 22 Feb 2012 11:27:55 GMT Frederik Heber [3dfd9c] * src/Parser/PdbParser.cpp (modified) * tests/regression/Parser/Pdb/post/tensid.pdb (added) * tests/regression/Parser/Pdb/pre/tensid.pdb (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-various.at (modified) BUGFIX: PdbParser stumbles over CONECT because it reads space- ... Wed, 22 Feb 2012 11:26:49 GMT Frederik Heber [ea7a50] * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor_impl.hpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor_impl.hpp (modified) * src/World.hpp (modified) * src/documentation/constructs/descriptors.dox (modified) Rewrote some of the descriptors such that they access World's AtomSet ... Fri, 17 Feb 2012 15:24:20 GMT Frederik Heber [52ed5b] * src/Atom/atom_bondedparticle.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) Ids handed out by molecule now start with 1. - this required some ... Fri, 17 Feb 2012 15:24:19 GMT Frederik Heber [cdaae6] * src/Atom/atom_bondedparticle.cpp (modified) * tests/regression/Molecules/BondFile/pre/test.dbond (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified) * tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) * tests/regression/Molecules/SaveBonds/post/test.dbond (modified) FIX: BondedParticle::OutputAdjacency() and ::OutputBonds() give ... Fri, 17 Feb 2012 15:24:18 GMT Frederik Heber [560bbe] * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/documentation/constructs/molecules.dox (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * tests/regression/Tesselation/BigNonConvex/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/BigNonConvex/post/NonConvexEnvelope.r3d (modified) AtomicInfo now also (re)stores ParticleInfo::Nr, molecule has own ... Fri, 17 Feb 2012 15:24:18 GMT Frederik Heber [ac5c36] * src/World.hpp (modified) FIX: Forgot to remove now unused idpool functions, were replaced by ... Fri, 17 Feb 2012 15:24:18 GMT Frederik Heber [7d46e3] * src/RandomNumbers/RandomNumberEngine_Encapsulation.hpp (modified) MEMFIX: RandomNumberEngine_Encapsulation::clone() did leak params ... Fri, 17 Feb 2012 15:24:18 GMT Frederik Heber [b97a60] * src/IdPool.hpp (modified) * src/IdPool_impl.hpp (modified) * src/IdPool_policy.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * src/documentation/constructs/world.dox (modified) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/post/test.xyz (modified) Modified IdPool implementation to give either unique or continuous ... Fri, 17 Feb 2012 15:24:18 GMT Frederik Heber [3867a7] * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * src/Atom/atom.cpp (modified) AtomicInfo now stores Father by id not ref. - this migh have caused ... Fri, 17 Feb 2012 15:24:18 GMT Frederik Heber [9f8b01] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) FIX: TremoloParser::processNeighbors() always ran through all ... Fri, 17 Feb 2012 15:24:18 GMT Frederik Heber [812155] * src/Parser/TremoloParser.cpp (modified) TremoloParser::save() redistributes ids in a continuous manner. - ... Fri, 17 Feb 2012 15:24:17 GMT Frederik Heber [8bf9c6] * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) All additionalAtomData maps now have const atomId_t as key. Fri, 17 Feb 2012 15:24:17 GMT Frederik Heber [2ad1ec] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_observable.hpp (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/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/qt-gui.dox (added) * src/documentation/userinterfaces/graphical.dox (modified) Rewrite of how GLWorldScene and subsidiaries get notified of changed ... Fri, 17 Feb 2012 15:24:17 GMT Frederik Heber [3f7587] * src/Bond/bond.cpp (modified) * src/Bond/bond.hpp (modified) * src/Bond/bond_observable.cpp (added) * src/Bond/bond_observable.hpp (added) * src/Makefile.am (modified) Made bond also an Observable. - for the moment this is not used. Fri, 17 Feb 2012 15:24:17 GMT Frederik Heber [74ec1f] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_observable.hpp (modified) BUGFIX: Added new channel BondDegreeChanged to AtomObservable, added ... Fri, 06 Jan 2012 14:02:08 GMT Frederik Heber [c0e28c] * src/Parser/FormatParser_common.cpp (modified) * src/Parser/FormatParser_common.hpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/PdbParser.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Mpqc/post/doublewater.in (added) * tests/regression/Parser/Mpqc/pre/water.in (added) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at (added) * tests/regression/Parser/Pcp/post/doubletest.conf (added) * tests/regression/Parser/Pcp/post/doublewater.conf (added) * tests/regression/Parser/Pcp/pre/water.conf (added) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load-multiply.at (added) * tests/regression/Parser/Pdb/post/doublewater.pdb (added) * tests/regression/Parser/Pdb/pre/water.pdb (added) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-multiply.at (added) * tests/regression/Parser/Psi3/post/doublewater.psi (added) * tests/regression/Parser/Psi3/pre/water.psi (added) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load-multiply.at (added) * tests/regression/Parser/Tremolo/post/doublewater.data (added) * tests/regression/Parser/Tremolo/pre/water.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at (added) * tests/regression/Parser/Xyz/post/doublewater.xyz (added) * tests/regression/Parser/Xyz/pre/water.xyz (added) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-multiply.at (added) * tests/regression/Parser/testsuite-parser.at (modified) FIX: One could not load another pdb file due to local ids messing up. ... Fri, 06 Jan 2012 14:02:04 GMT Frederik Heber [fbbcde] * LinearAlgebra/configure.ac (modified) * LinearAlgebra/src/unittests/Makefile.am (modified) * configure.ac (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/types.hpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) FIX: TestRunner is now compiled based on AM_CONDITIONAL set by HAVE_ECUT. Wed, 04 Jan 2012 14:28:41 GMT Frederik Heber [e65b26] * src/LinkedCell/LinkedCell_Model.cpp (modified) FIX: LinkedCell_Model::getNeighborhoodBounds() had wrong relative ... Wed, 04 Jan 2012 14:28:41 GMT Frederik Heber [c9c3c9] * src/cleanUp.cpp (modified) MEMFIX: Forgot to purge AtomObserver instance. Wed, 04 Jan 2012 14:28:41 GMT Frederik Heber [5972c3] * src/LinkedCell/LinkedCell_Model.cpp (modified) MEMFIX: LinkedCell_Model did not release N (Linked cell array). Wed, 04 Jan 2012 14:28:41 GMT Frederik Heber [b6f5bc] * src/IdPool_impl.hpp (modified) FIX: Fixes to idpool implementation that did not initialize all its ... Wed, 04 Jan 2012 14:28:41 GMT Frederik Heber [7111d4] * src/LinkedCell/LinkedCell_Model.cpp (modified) FIX: LinkedCell_Model::setPartition() did not assure Dimensions is ... Wed, 04 Jan 2012 14:28:41 GMT Frederik Heber [c9cafa] * src/Atom/atom_atominfo.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/molecule_graph.cpp (modified) Some warning fixes. comparison signed/unsigned: - ... Wed, 04 Jan 2012 14:28:41 GMT Frederik Heber [b75386] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) Verbosity fixes to LinkedCell_Model and _View. Wed, 04 Jan 2012 14:28:40 GMT Frederik Heber [57a770] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) Corrected verbosity levels of GLMoleculeObject..., GLWorldScene, and ... Wed, 04 Jan 2012 14:28:40 GMT Frederik Heber [0aa122] * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.cpp (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/ValueStorage.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/pyMoleCuilder.cpp (modified) * src/Actions/unittests/ActionRegistryUnitTest.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Actions/unittests/AtomsCalculationUnitTest.cpp (modified) * src/Actions/unittests/ManipulateAtomsUnitTest.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisBondsUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Analysis/unittests/CountBondsUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/MoleculeDescriptorUnitTest.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Element/unittests/PeriodentafelUnitTest.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/analyzer.cpp (modified) * src/Fragmentation/datacreator.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/joiner.cpp (modified) * src/Fragmentation/unittests/KeySetsContainerUnitTest.cpp (modified) * src/Fragmentation/unittests/MatrixContainerUnitTest.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BreadthFirstSearchAdd.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/CheckAgainstAdjacencyFile.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/BondGraphUnitTest.cpp (modified) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (modified) * src/Helpers/defs.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/AtomStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/Parameters/StringParameter.cpp (modified) * src/Parser/Parameters/unittests/ContinuousParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ContinuousValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteParameterUnitTest.cpp (modified) * src/Parser/Parameters/unittests/DiscreteValueUnitTest.cpp (modified) * src/Parser/Parameters/unittests/ParameterStorageUnitTest.cpp (modified) * src/Parser/Parameters/unittests/StringParameterUnitTest.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp (modified) * src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/ShapeUnitTest.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BoxCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/TypeEnumContainer.cpp (modified) * src/UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Menu/Menu.cpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * src/UIElements/Menu/MenuInterface.cpp (modified) * src/UIElements/Menu/Qt4/QtMenuPipe.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/DisplayMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SeparatorMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/SubMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenu.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp (modified) * src/UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/EmptyQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BoxQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/RandomNumberDistribution_ParametersQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/AtomQuery.cpp (modified) * src/UIElements/Query/AtomsQuery.cpp (modified) * src/UIElements/Query/BooleanQuery.cpp (modified) * src/UIElements/Query/BoxQuery.cpp (modified) * src/UIElements/Query/DoubleQuery.cpp (modified) * src/UIElements/Query/DoublesQuery.cpp (modified) * src/UIElements/Query/ElementQuery.cpp (modified) * src/UIElements/Query/ElementsQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/FileQuery.cpp (modified) * src/UIElements/Query/IntQuery.cpp (modified) * src/UIElements/Query/IntsQuery.cpp (modified) * src/UIElements/Query/MoleculeQuery.cpp (modified) * src/UIElements/Query/MoleculesQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/Query/RandomNumberDistribution_ParametersQuery.cpp (modified) * src/UIElements/Query/StringQuery.cpp (modified) * src/UIElements/Query/StringsQuery.cpp (modified) * src/UIElements/Query/UnsignedIntQuery.cpp (modified) * src/UIElements/Query/UnsignedIntsQuery.cpp (modified) * src/UIElements/Query/VectorQuery.cpp (modified) * src/UIElements/Query/VectorsQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BoxTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RandomNumberDistribution_ParametersTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeView.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtWorldView.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/FormulaUnitTest.cpp (modified) * src/unittests/ListOfBondsUnitTest.cpp (modified) * src/unittests/TestRunnerMain.cpp (modified) * src/unittests/UnitTestMain.cpp (modified) * src/unittests/WorldTimeUnitTest.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) Updated all source files's copyright note to current year 2012. Mon, 02 Jan 2012 13:35:16 GMT Frederik Heber [e215c1] * src/LinkedCell/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) DISTCHECKFIX: Forgot to add LinkedCell header files to some targets. ... Mon, 02 Jan 2012 13:34:58 GMT Frederik Heber [69459d] * src/LinkedCell/LinkedCell_View.hpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) Added unit test on changing box to LinkedCell_ControllerUnitTest. - ... Mon, 02 Jan 2012 13:34:58 GMT Frederik Heber [2ced6b] * src/LinkedCell/unittests/Makefile.am (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (added) * src/LinkedCell/unittests/stubs/AtomStub.cpp (moved) * src/LinkedCell/unittests/stubs/LinkedCell_ModelStub.cpp (deleted) * src/LinkedCell/unittests/stubs/LinkedCell_ViewStub.cpp (deleted) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (added) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (added) * src/LinkedCell/unittests/stubs/WorldStub.cpp (added) Replaced Molecuilder library dependencies by stubs in ... Mon, 02 Jan 2012 13:34:58 GMT Frederik Heber [b1c5ddb] * src/Atom/TesselPoint.hpp (modified) FIX: Made TesselPoint's dstor virtual. - this caused undefined ... Mon, 02 Jan 2012 13:34:58 GMT Frederik Heber [cbdcb1] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/LinkedCell_View.hpp (modified) * src/LinkedCell/LinkedCell_View_ModelWrapper.hpp (added) * src/LinkedCell/Makefile.am (modified) * src/LinkedCell/unittests/stubs/LinkedCell_ViewStub.cpp (modified) Added LinkedCell_View_ModelWrapper to safely keep LinkedCell_Model ... Mon, 02 Jan 2012 13:34:58 GMT Frederik Heber [4a8169] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Controller.hpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp (modified) LinkedCell_Controller is now an Observer. - new function ... Mon, 02 Jan 2012 13:34:58 GMT Frederik Heber [99f4ee] * src/Atom/unittests/Makefile.am (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/unittests/BoxUnitTest.cpp (modified) * src/unittests/BoxUnitTest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/stubs/ObserverStub.cpp (moved) * src/unittests/stubs/ObserverStub.hpp (moved) Class Box is now also an Observable. - it has two channels to ... Mon, 02 Jan 2012 13:34:58 GMT Frederik Heber [9ed706] * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/LinkedCell_View.hpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.hpp (modified) * src/LinkedCell/unittests/stubs/LinkedCell_ViewStub.cpp (modified) Implemented counting of active LinkedCell_View instances in static ... Mon, 02 Jan 2012 13:34:58 GMT Frederik Heber [c29915] * src/LinkedCell/LinkedCell_Model.hpp (modified) LinkedCell_Model cstors are now private but LinkedCell_Controller is ... Mon, 02 Jan 2012 13:34:57 GMT Frederik Heber [455043] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Controller.hpp (modified) Changed MapEdgelengthModel to contain const ref as value. - ... Mon, 02 Jan 2012 13:34:42 GMT Frederik Heber [54f3d1] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.hpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.hpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.hpp (modified) Removed short-wiring of updates as they are now passed through ... Mon, 02 Jan 2012 13:34:42 GMT Frederik Heber [8c31865] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (added) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.hpp (added) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.hpp (modified) * src/LinkedCell/LinkedCell_Model_inline.hpp (modified) * src/LinkedCell/Makefile.am (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) Added new class LinkedCellArrayCache that performs the lazy updates ... Mon, 02 Jan 2012 13:34:42 GMT Frederik Heber [e776dc] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (added) * src/LinkedCell/LinkedCell_Model_Update.hpp (added) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (added) * src/LinkedCell/LinkedCell_Model_changeModel.hpp (added) * src/LinkedCell/Makefile.am (modified) Added internal classes Update and changeModel to LinkedCell_Model. ... Mon, 02 Jan 2012 13:34:41 GMT Frederik Heber [cf6530] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp (modified) Implemented LinkedCell_Model::moveNode_internal(). - updated unit ... Mon, 02 Jan 2012 13:34:41 GMT Frederik Heber [a5b2b6b] * src/LinkedCell/LinkedCell_Model.cpp (modified) Simplified LinkedCell_Model::deleteNode_internal(). - this is ... Mon, 02 Jan 2012 13:34:41 GMT Frederik Heber [db8960] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) Shifted functionality of adding, moving, and deleting nodes to ... Mon, 02 Jan 2012 13:34:29 GMT Frederik Heber [bbab87] * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.hpp (modified) Added test for new descriptor AtomsWithinDistanceOf to ... Mon, 02 Jan 2012 13:34:29 GMT Frederik Heber [7afb77] * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (added) * src/Descriptors/AtomsWithinDistanceOfDescriptor.hpp (added) * src/Descriptors/AtomsWithinDistanceOfDescriptor_impl.hpp (added) * src/Makefile.am (modified) * src/documentation/constructs/descriptors.dox (modified) Added AtomsWithinDistanceOf descriptor. - this is basically just a ... Mon, 02 Jan 2012 13:34:29 GMT Frederik Heber [4834f4] * src/World.cpp (modified) * src/World.hpp (modified) World now has a LinkedCell_Controller and function getLinkedCell(). ... Mon, 02 Jan 2012 13:34:29 GMT Frederik Heber [53d894] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) Changed LinkedCell_Model::getNeighborhoodBounds() and ... Mon, 02 Jan 2012 13:34:29 GMT Frederik Heber [c80643] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Controller.hpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp (modified) LinkedCell_Controller::getView() now needs a PointCloud set. - this ... Mon, 02 Jan 2012 13:34:29 GMT Frederik Heber [4459fc] * src/LinkedCell/LinkedCell.hpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/Makefile.am (modified) * src/LinkedCell/tripleIndex.cpp (added) * src/LinkedCell/tripleIndex.hpp (added) * src/LinkedCell/types.hpp (modified) Refactored typedef tripleIndex into own structure. - we need the ... Mon, 02 Jan 2012 13:34:28 GMT Frederik Heber [c8f6b6] * src/LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp (modified) Small fixes to LinkedCell_ViewUnitTest. Mon, 02 Jan 2012 13:34:28 GMT Frederik Heber [b49568] * src/Descriptors/AtomOfMoleculeDescriptor.cpp (added) * src/Descriptors/AtomOfMoleculeDescriptor.hpp (added) * src/Descriptors/AtomOfMoleculeDescriptor_impl.hpp (added) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.hpp (modified) * src/Makefile.am (modified) * src/documentation/constructs/descriptors.dox (modified) Added new descriptor AtomOfMolecule. - also added new unit test ... Mon, 02 Jan 2012 13:34:28 GMT Frederik Heber [d78531] * src/LinkedCell/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Library LinkedCell_refactored is now contained in lib LinkedCell. Mon, 02 Jan 2012 13:34:28 GMT Frederik Heber [6bd7e0] * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/analysis_correlation.hpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/linkedcell.hpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.cpp (modified) * src/LinkedCell/unittests/linkedcellUnitTest.hpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/CandidateForTesselation.hpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/boundary.hpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/ellipsoid.hpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/tesselationhelpers.hpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/triangleintersectionlist.hpp (modified) * src/Tesselation/unittests/TesselationUnitTest.cpp (modified) * src/Tesselation/unittests/TesselationUnitTest.hpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp (modified) * src/molecule.hpp (modified) Renamed old LinkedCell class to LinkedCell_deprecated. - this is ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [f55ae5] * src/LinkedCell/LinkedCell_Model.cpp (modified) Implemented LinkedCell_Model::recieveNotification(). - i.e. it now ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [029870] * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell.hpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) * src/LinkedCell/types.hpp (modified) * src/LinkedCell/unittests/LinkedCellUnitTest.cpp (modified) FIX: LinkedCell and LinkedCell_Model now store _const_ TesselPoint ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [402f2c] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) LinkedCell_Model now signOn/Off to World and AtomObserver. Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [97c2550] * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomObserver.hpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (added) * src/Atom/unittests/AtomObserverUnitTest.hpp (added) * src/Atom/unittests/Makefile.am (added) * src/Atom/unittests/stubs/ObserverStub.cpp (added) * src/Atom/unittests/stubs/ObserverStub.hpp (added) * src/unittests/Makefile.am (modified) Added unit test for AtomObserver. - added position and element ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [5dfabd] * src/Atom/AtomObserver.cpp (added) * src/Atom/AtomObserver.hpp (added) * src/Atom/Makefile.am (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added singleton class AtomObserver that acts as relay station to all ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [2614e2a] * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model.hpp (modified) * src/LinkedCell/unittests/stubs/LinkedCell_ModelStub.cpp (modified) LinkedCell_Model now inherits Observer. - implemented facade for ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [fe8253] * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Controller.hpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp (modified) Added first reasonable heuristic, and added required implementation ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [9a5649] * src/LinkedCell/unittests/Makefile.am (modified) * src/LinkedCell/unittests/stubs/LinkedCellStub.cpp (added) * src/LinkedCell/unittests/stubs/LinkedCell_ModelStub.cpp (added) * src/LinkedCell/unittests/stubs/LinkedCell_ViewStub.cpp (added) LinkedCell_ControllerUnitTest only depends on stubs now. - i.e. we ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [fea945] * src/LinkedCell/LinkedCell_Controller.cpp (added) * src/LinkedCell/LinkedCell_Controller.hpp (added) * src/LinkedCell/Makefile.am (modified) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp (added) * src/LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp (added) * src/LinkedCell/unittests/Makefile.am (modified) Added simple implementation for LinkedCell_Controller. - ... Mon, 02 Jan 2012 13:00:05 GMT Frederik Heber [6b91e64] * src/LinkedCell/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Added convenience library for files of new LinkedCell implementation. ...