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AbstractBitmapRepresentation AbstractBitwiseBitmap AbstractEdgesFilter AbstractEdgesGenerator AbstractGraphTraversal AbstractNodes AbstractSearchState AccumulatorVirialOverlapSingleAverage AdjacencyMatrixRepresentation Algorithms AnalyticalDerivativeEnergyParacetamol ApplicationLauncher ApplicationUI ApplicationUI.ImagePanel ApplicationView ArrayReader1D ArrayReader2D AtomActionTransformed AtomDecompositionMD AtomPairSet BasisBigCell BasisMonoclinicParacetamol BasisNMOneCell BasisOrthorhombicParacetamol BCTraversal BFTraversal Bitmap BitmapFactory BitmapOfBigInteger BitmapOfLong BitmapOfLongVector BitmapUtils BnPYHardSphere BnPYLJ BoltzmannProcessor BoxAgentSourceCellManagerThreaded BoxCluster CalcHarmonicA CalcJacobian CBMCGrowSolidHexane CBMCGrowStraightAlkane Chain ChargeAgentSourceParacetamol CheckCBMCHexane ClusterAbstract ClusterBonds ClusterCollapsedTreeNode ClusterCoupled ClusterCoupledFlipped ClusterDiagram ClusterDiagram ClusterDiagram2 ClusterDiagramTree ClusterGenerator ClusterGenerator ClusterGenerator2 ClusterOperations ClusterSum ClusterSumEF ClusterSumPolarizable ClusterSumStickyEF ClusterTree ClusterTreeBonds ClusterTreeEF ClusterTreeNode ClusterWeight ClusterWeight.Factory ClusterWeightAbs ClusterWeightUmbrella ColorMap ConfigurationAligned ConfigurationCluster ConfigurationClusterMove ConfigurationFileXYZ ConfigurationMonoclinicLattice ConfigurationMonoclinicLattice.MyLattice ConfigurationOrthorhombicLattice ConfigurationOrthorhombicLattice.MyLattice ConformationHexane ConformationParacetamol ConformationParacetamolMonoclinic ConformationParacetamolOrthorhombic ConjugateGradients Controller CoordinateDefinition CoordinateDefinition.BasisCell CoordinateDefinition.SiteSource CoordinateDefinitionHexane CoordinateDefinitionLeaf CoordinateDefinitionLeafSuperBox CoordinateDefinitionMolecule CoordinateDefinitionMolecule.MoleculeSiteSource CoordinateDefinitionParacetamol CoordinateDefinitionParacetamol.OrientationAgentSource CoordinatePairLeafSet CoordinatePairMoleculeSet CoordinatePairSet CopyOfOrthogonalPolynomial CustomTestCase DataCutter DataProcessorBoltzmannFactor DataProcessorCvMD DataProcessorPhi DataProcessorSum DataSourceVirialOverlap DataSourceVirialOverlapRejected DefaultSVGConverterController DensityOfState DensityOfStatesPolynomial DerivativeEnergyFunction DerivativeEnergyFunction.MyAgentSource DestinationType DeviceButtonSingle DeviceCellNum3DSlider DeviceCellNumXYSlider DeviceEigenvaluesSlider DeviceWaveVectorSlider DFTraversal DiagramSource DialogView EdgeAttributes Edges EdgesFilter EdgesGenerator EdgesMetadata EdgesRepresentation EdgesRepresentationFactory EdgesSetVisitor EdgeVisitor EinsteinCrystalExpansionAnalysis EnergyMap EnergyMapCluster FerrenbergSwendsen FilterFactory FiniteDifferenceDerivativeCG FiniteDifferenceDerivativeCG.MyAgentSource FrameView Full Graph GraphCoefficient GraphFactory GraphPairProperty GraphProperty GraphSet GraphSetFactory GraphSetIO GraphTraversal HarmonicCrystal HarmonicCrystalMonoclinic HarmonicCrystalOrthorhombic HarmonicCrystalOrthorhombic.LatticeEnergy HarmonicCrystalSoftSphereFCC Heisenberg HessianDB HexaneVolumeFraction HydrogenP IAPIPotential IntegratorDimerMin IntegratorDimerRT IntegratorEnergyMap IntegratorHarmonic IntegratorOverlap IntegratorOverlapRejected IntegratorTMMC IntegratorVelocityVerletThreaded IPotentialCalculationThreaded JGoodiesSettings LatticeEnergyParacetamol LatticeSumCrystalParacetamol LeftPanelView LJMD3DThreaded LJMD3DThreaded LJMD3DThreadedforCluster LJMD3DThreadedforCluster LJTSRefLJ LJTSRefLJ.VirialLJParam MacrostateManager Main Main.AbstractOptionHandler Main.ColorOptionHandler Main.FloatOptionHandler Main.NoValueOptionHandler Main.OptionHandler Main.RectangleOptionHandler Main.SingleValueOptionHandler Main.TimeOptionHandler MainPanelView Match MayerEGeneral MayerEHardSphere MayerESpherical MayerFunction MayerFunctionSum MayerFunctionSumGeneral MayerFunctionTemperature MayerGeneral MayerGeneralSpherical MayerHardSphere MayerSSSeries MCMoveAtomCoupled MCMoveAtomCoupledBennet MCMoveAtomCoupledUmbrella MCMoveAtomSuperBox MCMoveCBMC MCMoveClusterAtom MCMoveClusterAtomMulti MCMoveClusterAtomRotateMulti MCMoveClusterDiagram MCMoveClusterMolecule MCMoveClusterMoleculeMulti MCMoveClusterReptateMulti MCMoveClusterRotateMolecule3D MCMoveClusterRotateMoleculeMulti MCMoveClusterTorsionMulti MCMoveClusterWiggleMulti MCMoveCombinedCbmcTranslation MCMoveHarmonic MCMoveHarmonicStep MCMoveMoleculeCoupled MCMoveMoleculeCoupledDLPOLY MCMovePhaseAngle MCMoveReptate MCMoveSingleMode MCMoveSpinFlip MCMoveSwapCluster MCMoveSwapCluster.SwapFactory MCMoveWV MCParacetamolMonoclinicDLMULTI MCParacetamolMonoclinicDLMULTIEquilibration MCParacetamolMonoclinicDLMULTISimCalcS MCParacetamolOrthorhombicDLMULTI MCParacetamolOrthorhombicDLMULTIEquilibration MCParacetamolOrthorhombicDLMULTISimCalcS MCParacetamolOrthorhombicMoveHarmonic MCParacetamolOrthorhombicMoveHarmonicStep MDParacetamolMonoclinic MDParacetamolOrthorhombic MEAM_3DMDwithGB MEAM_3DMDwithSnAgGB MEAM_3DMDwithSnCuGB MEAM_MC MEAMMd3D MEAMMd3DforCluster MEAMMd3DThreaded MEAMMd3DThreadedforCluster MenuBarView Messages MeterAPIPotentialEnergy MeterAtomicDisplacement MeterBoltzmannHarmonic MeterBoltzmannTarget MeterClusterWeight MeterDirectSamplingHarmonic MeterDirectSamplingTarget MeterHarmonicCoordinate MeterHarmonicEnergy MeterHarmonicEnergyFromMove MeterHarmonicSingleEnergy MeterJacobian MeterNormalMode MeterOverlap MeterPressureSuperBox MeterSamplingHarmonic MeterSamplingTarget MeterSamplingWeight MeterSpin MeterVirial MeterVirialRejected MeterWorkBennetHarmonic MeterWorkBennetTarget MeterWorkHarmonicBennet MeterWorkHarmonicPhaseSpace MeterWorkHarmonicTargetandReweighting MeterWorkHarmonicUmbrella MeterWorkTargetBennet MeterWorkTargetHarmonicandReweighting MeterWorkTargetPhaseSpace MeterWorkTargetUmbrella MeterWorkUmbrellaHarmonic MeterWorkUmbrellaTarget Model ModelFactory ModifierCells3D ModifierXCells2D ModifierYCells2D MoleculeActionRelaxWater3P MSDCoordWriter MSDProcessor MyEigenvalueDecomposition NaiveEdgesGenerator NautyEdgesGenerator NautyInfo NeighborCellManagerThreaded NeighborListManagerThreaded NodeAttributes NodePair Nodes NodesVisitor NonLinearConjugateGradients NormalModeAnalysisDisplay1D NormalModeAnalysisDisplay1D.Applet NormalModeAnalysisDisplay1DGraphic NormalModeAnalysisDisplay1DGraphic.Applet NormalModeAnalysisDisplay2D NormalModeAnalysisDisplay2DGraphic NormalModeAnalysisDisplay2DGraphic.Applet NormalModeAnalysisDisplay3D NormalModeAnalysisDisplay3D.Applet NormalModeAnalysisDisplay3DGraphic NormalModeAnalysisDisplay3DGraphic.Applet NormalModeEigenGetter NormalModeEigenGetter NormalModes NormalModes1DHR NormalModes2D NormalModes3D NormalModesFromFile NormalModesPotential NormalModesPotentialParacetamol NormalModesPotentialParacetamol.Lattice2ndDerivative NormalModesSoftSpherical NormalModesVariable NPTraversal NumericalDerivativeEnergyParacetamol Operations OrthogonalPolynomial P0Cluster P1Constraint P1LepsHarmonic P1MagneticField P2ElectrostaticDreiding P2HC2Yukawa P2Spin P2XOrder P2Yukawa ParameterSetMEAM PCEnergySumEinsteinCrystalExpansion PercusYevick PermutationIterator PermutationIterator PermutationRangeIterator PermutatorTest PotentialCalculationClusterWeightSum PotentialCalculationForcePressureSumGB PotentialCalculationForceSumThreaded PotentialMasterListDimer PotentialMasterListThreaded PotentialMasterListThreaded PotentialMasterListThreaded.NeighborListAgentSourceThreaded PotentialMasterListWorker PotentialMasterListWorker PotentialMEAM PotentialThreaded PreconditionedConjugateGradient PrimitiveHexane ProcessInfo ProcessWrapper ReaderIn ReeHooverMC ReeHooverMC.VirialParam RightPanelView Ring SearchState ShowStep SimBennet SimBennet.SimBennetParam SimCalcJ SimCalcS SimCalcSLJ SimCalcSMorse SimCalcSSoftSphere2D SimCalcSSoftSphereFCC SimCalcSSoftSphereFCCSuperBox SimDimerLJadatom SimDimerLJadatomCluster SimDimerLJgb SimDimerMEAMadatom SimDimerMEAMadatomCluster SimDimerMEAMGB SimDimerMEAMGBCluster SimFluidSoftSphere SimHarmonic SimHarmonicHexane SimHarmonicUmbrella SimHarmonicUmbrella.SimBennetParam SimModesJ SimOverlap SimOverlap.SimOverlapParam SimOverlapLJ SimOverlapLJ.SimOverlapParam SimOverlapLJModule SimOverlapLJModule.APIPotentialReference SimOverlapLJModule.APIPotentialTarget SimOverlapLJModule.MeterPotentialEnergyDifference SimOverlapLJModule.SimOverlapParam SimOverlapModule SimOverlapSoftSphere SimOverlapSoftSphere.SimOverlapParam SimOverlapSoftSphereReweighting SimOverlapSoftSphereReweighting.SimOverlapParam SimOverlapSoftSphereSuperBox SimOverlapSoftSphereSuperBox.SimOverlapParam SimpleEdgeAttributes SimpleEdges SimpleEdgesMetadata SimpleGraphCoefficient SimpleGraphSet SimpleNodes SimpleProcessWrapper SimTarget SimTargetUmbrella SimTargetUmbrella.SimBennetParam SimulationOrthorhombicParacetamol SimulationVirial SimulationVirialDiagram SimulationVirialMultiOverlap SimulationVirialOverlap SimulationVirialOverlapRejected SimulationVirialPT SimulationVirialUmbrella SimUmbrella SimUmbrella.SimBennetParam SimUmbrellaSoftSphere SimUmbrellaSoftSphere.SimBennetParam SingleAssociationSiteFluid SingleAssociationSiteFluid.VirialAssociatingFluidParam SingleAssociationSiteFluid2 SingleAssociationSiteFluid2.VirialAssociatingFluidParam SingleAssociationSiteFluid4Points SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam SpeciesAlkane SpeciesFactory SpeciesFactoryOrientedSpheres SpeciesFactorySiepmannSpheres SpeciesFactorySpheres SpeciesFactorySpheres2 SpeciesFactoryTangentSpheres SpeciesFactoryWater3P SpeciesFactoryWater4P SpeciesFactoryWaterGCPM SpeciesHexane SpeciesParacetamol Standard SteepestDescent StoredEdgesGenerator SVGApplication SVGClusterMap SVGContextMenu SVGConverter SVGConverter.SVGFileFilter SVGConverterController SVGConverterDocumentSource SVGConverterException SVGConverterFileSource SVGConverterSource SVGConverterURLSource SVGDraw SVGState TableView Tagged TagsList TestBitmapOfLong TestBitmapOfLongVector TestCGParacetamolMinEnergy TestFiniteDifferenceDerivative TestHC2YukawaMC3D TestHexane TestHexaneCBMCOnly TestHexaneFileConfig TestHexaneHarmonic TestHexaneHarmonic.DataProcessorFoo TestLJAssociationMC3D_NPT TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam TestNaiveEdgesGenerator TestNautyEdgesGenerator TestNonLinearConjugateGradients TestSetToUHexane TestSimpleProcessWrapper TestStoredGraphSets TestYukawaMC3D TestYukawaMD3D ThreadsMD ToolBarView TreeView UllmanSearchState UpperTriangleRepresentation VF2SearchState VFSearchState View ViewFactory Virial2CLJQ Virial2CLJQ.Virial2CLJQParam Virial2TestSuite VirialAlkane VirialAlkane.VirialSiepmannSpheresParam VirialAlkaneMix VirialAlkaneMix.VirialAlkaneMixParam VirialAlkaneMix2 VirialAlkaneMix2.VirialAlkaneMixParam VirialAlkaneMix2_Kong VirialAlkaneMix2_Kong.VirialAlkaneMixParam VirialAlkaneMix_Kong VirialAlkaneMix_Kong.VirialAlkaneMixParam VirialAssociatingFluid VirialAssociatingFluid.VirialAssociatingFluidParam VirialAssociatingFluid4points VirialAssociatingFluid4points.VirialAssociatingFluidParam VirialGCPM VirialGCPM.VirialGCPMParam VirialGCPMGraphic VirialHardAssociationCone VirialHardAssociationCone.VirialLJParam VirialLJ VirialLJ.VirialLJParam VirialLJMultiOverlap VirialLJMultiOverlap.VirialMixParam VirialLJRejected VirialLJRejected.VirialLJParam VirialLJSeries VirialLJSeries.VirialLJParam VirialLJTest VirialLJXS VirialLJXS.VirialLJParam VirialRowleyAlcohol VirialRowleyAlcohol.VirialParam VirialTangentSpheres VirialTangentSpheres.VirialTangentSpheresParam VirialTraPPEAlcohol VirialTraPPEAlcohol.VirialParam VirialWaterOverlap WaveVectorFactory WaveVectorFactory1D WaveVectorFactory2D WaveVectorFactoryFcc WaveVectorFactoryFromFile WaveVectorFactorySimple WaveVectorFactorySuperBox WizardView WriteS Zeolite zeoliteSimGraphic ZeoliteSimStart ZeoliteSimulation