# # ChangeLog for src # # Generated by Trac 1.4.4 # Apr 11, 2025, 3:28:25 PM Tue, 03 Apr 2012 08:00:19 GMT Frederik Heber [e791dc] * src/Analysis/analysis_correlation.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Removed molecule::doCountAtom() and added ... Tue, 03 Apr 2012 08:00:19 GMT Frederik Heber [108968] * src/Graph/BondGraph.cpp (modified) * src/Graph/BondGraph.hpp (modified) FIX: Rewrite of BondGraph's CreateAdjacency() and ... Tue, 03 Apr 2012 08:00:19 GMT Frederik Heber [08a0f52] * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) AtomInfo has new functions getElement() and getElementNo(). - ... Tue, 03 Apr 2012 07:58:43 GMT Frederik Heber [ccb487] * src/Parser/TremoloParser.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * tests/regression/Domain/RepeatBox/post/ec.data (modified) * tests/regression/Domain/RepeatBox/pre/ec.data (modified) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/Copy/post/tensid-undo.data (modified) * tests/regression/Molecules/Copy/post/tensid.data (modified) * tests/regression/Molecules/Copy/pre/tensid.data (modified) * tests/regression/Molecules/CreateMicelle/post/tensid.data (modified) * tests/regression/Molecules/CreateMicelle/pre/tensid.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data (modified) TremoloParser now always writes current domain as "# Box ..." into ... Tue, 03 Apr 2012 07:58:43 GMT Frederik Heber [a275b3] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) TremoloParser uses ElementKeys. - functions parseKnownTypes() and ... Tue, 03 Apr 2012 07:58:43 GMT Frederik Heber [d9005c1] * src/Parser/Exceptions.hpp (added) * src/Parser/Makefile.am (modified) * src/Parser/TremoloParser_ElementKeys.cpp (added) * src/Parser/TremoloParser_ElementKeys.hpp (added) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp (added) * src/Parser/unittests/ParserTremolo_ElementKeysUnitTest.hpp (added) Extracted TremoloParser::knownTypes into distinct class ElementKeys, ... Tue, 03 Apr 2012 07:55:55 GMT Frederik Heber [ebc499] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (added) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.def (added) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.hpp (added) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (added) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.def (added) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.hpp (added) * src/World.cpp (modified) * src/World.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/InvertAtoms/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/InvertAtoms/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/InvertAtoms/pre/box.xyz (added) * tests/regression/Selection/Atoms/InvertAtoms/testsuite-selection-invert-atoms.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) * tests/regression/Selection/Molecules/InvertMolecules/post/mol0_missing.xyz (added) * tests/regression/Selection/Molecules/InvertMolecules/post/mol0_present.xyz (added) * tests/regression/Selection/Molecules/InvertMolecules/pre/box.xyz (added) * tests/regression/Selection/Molecules/InvertMolecules/testsuite-selection-invert-molecules.at (added) * tests/regression/Selection/Molecules/testsuite-selection-molecules.at (modified) Added InvertMoleculesAction and InvertAtomsAction. - World has two ... Tue, 03 Apr 2012 07:55:43 GMT Frederik Heber [61c364] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.def (added) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.hpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.def (added) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.hpp (added) * src/Descriptors/AtomOrderDescriptor.cpp (added) * src/Descriptors/AtomOrderDescriptor.hpp (added) * src/Descriptors/AtomOrderDescriptor_impl.hpp (added) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.hpp (modified) * src/Makefile.am (modified) * src/World.hpp (modified) * tests/Python/AllActions/moltest.py (modified) * tests/Python/AllActions/moltest_check.py (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomByOrder/post/empty.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id1_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id1_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id2_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id2_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id3_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id3_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id4_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id4_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id5_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id5_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id6_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id6_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id7_missing.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/id7_present.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/pre/test.xyz (added) * tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-select-atom-by-order.at (added) * tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-unselect-atom-by-order.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added AtomOrderDescription along with SelectionAtomByOrder. - added ... Mon, 02 Apr 2012 12:33:13 GMT Frederik Heber [8de597] * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) FIX: FileQtQueryPipe demanded QFileDialog::ExistingFile. - for ... Mon, 02 Apr 2012 10:35:51 GMT Frederik Heber [510f81] * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) Merge branch 'Fix_Tesselation_InsideOutSideUnitTest' into Candidate_v123 Mon, 02 Apr 2012 10:35:29 GMT Frederik Heber [22425a] * src/Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp (modified) DISTFIX: Tesselation_InsideOutsideUnitTest still wrote temporary file. Mon, 02 Apr 2012 08:37:59 GMT Frederik Heber [7256a2] * src/Filling/Makefile.am (modified) * src/LinkedCell/Makefile.am (modified) * src/Shapes/Makefile.am (modified) DISTFIX: Forgot to include various header files in Makefile.am's. - ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [896f4a] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.def (modified) FillRegularGridAction now uses RandomInserter to fill in the ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [48ab414] * src/Filling/Inserter/RandomInserter.cpp (added) * src/Filling/Inserter/RandomInserter.hpp (added) * src/Filling/Makefile.am (modified) Implemented working RandomInserter. - we copy&paste most of the ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [4fbc4eb] * src/Filling/Filler.cpp (modified) FIX: Filler::operator() now shifts filler cluster out of domain ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [e32fa6] * src/Filling/Filler.cpp (modified) * src/Filling/Inserter/Inserter.cpp (modified) * src/Filling/Inserter/Inserter.hpp (modified) * src/Filling/Inserter/InserterBase.hpp (modified) * src/Filling/Inserter/SimpleInserter.cpp (modified) * src/Filling/Inserter/SimpleInserter.hpp (modified) Modified Filler:operator() such that Inserters only modify position, ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [68abe5] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Filling/Filler.cpp (modified) * src/Filling/Filler.hpp (modified) * src/Filling/Inserter/Inserter.cpp (modified) * src/Filling/Inserter/Inserter.hpp (modified) * src/Filling/Inserter/InserterBase.hpp (modified) * src/Filling/Inserter/SimpleInserter.cpp (modified) * src/Filling/Inserter/SimpleInserter.hpp (modified) Made Inserter::operator(), Filler::operator() return bool, used by ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [f61f61] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Filling/Inserter/Inserter.cpp (added) * src/Filling/Inserter/Inserter.hpp (modified) * src/Filling/Inserter/InserterBase.hpp (added) * src/Filling/Inserter/SimpleInserter.hpp (modified) * src/Filling/Makefile.am (modified) * src/Filling/unittests/FillerUnitTest.cpp (modified) Refactored implementation of Inserter into pimpl pattern. - this is ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [901d87] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Filling/Filler.cpp (modified) * src/Filling/Filler.hpp (modified) * src/Filling/Inserter/Inserter.hpp (added) * src/Filling/Inserter/SimpleInserter.cpp (added) * src/Filling/Inserter/SimpleInserter.hpp (added) * src/Filling/Makefile.am (modified) * src/Filling/unittests/FillerUnitTest.cpp (modified) * src/Filling/unittests/FillerUnitTest.hpp (modified) Refactored insertion of cluster into Inserter class. - this is to ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [dba7b0] * src/documentation/constructs/filling.dox (modified) Extended filling documentation for Inserter. Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [da1e92] * src/Shapes/Shape.cpp (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp (added) * src/Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp (added) * src/unittests/Makefile.am (modified) Shape::getVolume() and ::getSurfaceArea() use Approximators if ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [4c6e70] * src/Makefile.am (modified) * src/Tesselation/ApproximateShapeArea.cpp (added) * src/Tesselation/ApproximateShapeArea.hpp (added) * src/Tesselation/ApproximateShapeVolume.cpp (added) * src/Tesselation/ApproximateShapeVolume.hpp (added) Added functors for calculating surface area and volume of a Shape. ... Fri, 30 Mar 2012 09:18:26 GMT Frederik Heber [595cfd] * src/Filling/Generators/NodeGenerator.cpp (added) * src/Filling/Generators/NodeGenerator.hpp (added) * src/Filling/Makefile.am (modified) Added NodeGenerator. Fri, 30 Mar 2012 09:18:25 GMT Frederik Heber [c67c65] * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) Added preliminary getVolume() and getSurfaceArea() implementation to ... Fri, 30 Mar 2012 09:18:25 GMT Frederik Heber [7672551] * LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) * LinearAlgebra/src/LinearAlgebra/Line.hpp (modified) * LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (added) * LinearAlgebra/src/LinearAlgebra/LinePoint.hpp (added) * LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (modified) * LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (modified) * LinearAlgebra/src/LinearAlgebra/Makefile.am (modified) * LinearAlgebra/src/documentation/lines.dox (added) * LinearAlgebra/src/documentation/mainpage.dox (modified) * src/Shapes/Shape_impl.hpp (modified) Split off class definition of LinePoint from module Line.cpp - ... Fri, 30 Mar 2012 09:18:25 GMT Frederik Heber [e9ad43] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.def (modified) FillRegularGridAction now expects the filler as selected molecule, ... Fri, 30 Mar 2012 09:18:25 GMT Frederik Heber [345eda] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.def (modified) * tests/Python/AllActions/options.dat (modified) Enhanced FillRegularGridAction to avoid tesselated surfaces. - ... Fri, 30 Mar 2012 09:18:25 GMT Frederik Heber [5a4cbc] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Filling/Filler.cpp (modified) * src/Filling/Predicates/IsVoidNode_FillPredicate.cpp (modified) * src/IdPool_impl.hpp (modified) * src/Tesselation/boundary.cpp (modified) VERBOSITY: Increased verbosity threshold of some outputs connected to ... Fri, 30 Mar 2012 09:18:17 GMT Frederik Heber [a88452] * src/Actions/FillAction/FillRegularGridAction.cpp (added) * src/Actions/FillAction/FillRegularGridAction.def (added) * src/Actions/FillAction/FillRegularGridAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/Python/AllActions/options.dat (modified) Added new Action subfolder, menu, and CommandLine options map, and ... Fri, 30 Mar 2012 09:16:32 GMT Frederik Heber [d505a3] * src/Filling/Filler.cpp (added) * src/Filling/Filler.hpp (added) * src/Filling/Makefile.am (modified) * src/Filling/unittests/FillerUnitTest.cpp (added) * src/Filling/unittests/FillerUnitTest.hpp (added) * src/Filling/unittests/Makefile.am (modified) Added Filler as general method of filling a Shape. - ... Fri, 30 Mar 2012 09:16:32 GMT Frederik Heber [5d81e5] * src/Filling/Makefile.am (modified) * src/Filling/Mesh/CubeMesh.cpp (added) * src/Filling/Mesh/CubeMesh.hpp (added) Added CubeMesh derived from Mesh. - contains a count and a offset ... Fri, 30 Mar 2012 09:16:32 GMT Frederik Heber [dd3f4f] * src/Filling/Makefile.am (modified) * src/Filling/Mesh/Mesh.cpp (added) * src/Filling/Mesh/Mesh.hpp (added) Added class Mesh for containing a set of Shape-filling Vectors. Fri, 30 Mar 2012 09:16:32 GMT Frederik Heber [8f6e2a] * src/Filling/Cluster.cpp (added) * src/Filling/Cluster.hpp (added) * src/Filling/Makefile.am (modified) * src/Filling/unittests/ClusterUnitTest.cpp (added) * src/Filling/unittests/ClusterUnitTest.hpp (added) * src/Filling/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/unittests/stubs/AtomStub.cpp (moved) * src/unittests/stubs/WorldStub.cpp (moved) Added new class Cluster as atomIdset with a Shape. - inherits ... Fri, 30 Mar 2012 09:16:32 GMT Frederik Heber [9e5a306] * src/Filling/ClusterInterface.hpp (added) Added ClusterInterface. - this is preparatory for using a Cluster ... Fri, 30 Mar 2012 09:16:32 GMT Frederik Heber [7adddc] * src/Filling/Makefile.am (modified) * src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp (added) * src/Filling/Predicates/IsInsideSurface_FillPredicate.hpp (added) * src/Filling/unittests/IsInsideSurface_FillPredicateUnitTest.cpp (added) * src/Filling/unittests/IsInsideSurface_FillPredicateUnitTest.hpp (added) * src/Filling/unittests/Makefile.am (modified) Added IsInsideSurface_FillPredicate - added unit test. Fri, 30 Mar 2012 09:16:32 GMT Frederik Heber [83fd7d] * src/Filling/Makefile.am (modified) * src/Filling/Predicates/Ops_FillPredicate.cpp (added) * src/Filling/Predicates/Ops_FillPredicate.hpp (added) * src/Filling/Predicates/Ops_FillPredicate_impl.hpp (added) * src/Filling/unittests/Makefile.am (modified) * src/Filling/unittests/Ops_FillPredicateUnitTest.cpp (added) * src/Filling/unittests/Ops_FillPredicateUnitTest.hpp (added) Added Ops_FillPredicate. - added unit test. Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [baac79] * src/Filling/Makefile.am (modified) * src/Filling/Predicates/IsVoidNode_FillPredicate.cpp (added) * src/Filling/Predicates/IsVoidNode_FillPredicate.hpp (added) * src/Filling/unittests/IsVoidNode_FillPredicateUnitTest.cpp (added) * src/Filling/unittests/IsVoidNode_FillPredicateUnitTest.hpp (added) * src/Filling/unittests/Makefile.am (modified) Added IsVoidNode_FillPredicate. - added unit test. - added ... Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [6499b1] * src/Filling/Makefile.am (modified) * src/Filling/Predicates/IsInsideDomain_FillPredicate.cpp (added) * src/Filling/Predicates/IsInsideDomain_FillPredicate.hpp (added) * src/Filling/unittests/IsInsideDomain_FillPredicateUnitTest.cpp (added) * src/Filling/unittests/IsInsideDomain_FillPredicateUnitTest.hpp (added) * src/Filling/unittests/Makefile.am (modified) Added IsInsideDomain_FillPredicate. - added unit test. Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [600a52] * src/Filling/Makefile.am (modified) * src/Filling/Predicates/IsValidInDomain_FillPredicate.cpp (added) * src/Filling/Predicates/IsValidInDomain_FillPredicate.hpp (added) * src/Filling/unittests/IsValidInDomain_FillPredicateUnitTest.cpp (added) * src/Filling/unittests/IsValidInDomain_FillPredicateUnitTest.hpp (added) * src/Filling/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) Added IsInDomain_FillPredicate. - added unit test. Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [b00ab1] * src/Filling/Makefile.am (modified) * src/Filling/Predicates/AnyFillPredicate.cpp (added) * src/Filling/Predicates/AnyFillPredicate.hpp (added) AnyFillPredicate takes a specific boost::function as predicate. - ... Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [9c2cb3] * src/Filling/Makefile.am (modified) * src/Filling/Predicates/FillPredicate.cpp (added) * src/Filling/Predicates/FillPredicate.hpp (added) * src/Filling/Predicates/FillPredicateBase.hpp (added) * src/Filling/Predicates/FillPredicate_impl.hpp (added) FillPredicate is working base class, where FillPredicateBase.hpp is ... Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [0d57cbe] * src/Filling/Makefile.am (added) * src/Filling/NodeTypes.hpp (added) * src/Makefile.am (modified) Added Node and NodeSet for a position and a vector of Positions. Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [b380ed] * src/documentation/constructs/constructs.dox (modified) * src/documentation/constructs/filling.dox (added) DOCU: Added concept for new construct Filling. Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [9e1d01] * src/Atom/CopyAtoms/CopyAtomsInterface.hpp (added) * src/Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.cpp (added) * src/Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.hpp (added) * src/Atom/CopyAtoms/CopyAtoms_Simple.hpp (added) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (added) * src/Atom/CopyAtoms/CopyAtoms_withBonds.hpp (added) * src/Atom/Makefile.am (modified) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.cpp (added) * src/Atom/unittests/CopyAtomsInterfaceUnitTest.hpp (added) * src/Atom/unittests/Makefile.am (modified) * src/documentation/constructs/atoms.dox (modified) Added CopyAtoms structure. - this creates a copy of a vector of ... Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [c67ff9] * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/MoleculeUnitTest.cpp (added) * src/unittests/MoleculeUnitTest.hpp (added) Added molecule::getBoundingShape() and unit test MoleculeUnitTest on ... Fri, 30 Mar 2012 09:16:31 GMT Frederik Heber [8e1f901] * src/Fragmentation/Fragmentation.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) molecule uses AtomIdSet now, rename getAtoms -> getAtomIds(). - ... Fri, 30 Mar 2012 08:22:24 GMT Frederik Heber [5e6534] * src/AtomIdSet.cpp (added) * src/AtomIdSet.hpp (added) * src/Makefile.am (modified) * src/unittests/AtomIdSetUnitTest.cpp (added) * src/unittests/AtomIdSetUnitTest.hpp (added) * src/unittests/Makefile.am (modified) Refactored transform_iterator out of class molecule as AtomIdSet. - ... Wed, 28 Mar 2012 15:17:39 GMT Frederik Heber [d927ab] * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.hpp (modified) * src/Descriptors/AtomShapeDescriptor_impl.hpp (modified) Renamed AtomByShape -> AtomsByShape and speedup due to LinkedCell ... Wed, 28 Mar 2012 15:17:38 GMT Frederik Heber [5a8d61] * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Shapes/unittests/Shape_HomogeneousPointsUnitTest.cpp (added) * src/Shapes/unittests/Shape_HomogeneousPointsUnitTest.hpp (added) Added new function to all Shape: getHomogeneousPointsInVolume(). - ... Wed, 28 Mar 2012 15:17:38 GMT Frederik Heber [6acc2f3] * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) * src/Shapes/unittests/BaseShapesUnitTest.cpp (modified) * src/Shapes/unittests/ShapeOpsUnitTest.cpp (modified) * src/Shapes/unittests/ShapeOpsUnitTest.hpp (modified) Added getCenter() and getRadius to all Shapes. - also extended unit ... Wed, 28 Mar 2012 15:17:38 GMT Frederik Heber [84721b] * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Shapes/unittests/ShapeOpsUnitTest.cpp (added) * src/Shapes/unittests/ShapeOpsUnitTest.hpp (added) Added new unit test ShapeOpsUnitTest, testing all ShapeOps. - ... Wed, 28 Mar 2012 15:17:38 GMT Frederik Heber [571d04] * src/Shapes/unittests/BaseShapesUnitTest.cpp (moved) * src/Shapes/unittests/BaseShapesUnitTest.hpp (moved) * src/Shapes/unittests/Makefile.am (modified) Renamed ShapeUnitTest -> BaseShapesUnitTest. Wed, 28 Mar 2012 15:17:38 GMT Frederik Heber [735940] * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/Shape_impl.hpp (modified) FIX: Made practically all Shape... member functions const. - Shape: ... Wed, 28 Mar 2012 15:17:38 GMT Frederik Heber [b92e4a] * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/BaseShapes_impl.hpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/Shape.hpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeOps_impl.hpp (modified) * src/Shapes/ShapeType.hpp (added) * src/Shapes/Shape_impl.hpp (modified) Shape identify themselves via an enumerated Type. - this is ... Wed, 28 Mar 2012 13:25:11 GMT Frederik Heber [6a7fcbb] * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) FIX: Rewrote BoundaryTriangleSet::GetClosestPointInsideTriangle(). ... Wed, 28 Mar 2012 13:25:11 GMT Frederik Heber [c27ce7] * src/Tesselation/unittests/Makefile.am (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) BUG: Added another specific case to ... Wed, 28 Mar 2012 13:25:07 GMT Frederik Heber [6dc3fe] * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) Enhanced Tesselation_BoundaryTriangleUnitTest by check on ... Wed, 28 Mar 2012 13:23:33 GMT Frederik Heber [70a0ba] * LinearAlgebra/src/LinearAlgebra/defs.hpp (modified) * src/Tesselation/unittests/Makefile.am (modified) FIX: LINALG_MYEPSILON is too high for certain tesselation operations ... Wed, 28 Mar 2012 13:23:33 GMT Frederik Heber [03a713] * src/Tesselation/unittests/Makefile.am (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) BUG: Added failing test case to Tesselation_BoundaryTriangleUnitTest. ... Wed, 28 Mar 2012 13:23:11 GMT Frederik Heber [471dec] * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.hpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) Added BoundaryTriangleSet::IsInsideTriangle(). - this is ... Wed, 28 Mar 2012 12:10:52 GMT Frederik Heber [368207] * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Tesselation/unittests/Makefile.am (modified) FIX: Incorporated special case affecting ... 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- ...