# # ChangeLog for tests/regression # # Generated by Trac 1.4.4 # Apr 4, 2025, 5:43:10 AM Fri, 14 Dec 2012 17:39:30 GMT Frederik Heber [4882d5] * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Thermostats/ThermoStatContainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Molecules/VerletIntegration/post/test.conf (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) Rewrote VerletIntegrationAction to diminish dependence on ... Fri, 14 Dec 2012 17:38:49 GMT Frederik Heber [8b886f] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (added) * src/Actions/MoleculeAction/ChangeBondAngleAction.def (added) * src/Actions/MoleculeAction/ChangeBondAngleAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/ChangeBondAngle/post/water.pdb (added) * tests/regression/Molecules/ChangeBondAngle/pre/water.pdb (added) * tests/regression/Molecules/ChangeBondAngle/testsuite-molecules-change-bond-angle.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added ChangeBondAngleAction that changes the bond angle while keeping ... Fri, 14 Dec 2012 14:30:23 GMT Frederik Heber [f63e41] * src/Actions/BondAction/BondAddAction.cpp (added) * src/Actions/BondAction/BondAddAction.def (added) * src/Actions/BondAction/BondAddAction.hpp (added) * src/Actions/BondAction/BondRemoveAction.cpp (added) * src/Actions/BondAction/BondRemoveAction.def (added) * src/Actions/BondAction/BondRemoveAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/regression/Bond/Add/post/test.pdb (added) * tests/regression/Bond/Add/pre/test.pdb (added) * tests/regression/Bond/Add/testsuite-bond-add.at (added) * tests/regression/Bond/Remove/post/test.pdb (added) * tests/regression/Bond/Remove/pre/test.pdb (added) * tests/regression/Bond/Remove/testsuite-bond-remove.at (added) * tests/regression/Bond/testsuite-bond.at (added) * tests/regression/Makefile.am (modified) * tests/regression/testsuite.at (modified) Added Actions to add and remove a bond in between two atoms. - ... Fri, 14 Dec 2012 14:29:34 GMT Frederik Heber [7ace68] * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser.hpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * tests/regression/Parser/Psi3/pre/testtwocon.psi (modified) * tests/regression/Parser/Psi3/pre/testuhf.psi (modified) Added multiplicity guesser for Psi3Parser's UHF. - TESTFIX: changed ... Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber [05e2ed] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo/pre/bio.data (added) * tests/regression/Parser/Tremolo/pre/bio.potentials (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-improper.at (added) * tests/regression/Parser/testsuite-parser.at (modified) FIX: TremoloParser did not load/save imprData or torsion correctly. ... Fri, 14 Dec 2012 13:02:50 GMT Frederik Heber [67ab71] * src/Parser/TremoloParser.cpp (modified) * tests/regression/Parser/Tremolo-Potentials/post/test.data (modified) * tests/regression/Parser/Tremolo/post/test.data (modified) * tests/regression/Parser/Tremolo/post/test_xyz.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save.at (modified) FIX: default's resSeq in TremoloParser written inconsistently. - ... Fri, 14 Dec 2012 13:02:14 GMT Frederik Heber [0d97b4] * tests/regression/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at (modified) * tests/regression/Analysis/CalculateCellVolume/testsuite-analysis-calculate-cell-volume.at (modified) * tests/regression/Analysis/CalculateMolarMass/testsuite-analysis-calculate-molar-mass.at (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/testsuite-analysis-dipole-angular-correlation-periodic-boundaries.at (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (modified) * tests/regression/Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at (modified) * tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) * tests/regression/Analysis/PointCorrelation/testsuite-analysis-point-correlation.at (modified) * tests/regression/Analysis/PrincipalAxisSystem/testsuite-analysis-principal-axis-system.at (modified) * tests/regression/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/Atoms/ChangeElement/testsuite-atoms-change-element.at (modified) * tests/regression/Atoms/Remove/testsuite-atoms-remove.at (modified) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified) * tests/regression/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at (modified) * tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) * tests/regression/Domain/BoundInBox/testsuite-domain-bound-in-box.at (modified) * tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) * tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) * tests/regression/Domain/ChangeBox/testsuite-domain-change-box.at (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified) * tests/regression/Domain/SetBoundaryConditions/testsuite-domain-set-boundary-conditions.at (modified) * tests/regression/Domain/testsuite-domain.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (modified) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid-with-surface.at (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid.at (modified) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) * tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (modified) * tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-tremolo-dbond-file.at (modified) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at (modified) * tests/regression/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at (modified) * tests/regression/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at (modified) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified) * tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (modified) * tests/regression/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at (modified) * tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond.at (modified) * tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) * tests/regression/Options/ElementsDb/testsuite-options-elements-db.at (modified) * tests/regression/Options/ElementsDb/testsuite-options-no-elements-db.at (modified) * tests/regression/Options/Empty/testsuite-options-empty-configs.at (modified) * tests/regression/Options/FastParsing/testsuite-options-fast-parsing.at (modified) * tests/regression/Options/Help/testsuite-options-help.at (modified) * tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) * tests/regression/Options/SetDefaultName/testsuite-options-set-default-name.at (modified) * tests/regression/Options/SetWorldTime/testsuite-options-set-world-time.at (modified) * tests/regression/Options/Verbosity/testsuite-options-verbosity.at (modified) * tests/regression/Options/Warranty/testsuite-options-warranty.at (modified) * tests/regression/Options/testsuite-options.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-empty.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-save.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-empty.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load-multiply.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-save.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-CONECTs_empty_space.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-capital_letters_element.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-empty.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-multiply.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-various.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-save.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-with-conects.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-empty.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load-multiply.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-save.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-none.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-theory.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at (modified) * tests/regression/Parser/SetParameters/Psi3/testsuite-parser-set-parameters-psi3-reference.at (modified) * tests/regression/Parser/SetParameters/Psi3/testsuite-parser-set-parameters-psi3-wavefunction.at (modified) * tests/regression/Parser/Tremolo-Exttypes/testsuite-parser-tremolo-save-selected-atoms-as-exttypes.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-load.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-save.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials.at (modified) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at (modified) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-empty.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save-unique_usedfields.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-empty.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-multiply.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-various.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * tests/regression/Parser/testsuite-parser.at (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) * tests/regression/RandomNumbers/testsuite-randomnumbers.at (modified) * tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-select-all-atoms.at (modified) * tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-unselect-all-atoms.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-select-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-unselect-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-select-atoms-by-element.at (modified) * tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-unselect-atoms-by-element.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-select-atom-by-id-multiple.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-select-atom-by-id.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id-multiple.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id.at (modified) * tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-select-atom-by-order.at (modified) * tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-unselect-atom-by-order.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at (modified) * tests/regression/Selection/Atoms/InvertAtoms/testsuite-selection-invert-atoms.at (modified) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) * tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-select-all-molecules.at (modified) * tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-unselect-all-molecules.at (modified) * tests/regression/Selection/Molecules/ClearMolecules/testsuite-selection-clear-molecules.at (modified) * tests/regression/Selection/Molecules/InvertMolecules/testsuite-selection-invert-molecules.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-select-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-unselect-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-select-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-unselect-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-forward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-forward.at (modified) * tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-select-atoms-molecules.at (modified) * tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-unselect-atoms-molecules.at (modified) * tests/regression/Selection/Molecules/testsuite-selection-molecules.at (modified) * tests/regression/Selection/testsuite-selection.at (modified) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) * tests/regression/Tesselation/testsuite-tesselation.at (modified) * tests/regression/testsuite.at (modified) FIX: Disclaimer appeared twice in each testsuite. Second time removed. Thu, 13 Dec 2012 10:12:51 GMT Frederik Heber [79ac03] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/AdaptivityMap.hpp (modified) * src/Fragmentation/AtomMask.hpp (added) * src/Fragmentation/Exporters/ExportGraph.cpp (added) * src/Fragmentation/Exporters/ExportGraph.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToFiles.hpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (added) * src/Fragmentation/Exporters/ExportGraph_ToJobs.hpp (added) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/Graph.hpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (added) * src/Fragmentation/Homology/FragmentEdge.hpp (added) * src/Fragmentation/Homology/FragmentNode.cpp (added) * src/Fragmentation/Homology/FragmentNode.hpp (added) * src/Fragmentation/Homology/HomologyContainer.cpp (added) * src/Fragmentation/Homology/HomologyContainer.hpp (added) * src/Fragmentation/Homology/HomologyGraph.cpp (added) * src/Fragmentation/Homology/HomologyGraph.hpp (added) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (added) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp (added) * src/Fragmentation/Homology/unittests/Makefile.am (added) * src/Fragmentation/Homology/unittests/stubs/HomologyGraph_getFromKeysetStub.cpp (added) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Mask.hpp (added) * src/Fragmentation/MoleculeMask.hpp (added) * src/Fragmentation/SortIndex.cpp (added) * src/Fragmentation/SortIndex.hpp (added) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/fragmentation_helpers.hpp (modified) * src/Graph/AdjacencyList.cpp (added) * src/Graph/AdjacencyList.hpp (added) * src/Graph/CheckAgainstAdjacencyFile.cpp (deleted) * src/Graph/CheckAgainstAdjacencyFile.hpp (deleted) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.hpp (modified) * src/Graph/ListOfLocalAtoms.hpp (added) * src/Graph/Makefile.am (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (added) * src/Graph/unittests/AdjacencyListUnitTest.hpp (added) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.cpp (deleted) * src/Graph/unittests/CheckAgainstAdjacencyFileUnitTest.hpp (deleted) * src/Graph/unittests/Makefile.am (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeLeafClass.hpp (modified) * src/MoleculeListClass.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/Makefile.am (modified) * tests/CodeChecks/testsuite-header-dist.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) Merge branch 'Fragmentation_Homology' into Candidate_v1.3.7 ... Mon, 03 Dec 2012 09:50:01 GMT Frederik Heber [3aa8a5] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Graph/AdjacencyList.cpp (modified) * src/Graph/AdjacencyList.hpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.hpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) REFACTOR: AdjacencyList now just contains a single internal map. - ... Mon, 03 Dec 2012 09:49:06 GMT Frederik Heber [2a0eb0] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/AtomMask.hpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Fragmentation.hpp (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) FragmentationAction now works on selected atoms, split into ... Fri, 16 Nov 2012 11:10:27 GMT Frederik Heber [842aac] * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Actions/ShapeAction/CreateShapeAction.def (modified) * src/Actions/ShapeAction/SetShapeAction.cpp (deleted) * src/Actions/ShapeAction/SetShapeAction.def (deleted) * src/Actions/ShapeAction/SetShapeAction.hpp (deleted) * src/Shapes/ShapeFactory.cpp (modified) * src/Shapes/ShapeFactory.hpp (modified) * src/Shapes/unittests/ShapeFactoryUnitTest.cpp (modified) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) Refactoring: FillSurfaceAction uses ShapeRegistry Fri, 16 Nov 2012 11:10:07 GMT Frederik Heber [ff9e5a] * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/cleanUp.cpp (modified) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) Refactoring: AllAtomsInsideVolumeAction uses ShapeRegistry - ... Thu, 15 Nov 2012 17:31:07 GMT Frederik Heber [eff536] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.def (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.hpp (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.def (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.hpp (deleted) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (moved) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.def (added) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.hpp (added) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.def (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.hpp (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.def (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.hpp (deleted) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (moved) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.def (added) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.hpp (added) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) AllAtomsInsideCuboid/SphereAction > AllAtomsInsideVolumeAction (using ... Thu, 15 Nov 2012 17:31:07 GMT Frederik Heber [09eaac] * src/Actions/FillAction/FillSurfaceAction.cpp (moved) * src/Actions/FillAction/FillSurfaceAction.def (moved) * src/Actions/FillAction/FillSurfaceAction.hpp (moved) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) FillSphericalSurfaceAction > FillSurfaceAction (using shape factory) Fri, 26 Oct 2012 13:11:18 GMT Frederik Heber [f7c7cf] * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomById/post/id01_missing.xyz (added) * tests/regression/Selection/Atoms/AtomById/post/id01_present.xyz (added) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-select-atom-by-id-multiple.at (added) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id-multiple.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Selection(Not)AtomById now works on multiple ids. - this closed ... Fri, 26 Oct 2012 13:11:18 GMT Frederik Heber [3a51bd] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (added) * src/Actions/MoleculeAction/StretchBondAction.def (added) * src/Actions/MoleculeAction/StretchBondAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/StretchBond/post/ethane.xyz (added) * tests/regression/Molecules/StretchBond/pre/ethane.xyz (added) * tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added new StretchBondAction to stretch the bond within a molecule. ... Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [6253ed] * tests/CodeChecks/testsuite-config_h.at (modified) * tests/CodeChecks/testsuite-date_in_dox.at (modified) * tests/CodeChecks/testsuite-globallistofactions_hpp.at (modified) * tests/CodeChecks/testsuite-header-dist.at (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/CodeChecks/testsuite.at (modified) * tests/Fragmentations/Analyzing/heptan/testsuite-analyzing-heptan.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (modified) * tests/Fragmentations/Joining/heptan/testsuite-joining-heptan.at (modified) * tests/Fragmentations/testsuite.at (modified) * tests/JobMarket/testsuite-jobmarket-molecuilderrun.at (modified) * tests/JobMarket/testsuite-jobmarket-mpqc-jobs.at (modified) * tests/JobMarket/testsuite-jobmarket-stand-in-mpqc.at (modified) * tests/JobMarket/testsuite-jobmarket.at (modified) * tests/JobMarket/testsuite.at (modified) * tests/Python/AllActions/testsuite-python-allactions.at (modified) * tests/Python/AllActions/testsuite-python-options_dat.at (modified) * tests/Python/BoxMaker/testsuite-python-boxmaker.at (modified) * tests/Python/CommandHelp/testsuite-python-commandhelp.at (modified) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (modified) * tests/Python/testsuite.at (modified) * tests/Tesselations/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (modified) * tests/Tesselations/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (modified) * tests/Tesselations/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (modified) * tests/Tesselations/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (modified) * tests/Tesselations/benzene/testsuite-benzene.at (modified) * tests/Tesselations/cholesterol/testsuite-cholesterol.at (modified) * tests/Tesselations/cycloheptane/testsuite-cycloheptane.at (modified) * tests/Tesselations/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (modified) * tests/Tesselations/glucose/testsuite-glucose.at (modified) * tests/Tesselations/heptan/testsuite-heptan.at (modified) * tests/Tesselations/isoleucine/testsuite-isoleucine.at (modified) * tests/Tesselations/neohexane/testsuite-neohexane.at (modified) * tests/Tesselations/proline/testsuite-proline.at (modified) * tests/Tesselations/putrescine/testsuite-putrescine.at (modified) * tests/Tesselations/tartaric_acid/testsuite-tartaric_acid.at (modified) * tests/Tesselations/testsuite.at (modified) * tests/disclaimer.at (added) * tests/regression/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at (modified) * tests/regression/Analysis/CalculateCellVolume/testsuite-analysis-calculate-cell-volume.at (modified) * tests/regression/Analysis/CalculateMolarMass/testsuite-analysis-calculate-molar-mass.at (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/testsuite-analysis-dipole-angular-correlation-periodic-boundaries.at (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Analysis/DipoleCorrelation-Empty/testsuite-analysis-dipole-correlation-empty.at (modified) * tests/regression/Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at (modified) * tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) * tests/regression/Analysis/PointCorrelation/testsuite-analysis-point-correlation.at (modified) * tests/regression/Analysis/PrincipalAxisSystem/testsuite-analysis-principal-axis-system.at (modified) * tests/regression/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) * tests/regression/Atoms/ChangeElement/testsuite-atoms-change-element.at (modified) * tests/regression/Atoms/Remove/testsuite-atoms-remove.at (modified) * tests/regression/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at (modified) * tests/regression/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at (modified) * tests/regression/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at (modified) * tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at (modified) * tests/regression/Domain/BoundInBox/testsuite-domain-bound-in-box.at (modified) * tests/regression/Domain/CenterInBox/testsuite-domain-center-in-box.at (modified) * tests/regression/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at (modified) * tests/regression/Domain/ChangeBox/testsuite-domain-change-box.at (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/regression/Domain/ScaleBox/testsuite-domain-scale-box.at (modified) * tests/regression/Domain/SetBoundaryConditions/testsuite-domain-set-boundary-conditions.at (modified) * tests/regression/Domain/testsuite-domain.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at (modified) * tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at (modified) * tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid-with-surface.at (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid.at (modified) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) * tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (modified) * tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-tremolo-dbond-file.at (modified) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at (modified) * tests/regression/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at (modified) * tests/regression/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at (modified) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified) * tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (modified) * tests/regression/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at (modified) * tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified) * tests/regression/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) * tests/regression/Options/BondLengthTable/testsuite-options-bond-length-table.at (modified) * tests/regression/Options/ElementsDb/testsuite-options-elements-db.at (modified) * tests/regression/Options/ElementsDb/testsuite-options-no-elements-db.at (modified) * tests/regression/Options/Empty/testsuite-options-empty-configs.at (modified) * tests/regression/Options/FastParsing/testsuite-options-fast-parsing.at (modified) * tests/regression/Options/Help/testsuite-options-help.at (modified) * tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) * tests/regression/Options/SetDefaultName/testsuite-options-set-default-name.at (modified) * tests/regression/Options/SetWorldTime/testsuite-options-set-world-time.at (modified) * tests/regression/Options/Verbosity/testsuite-options-verbosity.at (modified) * tests/regression/Options/Warranty/testsuite-options-warranty.at (modified) * tests/regression/Options/testsuite-options.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-empty.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-save.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-empty.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load-multiply.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-multiple-timesteps.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-save.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-CONECTs_empty_space.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-capital_letters_element.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-empty.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-multiply.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-various.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-multiple-timesteps.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-save.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-with-conects.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-empty.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load-multiply.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-save.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-basis.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-maxiterations.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-none.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-theory.at (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at (modified) * tests/regression/Parser/SetParameters/Psi3/testsuite-parser-set-parameters-psi3-reference.at (modified) * tests/regression/Parser/SetParameters/Psi3/testsuite-parser-set-parameters-psi3-wavefunction.at (modified) * tests/regression/Parser/Tremolo-Exttypes/testsuite-parser-tremolo-save-selected-atoms-as-exttypes.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-load.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-save.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials.at (modified) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at (modified) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-empty.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save-unique_usedfields.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-empty.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-multiply.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-various.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-multiple-timesteps.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * tests/regression/Parser/testsuite-parser.at (modified) * tests/regression/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at (modified) * tests/regression/RandomNumbers/Engine/testsuite-set-random-number-engine.at (modified) * tests/regression/RandomNumbers/testsuite-randomnumbers.at (modified) * tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-select-all-atoms.at (modified) * tests/regression/Selection/Atoms/AllAtoms/testsuite-selection-unselect-all-atoms.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-select-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-unselect-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-select-atoms-by-element.at (modified) * tests/regression/Selection/Atoms/AtomByElement/testsuite-selection-unselect-atoms-by-element.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-select-atom-by-id.at (modified) * tests/regression/Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id.at (modified) * tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-select-atom-by-order.at (modified) * tests/regression/Selection/Atoms/AtomByOrder/testsuite-selection-unselect-atom-by-order.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at (modified) * tests/regression/Selection/Atoms/InvertAtoms/testsuite-selection-invert-atoms.at (modified) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) * tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-select-all-molecules.at (modified) * tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-unselect-all-molecules.at (modified) * tests/regression/Selection/Molecules/ClearMolecules/testsuite-selection-clear-molecules.at (modified) * tests/regression/Selection/Molecules/InvertMolecules/testsuite-selection-invert-molecules.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-select-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-unselect-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-select-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-unselect-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-forward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-forward.at (modified) * tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-select-atoms-molecules.at (modified) * tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-unselect-atoms-molecules.at (modified) * tests/regression/Selection/Molecules/testsuite-selection-molecules.at (modified) * tests/regression/Selection/testsuite-selection.at (modified) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) * tests/regression/Tesselation/testsuite-tesselation.at (modified) * tests/regression/testsuite.at (modified) FIX: Added license disclaimer to every testfile .at of the testsuite ... Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [e9dc19] * src/Parser/MpqcParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * tests/regression/Atoms/Add/post/test.in (modified) * tests/regression/Parser/Mpqc/post/doublewater.in (modified) * tests/regression/Parser/Mpqc/post/test.in (modified) FIX: MpqcParser now does not center the written set of atoms anymore. ... Wed, 26 Sep 2012 17:24:47 GMT Frederik Heber [e6e4a0] * src/Parser/TremoloParser.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * tests/regression/Atoms/Add/post/test.data (modified) * tests/regression/Parser/Tremolo-Potentials/post/test.data (modified) * tests/regression/Parser/Tremolo/post/test.data (modified) * tests/regression/Parser/Tremolo/pre/test.data (modified) FIX: TremoloParser did not treat key F properly in saveLine() and ... Wed, 26 Sep 2012 17:23:51 GMT Frederik Heber [125841] * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/unittests/BaseShapesUnitTest.cpp (modified) * tests/regression/Filling/SphericalSurface/post/tensid.data (modified) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) Made Sphere_impl::getHomogeneousPointsOnSurface() more accurate - ... Thu, 09 Aug 2012 12:51:10 GMT Michael Ankele [072f0e] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/WorldAction/OutputAsAction.cpp (moved) * src/Actions/WorldAction/OutputAsAction.def (moved) * src/Actions/WorldAction/OutputAsAction.hpp (moved) * tests/Python/AllActions/missing.dat (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-save.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-save.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-save.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-save.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * utils/Python/boxmaker.py.in (modified) Refactoring: renamed OutputAction -> OutputAsAction Wed, 11 Jul 2012 13:02:17 GMT Frederik Heber [bd81f9] * configure.ac (modified) * m4/ax_jobmarket.m4 (added) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (added) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (added) * src/Actions/FragmentationAction/FragmentationAutomationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/unittests/stubs/DummyUI.hpp (modified) * src/Atom/atom_observable.cpp (modified) * src/ControllerOptions_MPQCCommandJob.cpp (added) * src/ControllerOptions_MPQCCommandJob.hpp (added) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/MatrixContainer.hpp (modified) * src/Jobs/MPQCCommandJob.cpp (added) * src/Jobs/MPQCCommandJob.hpp (added) * src/Jobs/MPQCCommandJob_MPQCData.cpp (added) * src/Jobs/MPQCCommandJob_MPQCData.hpp (added) * src/Jobs/Makefile.am (added) * src/Jobs/unittests/MPQCCommandJobUnitTest.cpp (added) * src/Jobs/unittests/MPQCCommandJobUnitTest.hpp (added) * src/Jobs/unittests/MPQCDataUnitTest.cpp (added) * src/Jobs/unittests/MPQCDataUnitTest.hpp (added) * src/Jobs/unittests/Makefile.am (added) * src/Makefile.am (modified) * src/Server.cpp (added) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp (modified) * src/Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) * src/UIElements/CommandLineUI/Query/FilesCommandLineQuery.cpp (added) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (added) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Query/FilesQuery.cpp (added) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FilesTextQuery.cpp (added) * src/UIElements/TextUI/Query/TextQuery.hpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextDialog.hpp (modified) * src/controller.cpp (added) * src/controller_AddOn_MPQCCommandJob.cpp (added) * src/controller_MPQCCommandJob.cpp (added) * src/controller_MPQCCommandJob.hpp (added) * src/poolworker.cpp (added) * src/unittests/Makefile.am (modified) * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-globallistofactions_hpp.at (modified) * tests/Fragmentations/Makefile.am (modified) * tests/JobMarket/Makefile.am (added) * tests/JobMarket/atlocal.in (added) * tests/JobMarket/molecuilder.in (added) * tests/JobMarket/mpqc.cpp (added) * tests/JobMarket/pre/BondFragment00.in (added) * tests/JobMarket/pre/BondFragment00.out (added) * tests/JobMarket/pre/BondFragment01.out (added) * tests/JobMarket/pre/BondFragment02.out (added) * tests/JobMarket/pre/BondFragment03.out (added) * tests/JobMarket/pre/BondFragment04.out (added) * tests/JobMarket/pre/BondFragment05.out (added) * tests/JobMarket/pre/BondFragment06.out (added) * tests/JobMarket/pre/BondFragmentAdjacency.dat (added) * tests/JobMarket/pre/BondFragmentForces-Factors.dat (added) * tests/JobMarket/pre/BondFragmentKeySets.dat (added) * tests/JobMarket/testsuite-jobmarket-molecuilderrun.at (added) * tests/JobMarket/testsuite-jobmarket-mpqc-jobs.at (added) * tests/JobMarket/testsuite-jobmarket-stand-in-mpqc.at (added) * tests/JobMarket/testsuite-jobmarket.at (added) * tests/JobMarket/testsuite.at (added) * tests/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/Python/Makefile.am (modified) * tests/Tesselations/Makefile.am (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'Candidate_v1.3.0' into stable Conflicts: ... Tue, 10 Jul 2012 16:45:11 GMT Frederik Heber [5ffa05] * tests/CodeChecks/Makefile.am (modified) * tests/Fragmentations/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) * tests/Python/Makefile.am (modified) * tests/Tesselations/Makefile.am (modified) * tests/regression/Makefile.am (modified) DISTFIX: Now all package.m4 are created in build directory and ... Tue, 10 Jul 2012 15:41:00 GMT Frederik Heber [004d5c] * JobMarket/AUTHORS (deleted) * JobMarket/COPYING (deleted) * JobMarket/ChangeLog (deleted) * JobMarket/INSTALL (deleted) * JobMarket/JobMarket-debug.pc.in (deleted) * JobMarket/JobMarket.pc.in (deleted) * JobMarket/Makefile.am (deleted) * JobMarket/NEWS (deleted) * JobMarket/README (deleted) * JobMarket/bootstrap (deleted) * JobMarket/build-aux/README (deleted) * JobMarket/configure.ac (deleted) * JobMarket/configure.scan (deleted) * JobMarket/doc/Doxyfile (deleted) * JobMarket/doc/Makefile.am (deleted) * JobMarket/doc/am_doxygen_include.am (deleted) * JobMarket/libJobMarket_config.h.in (deleted) * JobMarket/m4 (deleted) * JobMarket/src/JobMarket/Connection.hpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerCommand.hpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerCommandRegistry.cpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerCommandRegistry.hpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerOptions.cpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerOptions.hpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerOptions_SystemCommandJob.cpp (deleted) * JobMarket/src/JobMarket/Controller/ControllerOptions_SystemCommandJob.hpp (deleted) * JobMarket/src/JobMarket/Controller/FragmentController.cpp (deleted) * JobMarket/src/JobMarket/Controller/FragmentController.hpp (deleted) * JobMarket/src/JobMarket/Controller/controller.cpp (deleted) * JobMarket/src/JobMarket/Controller/controller_AddOn.hpp (deleted) * JobMarket/src/JobMarket/Controller/controller_AddOn_SystemCommandJob.cpp (deleted) * JobMarket/src/JobMarket/Controller/controller_SystemCommandJob.cpp (deleted) * JobMarket/src/JobMarket/Controller/controller_SystemCommandJob.hpp (deleted) * JobMarket/src/JobMarket/Controller/controller_main.cpp (deleted) * JobMarket/src/JobMarket/Controller/controller_main.hpp (deleted) * JobMarket/src/JobMarket/ControllerChoices.hpp (deleted) * JobMarket/src/JobMarket/DefaultOptions.cpp (deleted) * JobMarket/src/JobMarket/DefaultOptions.hpp (deleted) * JobMarket/src/JobMarket/ExitflagContainer.hpp (deleted) * JobMarket/src/JobMarket/FragmentQueue.cpp (deleted) * JobMarket/src/JobMarket/FragmentQueue.hpp (deleted) * JobMarket/src/JobMarket/FragmentScheduler.cpp (deleted) * JobMarket/src/JobMarket/FragmentScheduler.hpp (deleted) * JobMarket/src/JobMarket/GlobalJobId.cpp (deleted) * JobMarket/src/JobMarket/GlobalJobId.hpp (deleted) * JobMarket/src/JobMarket/JobId.cpp (deleted) * JobMarket/src/JobMarket/JobId.hpp (deleted) * JobMarket/src/JobMarket/Jobs/FragmentJob.cpp (deleted) * JobMarket/src/JobMarket/Jobs/FragmentJob.hpp (deleted) * JobMarket/src/JobMarket/Jobs/SystemCommandJob.cpp (deleted) * JobMarket/src/JobMarket/Jobs/SystemCommandJob.hpp (deleted) * JobMarket/src/JobMarket/Listener.cpp (deleted) * JobMarket/src/JobMarket/Listener.hpp (deleted) * JobMarket/src/JobMarket/Makefile.am (deleted) * JobMarket/src/JobMarket/Operations/AsyncOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/AsyncOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/CheckResultsOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/CheckResultsOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/GetNextJobIdOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/GetNextJobIdOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/ReceiveResultsOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/ReceiveResultsOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/RemoveAllWorkerOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/RemoveAllWorkerOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/SendJobsOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/SendJobsOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/ShutdownOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Controllers/ShutdownOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Operation.hpp (deleted) * JobMarket/src/JobMarket/Operations/OperationQueue.cpp (deleted) * JobMarket/src/JobMarket/Operations/OperationQueue.hpp (deleted) * JobMarket/src/JobMarket/Operations/OperationRegistry.cpp (deleted) * JobMarket/src/JobMarket/Operations/OperationRegistry.hpp (deleted) * JobMarket/src/JobMarket/Operations/Servers/SendJobToWorkerOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Servers/SendJobToWorkerOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Servers/ShutdownWorkerOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Servers/ShutdownWorkerOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/SyncOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/SyncOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/EnrollInPoolOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/EnrollInPoolOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/ObtainJobOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/ObtainJobOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/RemoveFromPoolOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/RemoveFromPoolOperation.hpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/SubmitResultOperation.cpp (deleted) * JobMarket/src/JobMarket/Operations/Workers/SubmitResultOperation.hpp (deleted) * JobMarket/src/JobMarket/Pool/PoolWorker.cpp (deleted) * JobMarket/src/JobMarket/Pool/PoolWorker.hpp (deleted) * JobMarket/src/JobMarket/Pool/WorkerPool.cpp (deleted) * JobMarket/src/JobMarket/Pool/WorkerPool.hpp (deleted) * JobMarket/src/JobMarket/Results/FragmentResult.cpp (deleted) * JobMarket/src/JobMarket/Results/FragmentResult.hpp (deleted) * JobMarket/src/JobMarket/ServerOptions.cpp (deleted) * JobMarket/src/JobMarket/ServerOptions.hpp (deleted) * JobMarket/src/JobMarket/SignalHandler.cpp (deleted) * JobMarket/src/JobMarket/SignalHandler.hpp (deleted) * JobMarket/src/JobMarket/SignalOptions.cpp (deleted) * JobMarket/src/JobMarket/SignalOptions.hpp (deleted) * JobMarket/src/JobMarket/WorkerAddress.cpp (deleted) * JobMarket/src/JobMarket/WorkerAddress.hpp (deleted) * JobMarket/src/JobMarket/WorkerChoices.hpp (deleted) * JobMarket/src/JobMarket/WorkerOptions.cpp (deleted) * JobMarket/src/JobMarket/WorkerOptions.hpp (deleted) * JobMarket/src/JobMarket/atexit.cpp (deleted) * JobMarket/src/JobMarket/atexit.hpp (deleted) * JobMarket/src/JobMarket/poolworker.cpp (deleted) * JobMarket/src/JobMarket/poolworker_main.cpp (deleted) * JobMarket/src/JobMarket/poolworker_main.hpp (deleted) * JobMarket/src/JobMarket/server.cpp (deleted) * JobMarket/src/JobMarket/server_main.cpp (deleted) * JobMarket/src/JobMarket/server_main.hpp (deleted) * JobMarket/src/JobMarket/types.hpp (deleted) * JobMarket/src/documentation/Makefile.am (deleted) * JobMarket/src/documentation/jobmarket.dox (deleted) * JobMarket/src/documentation/mainpage.dox (deleted) * JobMarket/src/unittests/FragmentJobUnitTest.cpp (deleted) * JobMarket/src/unittests/FragmentJobUnitTest.hpp (deleted) * JobMarket/src/unittests/FragmentQueueUnitTest.cpp (deleted) * JobMarket/src/unittests/FragmentQueueUnitTest.hpp (deleted) * JobMarket/src/unittests/FragmentResultUnitTest.cpp (deleted) * JobMarket/src/unittests/FragmentResultUnitTest.hpp (deleted) * JobMarket/src/unittests/Makefile.am (deleted) * JobMarket/src/unittests/OperationQueueUnitTest.cpp (deleted) * JobMarket/src/unittests/OperationQueueUnitTest.hpp (deleted) * JobMarket/src/unittests/SystemCommandJobUnitTest.cpp (deleted) * JobMarket/src/unittests/SystemCommandJobUnitTest.hpp (deleted) * JobMarket/src/unittests/UnitTestMain.cpp (deleted) * JobMarket/src/unittests/WorkerAddressUnitTest.cpp (deleted) * JobMarket/src/unittests/WorkerAddressUnitTest.hpp (deleted) * JobMarket/src/unittests/WorkerPoolUnitTest.cpp (deleted) * JobMarket/src/unittests/WorkerPoolUnitTest.hpp (deleted) * JobMarket/src/unittests/stubs/AsyncOperationStub.hpp (deleted) * JobMarket/src/unittests/stubs/FragmentJobStub.cpp (deleted) * JobMarket/src/unittests/stubs/FragmentJobStub.hpp (deleted) * JobMarket/src/unittests/stubs/FragmentResultStub.cpp (deleted) * JobMarket/src/unittests/stubs/ObserverStub.cpp (deleted) * JobMarket/src/unittests/stubs/ObserverStub.hpp (deleted) * JobMarket/tests/CodeChecks/Makefile.am (deleted) * JobMarket/tests/CodeChecks/atlocal.in (deleted) * JobMarket/tests/CodeChecks/testsuite-config_h.at (deleted) * JobMarket/tests/CodeChecks/testsuite-date_in_dox.at (deleted) * JobMarket/tests/CodeChecks/testsuite-header-dist.at (deleted) * JobMarket/tests/CodeChecks/testsuite-memdebug.at (deleted) * JobMarket/tests/CodeChecks/testsuite-project-disclaimer.at (deleted) * JobMarket/tests/Makefile.am (deleted) * JobMarket/tests/regression/atlocal.in (deleted) * JobMarket/tests/regression/testsuite-addingjobs.at (deleted) * JobMarket/tests/regression/testsuite-checkstate.at (deleted) * JobMarket/tests/regression/testsuite-completerun.at (deleted) * JobMarket/tests/regression/testsuite-enrollinpool.at (deleted) * JobMarket/tests/regression/testsuite-getresults.at (deleted) * JobMarket/tests/regression/testsuite-resubmitjobs.at (deleted) * JobMarket/tests/regression/testsuite-server-shutdown.at (deleted) * JobMarket/tests/regression/testsuite-server-worker.at (deleted) * JobMarket/tests/regression/testsuite.at (deleted) * Makefile.am (modified) * configure.ac (modified) * m4/ax_jobmarket.m4 (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCCommandJob_MPQCData.cpp (modified) * src/Jobs/MPQCCommandJob_MPQCData.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Server.cpp (modified) * src/UIElements/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/poolworker.cpp (modified) * src/unittests/Makefile.am (modified) * tests/CodeChecks/testsuite-globallistofactions_hpp.at (modified) * tests/JobMarket/Makefile.am (moved) * tests/JobMarket/atlocal.in (added) * tests/JobMarket/molecuilder.in (added) * tests/JobMarket/mpqc.cpp (moved) * tests/JobMarket/pre/BondFragment00.in (moved) * tests/JobMarket/pre/BondFragment00.out (moved) * tests/JobMarket/pre/BondFragment01.out (moved) * tests/JobMarket/pre/BondFragment02.out (moved) * tests/JobMarket/pre/BondFragment03.out (moved) * tests/JobMarket/pre/BondFragment04.out (moved) * tests/JobMarket/pre/BondFragment05.out (moved) * tests/JobMarket/pre/BondFragment06.out (moved) * tests/JobMarket/pre/BondFragmentAdjacency.dat (moved) * tests/JobMarket/pre/BondFragmentForces-Factors.dat (moved) * tests/JobMarket/pre/BondFragmentKeySets.dat (moved) * tests/JobMarket/testsuite-jobmarket-molecuilderrun.at (moved) * tests/JobMarket/testsuite-jobmarket-mpqc-jobs.at (moved) * tests/JobMarket/testsuite-jobmarket-stand-in-mpqc.at (moved) * tests/JobMarket/testsuite-jobmarket.at (added) * tests/JobMarket/testsuite.at (moved) * tests/Makefile.am (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Removed JobMarket as it is now in its own repository. - added ... Fri, 06 Jul 2012 10:18:48 GMT Frederik Heber [edecba] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (added) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (added) * src/Actions/FragmentationAction/FragmentationAutomationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-molecuilderrun.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added Action to use the JobMarket for FragmentationAutomation. - ... Fri, 06 Jul 2012 10:18:47 GMT Frederik Heber [c8446c] * JobMarket/Makefile.am (modified) * JobMarket/configure.ac (modified) * JobMarket/tests/Makefile.am (added) * JobMarket/tests/regression/Makefile.am (added) * JobMarket/tests/regression/atlocal.in (added) * JobMarket/tests/regression/testsuite-addingjobs.at (moved) * JobMarket/tests/regression/testsuite-checkstate.at (moved) * JobMarket/tests/regression/testsuite-completerun.at (moved) * JobMarket/tests/regression/testsuite-enrollinpool.at (moved) * JobMarket/tests/regression/testsuite-getresults.at (moved) * JobMarket/tests/regression/testsuite-resubmitjobs.at (moved) * JobMarket/tests/regression/testsuite-server-shutdown.at (moved) * JobMarket/tests/regression/testsuite-server-worker.at (moved) * JobMarket/tests/regression/testsuite.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Moved basic Fragmentation/Automation regression tests over to ... Fri, 06 Jul 2012 10:18:43 GMT Frederik Heber [cc5db5] * Makefile.am (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/unittests/Makefile.am (modified) * src/Jobs/MPQCCommandJob.cpp (moved) * src/Jobs/MPQCCommandJob.hpp (moved) * src/Jobs/MPQCCommandJob_MPQCData.cpp (moved) * src/Jobs/MPQCCommandJob_MPQCData.hpp (moved) * src/Jobs/Makefile.am (added) * src/Jobs/unittests/MPQCCommandJobUnitTest.cpp (moved) * src/Jobs/unittests/MPQCCommandJobUnitTest.hpp (moved) * src/Jobs/unittests/MPQCDataUnitTest.cpp (moved) * src/Jobs/unittests/MPQCDataUnitTest.hpp (moved) * src/Jobs/unittests/Makefile.am (added) * src/Makefile.am (modified) * src/Server.cpp (moved) * src/controller.cpp (moved) * src/poolworker.cpp (moved) * src/unittests/Makefile.am (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-checkstate.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-enrollinpool.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-getresults.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-mpqc-jobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-resubmitjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-shutdown.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) Moved all MPQCCommand... to src/Jobs, controller,server,poolworker to ... Fri, 06 Jul 2012 09:29:15 GMT Frederik Heber [469f53] * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-enrollinpool.at (modified) Regression test FragmentationAutomation enroll-in-pool now also adds ... Mon, 02 Jul 2012 08:32:06 GMT Frederik Heber [af9b9ff] * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/controller.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-checkstate.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-enrollinpool.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-getresults.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-mpqc-jobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-resubmitjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-shutdown.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) Controller now also uses boost::program_options to parse command line ... Mon, 02 Jul 2012 08:32:04 GMT Frederik Heber [684bc1] * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/Server.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-checkstate.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-enrollinpool.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-getresults.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-mpqc-jobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-resubmitjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-shutdown.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) Server now also parses worker and controller port via ... Mon, 02 Jul 2012 08:32:03 GMT Frederik Heber [5ac92e] * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/poolworker.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-enrollinpool.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-mpqc-jobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-resubmitjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) PoolWorker now parses command line options via ... Mon, 02 Jul 2012 07:54:13 GMT Frederik Heber [bc1625] * tests/regression/Fragmentation/Automation/pre/BondFragmentAdjacency.dat (added) * tests/regression/Fragmentation/Automation/pre/BondFragmentForces-Factors.dat (added) * tests/regression/Fragmentation/Automation/pre/BondFragmentKeySets.dat (added) * tests/regression/Fragmentation/Automation/pre/Job00.in (deleted) * tests/regression/Fragmentation/Automation/pre/Job01.in (deleted) * tests/regression/Fragmentation/Automation/pre/Job02.in (deleted) * tests/regression/Fragmentation/Automation/pre/Job03.in (deleted) * tests/regression/Fragmentation/Automation/pre/Job04.in (deleted) * tests/regression/Fragmentation/Automation/pre/Job05.in (deleted) * tests/regression/Fragmentation/Automation/pre/Job06.in (deleted) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-mpqc-jobs.at (modified) Regression test mpqc-jobs now requires "correct" results from stand- ... Mon, 02 Jul 2012 07:54:13 GMT Frederik Heber [a98afb] * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-mpqc-jobs.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test to Fragmentation/Automation whether mpqc jobs ... Mon, 02 Jul 2012 07:54:13 GMT Frederik Heber [23d10f] * tests/regression/Fragmentation/Automation/mpqc.cpp (added) * tests/regression/Fragmentation/Automation/pre/BondFragment00.in (added) * tests/regression/Fragmentation/Automation/pre/BondFragment00.out (added) * tests/regression/Fragmentation/Automation/pre/BondFragment01.out (added) * tests/regression/Fragmentation/Automation/pre/BondFragment02.out (added) * tests/regression/Fragmentation/Automation/pre/BondFragment03.out (added) * tests/regression/Fragmentation/Automation/pre/BondFragment04.out (added) * tests/regression/Fragmentation/Automation/pre/BondFragment05.out (added) * tests/regression/Fragmentation/Automation/pre/BondFragment06.out (added) * tests/regression/Fragmentation/Automation/pre/Job00.in (added) * tests/regression/Fragmentation/Automation/pre/Job01.in (added) * tests/regression/Fragmentation/Automation/pre/Job02.in (added) * tests/regression/Fragmentation/Automation/pre/Job03.in (added) * tests/regression/Fragmentation/Automation/pre/Job04.in (added) * tests/regression/Fragmentation/Automation/pre/Job05.in (added) * tests/regression/Fragmentation/Automation/pre/Job06.in (added) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-stand-in-mpqc.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added stand-in mpqc program and regression test on it to ... Mon, 02 Jul 2012 07:54:11 GMT Frederik Heber [2344a3] * src/Fragmentation/Automation/FragmentQueue.cpp (modified) * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/FragmentScheduler.hpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-resubmitjobs.at (modified) FragmentScheduler is now an Observer of JobsQueue and pool. - ... Fri, 29 Jun 2012 13:23:20 GMT Frederik Heber [a06358c] * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-enrollinpool.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test Fragmentation/Automation for enrolling in pool. Fri, 29 Jun 2012 13:23:20 GMT Frederik Heber [e8f397] * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/Pool/PoolWorker.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-resubmitjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) PoolWorker is now truely listenting. - does now ... Fri, 29 Jun 2012 08:01:38 GMT Frederik Heber [fe95b7] * src/Fragmentation/Automation/FragmentQueue.cpp (modified) * src/Fragmentation/Automation/FragmentQueue.hpp (modified) * src/Fragmentation/Automation/unittests/FragmentQueueUnitTest.cpp (modified) * src/Fragmentation/Automation/unittests/FragmentQueueUnitTest.hpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-resubmitjobs.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) FragmentQueue can now resubmit jobs. - we keep an internal list of ... Wed, 27 Jun 2012 16:07:21 GMT Frederik Heber [41c1b7] * src/Fragmentation/Automation/Controller/Commands/EnrollInPoolOperation.cpp (added) * src/Fragmentation/Automation/Controller/Commands/EnrollInPoolOperation.hpp (added) * src/Fragmentation/Automation/Controller/Commands/ObtainJobOperation.cpp (added) * src/Fragmentation/Automation/Controller/Commands/ObtainJobOperation.hpp (added) * src/Fragmentation/Automation/Controller/Commands/SendJobToWorkerOperation.cpp (added) * src/Fragmentation/Automation/Controller/Commands/SendJobToWorkerOperation.hpp (added) * src/Fragmentation/Automation/Controller/Commands/ShutdownOperation.cpp (modified) * src/Fragmentation/Automation/Controller/Commands/SubmitResultOperation.cpp (added) * src/Fragmentation/Automation/Controller/Commands/SubmitResultOperation.hpp (added) * src/Fragmentation/Automation/Controller/Commands/WorkOnJobOperation.cpp (deleted) * src/Fragmentation/Automation/Controller/Commands/WorkOnJobOperation.hpp (deleted) * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/FragmentScheduler.hpp (modified) * src/Fragmentation/Automation/FragmentWorker.cpp (deleted) * src/Fragmentation/Automation/FragmentWorker.hpp (deleted) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/Pool/PoolWorker.cpp (added) * src/Fragmentation/Automation/Pool/PoolWorker.hpp (added) * src/Fragmentation/Automation/Pool/WorkerPool.cpp (modified) * src/Fragmentation/Automation/Pool/WorkerPool.hpp (modified) * src/Fragmentation/Automation/poolworker.cpp (added) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) HUGE: Added PoolWorker, removed (Fragment)Worker, and rewrote parts ... Wed, 27 Jun 2012 16:07:20 GMT Frederik Heber [554809] * src/Fragmentation/Automation/controller.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) createjobs now gets two options: command, argument. Wed, 27 Jun 2012 16:07:20 GMT Frederik Heber [d1dbfc] * src/Fragmentation/Automation/Controller/Commands/GetNextJobIdOperation.cpp (added) * src/Fragmentation/Automation/Controller/Commands/GetNextJobIdOperation.hpp (added) * src/Fragmentation/Automation/Controller/FragmentController.cpp (modified) * src/Fragmentation/Automation/ControllerChoices.hpp (modified) * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/FragmentScheduler.hpp (modified) * src/Fragmentation/Automation/GlobalJobId.cpp (modified) * src/Fragmentation/Automation/GlobalJobId.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/controller.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) New GetNextJobIdOperation for obtaining next available JobId from ... Wed, 27 Jun 2012 16:07:20 GMT Frederik Heber [ff60cfa] * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/GlobalJobId.cpp (added) * src/Fragmentation/Automation/GlobalJobId.hpp (added) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/controller.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) Controller has new function addjobs. - addjobs parses mpqc input ... Fri, 22 Jun 2012 08:19:29 GMT Frederik Heber [7ca772] * src/Fragmentation/Automation/Controller/CommandRegistry.cpp (added) * src/Fragmentation/Automation/Controller/CommandRegistry.hpp (added) * src/Fragmentation/Automation/Controller/FragmentController.cpp (modified) * src/Fragmentation/Automation/Controller/FragmentController.hpp (modified) * src/Fragmentation/Automation/Controller/JobAdder.cpp (deleted) * src/Fragmentation/Automation/Controller/ResultChecker.cpp (deleted) * src/Fragmentation/Automation/Controller/ResultGetter.cpp (deleted) * src/Fragmentation/Automation/Controller/Shutdowner.cpp (deleted) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/controller.cpp (added) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-checkstate.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-getresults.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-shutdown.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) Operations are now contained in CommandRegistry in ... Mon, 18 Jun 2012 10:53:30 GMT Frederik Heber [ca331c] * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.def (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/output.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/post/undo.data (added) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at (added) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (modified) * tests/regression/Parser/Tremolo/post/water-neighbors.data (added) * tests/regression/Parser/testsuite-parser.at (modified) Added Undo/Redo capability to SetTremoloAtomdataAction. - ... Mon, 18 Jun 2012 10:53:29 GMT Frederik Heber [5b0581] * src/Parser/TremoloParser.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo/post/output.data (added) * tests/regression/Parser/Tremolo/pre/water-neighbors.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-save-unique_usedfields.at (added) * tests/regression/Parser/testsuite-parser.at (modified) FIX: TremoloParser did not make usedFields unique when neighbors=4 ... Wed, 13 Jun 2012 17:39:28 GMT Frederik Heber [770ec6] * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.def (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/Specific/KeyValueValidator.cpp (added) * src/Parameters/Validators/Specific/KeyValueValidator.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc-none.at (added) * tests/regression/Parser/SetParameters/Mpqc/testsuite-parser-set-parameters-mpqc.at (modified) * tests/regression/Parser/testsuite-parser.at (modified) KeyValueValidator implemented. - SetParserParameters now receives ... Wed, 13 Jun 2012 17:39:13 GMT Frederik Heber [23958d] * src/Actions/AnalysisAction/CalculateBoundingBoxAction.def (modified) * src/Actions/AnalysisAction/CalculateCellVolumeAction.def (modified) * src/Actions/AnalysisAction/CalculateMolarMassAction.def (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.def (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.def (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.def (modified) * src/Actions/AnalysisAction/PointCorrelationAction.def (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.def (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (modified) * src/Actions/AtomAction/AddAction.def (modified) * src/Actions/AtomAction/ChangeElementAction.def (modified) * src/Actions/AtomAction/RemoveAction.def (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.def (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.def (modified) * src/Actions/AtomAction/TranslateAction.def (modified) * src/Actions/CommandAction/BondLengthTableAction.def (modified) * src/Actions/CommandAction/ElementDbAction.def (modified) * src/Actions/CommandAction/FastParsingAction.def (modified) * src/Actions/CommandAction/HelpAction.def (modified) * src/Actions/CommandAction/VerboseAction.def (modified) * src/Actions/CommandAction/VersionAction.def (modified) * src/Actions/CommandAction/WarrantyAction.def (modified) * src/Actions/FillAction/FillRegularGridAction.def (modified) * src/Actions/FillAction/FillSphericalSurfaceAction.def (modified) * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/GraphAction/CreateAdjacencyAction.def (modified) * src/Actions/GraphAction/DepthFirstSearchAction.def (modified) * src/Actions/GraphAction/SubgraphDissectionAction.def (modified) * src/Actions/MoleculeAction/BondFileAction.def (modified) * src/Actions/MoleculeAction/ChangeNameAction.def (modified) * src/Actions/MoleculeAction/CopyAction.def (modified) * src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.def (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def (modified) * src/Actions/MoleculeAction/LoadAction.def (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.def (modified) * src/Actions/MoleculeAction/SaveBondsAction.def (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.def (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.def (modified) * src/Actions/MoleculeAction/SuspendInWaterAction.def (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.def (modified) * src/Actions/ParserAction/ParseTremoloPotentialsAction.def (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.def (modified) * src/Actions/ParserAction/SetOutputFormatsAction.def (modified) * src/Actions/ParserAction/SetParserParametersAction.def (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.def (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.def (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.def (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.def (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.def (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.def (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.def (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.def (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.def (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.def (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.def (modified) * src/Actions/WorldAction/BoundInBoxAction.def (modified) * src/Actions/WorldAction/CenterInBoxAction.def (modified) * src/Actions/WorldAction/CenterOnEdgeAction.def (modified) * src/Actions/WorldAction/ChangeBoxAction.def (modified) * src/Actions/WorldAction/InputAction.def (modified) * src/Actions/WorldAction/OutputAction.def (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * src/Actions/WorldAction/ScaleBoxAction.def (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.def (modified) * src/Actions/WorldAction/SetDefaultNameAction.def (modified) * src/Actions/WorldAction/SetWorldTimeAction.def (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/Validators/GenericValidators.hpp (added) * src/Parameters/Validators/Specific/ActionNameValidator.hpp (added) * src/Parameters/Validators/Specific/AtomDataValidator.hpp (added) * src/Parameters/Validators/Specific/AtomIdValidator.hpp (added) * src/Parameters/Validators/Specific/BoxConditionValidator.hpp (added) * src/Parameters/Validators/Specific/BoxLengthValidator.hpp (modified) * src/Parameters/Validators/Specific/BoxVectorValidator.hpp (added) * src/Parameters/Validators/Specific/FilePresentValidator.hpp (modified) * src/Parameters/Validators/Specific/FileSuffixValidator.hpp (added) * src/Parameters/Validators/Specific/FormulaValidator.hpp (added) * src/Parameters/Validators/Specific/KeyValueValidator.hpp (added) * src/Parameters/Validators/Specific/MoleculeIdValidator.hpp (added) * src/Parameters/Validators/Specific/ParserFileValidator.hpp (added) * src/Parameters/Validators/Specific/ParserTypeValidator.hpp (added) * src/Parameters/Validators/Specific/RandomNumberValidators.hpp (added) * src/Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.hpp (added) * src/Parameters/Validators/Specific/RealSpaceMatrixSymmetricValidator.hpp (added) * src/Parameters/Validators/Specific/RotationAngleValidator.hpp (added) * src/Parameters/Validators/Specific/TimeStepPresentValidator.hpp (added) * src/Parameters/Validators/Specific/VectorPositiveComponentsValidator.hpp (added) * src/Parameters/Validators/Specific/VectorZeroOneComponentsValidator.hpp (added) * src/Parameters/Validators/UniqueValidator.hpp (added) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-save.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-select-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-unselect-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-forward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-forward.at (modified) HUGE: All .def files now contain a useful paramvalids line. - many ... Wed, 13 Jun 2012 17:39:11 GMT Frederik Heber [e1f414] * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.def (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) FIX: RepeatBoxAction requires std::vector< unsigned int > for ... Wed, 13 Jun 2012 17:39:04 GMT Frederik Heber [97f9b9] * src/Actions/WorldAction/SetBoundaryConditionsAction.def (modified) * src/Box.cpp (modified) * src/Box.hpp (modified) * src/Box_BoundaryConditions.cpp (modified) * src/Box_BoundaryConditions.hpp (modified) * src/unittests/Box_BoundaryConditionsUnitTest.cpp (modified) * tests/regression/Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at (modified) * tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) * tests/regression/Domain/SetBoundaryConditions/testsuite-domain-set-boundary-conditions.at (modified) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (modified) SetBoundaryConditionsAction requires vector instead of string ... Wed, 13 Jun 2012 17:39:03 GMT Frederik Heber [8ea3e7] * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.def (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) CopyMolecule can now copy all currently selected molecules. - this ... Wed, 13 Jun 2012 17:39:02 GMT Frederik Heber [2382d7] * src/Actions/FillAction/FillRegularGridAction.def (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Filling/Mesh/CubeMesh.hpp (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid-with-surface.at (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid.at (modified) FillRegularGrid now uses std::vector instead of Vector. ... Wed, 13 Jun 2012 17:39:01 GMT Frederik Heber [7951b9] * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.def (modified) * tests/regression/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified) Rewrote SurfaceCorrelationAction such that selected atoms are used in ... Mon, 11 Jun 2012 09:53:19 GMT Frederik Heber [f10b0c] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (modified) * src/Actions/AtomAction/ChangeElementAction.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/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSphericalSurfaceAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.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/ParserAction/ParseTremoloPotentialsAction.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.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/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/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.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/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/unittests/stubs/DummyUI.hpp (modified) * src/Parameters/Parameter.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/StreamOperators.hpp (added) * src/Parameters/Value.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * src/Parameters/VectorFromString.hpp (deleted) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (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/CommandLineQuery.hpp (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/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/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/AtomsQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BooleanQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/BoxQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/DoubleQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/ElementsQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/FileQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/IntQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculeQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/MoleculesQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/QtQueryListPipe.hpp (modified) * src/UIElements/Qt4/Pipe/QtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/RandomNumberDistribution_ParametersQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/StringQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/UnsignedIntQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorQtQueryPipe.hpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.cpp (modified) * src/UIElements/Qt4/Pipe/VectorsQtQueryPipe.hpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/QtDialog.hpp (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/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/QtQuery.hpp (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/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/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/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/TextQuery.hpp (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/TextDialog.hpp (modified) * tests/regression/Atoms/Add/testsuite-atoms-add.at (modified) disastrously big and ugly commit - using new Parameter classes: ... Thu, 17 May 2012 15:21:50 GMT Frederik Heber [167b63] * src/Fragmentation/Automation/Controller/Commands/CheckResultsOperation.cpp (added) * src/Fragmentation/Automation/Controller/Commands/CheckResultsOperation.hpp (added) * src/Fragmentation/Automation/Controller/Commands/ReceiveJobsOperation.cpp (added) * src/Fragmentation/Automation/Controller/Commands/ReceiveJobsOperation.hpp (added) * src/Fragmentation/Automation/Controller/Commands/SendResultsOperation.cpp (added) * src/Fragmentation/Automation/Controller/Commands/SendResultsOperation.hpp (added) * src/Fragmentation/Automation/Controller/Commands/ShutdownOperation.cpp (added) * src/Fragmentation/Automation/Controller/Commands/ShutdownOperation.hpp (added) * src/Fragmentation/Automation/Controller/FragmentController.cpp (modified) * src/Fragmentation/Automation/Controller/FragmentController.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) Extracted all other derived Operation's too and placed into folder ... Thu, 17 May 2012 15:21:12 GMT Frederik Heber [5adb84] * src/Fragmentation/Automation/FragmentController.cpp (modified) * src/Fragmentation/Automation/FragmentController.hpp (modified) * src/Fragmentation/Automation/JobAdder.cpp (modified) * src/Fragmentation/Automation/ResultChecker.cpp (modified) * src/Fragmentation/Automation/ResultGetter.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (modified) Factored out Operation and derived all operations from it. - a ... Fri, 04 May 2012 14:19:07 GMT Frederik Heber [fb2324] * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-completerun.at (added) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test Fragmentation/Automation with a complete run of ... Fri, 04 May 2012 14:19:07 GMT Frederik Heber [c837ad0] * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-getresults.at (added) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test Fragmentation/Automation on getting results. Fri, 04 May 2012 14:19:07 GMT Frederik Heber [db34f2] * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-checkstate.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test Fragmentation/Automation on checking state. Fri, 04 May 2012 14:19:07 GMT Frederik Heber [6772eb] * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-addingjobs.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test Fragmentation/Automation on adding jobs to Server. Fri, 04 May 2012 14:19:07 GMT Frederik Heber [03195a] * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-shutdown.at (added) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test Fragmentation/Automation on Server shutdown ... Fri, 04 May 2012 14:19:07 GMT Frederik Heber [0196c6] * src/Fragmentation/Automation/ControllerChoices.hpp (modified) * src/Fragmentation/Automation/FragmentController.cpp (modified) * src/Fragmentation/Automation/FragmentController.hpp (modified) * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/Shutdowner.cpp (added) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (modified) Added Shutdown as choice to ControllerChoices. - new helper app ... Fri, 04 May 2012 14:19:07 GMT Frederik Heber [e70b9d] * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation-server-worker.at (moved) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Renamed regression test Fragmentation/Automation. - there are more ... Fri, 04 May 2012 14:19:07 GMT Frederik Heber [778abb] * src/Fragmentation/Automation/ControllerChoices.hpp (added) * src/Fragmentation/Automation/FragmentController.cpp (modified) * src/Fragmentation/Automation/FragmentController.hpp (modified) * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/FragmentScheduler.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/ResultGetter.cpp (added) * src/Fragmentation/Automation/Server.cpp (modified) * src/Fragmentation/Automation/types.hpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation.at (modified) Added ResultGetter and capabilities to receive calculated results to ... Fri, 04 May 2012 14:19:07 GMT Frederik Heber [3c4a5e] * src/Fragmentation/Automation/FragmentController.cpp (modified) * src/Fragmentation/Automation/FragmentController.hpp (modified) * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/FragmentScheduler.hpp (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/ResultChecker.cpp (added) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation.at (modified) Added ResultChecker and capability to check on computed jobs. - ... Fri, 04 May 2012 14:19:07 GMT Frederik Heber [db03d9] * src/Fragmentation/Automation/FragmentController.cpp (added) * src/Fragmentation/Automation/FragmentController.hpp (added) * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/FragmentScheduler.hpp (modified) * src/Fragmentation/Automation/FragmentWorker.hpp (modified) * src/Fragmentation/Automation/JobAdder.cpp (added) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Automation/Server.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation.at (modified) Added possibility to add jobs via a FragmentController. - Server ... Fri, 04 May 2012 14:19:06 GMT Frederik Heber [ef2767] * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/FragmentScheduler.hpp (modified) * src/Fragmentation/Automation/FragmentWorker.cpp (modified) * src/Fragmentation/Automation/FragmentWorker.hpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation.at (modified) Server and Worker now also correctly exchange result. - Server uses ... Fri, 04 May 2012 14:19:06 GMT Frederik Heber [0bdd51b] * src/Fragmentation/Automation/FragmentScheduler.cpp (modified) * src/Fragmentation/Automation/FragmentWorker.cpp (modified) * src/Fragmentation/Automation/FragmentWorker.hpp (modified) * src/Fragmentation/Automation/Worker.cpp (modified) * tests/regression/Fragmentation/Automation/testsuite-fragmentation-automation.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test for Server/Client construct. - currently we ... Fri, 06 Apr 2012 11:45:30 GMT Frederik Heber [531f27] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (added) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.def (added) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.hpp (added) * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo-Exttypes/post/test-right.exttypes (added) * tests/regression/Parser/Tremolo-Exttypes/post/test-wrong.exttypes (added) * tests/regression/Parser/Tremolo-Exttypes/pre/test.xyz (added) * tests/regression/Parser/Tremolo-Exttypes/testsuite-parser-tremolo-save-selected-atoms-as-exttypes.at (added) * tests/regression/Parser/testsuite-parser.at (modified) Added SaveSelectedAtomsAsExtTypesAction that creates a tremolo- ... Fri, 06 Apr 2012 11:44:51 GMT Frederik Heber [80ca29] * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.def (modified) * src/Actions/FillAction/FillSphericalSurfaceAction.cpp (modified) * src/Actions/FillAction/FillSphericalSurfaceAction.def (modified) * tests/regression/Filling/RegularGrid/post/double_sles-undo.data (added) * tests/regression/Filling/RegularGrid/post/single_sles-undo.data (added) * tests/regression/Filling/RegularGrid/post/solved_double_sles.data (added) * tests/regression/Filling/RegularGrid/post/solved_single_sles.data (added) * tests/regression/Filling/RegularGrid/post/tensid.data (deleted) * tests/regression/Filling/RegularGrid/pre/double_sles.data (added) * tests/regression/Filling/RegularGrid/pre/single_sles.data (added) * tests/regression/Filling/RegularGrid/pre/sles.potentials (moved) * tests/regression/Filling/RegularGrid/pre/tensid.data (deleted) * tests/regression/Filling/RegularGrid/pre/water.data (modified) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid-with-surface.at (added) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid.at (modified) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Added regression test Filling/RegularGrid with and without a ... Fri, 06 Apr 2012 11:44:51 GMT Frederik Heber [72e4c95] * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) tempcommit: regression tests Filling/SphericalSurface Undo/Redo were ... Fri, 06 Apr 2012 11:44:09 GMT Frederik Heber [91be2d] * tests/regression/Filling/SphericalSurface/post/tensid-undo.data (added) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (modified) Added Undo/Redo check to regression test Filling/SphericalSurface. ... Fri, 06 Apr 2012 11:44:09 GMT Frederik Heber [4187a7] * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/CreateMicelleAction.cpp (deleted) * src/Actions/MoleculeAction/CreateMicelleAction.def (deleted) * src/Actions/MoleculeAction/CreateMicelleAction.hpp (deleted) * tests/regression/Filling/SphericalSurface/post/tensid.data (added) * tests/regression/Filling/SphericalSurface/pre/tensid.data (added) * tests/regression/Filling/SphericalSurface/pre/tensid.potentials (moved) * tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at (added) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/CreateMicelle/post/tensid.data (deleted) * tests/regression/Molecules/CreateMicelle/pre/tensid.data (deleted) * tests/regression/Molecules/CreateMicelle/testsuite-molecules-create-micelle.at (deleted) * tests/regression/Molecules/testsuite-molecules.at (modified) Removed MoleculeAction/CreateMicelleAction, is replaced by ... Fri, 06 Apr 2012 11:44:00 GMT Frederik Heber [4a4f3d] * tests/regression/Filling/RegularGrid/post/tensid.data (added) * tests/regression/Filling/RegularGrid/pre/tensid.data (added) * tests/regression/Filling/RegularGrid/pre/tensid.potentials (added) * tests/regression/Filling/RegularGrid/pre/water.data (added) * tests/regression/Filling/RegularGrid/testsuite-molecules-fill-regular-grid.at (added) * tests/regression/Filling/testsuite-filling.at (modified) * tests/regression/Makefile.am (modified) Added regression test Filling/RegularGrid with undo, redo. Thu, 05 Apr 2012 15:56:03 GMT Frederik Heber [259887] * src/Parser/XyzParser.cpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-various.at (added) * tests/regression/Parser/testsuite-parser.at (modified) FIX: XyzParser stumbled over empty comment line. - FormatParser< ... Thu, 05 Apr 2012 15:55:48 GMT Frederik Heber [2034f3] * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/unittests/Makefile.am (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * tests/regression/Filling/FillVoidWithMolecule/post/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data (modified) * tests/regression/Filling/FillVoidWithMolecule/pre/tensid.potentials (added) * tests/regression/Molecules/Copy/post/tensid-undo.data (deleted) * tests/regression/Molecules/Copy/post/tensid.data (modified) * tests/regression/Molecules/Copy/pre/tensid.data (modified) * tests/regression/Molecules/Copy/pre/tensid.potentials (modified) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Molecules/CreateMicelle/post/tensid.data (modified) * tests/regression/Molecules/CreateMicelle/pre/tensid.data (modified) * tests/regression/Molecules/CreateMicelle/pre/tensid.potentials (modified) Added AtomInfo::charge along with getter and setter. - charge is ... 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 07:55:55 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 ... Wed, 28 Mar 2012 15:17:39 GMT Frederik Heber [3e1b7b] * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsinsidetinysphere.xyz (added) * tests/regression/Selection/Atoms/AtomsInsideSphere/post/allatomsoutsidetinysphere.xyz (added) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (added) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added regression test on select-atoms-inside-sphere with a small ... 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 11:29:05 GMT Frederik Heber [b49c5d] * tests/regression/Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at (modified) * tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) Regression test Analysis/PairCorrelation sets BC explicitly to Wrap. ... 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 11:29:04 GMT Frederik Heber [a8ae6d] * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_X.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0000.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0001.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0002.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0003.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0004.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0005.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0006.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0007.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0008.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0009.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0010.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0011.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0012.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0013.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0014.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0015.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0016.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0017.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0018.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0019.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0020.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0021.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0022.dat (added) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/post/water_histogram_Y.0023.dat (added) * 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tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) TESTFIX: Separated regression test Analysis/DipoleAngularCorrelation. ... 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 11:28:42 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 11:27:55 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- ... 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 [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, 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. ... Mon, 02 Jan 2012 13:35:16 GMT Frederik Heber [c48a51f] * tests/regression/Makefile.am (modified) DISTCHECKFIX: Forgot to remove folder Python from ... Wed, 28 Dec 2011 15:25:49 GMT Frederik Heber [afa9d8] * tests/regression/Molecules/BondFile/post/test.pdb (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified) * tests/regression/Tesselation/BigNonConvex/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) TESTFIX: Fixed regression tests Molecules/BondFile and ... Wed, 28 Dec 2011 15:25:48 GMT Frederik Heber [30c753] * configure.ac (modified) * src/Dynamics/LinearInterpolationBetweenSteps.hpp (modified) * src/Dynamics/VerletForceIntegration.hpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * tests/regression/Molecules/BondFile/testsuite-molecules-fragmentation-bond-file.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) Removed atomSet atoms in class molecule and replaced by a ... Wed, 28 Dec 2011 15:24:57 GMT Frederik Heber [c015b3] * configure.ac (modified) * src/Actions/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * tests/Makefile.am (modified) * tests/Python/AllActions/getPossibleOptions.sh (moved) * tests/Python/AllActions/listcmds.py (moved) * tests/Python/AllActions/missing.dat (moved) * tests/Python/AllActions/moltest.py (moved) * tests/Python/AllActions/moltest_check.py (moved) * tests/Python/AllActions/options.dat (moved) * tests/Python/AllActions/testsuite-python-allactions.at (added) * tests/Python/AllActions/testsuite-python-options_dat.at (added) * tests/Python/BoxMaker/post/out.data (moved) * tests/Python/BoxMaker/post/out.xyz (moved) * tests/Python/BoxMaker/pre/argon.data (moved) * tests/Python/BoxMaker/pre/argon.potentials (moved) * tests/Python/BoxMaker/pre/argon.tremolo (moved) * tests/Python/BoxMaker/testsuite-python-boxmaker.at (added) * tests/Python/CommandHelp/testsuite-python-commandhelp.at (moved) * tests/Python/Makefile.am (added) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (moved) * tests/Python/atlocal.in (added) * tests/Python/run.in (moved) * tests/Python/testsuite.at (added) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (deleted) * tests/regression/Python/AllActions/testsuite-python-options_dat.at (deleted) * tests/regression/Python/BoxMaker/testsuite-python-boxmaker.at (deleted) * tests/regression/Python/testsuite-python.at (deleted) * tests/regression/testsuite.at (modified) * utils/Makefile.am (modified) Added enable-switches for Qt-based GUI and python module and scripts. ... Thu, 10 Nov 2011 10:21:23 GMT Frederik Heber [0d571d7] * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) DISTCHECKFIX: Forgot to set write permissions for new ec.data test ... Thu, 10 Nov 2011 10:21:23 GMT Frederik Heber [a55be1] * tests/regression/Makefile.am (modified) DISTCHECKFIX: testsuite does not depends on run scripts. - ... Tue, 08 Nov 2011 11:45:15 GMT Frederik Heber [12facf] * src/Actions/hello.cpp (deleted) * src/Makefile.am (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/Pythontest/testsuite-python-pythontest.at (deleted) * tests/regression/Python/testsuite-python.at (modified) Removed now obsolete Pythontest including regression test. - as ... Mon, 07 Nov 2011 18:33:50 GMT Frederik Heber [5ab796] * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/moltest_check.py (added) * tests/regression/Python/AllActions/options.dat (modified) * tests/regression/Python/AllActions/testsuite-python-options_dat.at (added) * tests/regression/Python/testsuite-python.at (modified) Added regression test on whether all options in the python module are ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [f89b45] * src/Actions/AnalysisAction/CalculateBoundingBoxAction.cpp (added) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.def (added) * src/Actions/AnalysisAction/CalculateBoundingBoxAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/pyMoleCuilder.cpp (modified) * tests/regression/Analysis/CalculateBoundingBox/testsuite-analysis-calculate-bounding-box.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/listcmds.py (added) * tests/regression/Python/AllActions/moltest.py (modified) * tests/regression/Python/AllActions/options.dat (modified) * tests/regression/Python/AllActions/testsuite-python-allactions.at (modified) Added Reaction CalculateBoundingBoxAction. - calculate bounding box ... Mon, 07 Nov 2011 16:13:18 GMT Frederik Heber [55f299] * src/Actions/AnalysisAction/CalculateMolarMassAction.cpp (added) * src/Actions/AnalysisAction/CalculateMolarMassAction.def (added) * src/Actions/AnalysisAction/CalculateMolarMassAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Analysis/CalculateMolarMass/pre/argon.xyz (added) * tests/regression/Analysis/CalculateMolarMass/pre/water.xyz (added) * tests/regression/Analysis/CalculateMolarMass/testsuite-analysis-calculate-molar-mass.at (added) * tests/regression/Analysis/testsuite-analysis.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Python/AllActions/options.dat (modified) Added Reaction CalculateMolarMassAction. - calculate molar mass ...