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Project: etomica
  • etomica-master
    • gradle
      • wrapper
        • gradle-wrapper.properties
      • ColoredTestOutput.gradle
    • libs
    • etomica-apps
      • src
        • main
          • java
            • etomica
              • overlap
                • MeterOverlap.java
                • IntegratorOverlap.java
                • AlphaSource.java
                • DataOverlap.java
              • eigenstuff
                • MyEigenvalueDecomposition.java
                • ReaderIn.java
              • gaussianwork
                • MCMoveMultiHarmonic.java
                • MeterWorkBAandReweighting.java
                • MeterBoltzmannA.java
                • SimOverlapMultiHarmonicOptRefPref.java
                • SimOverlapMultiHarmonic.java
                • MeterBoltzmannB.java
                • MeterWorkABandReweighting.java
              • dimer
                • SimDimerMEAMGB.java
                • SimDimerLJgb.java
                • SimDimerLJadatomCluster.java
                • SimDimerMEAMadatom.java
                • EnergyMap.java
                • PotentialMasterListDimer.java
                • IntegratorEnergyMap.java
                • SimDimerMEAMadatomCluster.java
                • P1LepsHarmonic.java
                • SimDimerMEAMGBCluster.java
                • SimDimerLJadatom.java
                • IntegratorDimerRT.java
                • EnergyMapCluster.java
                • IntegratorDimerMin.java
                • PotentialCalculationForcePressureSumGB.java
              • freeenergy
                • npath
                  • IntegratorImageMultistepMD.java
                  • ConfigFromFileLAMMPS.java
                  • P1ImageHarmonic.java
                  • IntegratorMDHarmonicMC.java
                  • MCMoveAtomNPath.java
                  • IntegratorImageHarmonicMD.java
                  • SimIdealGas.java
                  • MCMoveAtomCoupled.java
                  • SimFe.java
                  • DataSourceEnergies.java
                  • SimLattice.java
                  • PotentialCalculationDUDW.java
                  • MCMoveAtomSwap.java
                  • SimLJ.java
              • yukawa
                • P2HC2Yukawa.java
                • TestYukawaMD3D.java
                • TestYukawaMC3D.java
                • P2Yukawa.java
                • TestHC2YukawaMC3D.java
              • threads
                • ThreadsMD.java
                • AtomDecompositionMD.java
              • dielectric
                • DLJ_NVT_1site.java
                • TIP4P_NVT.java
                • DHS_NVT.java
              • association
                • MCMoveBiasUB.java
                • BiasVolume.java
                • MCMoveMoleculeSmer.java
                • BiasVolumeSphereOrientedDoubleSites.java
                • MCMoveBiasUBMolecule.java
                • MCMoveSmerRotate.java
                • BiasVolumeSphereOriented.java
                • AssociationDefinition.java
                • AssociationHelperMolecule.java
                • MCMoveVolumeAssociatedMolecule.java
                • MCMoveMoleculeMonomer.java
                • MCMoveVolumeAssociated.java
                • TestLJAssociationMC3D_NPT_DoubleSites.java
                • ColorSchemeSmerByLength.java
                • AssociationManager.java
                • AssociationHelperDouble.java
                • BiasVolumeAceticAcid.java
                • IAssociationHelper.java
                • MCMoveRotateAssociated.java
                • MCMoveSmer.java
                • AtomSourceRandomMonomer.java
                • TestLJAssociationMC3D_NVTOld.java
                • MCMoveAtomMonomer.java
                • BiasVolumeSphere.java
                • AceticAcid
                  • Wertheim2SiteAceticAcid.java
                  • TestAceticAcidMC3D_NPT.java
                • MoleculeSourceRandomDimer.java
                • ColorSchemeSmer.java
                • MoleculeSourceRandomMonomer.java
                • MCMoveAtomNoSmer.java
                • AssociationDefinitionMolecule.java
                • TestLJAssociationMC3D_NPT.java
                • TestIGAssociationMC3D_NPT_DoubleSites.java
                • AssociationManagerMolecule.java
                • MeterDimerMoleFraction.java
                • IAssociationHelperMolecule.java
                • AtomSourceRandomSmer.java
                • BiasVolume2SiteAceticAcid.java
                • AssociationHelperBranched.java
                • AssociationHelperSingle.java
                • MCMoveDimerRotate.java
                • MCMoveMoleculeRotateAssociated.java
                • MCMoveDimer.java
                • MCMoveAtomDimer.java
                • MCMoveAtomSmer.java
                • AtomSourceRandomDimer.java
                • BiasVolumeMolecule.java
                • BiasVolumeCube.java
                • GCPMWater
                  • WertheimGCPM3PtEBondDecomp.java
                  • WertheimGCPM4PtEBondDecompFinal.java
                  • WertheimGCPM4PtThreeSiteEDecompDirectSampling.java
                  • WertheimGCPM4PtEBondDecomp.java
                  • WertheimGCPM3PtThreeSite.java
                  • WertheimGCPM4PtThreeSite.java
                • MCMoveRotateNoSmer.java
              • kmc
                • IntegratorKMCCluster.java
                • IntegratorKMC.java
                • SimKMCmaster.java
                • SimKMCLJadatom.java
                • SimKMCworker.java
                • SimKMCMEAMadatom.java
              • AlkaneEH
                • DLJ_NVT_1site.java
                • ConformationAlkaneEH.java
                • CH4NVT.java
                • SpeciesAlkaneEH.java
                • ConformationMethane.java
                • SpeciesMethane.java
                • DHS_NVT.java
              • paracetamol
                • LatticeEnergyParacetamol.java
                • MCParacetamolMonoclinicDLMULTISimCalcS.java
                • NormalModeEigenGetter.java
                • MCParacetamolMonoclinicDLMULTIEquilibration.java
                • ConformationParacetamolOrthorhombic.java
                • MCMoveMoleculeCoupledDLPOLY.java
                • HarmonicCrystalMonoclinic.java
                • HydrogenP.java
                • ConfigurationMonoclinicLattice.java
                • ChargeAgentSourceParacetamol.java
                • LatticeSumCrystalParacetamol.java
                • MCParacetamolOrthorhombicMoveHarmonic.java
                • ConformationParacetamolMonoclinic.java
                • MDParacetamolOrthorhombic.java
                • ConfigurationOrthorhombicLattice.java
                • SimulationOrthorhombicParacetamol.java
                • BasisOrthorhombicParacetamol.java
                • ConformationParacetamol.java
                • SpeciesParacetamol.java
                • MDParacetamolMonoclinic.java
                • P2ElectrostaticDreiding.java
                • MCParacetamolMonoclinicDLMULTI.java
                • NormalModesPotentialParacetamol.java
                • MCParacetamolOrthorhombicDLMULTIEquilibration.java
                • MCParacetamolOrthorhombicMoveHarmonicStep.java
                • MCParacetamolOrthorhombicDLMULTISimCalcS.java
                • HarmonicCrystalOrthorhombic.java
                • MCParacetamolOrthorhombicDLMULTI.java
                • NumericalDerivativeEnergyParacetamol.java
                • CoordinateDefinitionParacetamol.java
                • AnalyticalDerivativeEnergyParacetamol.java
                • AtomActionTransformed.java
                • BasisMonoclinicParacetamol.java
              • tmmc
                • MacrostateManager.java
                • IntegratorTMMC.java
              • models
                • traPPE
                  • MethanolPotentialHelper.java
                  • ConformationMethanol.java
                  • SpeciesMethanol.java
                  • SpeciesFactoryMethanol.java
                • OPLS
                  • SpeciesAceticAcid.java
                  • P2AceticAcidTwoSite.java
                  • ConformationAceticAcid.java
                  • AceticAcidModPotentialHelper.java
                  • P2HardAssociationRefAceticAcidTwoSite.java
                  • AceticAcidPotentialHelper.java
                  • DipoleSourceAceticAcid.java
                • oneDHardRods
                  • MeterDifferentImageSubtractDoubleSize.java
                  • MeterWidomModeImaginary.java
                  • MeterNMCBaskets.java
                  • MeterOverlapSameGaussian.java
                  • MCMoveChangeMultipleWV.java
                  • SimDegFreeBinning.java
                  • SimDifferentImageSsFccBigCell.java
                  • SimDifferentImageSsFcc.java
                  • TestDifferentImage1DHRAdd.java
                  • TestDifferentImage1DHRSubtract.java
                  • HarmonicCrystalSsFccDoubleSize.java
                  • MeterDifferentImageAddDoubleSize.java
                  • MCMoveCompareMultipleWV.java
                  • MeterCompareWVShortcut.java
                  • MeterOverlap.java
                  • DoubleIntegral.java
                  • MakeData.java
                  • MeterOverlapSameGaussian1D.java
                  • SimOverlapSsNxy.java
                  • MeterWidomMode.java
                  • DoubleIntegralEtas.java
                  • SimDifferentImage.java
                  • SimOverlapMultipleWaveVectors.java
                  • MeterNormalModeCoordinate.java
                  • MeterDifferentImageSubtract1D.java
                  • MeterDifferentImageSubtract.java
                  • HarmonicCrystalSsFccBigCellNxy.java
                  • MeterWidomModeReal.java
                  • SimDifferentImage1DHR.java
                  • MeterDifferentImageAdd.java
                  • MCMoveChangeMultipleModes.java
                  • SimExtensiveTest.java
                  • SimDegreeFreedom.java
                  • MeterCompareMultipleWVBrute.java
                  • MeterF.java
                  • SimOverlapMultipleWV3DLJ.java
                  • SimDifferentImageSsFccDoubleSize.java
                  • MeterDifferentImageAdd1D.java
                  • SimWidomMode.java
                  • WriteHistograms.java
                  • SimDegreeFreedom3D.java
                  • SimDifferentImage1D.java
                • nitrogen
                  • ConformationNitrogenShellModel.java
                  • SimDirectBetaN2RPAngleToNoAngle.java
                  • SimDirectBetaN2RP.java
                  • MCMoveMoleculeCoupledInitPert.java
                  • HarmonicAlphaNitrogenModelPairMoleculeSequential.java
                  • SimDirectBetaN2RPInitPert.java
                  • HarmonicAlphaNitrogenModelDecomposed.java
                  • HarmonicBetaNitrogenModelPairMoleculeSequential.java
                  • HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS.java
                  • MCMoveMoleculeCoupledSuperBox.java
                  • HarmonicBetaNitrogenModelLatticeSum.java
                  • P2Nitrogen.java
                  • MCMoveRotateMolecule3DFixedAngle.java
                  • HarmonicAlphaNitrogenModelPairMoleculeSequentialLS.java
                  • MinimizationBetaNitrogenModel.java
                  • FindBetaN2AngleFromParameter.java
                  • FiniteDifferenceDerivativeCGNitrogenBeta.java
                  • MeterDirectInitPert.java
                  • HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS.java
                  • MinimizeBetaNitrogenLatticeParameterLSFromFile.java
                  • CalcAnalytical2ndDerivativeNitrogen.java
                  • SimulationBetaNitrogenModelTest.java
                  • MCMoveRotateMolecule3DN2AveCosThetaConstraint.java
                  • SimDirectDisorderedAlphaN2RPInitPert.java
                  • BetaPhaseLatticeParameterNA.java
                  • MCMoveVolumeN2.java
                  • SimOverlapBetaN2RPScaling.java
                  • HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2.java
                  • SimOverlapDisorderedAlphaN2TP.java
                  • MeterTargetRPMolecule.java
                  • HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS.java
                  • TestRotationVector.java
                  • MeterOrientationOrderParameter.java
                  • MCMoveRotateMolecule3DSuperBox.java
                  • MeterOrientationDistribution.java
                  • MeterTargetTPMolecule.java
                  • MCMoveRotateMolecule3DConstraint.java
                  • HarmonicBetaNitrogenModelPairMoleculeSequentialLS.java
                  • FindPairMoleculeIndex.java
                  • MeterNormalizedCoordBeta.java
                  • CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen.java
                  • MinimizeGammaNitrogenLatticeParameter.java
                  • CoordinateDefinitionNitrogen.java
                  • HarmonicAlphaNitrogenModelPairMolecule.java
                  • SpeciesN2.java
                  • MinimizeBetaNitrogenTranslationDOF.java
                  • HarmonicBetaNitrogenModel.java
                  • HarmonicAlphaNitrogenModel.java
                  • MeterBoltzmann.java
                  • CalcNumerical2ndDerivativeNitrogen.java
                  • SimOverlapBetaN2RP.java
                  • SimOverlapDisorderedAlphaN2RPScaling.java
                  • SimulationBetaNitrogenModel.java
                  • MeterRotPerturbMolecule.java
                  • BetaPhaseLatticeParameterLS.java
                  • HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2.java
                  • CoordinateDefinitionNitrogenSuperBox.java
                  • MinimizeBetaNitrogenLatticeParameterFromFile.java
                  • HarmonicBetaNitrogenModelDecomposed.java
                  • SimOverlapNitrogenModel.java
                  • SimOverlapAlphaN2TP.java
                  • PRotConstraint.java
                  • P2NitrogenAnisotropic.java
                  • BoundaryRectangularPeriodicSwitch.java
                  • P2NitrogenAB.java
                  • SimOverlapBetaN2TP.java
                  • HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS.java
                  • MeterBoltzmannRotPerturb.java
                  • LatticeSumCrystalMolecular.java
                  • MeterRotationDistributionGroup.java
                  • FindTransitionTemperature.java
                  • BoundaryDeformablePeriodicSwitch.java
                  • SpeciesN2B.java
                  • AtomActionTransformed.java
                  • SimulationAlphaNitrogenModel.java
                  • MeterBoltzmannDirect.java
                  • CalcNumerical2ndDerivative.java
                  • FindPairMoleculeIndexBetaN2.java
                  • HarmonicAlphaNitrogenModelLatticeSum.java
                  • P2NitrogenShellModel.java
                  • BetaPhaseLatticeParameter.java
                  • ConformationNitrogen.java
                  • SimulationGammaNitrogenModel.java
                  • P0LatticeEnergyCorrec.java
                  • MeterNormalizedCoord.java
                  • MinimizeBetaNitrogenLatticeParameter.java
                  • MinimizationBetaNitrogenModelLS.java
                  • HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS.java
                  • SpeciesN2ShellModel.java
                • clathrates
                  • MinimizationTIP4P.java
                  • ClathrateHarmonicFE.java
                • rowley
                  • MethanolPotentialHelper.java
                  • SpeciesEthanol.java
                  • MassProductionVirialRowleyAlcohol.java
                  • SpeciesFactoryEthanol.java
                  • ConformationMethanol.java
                  • MethanolRouteParams.java
                  • SpeciesMethanol.java
                  • SpeciesFactoryMethanol.java
                  • P2RepRowley.java
                  • EthanolPotentialHelper.java
                  • EthanolRouteParams.java
                  • ConformationEthanol.java
                  • DimerApproach.java
                • hexane
                  • TestHexaneCBMCOnly.java
                  • MCMoveCombinedCbmcTranslation.java
                  • CBMCGrowSolidHexane.java
                  • MCMoveReptate.java
                  • TestHexane.java
                  • HexaneVolumeFraction.java
                  • SpeciesHexane.java
                  • ConformationHexane.java
                  • SimHarmonicHexane.java
                  • CheckCBMCHexane.java
                  • PrimitiveHexane.java
                  • TestSetToUHexane.java
                  • CoordinateDefinitionHexane.java
                  • CBMCGrowStraightAlkane.java
                  • ShowStep.java
                  • TestHexaneHarmonic.java
                  • TestHexaneFileConfig.java
                  • package.html
                  • MCMoveCBMC.java
              • liquidLJ
                • MeterWidomInsertionCorrection.java
                • Potential2SoftSphericalLSMultiLatSlanty.java
                • LjMd3Dv2y.java
                • DataProcessorReweightRatio.java
                • PotentialCalculationSumCutoff.java
                • MeterWidomInsertionP.java
                • Potential2SoftSphericalLSMultiLat.java
                • LjMd3D.java
                • DataProcessorReweight.java
                • MeterPUCutLS.java
                • ValueCache.java
                • Potential2SoftSphericalLSMulti.java
                • PotentialCalculationSumCutoffLS.java
                • MeterPU.java
                • LjMC3D.java
                • PotentialCalculationEnergySumCutoff.java
                • MeterPotentialEnergyCutoff.java
                • MeterPUCut.java
              • zeolite
                • DataCutter.java
                • ZeoliteSimStart.java
                • DeviceButtonSingle.java
                • ConfigurationFileXYZ.java
                • ZeoliteSimulation.java
                • MSDProcessor.java
                • Zeolite.java
                • zeoliteSimGraphic.java
                • MSDCoordWriter.java
              • rotation
                • WaterDropletMatrix.java
                • ConfigurationWater108TIP4P.java
                • WaterTrimerRattle.java
                • SingleDipole.java
                • SingleWaterShake.java
                • WaterDroplet.java
                • IntegratorVelocityVerletQuaternion.java
                • WaterTrimer.java
                • WaterDropletShake.java
                • SingleDumbellRattle.java
                • WaterDropletRattle.java
                • ConfigurationWater3_3P.java
                • ConfigurationWater3.java
                • SingleWaterMatrix.java
                • P2LJDipole.java
                • ConfigurationWater256.java
                • SingleWater.java
                • SingleWaterRattle.java
                • SingleDumbellShake.java
                • WaterTrimerShake.java
                • ConfigurationWater108.java
                • DipoleBox.java
                • WaterBox.java
                • DipoleBoxMatrix.java
              • densityofstate
                • FerrenbergSwendsen.java
                • DensityOfState.java
                • DataProcessorPhi.java
                • CopyOfOrthogonalPolynomial.java
                • OrthogonalPolynomial.java
                • DensityOfStatesPolynomial.java
              • threaded
                • IPotentialCalculationThreaded.java
                • atom
                  • LJMD3DThreaded.java
                  • PotentialMasterListWorker.java
                  • PotentialMasterListThreaded.java
                  • LJMD3DThreadedforCluster.java
                • IntegratorVelocityVerletThreaded.java
                • PotentialCalculationForceSumThreaded.java
                • PotentialThreaded.java
                • domain
                  • BoxAgentSourceCellManagerThreaded.java
                  • NeighborCellManagerThreaded.java
                  • MEAMMd3DThreadedforCluster.java
                  • LJMD3DThreaded.java
                  • PotentialMasterListWorker.java
                  • NeighborListManagerThreaded.java
                  • MEAMMd3DThreaded.java
                  • PotentialMasterListThreaded.java
                  • LJMD3DThreadedforCluster.java
              • meam
                • ParameterSetMEAM.java
                • P2EAM.java
                • PotentialEAM_LS.java
                • EFSTungsten.java
                • MEAM_3DMDwithSnAgGB.java
                • PotentialMEAM.java
                • PotentialEAM.java
                • MEAMMd3DforCluster.java
                • PotentialEFS.java
                • MEAM_MC.java
                • PotentialCalculationEnergySumEAM.java
                • MEAM_3DMDwithSnCuGB.java
                • DataProcessorCvMD.java
                • MEAMMd3D.java
                • MEAM_3DMDwithGB.java
                • PotentialCuLREP.java
              • mappedRdf
                • PotentialCalculationMappedRdf.java
                • MappedRdf.java
                • MeterMappedRdf.java
              • normalmode
                • SimModesJ.java
                • DataSourceImposedFEHistogram.java
                • SimOverlapSoftSphereSuperBox.java
                • MinimizeHCP.java
                • NormalModeAnalysisDisplay2DGraphic.java
                • HarmonicCrystal.java
                • IntegratorHardMDMC.java
                • NormalModeEigenGetter.java
                • WaveVectorFactory1D.java
                • MeterWorkBennetHarmonic.java
                • MeterDisplacementRMS.java
                • MeterTiltRotationStdev.java
                • NormalModes2D.java
                • DataSourceImposedFEFit.java
                • NormalModes3D.java
                • MCMoveVolumeMonoclinicAngle.java
                • PotentialCalculationEFSSP.java
                • DeviceEigenvaluesSlider.java
                • DataSourceFEHistogram.java
                • CoordinateDefinition.java
                • MeterSolidMirror.java
                • MeterSamplingTarget.java
                • NormalModeAnalysisDisplay2D.java
                • MeterDirectSamplingTarget.java
                • SimOverlapSoftSphereHCP.java
                • MeterPhiDeviation.java
                • SimEinStep2HCP.java
                • MCMovePhaseAngle.java
                • MeterWorkUmbrellaHarmonic.java
                • HarmonicCrystalSoftSphereBCC.java
                • MeterTargetTP.java
                • SimEinStep1.java
                • PotentialCalculationLJSP.java
                • HarmonicCrystalSoftSphereFCC.java
                • IAPIPotential.java
                • ArrayReader1D.java
                • P1Constraint.java
                • MeterHarmonicSingleEnergy.java
                • MeterSolidProps.java
                • MCMoveVolumeSolid.java
                • MeterHarmonicCoordinate.java
                • DataSourceMuRoot1.java
                • DeviceCellNumXYSlider.java
                • MeterAPIPotentialEnergy.java
                • MCMoveEinsteinCrystal.java
                • NormalModeAnalysisDisplay1DGraphic.java
                • MeterDisplacementMoleculeRMS.java
                • CalcJacobian.java
                • DataSourcePMu.java
                • MCMoveVolumeMonoclinicScaled.java
                • SimOverlap.java
                • SimUmbrella.java
                • SimCalcSSoftSphereFCC.java
                • NormalModes.java
                • NormalModesPotential.java
                • WaveVectorFactoryFromFile.java
                • MCMoveVolumeSolidNPTMolecularOriented.java
                • DeviceCellNum3DSlider.java
                • MCMoveAtomSuperBox.java
                • MeterMaxExpansion.java
                • HTTPSoftSphereApplet.java
                • HarmonicCrystalSoftSphereHCP.java
                • MCMoveHarmonic.java
                • MeterNormalMode.java
                • SimTarget.java
                • SimCalcSSoftSphere2D.java
                • CoordinateDefinitionLeafSuperBox.java
                • DeviceWaveVectorSlider.java
                • HessianFromFile.java
                • MeterDP.java
                • CoordinateDefinitionLeaf.java
                • MeterDirectSamplingHarmonic.java
                • CoordinateDefinitionMoleculeVolumeFluctuation.java
                • SimLJHTTISuper.java
                • SimCalcSLJ.java
                • SimOverlapSoftSphereEin.java
                • DataSourceMuRoot.java
                • SimLJVacancy.java
                • SimOverlapSoftSphereReweighting.java
                • SimCalcJ.java
                • MeterWorkHarmonicPhaseSpace.java
                • WaveVectorFactorySimple.java
                • SimOverlapModule.java
                • SimEinStep2.java
                • NormalModesMolecular.java
                • MeterBoltzmannHarmonic.java
                • NormalModesFromFile.java
                • SimOverlapSoftSphereTPHCP.java
                • SimHarmonic.java
                • SoftSphereSolidEOSCalculator.java
                • WaveVectorFactorySuperBox.java
                • MCMoveRotateMoleculePhiTheta.java
                • CoordinateDefinitionMolecule.java
                • IntegratorHarmonic.java
                • ArrayA2B.java
                • SimHarmonicUmbrella.java
                • HSDimerNPT.java
                • MCMoveAtomCoupled.java
                • SimCalcS.java
                • MeterPlaneSlip.java
                • NormalModeAnalysisDisplay3D.java
                • ModifierCells3D.java
                • MeterSolidPropsLJ.java
                • MeterDADB.java
                • LatticeSumMolecularCrystal.java
                • ArrayB2A.java
                • MeterThetaDeviation.java
                • NormalModes1DHR.java
                • P1ConstraintNbrHcp.java
                • PotentialCalculationSolidSuperCutLS.java
                • SimLJHTTISuperHCP.java
                • DataSourceAvgPressure2.java
                • MCMoveVolumeMonoclinic.java
                • SoftSphereSolidEOS.java
                • SimOverlapSSnxy.java
                • MeterBoltzmann.java
                • MeterTiltRotation.java
                • MCMoveHarmonicEin.java
                • P1ConstraintNbr.java
                • MeterOverlapSwitch.java
                • LJVacancyMin.java
                • SimOverlapSoftSphereTPSlantedBox.java
                • DataSourceAvgPressure.java
                • MeterHarmonicEnergyFromMove.java
                • SimOverlapLJ.java
                • SimTargetUmbrella.java
                • MeterDDP.java
                • MeterWorkTargetPhaseSpace.java
                • DataProcessorBoltzmannFactor.java
                • MeterWorkHarmonicBennet.java
                • ModifierXCells2D.java
                • SpeciesHSDimer.java
                • MeterWorkUmbrellaTarget.java
                • P2XOrder.java
                • HarmonicCrystalSsFccNxy.java
                • SimOverlapSoftSphereEinHarm.java
                • MeterSolidDACut.java
                • SimOverlapSoftSphereSoftness.java
                • NormalModeAnalysisDisplay3DGraphic.java
                • MCMoveWV.java
                • MeterWorkHarmonicTargetandReweighting.java
                • HTTPSoftSphereSim.java
                • NormalModeAnalysisDisplay1D.java
                • ConformationHSDimer.java
                • SimEinStep1HCP.java
                • PotentialCalculationSolidSuper.java
                • HSNPT.java
                • MeterSolidDA.java
                • MeterWorkHarmonicUmbrella.java
                • MCMoveSingleMode.java
                • MeterWorkBennetTarget.java
                • MeterBoltzmannHTTP.java
                • SimCalcSMorse.java
                • MeterWorkTargetUmbrella.java
                • SimOverlapLJModule.java
                • BoltzmannProcessor.java
                • MeterTilt.java
                • SimHSMDVacancy.java
                • MeterBoltzmannTarget.java
                • MeterHarmonicEnergy.java
                • WaveVectorFactoryFcc.java
                • MeterTiltHistogram.java
                • MCMoveVolumeSolidNPTMolecular.java
                • HessianDB.java
                • ArrayReader2D.java
                • MeterWorkTargetBennet.java
                • DataSourcePN.java
                • DataSourceFE.java
                • MCMoveHarmonicStep.java
                • MeterJacobian.java
                • CoordinateDefinitionHSDimer.java
                • MeterAtomicDisplacement.java
                • WriteS.java
                • PotentialCalculationSolidSuperCut.java
                • BasisBigCell.java
                • SimCalcSSoftSphereFCCSuperBox.java
                • MeterWorkTargetHarmonicandReweighting.java
                • MeterPressureSuperBox.java
                • MeterTiltRotationHistogram.java
                • DataSourceMuRootPMatch.java
                • SimOverlapSoftSphere.java
                • NormalModesVariable.java
                • SimUmbrellaSoftSphere.java
                • DataProcessorSum.java
                • SimBennet.java
                • NormalModesSoftSpherical.java
                • nptdemo
                  • HSNPT2DGraphic.java
                  • HSNPT2DSim.java
                  • ColorSchemeScaledOverlap.java
                  • DisplayBoxCanvas2DNpTScaling.java
                • ModifierYCells2D.java
                • WaveVectorFactory2D.java
                • CalcHarmonicA.java
                • MCMoveAtomCoupledBennet.java
                • MCMoveMoleculeCoupled.java
                • SimOverlapSoftSphereDP.java
                • WaveVectorFactory.java
                • MCMoveAtomCoupledUmbrella.java
                • MeterSamplingHarmonic.java
                • SimFluidSoftSphere.java
                • SimOverlapSoftSphereTP.java
              • metastable
                • LJmuVT.java
                • DataProcessorXY.java
                • LJNPT.java
                • LJNVT.java
                • MeterDensityDistribution.java
              • surfacetension
                • SurfaceTensionMapped.java
                • ActionRecenter.java
                • FitTanh.java
                • LJMC.java
                • DataProcessorSurfaceTension.java
              • veos
                • QSeries.java
                • bigdecimal
                  • Wigner3j.java
                  • Factorial.java
                  • Bernoulli.java
                  • Ifactor.java
                  • BigComplex.java
                  • RatPoly.java
                  • Euler.java
                  • BigSurdVec.java
                  • Harmonic.java
                  • PartitionsP.java
                  • Wigner3jGUI.java
                  • EulerPhi.java
                  • BigDecimalMath.java
                  • Prime.java
                  • BigIntegerMath.java
                  • Rational.java
                  • BigSurd.java
                  • BigIntegerPoly.java
                • MyBigDecimal.java
                • BigValue.java
                • HardRods.java
                • BetaSource.java
                • IBigValue.java
                • VanderWaals.java
                • Ushcats.java
              • mappedvirial
                • PotentialCalculationMappedVirial.java
                • MeterMeanForce.java
                • MeterMappedVirial.java
                • PotentialCalculationMappedVirialV.java
                • MeterMappedU.java
                • MappedVirialLJ.java
                • MappedVirialLJVGr.java
                • PotentialCalculationMappedEnergy.java
                • MappedU.java
                • MeterMappedVirialV.java
              • virial
                • MeterVirialIC.java
                • PotentialGroup3PI.java
                • B2ForSphericallySymmetricUByTrapezoidRule.java
                • PercusYevick.java
                • ClusterBondsNonAdditive.java
                • overlap
                  • DataSourceVirialOverlap.java
                  • DataProcessorVirialOverlap.java
                  • AccumulatorVirialOverlapSingleAverage.java
                  • DataVirialOverlap.java
                  • IntegratorOverlap.java
                • MayerFunctionMolecularThreeBody.java
                • ClusterChainHS.java
                • BnPYCHe.java
                • IsFFT.java
                • CalcFFT.java
                • ConformationNaphthaleneTraPPE.java
                • MayerPTAtt.java
                • MCMoveClusterTorsionMulti.java
                • PercusYevick1QC.java
                • ClusterWheatley.java
                • MayerEHardSphere.java
                • MayerFunctionTemperature.java
                • ClusterCoupledAtomFlipped.java
                • ClusterWheatleyMultibodyBD.java
                • MCMoveClusterMolecule.java
                • ClusterWheatleySoftDerivatives.java
                • MCMoveClusterAtomChainHSTail.java
                • BnJHBVArgon_Analytic.java
                • ClusterWeight.java
                • MCMoveClusterWiggleMulti.java
                • SpeciesAlkane.java
                • SpeciesFactorySpheres.java
                • ClusterSumShell.java
                • B4FFTLJ.java
                • CoordinatePairSet.java
                • PotentialEmulCached.java
                • ClusterChainSoft.java
                • SpeciesFactoryOrientedSpheres.java
                • IEGenerator.java
                • ClusterSumPolarizableWertheimProduct.java
                • ClusterWheatleySoftDerivativesBD.java
                • Conformation7SiteRigidSF6.java
                • ClusterSumPolarizable.java
                • MCMoveClusterPolyhedraChain.java
                • ClusterSumAssociation.java
                • ClusterSumMultibodyShell.java
                • ConformationPh3site.java
                • ClusterWheatleyMultibodyDerivativesBD.java
                • MayerFunctionNonAdditiveFull.java
                • PotentialNonAdditive.java
                • ClusterDifference.java
                • BnPYLJ.java
                • MCMoveClusterAtomMulti.java
                • MCMoveClusterAtomHSChainMix.java
                • MayerWell.java
                • ClusterWheatleyMultibody.java
                • MayerSSSeries.java
                • MCMoveClusterRingRegrow.java
                • HNCGenerator.java
                • ClusterSumPolarizableWertheimProduct4PtFinal.java
                • GUI
                  • views
                    • ViewConsoleOutputBox.java
                    • ViewAlertMsgBoxSpeciesRemoval.java
                    • ViewSpeciesSelection.java
                    • ViewAlkaneLengthSelection.java
                    • ViewSimEnvironmentSelection.java
                    • ViewAlertMsgBox.java
                    • AppViewMixtureBuilder.java
                  • containers
                    • PanelMainFrame.java
                    • AppFrameMixtureBuilder.java
                  • models
                    • MolecularModelLJ_SpeciesLJ.java
                    • IMolecularModel_SpeciesFactory.java
                    • MolecularModelTRAPPE_SpeciesAlkane.java
                    • ModelTemperatureAndSteps.java
                    • ViewSpeciesSelection.java
                    • MolecularModel2CLJQ_SpeciesLJ.java
                    • MolecularModel2CLJQ_SpeciesCO2.java
                    • ModelPotParamDisplayTable.java
                    • ModelMoleculeListDisplayTable_new.java
                    • ModelSimulationEnvironment.java
                    • MolecularModelTrappe_SpeciesCO2.java
                    • EnumPotentialParamDescription.java
                    • MolecularModel2CLJQ_SpeciesEthane.java
                    • ModelSpeciesSelection.java
                    • MolecularModelSKS_SpeciesAlkane.java
                    • MolecularModelExp6_SpeciesAlkane.java
                    • ModelMoleculeListDisplayTable.java
                    • ModelAlertMsgDialog.java
                    • MolecularModelLJQ_SpeciesLJ.java
                    • EnumSiteName.java
                    • ModelAlkaneLengthSelection.java
                    • AppModelMixtureBuilder.java
                    • MolecularModelEMP2_SpeciesCO2.java
                    • MolecularModelSPCE_SpeciesH2O.java
                    • ModelSelectedSpecies.java
                    • ModelSimulationConstructor.java
                  • components
                    • CollectionPotentialAtomicLike.java
                    • CollectionBondedPotentialAlkanes.java
                    • ArrayMoleculeDisplayList.java
                    • BuilderCollectionPotential.java
                    • CollectionBondedPotentialAlcohols.java
                    • SimpleElementForSimilarSpecies.java
                    • ACollectionBondedPotential.java
                    • CollectionPotentialAtomicUnlike.java
                    • ICollectionPotential.java
                    • ExceptionSingleSiteAtomicPotential.java
                    • ExceptionDoNotRemoveSpecies.java
                    • CollectionPotentialMolecularLike.java
                    • ExceptionSameSpeciesSamePotential.java
                    • CollectionPotentialMolecularUnlike.java
                    • SimulationRunner.java
                    • HashMapPotentialNonBonded.java
                  • controllers
                    • AppControllerMixtureBuilder.java
                    • ControllerSimEnvironmentSelection.java
                    • ControllerAlertMsgBox.java
                    • ControllerAlkaneLengthSelection.java
                    • ControllerAlertMsgBoxSpeciesRemoval.java
                    • ControllerSpeciesSelection.java
                  • ApplicationMixtureBuilder.java
                • MeterVirialSWWE.java
                • MCMoveClusterRingScale.java
                • B3ForSphericallySymmetricU.java
                • Species7SiteRigidSF6.java
                • ClusterWheatleyHS.java
                • ConfigurationClusterChain.java
                • AtomPairSet.java
                • MuGeneral.java
                • SpeciesAnthracene3site464.java
                • MayerHSMixture.java
                • ClusterSumHS.java
                • MCMoveClusterRotateMoleculeMulti.java
                • BnHSIonic.java
                • MeterVirialExternalField.java
                • ClusterWheatleyMultibodyMix.java
                • MeterVirialExternalFieldOverlapRho.java
                • MCMoveChangeBondLength.java
                • MeterSamplingWeight.java
                • CoordinatePairMoleculeSet.java
                • MCMoveClusterAtom.java
                • MCMoveClusterAtomHSTree.java
                • MCMoveClusterDiagram.java
                • ClusterTreeBonds.java
                • ClusterExchange.java
                • CoordinatePairLeafSet.java
                • ClusterAbstractMultivalue.java
                • ClusterWheatleySoftMix.java
                • SpeciesTraPPEPhenanthrene.java
                • B3LJ.java
                • ClusterSumEF.java
                • PYGenerator.java
                • ClusterSumExternalField.java
                • SpeciesFactoryWater3P.java
                • ConformationPhenanthreneTraPPE.java
                • ClusterCoupledFlippedPartial.java
                • MayerFunctionSum.java
                • MeterVirialBDBin.java
                • ClusterWheatleyPartitionScreening.java
                • SpeciesAnthracene3site545.java
                • P1IntraLambda.java
                • MayerDFDTSpherical.java
                • ClusterSumMultibody.java
                • MCMoveClusterMoleculeLayerMove.java
                • ClusterSumNonAdditiveTrimerEnergy.java
                • B6FFTLJ.java
                • MayerFunctionSumGeneral.java
                • BoxCluster.java
                • MCMoveClusterAtomRotateMulti.java
                • SpeciesFactorySpheres2.java
                • MayerFunctionThreeBody.java
                • BnHNCLJ.java
                • SpeciesTraPPENaphthalene.java
                • MayerFunctionSphericalThreeBody.java
                • SpeciesFactoryWaterGCPM.java
                • MCMoveClusterRingRegrowExchange.java
                • B3NonAddForSphericallySymmetricU.java
                • B2Ionic.java
                • MCMoveClusterPolyhedraTree.java
                • MayerSphericalPTAtt.java
                • MayerEGeneral.java
                • PotentialGroupPI.java
                • MayerSphericalPlus.java
                • ClusterSum.java
                • B5FFTLJ.java
                • ClusterWheatleyMultibodyDerivatives.java
                • MeterVirialBDBinMultiThreaded.java
                • MCMoveClusterAtomHSTreeMix.java
                • ConformationCO2.java
                • MeterVirialExternalFieldConfined.java
                • MCMoveClusterAngleBend.java
                • MayerPUGeneral.java
                • ConfigurationCluster.java
                • MeterVirial.java
                • MayerD2FDT2Spherical.java
                • simulations
                  • VirialHeNonAdditive.java
                  • VirialHePCKLJSTempDeriv.java
                  • VirialCPSHeliumNonAdditive.java
                  • VirialCO2NaphthaleneLJQ.java
                  • VirialAnthraceneTraPPE.java
                  • VirialGCPMGraphic.java
                  • VirialLJSeries.java
                  • VirialPh464.java
                  • DoubleAssociationSitesFluid4Pt.java
                  • VirialH2OGCPMD.java
                  • ModifierTPI.java
                  • VirialAlkaneMix.java
                  • VirialN2CH4UAMix.java
                  • VirialHeNonAdditiveWheatley.java
                  • SingleAssociationSiteFluid3Pt.java
                  • LJTSRefLJ.java
                  • VirialH2O.java
                  • VirialMethaneEH.java
                  • VirialHePYCorrection.java
                  • VirialCO2anthracene545.java
                  • VirialCO2H2OSC.java
                  • VirialCPSHeliumNonAdditiveClassical.java
                  • VirialCH4AlkaneEHMix.java
                  • VirialB2WaterTIP4P_DHS_difference.java
                  • VirialLJD.java
                  • VirialO2.java
                  • VirialHePI.java
                  • VirialCO2CH4Mix.java
                  • VirialAlkaneFlex.java
                  • VirialN2CH4Mix.java
                  • VirialHardAssociationConeDoubleSites.java
                  • VirialCO2H2OGCPMX.java
                  • VirialHePIXCEven.java
                  • VirialCO2H2OGCPM.java
                  • VirialAnthracene464.java
                  • ShapeParser.java
                  • SimulationVirialOverlap.java
                  • ReeHooverMC.java
                  • VirialH2PI.java
                  • VirialHS.java
                  • FourAssociationSitesFluid2Pt.java
                  • VirialCO2AnthraceneTraPPE.java
                  • VirialExternalFieldConfinedOverlap.java
                  • VirialAceticAcidFlex.java
                  • VirialN2AlkaneUAMix.java
                  • VirialAceticAcid.java
                  • VirialCO2anthracene464.java
                  • SimulationVirialOverlap2.java
                  • VirialN2PI.java
                  • VirialO2PI.java
                  • VirialHSOrC.java
                  • VirialCO2CH4UAMixWheatley.java
                  • VirialPolyhedra.java
                  • VirialB3C2HSDipole.java
                  • VirialCO2SKSMix.java
                  • SingleAssociationSiteFluid.java
                  • VirialAlkaneMix_Kong.java
                  • SimulationVirial.java
                  • VirialSQWRecalcSmallMem.java
                  • SingleAssociationSiteFluid4Pt.java
                  • VirialCO2AlkaneEHMix.java
                  • VirialHePIXCOdd.java
                  • DirectSamplingTargetQCArReferenceAzizAr.java
                  • VirialAlkaneSKS.java
                  • VirialGCPM.java
                  • VirialAlkaneMix2.java
                  • VirialLJOrC.java
                  • VirialHePCKLJSPYCorrection.java
                  • VirialB3C2TIP4Pwater.java
                  • VirialLJ.java
                  • VirialH2PIBoltzmann.java
                  • VirialSwsPT.java
                  • VirialAnthracene545.java
                  • VirialAlkane.java
                  • VirialCO2PI.java
                  • VirialHePI_PotentialCorrection.java
                  • VirialLJPYCorrection.java
                  • VirialCO2NaphthaleneTraPPE.java
                  • VirialSWWE.java
                  • VirialCPSHeliumNonAdditiveClassical_Correction.java
                  • VirialHePIGraphic.java
                  • VirialHePIXC.java
                  • SimulationVirialDiagram.java
                  • VirialCO2AlkaneUAMix.java
                  • SingleAssociationSiteFluid2.java
                  • VirialExternalFieldConfinedOverlapRho.java
                  • VirialN2TraPPE.java
                  • VirialCO2.java
                  • SingleAssociationSiteFluidGraph.java
                  • VirialHePCKLJS.java
                  • VirialHardAssociationCone.java
                  • VirialCO2TraPPE.java
                  • SingleAssociationSiteFluid2Pt.java
                  • VirialH2PYCorrection.java
                  • VirialCO2N2Mix.java
                  • VirialB3C1TIP4Pwater.java
                  • VirialHSMixture.java
                  • TestLJAssociationMC3D_NPT.java
                  • VirialCO2CH4UAMix.java
                  • VirialAlkaneFull.java
                  • VirialN2AlkaneUARigid.java
                  • VirialSQWBinMultiThreaded.java
                  • VirialLJMultiOverlap.java
                  • DoubleAssociationSitesFluid3Pt.java
                  • VirialAlkaneMix2_Kong.java
                  • VirialCO2LJQ.java
                  • Virial2CLJQ.java
                  • BnFlexibleContributionTraPPEUAMethanol.java
                  • VirialWaterOverlap.java
                  • VirialSQWBinMultiRecalcW.java
                  • VirialEmulNonAdditive.java
                  • VirialN2.java
                  • VirialHeSC.java
                  • SimulationVirialMultiOverlap.java
                  • VirialAlkaneEHTest.java
                  • VirialPhenanthreneTraPPE.java
                  • DoubleAssociationSitesFluid2Pt.java
                  • VirialN2AlkaneEHMix.java
                  • SimulationVirialUmbrella.java
                  • VirialPolyhedra2.java
                  • VirialSF6LJAlkaneUAMix.java
                  • VirialPh545.java
                  • VirialTraPPEAlcohol.java
                  • VirialH2PIXC.java
                  • VirialHePCKLJSCHNCCorrection.java
                  • VirialH2PISimple.java
                  • VirialRowleyAlcohol.java
                  • VirialLJOrICPYC.java
                  • VirialExternalFieldOverlapRho.java
                  • VirialLJBridge.java
                  • VirialLJCHNCCorrection.java
                  • VirialB3C1HSDipole.java
                  • VirialNaphthaleneTraPPE.java
                  • VirialAssociatingFluid4points.java
                  • VirialExternalFieldConfinedOverlapSW.java
                  • Virial7SiteRigidSF6.java
                  • VirialAssociatingFluid.java
                  • VirialHSBinMultiThreaded.java
                  • SingleAssociationSiteFluid4Points.java
                  • VirialSW.java
                • ClusterWeightAbs.java
                • ClusterPY.java
                • MeterVirialBinMultiThreaded.java
                • ClusterCoupledFlipped.java
                • paralleltempering
                  • MCMoveSwapCluster.java
                • MuFGeneral.java
                • SpeciesFactory.java
                • MCMoveClusterAngleBendAceticAcid.java
                • ClusterSumIC.java
                • SpeciesTraPPEAnthracene.java
                • ClusterWeightSumWall.java
                • BnSCALJ.java
                • MCMoveClusterRotateMolecule3D.java
                • MCMoveClusterAtomHSChain.java
                • SpeciesFactorySiepmannSpheres.java
                • ClusterCoupledFlippedMultivalue.java
                • MCMoveClusterTorsionAceticAcid.java
                • ClusterSumPolarizableWertheimProduct4Pt.java
                • MayerFunctionProductGeneral.java
                • MCMoveClusterMoleculeMulti.java
                • MeterVirialBD.java
                • ClusterTreeEF.java
                • MayerFunctionNonAdditive.java
                • MayerENonGeneral.java
                • ConformationAnthraceneTraPPE.java
                • BnIETP2Spherical.java
                • MCMoveClusterWiggleAlkaneEH.java
                • MeterVirialExternalFieldOverlapConfinedRho.java
                • MayerDFQFHDTSpherical.java
                • MCMoveClusterRotateCH3.java
                • ConfigurationClusterAceticAcid.java
                • OrnsteinZernike.java
                • MeterVirialExternalFieldSW.java
                • ConfigurationClusterWertheimGCPM.java
                • SpeciesPh3site545.java
                • ClusterICPYC.java
                • ConfigurationClusterMove.java
                • ConformationMethane.java
                • MayerESpherical.java
                • ConfigurationClusterChainFourSites.java
                • SpeciesMethane.java
                • ClusterSumStickyEF.java
                • MeterVirialExternalFieldOverlapConfined.java
                • ClusterWheatleySoftBDMix.java
                • BnPYHardSphere.java
                • MCMoveClusterAtomSQWTree.java
                • ClusterWeightUmbrella.java
                • MCMoveClusterReptateMulti.java
                • MayerGeneralSpherical.java
                • ClusterAbstract.java
                • MCMoveClusterRingRegrowOrientation.java
                • MayerGeneralAtomic.java
                • HypernettedChain.java
                • ClusterWheatleySoftBD.java
                • BnPY_1QC_Helium.java
                • MCMoveClusterRingPartialRegrow.java
                • ClusterTree.java
                • SpeciesFactoryWater4P.java
                • ClusterWheatleyExtendSW.java
                • MCMoveClusterAtomHSRing.java
                • SpeciesTraPPECO2.java
                • ClusterBonds.java
                • PotentialCommonAtomic.java
                • MayerXSpherical.java
                • cluster
                  • ClusterTreeNode.java
                  • VirialDiagrams.java
                  • Full.java
                  • MayerIonicDiagram4qbonds.java
                  • ClusterOperations.java
                  • WertheimDiagrams2SiteRho.java
                  • MayerIonicDiagram2qbonds.java
                  • DiagramSource.java
                  • ExternalVirialDiagrams.java
                  • DCF.java
                  • ClusterAssociation.java
                  • ClusterDiagram.java
                  • Standard.java
                  • ExchangeSplit.java
                  • WertheimDiagrams3SiteRho.java
                  • ClusterCollapsedTreeNode.java
                  • BondConnectedSubstitution.java
                  • Ring.java
                  • PermutationIterator.java
                  • Chain.java
                  • BondConnectedSubstitutionNaphthalene.java
                  • MayerIonicDiagram1qbond.java
                  • VirialDiagramsMix2.java
                  • VirialDiagramsPT.java
                  • CondenseExchange.java
                  • VirialDiagramsMix.java
                  • ClusterDiagramTree.java
                  • ClusterGenerator.java
                  • BondConnectedSubstitution3Site.java
                • MCMoveClusterAtomSQWChain.java
                • MayerFunction.java
                • ConfigurationClusterWertheimGCPMDirectSampling.java
                • MeterVirialExternalFieldOverlapConfinedSW.java
                • MCMoveClusterTorsionAlkaneEH.java
                • MayerGeneral.java
                • MCMoveClusterAtomQ.java
                • ClusterWheatleySoft.java
                • SpeciesPh3site464.java
                • ConformationAnthracene3site.java
                • MCMoveClusterWiggleAceticAcid.java
                • IntSet.java
                • MeterVirialExternalFieldRho.java
                • MoleculeActionRelaxWater3P.java
                • ClusterSinglyConnected.java
                • MeterVirialEBinMultiThreaded.java
                • ConfigurationClusterWertheimGCPM4Pt.java
                • SpeciesFactoryTangentSpheres.java
                • ClusterMultiToSingle.java
                • MCMoveClusterAtomDiscrete.java
                • MayerHardSphere.java
              • thermointegration
                • LjMc3D.java
                • IntegratorThermodynamicPEvsT.java
                • IntegratorThermodynamic.java
              • interfacial
                • IntegratorFixedWall.java
                • LJMD.java
                • P1Wall.java
                • MeterWallPosition.java
                • LJMC.java
                • ConfigurationLammps.java
                • MCMoveAtomNbr.java
                • MeterWallForce.java
                • WriteConfigurationInterfacial.java
                • FixedWall.java
              • spin
                • P1MagneticField.java
                • MeterSpin.java
                • MCMoveSpinFlip.java
                • ConfigurationAligned.java
                • P2Spin.java
                • Heisenberg.java
              • conjugategradient
                • TestNonLinearConjugateGradients.java
                • SteepestDescent.java
                • TestFiniteDifferenceDerivative.java
                • PreconditionedConjugateGradient.java
                • ConjugateGradients.java
                • FiniteDifferenceDerivativeCG.java
                • DerivativeEnergyFunction.java
                • NonLinearConjugateGradients.java
        • test
          • java
            • etomica
              • virial
                • ClusterWheatleySoftDerivativesTest.java
                • simulations
                  • VirialLJTest.java
                • ClusterWheatleyMultibodyDerivativesTest.java
    • etomica-core
      • src
        • main
          • resources
            • tests
          • java
            • etomica
              • molecule
                • MoleculeToMoleculeListSpecies.java
                • MoleculesetArray.java
                • MoleculePair.java
                • MoleculeAgentManager.java
                • MoleculeToMoleculeList.java
                • IMoleculeOriented.java
                • MoleculeToMoleculeSetFixed.java
                • IMoleculeKinetic.java
                • MoleculePositionCOM.java
                • iterator
                  • MoleculeIteratorAll.java
                  • MoleculesetIterator.java
                  • MpiIntraspeciesAA.java
                  • MpiInterspecies1A.java
                  • MoleculeIterator.java
                  • MoleculesetIteratorBasisDependent.java
                  • MoleculeIteratorArrayListSimple.java
                  • MpiInnerVariable.java
                  • MoleculeIteratorBoxDependent.java
                  • MpiInterArrayList.java
                  • MpiInterspeciesAA.java
                  • MpiMolecule.java
                  • MoleculeIteratorMolecule.java
                  • MoleculeIteratorSinglet.java
                  • MpiInnerFixed.java
                  • MoleculesetIteratorTargetable.java
                  • MoleculeIteratorAllMolecules.java
                  • MoleculesetIteratorPDT.java
                  • IteratorFactory.java
                  • MoleculeIteratorMoleculeDependent.java
                  • MpiIntraArrayList.java
                  • MoleculeIteratorArrayList.java
                  • MpiIntraspecies1A.java
                  • MoleculesetIteratorBoxDependent.java
                • MoleculeOrientedDynamic.java
                • OrientationCalc.java
                • IMoleculePositionDefinition.java
                • IMoleculeList.java
                • DipoleSource.java
                • MoleculePositionGeometricCenterAlkaneEH.java
                • MoleculePositionGeometricCenterPBC.java
                • IMoleculeOrientedKinetic.java
                • MoleculeSetSinglet.java
                • Molecule.java
                • IMoleculePositioned.java
                • IMolecule.java
                • MoleculeToIndex.java
                • MoleculePositionGeometricCenter.java
                • MoleculePositionFirstAtom.java
                • MoleculeSource.java
                • MoleculeListWrapper.java
                • OrientationCalcQuaternion.java
                • MoleculeSourceRandomMolecule.java
                • MoleculeOriented.java
                • OrientationCalcAtom.java
                • MoleculeArrayList.java
              • atom
                • AtomSourceRandomLeaf.java
                • AtomTypeAgentManager.java
                • AtomToParentChildList.java
                • AtomHydrogen.java
                • AtomOrientedDynamic.java
                • AtomOriented.java
                • AtomToIndex.java
                • DiameterHashByElementType.java
                • IAtomList.java
                • AtomPair.java
                • IAtom.java
                • AtomType.java
                • iterator
                  • AtomLeafsetIterator.java
                  • ApiLeafAtoms.java
                  • AtomIteratorArrayListSimple.java
                  • ANIntragroupExchange.java
                  • AtomsetIteratorBoxDependent.java
                  • AtomIteratorBasisFilteredType.java
                  • Atomset3IteratorIndexList.java
                  • ApiIntergroupExchange.java
                  • AtomsetIteratorBasisDependent.java
                  • AtomIteratorBasisFilteredType2.java
                  • ApiIndexList.java
                  • AtomIteratorSinglet.java
                  • AtomIteratorBasisAdjustableStart.java
                  • ApiBuilder.java
                  • AtomsetIteratorTargetable.java
                  • ApiInnerVariable.java
                  • AtomsetIteratorDirectable.java
                  • AtomIteratorLeafAtoms.java
                  • AtomIteratorNull.java
                  • ApiIntergroupCoupled.java
                  • AtomIteratorBasisDependent.java
                  • AtomIteratorBasis.java
                  • AtomsetIteratorAllLeafAtoms.java
                  • AtomsetIterator.java
                  • TripletInnerSequential.java
                  • Atomset4IteratorIndexList.java
                  • ApiIntragroup.java
                  • AtomsetIteratorPDT.java
                  • AtomIteratorArrayList.java
                  • AtomIteratorLeafFilteredType.java
                  • AtomIterator.java
                  • ApiInterArrayList.java
                  • ApiIntergroup.java
                  • ApiIntraArrayList.java
                  • AtomIteratorAtomDependent.java
                  • AtomIteratorArrayListAdjacent.java
                  • package.html
                  • ApiIntergroupIntraSpecies.java
                  • ANIntergroupCoupled.java
                  • ANIntergroupExchange.java
                  • AtomIteratorBoxDependent.java
                  • AtomIteratorAllLeafType.java
                • AtomToAtomSetFixed.java
                • DiameterHash.java
                • DiameterHashByType.java
                • Atom.java
                • AtomSetSinglet.java
                • AtomOrientedQuaternion.java
                • AtomTypeOriented.java
                • AtomToAtomLeafList.java
                • AtomArrayList.java
                • IAtomKinetic.java
                • AtomSourceRandomSpecies.java
                • DiameterHashByElement.java
                • AtomListWrapper.java
                • IAtomOriented.java
                • AtomFilterCollective.java
                • AtomToIndexChild.java
                • AtomLeafDynamic.java
                • AtomSource.java
                • AtomTypeSpheroPolyhedron.java
                • AtomGroupVelocityAverage.java
                • AtomsetArray.java
                • IAtomOrientedKinetic.java
                • package.html
                • AtomFilter.java
                • AtomLeafAgentManager.java
              • species
                • ISpecies.java
                • SpeciesSpheresMono.java
                • SpeciesSpheresRotatingMolecule.java
                • Species.java
                • SpeciesSpheresCustom.java
                • SpeciesSpheresHetero.java
                • SpeciesSpheres.java
                • SpeciesOriented.java
                • ISpeciesOriented.java
                • SpeciesAgentManager.java
                • SpeciesSpheresRotating.java
                • SpeciesPolyhedron.java
              • space1d
                • Space1D.java
                • Tensor1D.java
                • Vector1D.java
                • package-info.java
                • Orientation1D.java
                • RotationTensor1D.java
              • space
                • Tensor.java
                • BoundaryDeformablePeriodic.java
                • RotationTensor.java
                • BoundaryDeformableLattice.java
                • BoundaryEventListener.java
                • BoundaryRectangular.java
                • IOrientation.java
                • BoundaryRectangularPore.java
                • BoundaryEventManager.java
                • BoundaryRectangularNonperiodic.java
                • Space.java
                • package-info.java
                • BoundaryEvent.java
                • BoundaryRectangularSlit.java
                • Vector.java
                • BoundaryRectangularPeriodic.java
                • Boundary.java
              • modifier
                • ModifierNMolecule.java
                • ModifierGeneral.java
                • ModifierFunctionWrapper.java
                • ModifyBooleanAction.java
                • ModifierBoolean.java
                • ModifyAction.java
                • package.html
                • Modifier.java
              • box
                • AtomSetAllMolecules.java
                • BoxEvent.java
                • BoxAtomEvent.java
                • BoxAgentSourceAtomManager.java
                • RandomPositionSourceDeformable.java
                • BoxMoleculeEvent.java
                • RandomPositionSource.java
                • BoxEventListener.java
                • BoxAtomIndexEvent.java
                • BoxAgentManager.java
                • BoxAgentSourceMoleculeManager.java
                • BoxEventListenerAdapter.java
                • RandomPositionSourceRectangular.java
                • package-info.java
                • BoxIndexEvent.java
                • BoxMoleculeCountEvent.java
                • BoxCellManager.java
                • BoxMoleculeIndexEvent.java
                • BoxEventManager.java
                • Box.java
              • simulation
                • SimulationIndexEvent.java
                • SimulationSpeciesEvent.java
                • Simulation.java
                • SimulationAtomTypeIndexEvent.java
                • SimulationContainer.java
                • SimulationEvent.java
                • SimulationEventManager.java
                • SimulationSpeciesIndexEvent.java
                • SimulationBoxEvent.java
                • SimulationAtomTypeEvent.java
                • SimulationListener.java
                • prototypes
                  • SWMD2D.java
                  • LJMD2D.java
                  • GEMCWithRotation.java
                  • DemoSim.java
                  • HSMD2D_noNbr.java
                  • SoftSphere3d.java
                  • LJMD3D.java
                  • ChainHSMD3D.java
                  • SWMD3D.java
                  • HSMD2D.java
                  • HSMC2D.java
                  • HSMD3DNoNbr.java
                  • HSMD3D.java
              • models
                • water
                  • P2WaterTIP4PHardCore.java
                  • SpeciesWater4POriented.java
                  • ConformationWaterGCPM.java
                  • ConformationWaterTIP4P.java
                  • SpeciesWater3P.java
                  • SpeciesWater4PCOM.java
                  • ConformationWaterGCPMCOM.java
                  • PNWaterGCPMThreeSite.java
                  • SpeciesWater3POriented.java
                  • P2WaterTIP4PSoft.java
                  • ConformationWater3P.java
                  • P2HardAssociationGCPMReference.java
                  • ChargeAgentSourceTIP4PWater.java
                  • TestEwaldTIP4PWater.java
                  • P2WaterSPCE.java
                  • package-info.java
                  • DipoleSourceWater.java
                  • P2WaterTIP4P.java
                  • SpeciesWater4P.java
                  • P2Water3P.java
                  • ConfigurationFileTIP4P.java
                  • P2Water3PSoft.java
                  • P2WaterSzalewicz.java
                  • OrientationCalcWater4P.java
                  • PNWaterGCPM.java
                  • P2Water4PSoft.java
                  • P2Water4P.java
                  • P2WaterSPCSoft.java
                  • P2WaterSPC.java
                  • OrientationCalcWater3P.java
                • package-info.java
                • co2
                  • PNGCPMX.java
                  • P2CO2H2OWheatley.java
                  • package-info.java
                  • PNGCPM.java
                  • PNCO2GCPM.java
                  • P2CO2Hellmann.java
              • graphics
                • DeviceTable.java
                • DeviceToggleRadioButtons.java
                • DisplayTextBoxesCAE.java
                • ActionGraphic.java
                • DeviceTableModelGeneric.java
                • Device.java
                • ColorSchemeNeighbor.java
                • SimulationPanel.java
                • DeviceBox.java
                • DisplayTextBox.java
                • ColorSchemeCell.java
                • SimulationGraphic.java
                • ColorScheme.java
                • ActionVelocityWindow.java
                • DeviceTrioControllerButton.java
                • DisplayBoxCanvas1D.java
                • ColorSchemeCollective.java
                • DisplayPolytopeCanvasG3DSys.java
                • images
                • DisplayBoxCanvasG3DSys.java
                • DisplayPolytope.java
                • DisplayTable.java
                • DataTagBag.java
                • DisplayPolytopeCanvas2D.java
                • DisplayTimer.java
                • ColorSchemeRandom.java
                • ColorSchemeByType.java
                • BondListener.java
                • Display.java
                • ColorSchemeRandomByMolecule.java
                • BondManager.java
                • DeviceNSelector.java
                • DevicePlotPoints.java
                • ColorSchemeNeighborCell.java
                • DisplayScrollingGraph.java
                • DeviceBoxValueChangedListener.java
                • ColorSchemeTemperature.java
                • ColorSchemeCollectiveAgent.java
                • DeviceSlider.java
                • AboutBoxWindow.java
                • DimensionedDoubleEditor.java
                • ColorSchemeCoordination.java
                • DeviceThermoSlider.java
                • DisplayBoxSpin2D.java
                • DeviceButton.java
                • DeviceButtonGroup.java
                • ColorSchemeNull.java
                • DeviceControllerButton.java
                • DisplayBox.java
                • ColorSchemeOverlap.java
                • DisplayPlot.java
                • ColorSchemeColliders.java
                • ActionHistoryWindow.java
                • GraphicalElement.java
                • OverflowShift.java
                • DeviceSpinner.java
                • PropertyText.java
                • DeviceSelector.java
                • Drawable.java
                • DeviceCheckBox.java
                • DefaultToolbar.java
                • EtomicaTheme.java
                • DeviceBoxValueChangedEvent.java
                • DeviceToggleButton.java
                • ActionConfigWindow.java
                • DisplayCanvas.java
                • DecimalSlider.java
                • DisplayBoxCanvas2D.java
                • DeviceDelaySlider.java
                • DeviceThermoSelector.java
                • EtomicaPlot.java
              • units
                • Bar.java
                • Dalton.java
                • Angstrom.java
                • Barye.java
                • Hertz.java
                • Dyne.java
                • CubicMeter.java
                • Poise.java
                • Candela.java
                • Erg.java
                • Decimal.java
                • UnitRatio.java
                • BohrRadius.java
                • dimensions
                  • DimensionRatio.java
                  • Current.java
                  • LuminousIntensity.java
                  • Dipole.java
                  • Fraction.java
                  • Temperature.java
                  • Momentum.java
                  • Power.java
                  • Pressure2D.java
                  • Time.java
                  • Area.java
                  • ElectricPotential.java
                  • Mass.java
                  • CompoundDimension.java
                  • Frequency.java
                  • Dimension.java
                  • Quantity.java
                  • Volume.java
                  • Pressure.java
                  • Wavenumber.java
                  • Null.java
                  • Undefined.java
                  • Viscosity.java
                  • Energy.java
                  • Dimensioned.java
                  • Charge.java
                  • Length.java
                  • Force.java
                  • Angle.java
                  • Velocity.java
                • Gram.java
                • ElectronVolt.java
                • Count.java
                • Liter.java
                • Picosecond.java
                • gui
                  • Lister.java
                  • package-info.java
                  • UnitFilter.java
                  • UnitGraphics.java
                • Debye.java
                • Kelvin.java
                • Hartree.java
                • Pixel.java
                • PrefixedUnit.java
                • Percent.java
                • package-info.java
                • Radian.java
                • CubicCentimeter.java
                • Prefix.java
                • Degree.java
                • Pascal.java
                • Electron.java
                • Meter.java
                • Second.java
                • Coulomb.java
                • Calorie.java
                • Ampere.java
                • Statcoulomb.java
                • Joule.java
                • systems
                  • CGS.java
                  • UnitSystem.java
                  • MKS.java
                  • package-info.java
                  • LJ.java
                • CompoundUnit.java
                • Unit.java
                • Mole.java
                • SimpleUnit.java
                • Volt.java
                • Watt.java
                • Newton.java
              • util
                • EventManager.java
                • IEvent.java
                • ScientificFormat.java
                • Grabber.java
                • Debug.java
                • Constants.java
                • ReadParameters.java
                • ParseArgs.java
                • Arrays.java
                • TreeList.java
                • ParameterParser.java
                • IListener.java
                • collections
                  • IndexMap.java
                • random
                  • RandomNumberGeneratorUnix.java
                  • IRandom.java
                  • RandomNumberGenerator.java
                  • RandomMersenneTwister.java
                • WriteParameters.java
                • ParameterBase.java
                • TreeLinker.java
                • Strings.java
                • package.html
              • config
                • ConformationChain2D.java
                • ConfigurationFileBinary.java
                • ConformationChainZigZag2.java
                • ConfigurationLatticeWithPlane.java
                • ConfigurationOrientedFile.java
                • ConformationLinear.java
                • ConformationChain.java
                • Configuration.java
                • ConfigurationLatticeSimple.java
                • IConformationOriented.java
                • ConformationChainZigZag.java
                • ConfigurationZincblende.java
                • GrainBoundaryConfiguration.java
                • ConformationWater.java
                • ConfigurationFile.java
                • ConformationChainLinear.java
                • ConfigurationReplicate.java
                • ConfigurationResourceFile.java
                • GrainBoundaryTiltConfiguration.java
                • ConfigurationLattice.java
                • package.html
                • ConformationGeneric.java
                • ConformationChain3D.java
                • IConformation.java
              • compatibility
                • FeatureRequirement.java
                • Requirement.java
                • FeatureSet.java
                • ClassRequirement.java
                • StringFeature.java
                • NumericFeature.java
                • RequirementSet.java
                • Feature.java
                • package.html
              • exception
                • MethodNotImplementedException.java
                • AbnormalCompletionException.java
                • ConfigurationOverlapException.java
                • package.html
              • lattice
                • LatticeOrthorhombicHexagonal.java
                • IndexIteratorReflecting.java
                • AbstractLattice.java
                • crystal
                  • PrimitiveCubic.java
                  • BasisHcp.java
                  • BasisCubicFccDiamond.java
                  • Basis.java
                  • BasisCubicBcc.java
                  • PrimitiveHCP4.java
                  • BasisHcpBaseCentered.java
                  • PrimitiveBcc.java
                  • BasisBetaSnA5.java
                  • BasisCubicDiamond.java
                  • PrimitiveGeneral.java
                  • BasisHcp4.java
                  • PrimitiveTriclinic.java
                  • BasisMonatomic.java
                  • PrimitiveHexagonal2D.java
                  • PrimitiveFcc.java
                  • PrimitiveOrthorhombic.java
                  • PrimitiveHexagonal.java
                  • PrimitiveOrthorhombicHexagonal.java
                  • BasisOrthorhombicHexagonal.java
                  • PrimitiveTrigonal.java
                  • PrimitiveTetragonal.java
                  • BasisCubicFcc.java
                  • package.html
                  • PrimitiveMonoclinic.java
                  • Primitive.java
                • CubicLattice.java
                • LatticePlane.java
                • BravaisLatticeCrystal.java
                • SiteFactory.java
                • RectangularLatticeNbrIterator.java
                • LatticeHcp.java
                • LatticeCubicDiamond.java
                • IndexIteratorTriangularPermutations.java
                • SpaceLattice.java
                • RectangularLatticeNbrIteratorSquare.java
                • CellLattice.java
                • LatticeSumCrystal.java
                • IndexIterator.java
                • RectangularLatticeNbrIteratorAdjacent.java
                • BravaisLattice.java
                • LatticeCubicBcc.java
                • LatticeHcp4.java
                • LatticeSum.java
                • FiniteLattice.java
                • IndexIteratorSizable.java
                • SiteIterator.java
                • IndexIteratorRectangular.java
                • IndexIteratorTriangular.java
                • RectangularLattice.java
                • package.html
                • IndexIteratorIncreasing.java
                • LatticeCubicSimple.java
                • LatticeCubicFcc.java
              • statmech
                • HardSphereSolid.java
                • MaxwellBoltzmann.java
                • HardSphere.java
                • LennardJones.java
                • HardSphereFluid.java
                • package-info.java
              • data
                • AccumulatorHistory.java
                • IDataInfoFactory.java
                • AccumulatorCounter.java
                • DataAccumulator.java
                • DataSourceAtomDistance.java
                • DataProcessorForked.java
                • AccumulatorAverageFixedOutputFile.java
                • DataSourceUniform.java
                • AccumulatorAverageBlockless.java
                • DataPumpListenerSmart.java
                • AccumulatorRatioAverageCovarianceFull.java
                • AccumulatorAverageCollapsingLogAB.java
                • DataTableAverages.java
                • IDataSink.java
                • AccumulatorAverageBootstrap.java
                • DataSet.java
                • IDataSource.java
                • HistogramDataSource.java
                • DataProcessorInterfacialTension.java
                • DataPumpListener.java
                • DataSplitter.java
                • DataSourceAcceptanceProbability.java
                • DataProcessor.java
                • AccumulatorAverageFixed.java
                • DataSourcePoints.java
                • DataSourcePositioned.java
                • DataDump.java
                • DataGroupFilter.java
                • DataSourceTensorVirialHard.java
                • DataPump.java
                • DataSourceCountSteps.java
                • FunctionData.java
                • DataStreamAction.java
                • AccumulatorAverageBlocklessSlim.java
                • AccumulatorAverageCovariance.java
                • DataPumpListenerPowStrict.java
                • AccumulatorRatioAverageCovariance.java
                • DataSourcePositionedBoltzmannFactor.java
                • AccumulatorAverageCollapsingLog.java
                • IData.java
                • histogram
                  • HistogramDiscrete.java
                  • HistogramReweightedData.java
                  • HistogramExpanding.java
                  • HistogramCollapsing.java
                  • HistogramNotSoSimple.java
                  • Histogram.java
                  • HistogramSimple.java
                • DataTableListener.java
                • DataSourceIndependent.java
                • types
                  • CastToDouble.java
                  • CastGroupToDoubleArray.java
                  • DataVector.java
                  • CastGroupOfTablesToDataTable.java
                  • CastToGroup.java
                  • DataTable.java
                  • DataTensor.java
                  • DataDoubleArray.java
                  • DataDouble.java
                  • DataGroup.java
                  • CastToDoubleArray.java
                  • DataFunction.java
                  • CastToTable.java
                  • package.html
                  • DataDoubleBDArray.java
                • AccumulatorHistogram.java
                • DataLogger.java
                • DataProcessorChemicalPotential.java
                • DataSourceCountTime.java
                • DataPipeForked.java
                • DataFork.java
                • DataGroupSplitter.java
                • DataSourceScalar.java
                • DataSourceRmsVelocity.java
                • DataInfoFactory.java
                • DataPipe.java
                • history
                  • HistoryCollapsingDiscard.java
                  • HistoryComplete.java
                  • HistoryScrolling.java
                  • HistoryCollapsing.java
                  • HistoryCollapsingAverage.java
                  • History.java
                • IDataInfo.java
                • DataDistributer.java
                • DataSourceGroup.java
                • DataArrayWriter.java
                • DataSourceAcceptanceRatio.java
                • DataProcessorFunction.java
                • DataSourceMolecular.java
                • DataSourceFunction.java
                • meter
                  • MeterDipoleSumSquaredMappedAverage.java
                  • MeterPressureByVolumeChange.java
                  • MeterDipoleSumSquared1site.java
                  • MeterMeanSquareDisplacement.java
                  • MeterLocalMoleFraction.java
                  • MeterPositionCOM.java
                  • MeterPressureTensorFromIntegrator.java
                  • MeterPotentialEnergy.java
                  • PotentialCalculationRDF.java
                  • MeterLocalDensity.java
                  • MeterMomentumCOM.java
                  • MeterStructureFactor.java
                  • DataSourceCollisional.java
                  • MeterRDFPC.java
                  • MeterPressureHardTensor.java
                  • MeterPressureMolecular.java
                  • MeterMoleFraction.java
                  • MeterProfileByVolume.java
                  • MeterWidomInsertion.java
                  • MeterDihedralAngle.java
                  • MeterTemperature.java
                  • MeterVolume.java
                  • MeterPressure.java
                  • MeterProfile.java
                  • MeterHyperVirial.java
                  • MeterProfileByAtoms.java
                  • MeterKineticEnergyRigid.java
                  • MeterAvgBondLength.java
                  • MeterKineticEnergy.java
                  • MeterDensity.java
                  • MeterEnergy.java
                  • MeterDipoleSumSquaredTIP4PWater.java
                  • MeterRMSD.java
                  • MeterNMolecules.java
                  • MeterPotentialEnergyFromIntegrator.java
                  • MeterPressureTensor.java
                  • MeterRDF.java
                  • package.html
                  • MeterPressureHard.java
                  • MeterKineticEnergyFromIntegrator.java
                  • MeterRadiusGyration.java
                  • MeterTensorVelocity.java
                • AccumulatorAverageCollapsing.java
                • DataSourceAtomic.java
                • package.html
                • AccumulatorAverage.java
                • DataSinkConsole.java
                • DataSourceCountCollisions.java
                • DataPumpListenerPow.java
                • DataTag.java
                • DataSourceIndependentSimple.java
                • DataSetListener.java
                • DataSinkTable.java
                • DataTableWriter.java
                • DataInfo.java
              • space3d
                • BoundaryTruncatedOctahedron.java
                • RotationTensor3D.java
                • Vector3D.java
                • Tensor3D.java
                • Orientation3D.java
                • package-info.java
                • IOrientationFull3D.java
                • IOrientation3D.java
                • OrientationFull3D.java
                • Space3D.java
              • action
                • WriteConfigurationBinary.java
                • PDBWriter.java
                • SimulationDataAction.java
                • BoxInflateAnisotropic.java
                • Undoable.java
                • IntegratorReset.java
                • BoxActionAdapter.java
                • AtomActionTranslateBy.java
                • BoxImposePbc.java
                • IAction.java
                • ControllerAction.java
                • SimulationActionAdapter.java
                • ResetAccumulatorsAveraged.java
                • Activity.java
                • AtomAction.java
                • BoxQuench.java
                • ActionIntegrate.java
                • BoxAction.java
                • activity
                  • ActivityGroupSeries.java
                  • ActivityGroupParallel.java
                  • Controller.java
                  • ControllerEvent.java
                  • ActivityIntegrate.java
                  • ActivityGroup.java
                  • package.html
                • WriteConfigurationOriented.java
                • ControllerActionAdapter.java
                • package-info.java
                • MoleculeActionTranslateTo.java
                • ControllerToggle.java
                • CalcVibrationalModes.java
                • ActionGroupSeries.java
                • MoleculeChildAtomAction.java
                • IntegratorActionAdapter.java
                • AtomActionRandomizeVelocity.java
                • IntegratorDimerApproach.java
                • ActionToggle.java
                • WriteConfiguration.java
                • SimulationAction.java
                • ActionGroup.java
                • AtomActionRotateBy.java
                • ResetAccumulators.java
                • BoxInflateDeformable.java
                • XYZWriter.java
                • IntegratorAction.java
                • BoxScaleMomenta.java
                • BoxRandomizeMomenta.java
                • BoxDeleteMolecules.java
                • BoxInflate.java
                • WriteConfigurationP2DLPOLY.java
                • SimulationRestart.java
                • WriteConfigurationDLPOLY.java
                • MoleculeAction.java
              • math
                • discrete
                  • FixedSumIterator.java
                  • CombinationIterator.java
                  • package-info.java
                  • PermutationIterator.java
                  • PermutationDegenerateIterator.java
                • geometry
                  • PolyhedronGeneral.java
                  • Parallelotope.java
                  • Rectangle.java
                  • Polygon.java
                  • Plane.java
                  • Hexahedron.java
                  • Rectangular.java
                  • Cube.java
                  • PolygonGeneral.java
                  • Hypersphere.java
                  • Polytope.java
                  • LineSegment.java
                  • package-info.java
                  • Point.java
                  • Polyhedron.java
                  • Sphere.java
                  • Square.java
                  • Parallelogram.java
                  • coordinate
                    • CoordinateConverter.java
                  • Shape.java
                  • Cuboid.java
                  • Circle.java
                  • Parallelepiped.java
                  • TruncatedOctahedron.java
                • function
                  • IFunction.java
                  • FunctionMultiDimensionalDifferentiable.java
                  • FunctionInvertible.java
                  • Function.java
                  • FunctionDifferentiable.java
                  • FunctionMultiDimensional.java
                  • FunctionChain.java
                • Complex.java
                • SpecialFunctions.java
                • DoubleRange.java
                • linearalgebra
                  • package-info.java
                • package-info.java
                • Quaternion.java
                • Gamma.java
                • Rational.java
                • numerical
                  • SteepestDescent.java
                  • FastFourierTransform.java
                  • LinearFit.java
                  • VirialOptimizer.java
                  • AkimaSplineSmootherDy.java
                  • ArrayReader1D.java
                  • AkimaSplineSmoother.java
                  • NewtonMinimization.java
                  • CalcGradientDifferentiable.java
                  • AkimaSplineSmootherApp.java
                  • AkimaSpline.java
                  • SineTransform.java
                  • AkimaSplineSmootherDyApp.java
                  • PadeApproximation.java
                  • AkimaSplineSmootherMain.java
                  • FiniteDifferenceDerivative.java
                  • FittingFunctionNonLinear.java
                  • PolynomialFit.java
              • tests
                • TestLJMC3D.java
                • TestLJGCMC3D.java
                • TestSWChain.java
                • TestHSMD3D.java
              • chem
                • elements
                  • Helium.java
                  • Sulfur.java
                  • Tin.java
                  • Carbon.java
                  • Iron.java
                  • Hydrogen.java
                  • Silver.java
                  • Tungsten.java
                  • Copper.java
                  • IElement.java
                  • Element.java
                  • Oxygen.java
                  • ElementSimple.java
                  • Sodium.java
                  • ElementChemical.java
                  • Chlorine.java
                  • package.html
                  • Fluorine.java
                  • Argon.java
                  • Nitrogen.java
                • electrostatics
                  • Electrostatic.java
                  • Charge.java
                  • package.html
                • models
                  • Model.java
                  • ModelChain.java
                  • package.html
                • package.html
              • spaceNd
                • VectorND.java
                • TensorND.java
              • potential
                • P2SquareWell.java
                • P2MoleculeSoftTruncatedSwitched.java
                • P2Morse.java
                • P1HardBoundary.java
                • PotentialNonAdditiveDifference.java
                • P2HardBondedList.java
                • PotentialCalculationForcePressureSum.java
                • PotentialEmul.java
                • PotentialAtomicSum.java
                • Potential1.java
                • P2SoftTruncated.java
                • P2HardAssociationConeReferenceFourSites.java
                • Potential2.java
                • P1IntraMolecular.java
                • EwaldSumMolecules.java
                • P2HydrogenHindePatkowski.java
                • P3CPSNonAdditiveHeSimplified.java
                • IPotentialAtomicMultibody.java
                • P3BondAngleDreiding.java
                • PotentialCalculationVirialSum.java
                • P3Induction.java
                • P1HardMovingBoundary.java
                • PotentialCalculationEnergySum.java
                • P2PenetrableSquareWell.java
                • PotentialGroupSoft.java
                • P1Harmonic.java
                • P2NitrogenHellmann.java
                • P3QChem.java
                • IPotentialMolecularTorque.java
                • PotentialN.java
                • P2PenetrableBond.java
                • IPotentialTorque.java
                • P2HardAssociationConeReference.java
                • PotentialCalculationPressureTensor.java
                • P4BondTorsion.java
                • P2Electrostatic.java
                • P2LennardJonesDreiding.java
                • Potential2Soft.java
                • P2Tether.java
                • P2Harmonic.java
                • P2WCA.java
                • PotentialPolarizable.java
                • IPotential0Lrc.java
                • P2SemiclassicalAtomic.java
                • P2SoftSphericalTruncated.java
                • PotentialTruncated.java
                • P2HardAssociationCone.java
                • P2EffectiveFeynmanHibbs.java
                • PotentialCalculationEnergySumBigDecimal.java
                • PotentialGroup.java
                • P2O2Bartolomei.java
                • PotentialMasterMonatomic.java
                • P2MoleculeMonatomic.java
                • PotentialHard.java
                • P2Fene.java
                • P2HardAssociationConeFourSitesSW.java
                • Potential0.java
                • P3CPSNonAdditiveHe.java
                • P2Exp6Buckingham.java
                • P2CO2EMP1.java
                • IPotential0MoleculeLrc.java
                • PotentialDLPOLY.java
                • P2CO2TraPPE.java
                • P2HardBond.java
                • P2SoftSphere.java
                • P2PenetrableSphere.java
                • P2ModifiedMorse.java
                • P2HardWrapper.java
                • P2SoftSphericalTruncatedShifted.java
                • PotentialCalculationHyperVirialSum.java
                • PotentialCalculationMolecularVirialSum.java
                • P1HydrogenMielke.java
                • Potential2SoftSphericalLS.java
                • P1IntraSimple.java
                • P3HydrogenGarberoglioMolecular.java
                • PotentialMolecularMonatomic.java
                • P1HarmonicSite.java
                • P3AdditiveQChem.java
                • P2LJDipole.java
                • P2LennardJones.java
                • IteratorDirective.java
                • P2CO2EMP2.java
                • P4BondTorsionOPLS.java
                • PotentialMolecular.java
                • P2LJQQ.java
                • P3HydrogenATM.java
                • P2HardAssociation.java
                • PotentialMasterLrc.java
                • IPotentialAtomic.java
                • PotentialArray.java
                • P2HardSphere.java
                • PotentialCalculationPhiSum.java
                • PotentialMaster.java
                • PotentialCalculationTorqueSum.java
                • P2HeSimplified.java
                • P2HardAssociationConeDoubleSites.java
                • P2HydrogenHindePatkowskiAtomic.java
                • P2DLPOLY.java
                • P3BondAngle.java
                • P3CPSNonAdditiveHeOrig.java
                • P2HardAssociationConeFourSites.java
                • P2HePCKLJS.java
                • P2SoftSphericalTruncatedSwitched.java
                • PotentialCalculationForceSum.java
                • PotentialSoft.java
                • P3NitrogenHellmannNonAdditive.java
                • P2WaterPotentialsJankowski.java
                • PotentialReactive.java
                • P2Exp6.java
                • P2HydrogenPatkowskiIso.java
                • P2SoftSphericalTruncatedForceShifted.java
                • P2TriangleWell.java
                • P2MoleculeTruncated.java
                • P3HydrogenManzhos.java
                • P2HydrogenPatkowskiAtomic.java
                • IPotential.java
                • P2HydrogenHinde.java
                • Potential0Lrc.java
                • P2ReactionFieldDipoleTruncated.java
                • P2RoughSphere.java
                • P4BondTorsionAlkaneXCCH.java
                • P2QChem.java
                • PotentialCalculation.java
                • P2QChemInterpolated.java
                • P2HardAssociationConeSW.java
                • P1HardPeriodic.java
                • PotentialCalculationMolecular.java
                • P2HSDipole.java
                • P2HardAssociationConeOneSite.java
                • P2HydrogenHindeAtomic.java
                • P1ExternalField.java
                • P2Dreiding.java
                • P1SoftBoundary.java
                • P3CPSNonAdditiveHeLessSimplified.java
                • P2CO2EMP.java
                • Potential2Spherical.java
                • P2Ideal.java
                • P2SquareWellRobust.java
                • P2SpheroPolyhedron.java
                • P2Anharmonic.java
                • Potential2HardSpherical.java
                • P2SemiclassicalMolecular.java
                • P2ReactionFieldDipole.java
                • PotentialArrayMolecular.java
                • P2LJQ.java
                • P3AxilrodTeller.java
                • P2ArgonAziz1993.java
                • PotentialArrayByType.java
                • P2HydrogenPatkowski.java
                • P2ElectrostaticWithHardCore.java
                • IPotentialMolecular.java
                • PotentialMolecularSoft.java
                • PotentialMolecularSum.java
                • Potential.java
                • P2DiscreteFeynmanHibbs.java
                • P2ArgonSlavicekEtAl2003.java
                • IPotentialMolecularSecondDerivative.java
                • EwaldSummation.java
                • P2DoubleWell.java
                • P2ArgonTangAndToennies2003.java
                • P22CLJQ.java
                • P4TorsionDreiding.java
                • Potential2SoftSpherical.java
              • nbr
                • CriterionTypesMulti.java
                • CriterionAll.java
                • molecule
                  • CriterionAdapterMolecular.java
                  • PotentialMasterNbrMolecular.java
                  • CriterionSpecies.java
                  • CriterionSpeciesPair.java
                  • CriterionAllMolecular.java
                  • NeighborCriterionMolecular.java
                  • CriterionSimpleMolecular.java
                  • package.html
                • PotentialGroupHybrid.java
                • CriterionMolecularNonAdjacent.java
                • CriterionPositionWall.java
                • CriterionTypesCombination.java
                • site
                  • Api1ASite.java
                  • AtomSite.java
                  • NeighborSiteManager.java
                  • PotentialMasterSite.java
                • CriterionSimple.java
                • CriterionInterMolecular.java
                • CriterionAdapter.java
                • CriterionTypePair.java
                • CriterionBondedSimple.java
                • PotentialMasterNbr.java
                • PotentialMasterHybrid.java
                • list
                  • NeighborListManager.java
                  • molecule
                    • NeighborCellManagerListMolecular.java
                    • NeighborListManagerSlantyMolecular.java
                    • MoleculePotentialList.java
                    • MoleculeNeighborLists.java
                    • NeighborListEventManagerMolecular.java
                    • INeighborListListenerMolecular.java
                    • NeighborListManagerMolecular.java
                    • PotentialMasterListMolecular.java
                    • package.html
                    • BoxAgentSourceCellManagerListMolecular.java
                  • INeighborListListener.java
                  • NeighborListManagerSlanty.java
                  • PotentialMasterList.java
                  • NeighborListEventManager.java
                  • BoxAgentSourceCellManagerList.java
                  • NeighborCellManagerList.java
                  • package.html
                  • AtomNeighborLists.java
                  • AtomPotentialList.java
                • PotentialGroupNbr.java
                • NeighborCriterion.java
                • CriterionNone.java
                • CriterionType.java
                • package.html
                • cell
                  • molecule
                    • MoleculesetIteratorCellular.java
                    • BoxAgentSourceCellManagerMolecular.java
                    • CellMolecular.java
                    • NeighborCellManagerMolecular.java
                    • MoleculeIteratorCell.java
                    • MpiAACell.java
                    • package.html
                    • Mpi1ACell.java
                  • AtomIteratorCell.java
                  • ApiAACell.java
                  • NeighborCellManager.java
                  • PotentialMasterCell.java
                  • Cell.java
                  • Api1ACell.java
                  • package.html
                  • BoxAgentSourceCellManager.java
                  • AtomsetIteratorCellular.java
                • CriterionMolecular.java
              • meta
                • ComponentIndex.java
                • SimulationModel.java
                • properties
                  • InstanceProperty.java
                  • Property.java
                  • AtomListProperty.java
                  • ArrayProperty.java
                  • VectorProperty.java
                  • MoleculeListProperty.java
                • DataSourceIndex.java
                • javadoc
                  • KeepSimJavadoc.java
                • annotations
                  • IgnoreProperty.java
                • WrapperIndex.java
                • Common.java
                • wrappers
                  • ObjectWrapper.java
                  • SimulationWrapper.java
                  • Wrapper.java
                • serializers
                  • VectorSerializer.java
              • integrator
                • IntegratorHard.java
                • IntegratorEventManager.java
                • IntegratorVerlet.java
                • IntegratorPT.java
                • IntegratorListenerMD.java
                • IntegratorMC.java
                • IntegratorRigidIterative.java
                • IntegratorGear4.java
                • IntegratorAnalytic.java
                • IntegratorGEMC.java
                • IntegratorConNVT.java
                • IntegratorVelocityVerletRattle.java
                • Integrator.java
                • IntegratorManagerMC.java
                • IntegratorEvent.java
                • IntegratorVelocityVerletShake.java
                • IntegratorListenerGroupSeries.java
                • IntegratorListenerAction.java
                • IntegratorListener.java
                • IntegratorMD.java
                • IntegratorBox.java
                • IntegratorVelocityVerlet.java
                • IntegratorRigidMatrixIterative.java
                • mcmove
                  • MCMoveMolecule.java
                  • MCMoveMoleculeExchange.java
                  • MCMoveTrialCompletedEvent.java
                  • MCMoveRotateMolecule3D.java
                  • MCMoveBoxSize.java
                  • MCMoveMolecular.java
                  • MCMoveInsertDeleteBiased.java
                  • MCMoveStep.java
                  • MCMoveAtom.java
                  • MCMoveOverlapListener.java
                  • MCMoveBoxStep.java
                  • MCMoveInsertDelete.java
                  • MCMoveTrialFailedEvent.java
                  • MCMoveManager.java
                  • MCMove.java
                  • MCMoveTracker.java
                  • MCMoveInsertDeleteLatticeVacancy.java
                  • MCMoveAtomInRegion.java
                  • MCMoveBox.java
                  • MCMoveSemigrand.java
                  • MCMoveRotate.java
                  • MCMoveWiggleAceticAcid.java
                  • MCMoveVolumeExchange.java
                  • MCMoveDimerRotate.java
                  • MCMoveStepTracker.java
                  • MCMoveSwapConfiguration.java
                  • MCMoveDimer.java
                  • MCMoveTrialInitiatedEvent.java
                  • MCMoveVolume.java
                  • package.html
                  • MCMoveEvent.java
                  • MCMoveInsertDeleteVacancy.java
                  • MCMoveIDBiasAction.java
                  • MCMoveStepDependent.java
                  • MCMoveTorsionAceticAcid.java
                • IntegratorGear4NPH.java
                • package.html
              • parser
                • ParserLAMMPS.java
                • ParmedStructure.java
                • ParmedParser.java
              • space2d
                • IOrientation2D.java
                • Space2D.java
                • RotationTensor2D.java
                • package-info.java
                • Orientation2D.java
                • Vector2D.java
                • Tensor2D.java
        • test
          • resources
            • etomica
              • integrationtests
              • potential
          • java
            • etomica
              • atom
                • MoleculeArrayListTest.java
                • iterator
                  • AtomIteratorArrayListAdjacentTest.java
                  • ListerMolecule.java
                  • MpiInterspeciesAATest.java
                  • Lister.java
                  • AtomIteratorBasisTest.java
                  • MpiInterspecies1ATest.java
                  • ApiBuilderTest.java
                  • IteratorTestAbstract.java
                  • MoleculeIteratorArrayListTest.java
                  • AtomIteratorArrayListTest.java
                  • MpiIntraspecies1ATest.java
                  • MpiIntraspeciesAATest.java
                  • AtomIteratorLeafAtomsTest.java
                  • MoleculeIteratorAllMoleculesTest.java
                  • MoleculeIteratorTestAbstract.java
                  • package.html
                  • MoleculeIteratorSingletTest.java
                  • AtomIteratorSingletTest.java
                  • ApiLeafAtomsTest.java
                • AtomArrayListTest.java
                • MoleculesetAction.java
              • species
                • SpeciesManagerTest.java
              • integrationtests
                • TestSnapshots.java
              • space
                • BoundaryDeformablePeriodicTest.java
              • models
                • water
                  • PNWaterGCPMTest.java
                  • P2WaterSPCETest.java
                  • P2WaterTIP4PTest.java
                  • P2WaterSPCTest.java
              • graphics
                • GraphicsSmokeTests.java
              • util
                • collections
                  • IndexMapTest.java
              • data
                • AccumulatorAverageFixedTest.java
                • AccumulatorAverageTestBase.java
                • types
                  • DataGroupTest.java
                • AccumulatorAverageCollapsingTest.java
                • meter
                  • MeterRMSDTest.java
              • space3d
                • Tensor3DTest.java
                • Vector3DTest.java
              • action
                • ActionGroupSeriesTest.java
              • math
                • discrete
                  • FixedSumIteratorTest.java
                • SpecialFunctionsTest.java
              • spaceNd
                • TensorNDTest.java
              • potential
                • EwaldSummationTest.java
              • UnitTestUtil.java
              • package.html
              • parser
                • ParmedParserTest.java
                • ParmedStructureTest.java
              • space2d
                • Tensor2DTest.java
    • etomica-graph
      • src
        • main
          • resources
            • etomica
              • graph
                • model
                  • impl
          • java
            • etomica
              • graph
                • iterators
                  • CartesianIterator.java
                  • StoredIterator.java
                  • ChainedIterator.java
                  • RangePermutator.java
                  • IsomorphismPrefilteredPartitionedIterator.java
                  • IteratorWrapper.java
                  • DefaultIterator.java
                  • CartesianPermutator.java
                  • filters
                    • FieldNodeCount.java
                    • LocalFilter.java
                    • GlobalFilter.java
                    • IdenticalGraphFilter.java
                    • PropertyFilter.java
                    • IsomorphismFilter.java
                  • PartitionedIterator.java
                  • DefaultPermutator.java
                  • FixedEdgeCountIterator.java
                  • EdgelessIterator.java
                  • IteratorToSet.java
                • operations
                  • DropOrphanNodes.java
                  • DifByConstant.java
                  • DifByEdge.java
                  • Sub.java
                  • Union.java
                  • Int.java
                  • IntParameters.java
                  • MulFlexible.java
                  • Parameters.java
                  • Decorate.java
                  • ComponentSubst.java
                  • UnaryChain.java
                  • RelabelParameters.java
                  • MaxIsomorph.java
                  • MulScalarParameters.java
                  • GraphOp.java
                  • PowParameters.java
                  • NCopy.java
                  • IsoFree.java
                  • RelabelWertheim.java
                  • ReeHoover.java
                  • Delete.java
                  • Conv.java
                  • Binary.java
                  • Unfactor.java
                  • ConvParameters.java
                  • Mul.java
                  • MulUnion.java
                  • Exclude.java
                  • SplitOne.java
                  • DeleteEdgeParameters.java
                  • SplitParameters.java
                  • SplitOneBiconnected.java
                  • BiComponentSubst.java
                  • DecorateWertheim2SiteRho.java
                  • ExcludeParameters.java
                  • DifByNode.java
                  • DeleteEdge.java
                  • MulScalar.java
                  • PCopy.java
                  • DecorateWertheimNaphthalene2Rho.java
                  • IdenticalFree.java
                  • SetPropertyFilter.java
                  • GraphOpMaxRoot.java
                  • Unary.java
                  • MaxIsomorphWertheim.java
                  • CombineABSite.java
                  • DecorateWertheim3SiteRho.java
                  • FactorOnce.java
                  • DecorateWertheim2Site.java
                  • AllIsomorphs.java
                  • Pow.java
                  • Sum.java
                  • ExpParameters.java
                  • Split.java
                  • GraphExtract.java
                  • Factor.java
                  • Exp.java
                  • DifParameters.java
                  • Relabel.java
                  • SplitGraph.java
                • viewer
                  • GraphMap.java
                  • ClusterViewer.java
                • util
                  • GraphNumber.java
                • property
                  • HasArticulationPoint.java
                  • IsFFT.java
                  • Property.java
                  • HasSimpleArticulationPoint.java
                  • HasNodalPoint.java
                  • NumFieldNodes.java
                  • HasEdgeCount.java
                  • HasArticulationPair.java
                  • FFTDecomposition.java
                  • FactorFFT.java
                  • FieldNodeCountMax.java
                  • NumRootNodes.java
                  • IsConnected.java
                  • IsBiconnected.java
                  • HasNoRootEdge.java
                  • IsArticulationPair.java
                  • IsArticulationPoint.java
                • engine
                  • impl
                    • EnvironmentImpl.java
                    • ParserImpl.java
                    • CommandVariableValueImpl.java
                    • BinaryOpByteImpl.java
                    • ConstructorColoredImpl.java
                    • ConstructorMonoImpl.java
                    • UnaryOpImpl.java
                    • CommandImpl.java
                    • AssignmentImpl.java
                    • PropertyImpl.java
                    • ConstructorImpl.java
                    • BinaryOpImpl.java
                    • UnaryOpTwoByteImpl.java
                    • UnaryOpByteMapImpl.java
                    • UnaryOpThreeColorImpl.java
                    • UnaryOpByteImpl.java
                    • CommandValueImpl.java
                    • UnaryOpColorImpl.java
                    • VariableImpl.java
                    • CommandPropertyValueImpl.java
                    • ValueImpl.java
                    • CommandVariableImpl.java
                  • Viewer.java
                  • Parser.java
                  • ConsoleContainer.java
                  • Console.java
                  • ConsoleReader.java
                  • Environment.java
                  • Launcher.java
                  • Interpreter.java
                  • ConsoleUI.java
                • traversal
                  • DepthFirst.java
                  • CVisitor.java
                  • BiconectedNodalPoint.java
                  • TraversalVisitor.java
                  • Biconnected.java
                  • BCVisitor.java
                  • AbstractTraversal.java
                  • BreadthFirst.java
                  • BitmapUtils.java
                  • Traversal.java
                • view
                  • rasterizer
                    • SVGConverterController.java
                    • SVGConverterDocumentSource.java
                    • SVGConverter.java
                    • DefaultSVGConverterController.java
                    • SVGConverterFileSource.java
                    • SVGConverterException.java
                    • Main.java
                    • DestinationType.java
                    • Messages.java
                    • SVGConverterURLSource.java
                    • SVGConverterSource.java
                • model
                  • comparators
                    • ComparatorNumRootNodes.java
                    • ComparatorNumNodes.java
                    • ComparatorBiConnected.java
                    • ComparatorNumFieldNodes.java
                    • ComparatorChain.java
                    • ComparatorNumEdges.java
                    • ComparatorNodeColors.java
                  • NodeVisitor.java
                  • impl
                    • EdgeImpl.java
                    • GraphImpl.java
                    • MetadataImpl.java
                    • CoefficientImpl.java
                    • AbstractBitmap.java
                    • BitmapOfLongVector.java
                    • BitmapOfLong.java
                    • NodeImpl.java
                  • Bitmap.java
                  • GraphIterator.java
                  • GraphList.java
                  • GraphFactory.java
                  • Edge.java
                  • EdgeVisitor.java
                  • Metadata.java
                  • Node.java
                  • Graph.java
                  • Coefficient.java
                  • BitmapFactory.java
                  • Permutator.java
                • isomorphism
                  • NodePair.java
                  • VFSearchState.java
                  • SearchState.java
                  • Match.java
                  • AbstractSearchState.java
                  • VF2SearchState.java
                  • UllmanSearchState.java
        • test
          • java
            • etomica
              • graph
                • GraphIteratorTest.java
                • EdgeCountFilterTest.java
                • DefaultIteratorTest.java
                • PartitionedIteratorTest.java
                • StoredIteratorTest.java
                • CartesianPermutatorTest.java
                • engine
                  • ParserTest.java
                • IsomorphismFilterTest.java
                • FixedEdgeCountIteratorTest.java
                • ConnectivityTest.java
                • DeleteTest.java
                • EdgelessIteratorTest.java
                • CustomTestCase.java
    • config
      • xsl
    • publish_javadoc.sh
    • LICENSE-MPL
    • benchmarks
      • src
        • main
          • java
            • etomica
              • space
                • BenchVector3D.java
              • simulation
                • BenchSimSWChain.java
                • BenchSimHSMD3D.java
                • BenchSimLJGCMC3D.java
                • BenchSimDCVGCMD.java
                • BenchSimSurfacetensionLJMC.java
                • BenchSimLJMC3D.java
              • Main.java
              • math
                • LnFactorialBenchmark.java
                • ErfcBenchmark.java
                • FactorialBenchmark.java
      • build.gradle
    • build.gradle
    • etomica-server
      • src
        • main
          • java
            • etomica
              • server
                • health
                  • BasicHealthCheck.java
                • EtomicaServerConfig.java
                • dao
                  • DataStreamStore.java
                  • SimulationStore.java
                • resources
                  • ConfigurationWebsocket.java
                  • PropertiesResource.java
                  • data
                    • DataStreamWebsocket.java
                    • DataStreamResource.java
                  • EchoServer.java
                  • ControlResource.java
                  • SimulationResource.java
                  • SimulationsIndexResource.java
                • representations
                  • PropertyUpdate.java
                  • StatusAction.java
                  • DataAndInfo.java
                  • ConstructionInfo.java
                  • SimClassInfo.java
                  • ConfigurationUpdate.java
                  • ConstructionParams.java
                  • SimulationConstructor.java
                • EtomicaServer.java
                • core
                  • construction
                    • Construction.java
                • serializers
                  • WrapperSerializer.java
                  • DataSerializer.java
                  • PropertySerializer.java
      • config
      • build.gradle
    • etomica-modules
      • src
        • main
          • java
            • etomica
              • modules
                • rosmosis
                  • IPotentialCalculationWallForce.java
                  • ConfigurationMembraneWater.java
                  • ReverseOsmosisGraphic.java
                  • MeterFlux.java
                  • PotentialCalculationForceSumWallForce.java
                  • ReverseOsmosisWater.java
                  • ReverseOsmosisWaterGraphic.java
                  • ReverseOsmosis.java
                  • MeterOsmoticPressure.java
                  • PotentialCalculationTorqueSumWallForce.java
                  • ConfigurationMembrane.java
                  • P1Tether.java
                • statistics
                  • DataAccPusher.java
                  • AccumulatorFactory.java
                  • HistoryStatistics.java
                  • DataAccCorrectedPusher.java
                  • DataProcessorBounds.java
                  • AccumulatorMimicMu.java
                  • StatisticsMCGraphic.java
                  • DataAccSamplesPusher.java
                  • DataCollector.java
                  • DataProcessorMu.java
                  • DataAccDiffCorrectedPusher.java
                  • DataAccDifficultyPusher.java
                • insertion
                  • InsertionGraphic.java
                  • Insertion.java
                • multiharmonic
                  • overlap
                    • MultiharmonicMC.java
                    • MultiharmonicGraphicMC.java
                    • DataOverlapCaching.java
                    • AccumulatorOverlapAverageUa2.java
                  • mbar
                    • MultiharmonicMC.java
                    • MeterMBAR.java
                    • MultiharmonicGraphicMC.java
                  • MCMoveMultiHarmonic.java
                  • MultiharmonicMC.java
                  • DataProcessorBounds.java
                  • MultiharmonicGraphicMC.java
                  • MultiharmonicGraphic.java
                  • DataProcessorDyDLnx.java
                  • DataProcessorVar.java
                  • Multiharmonic.java
                  • MeterFreeEnergy.java
                  • umbrella
                    • MultiharmonicMC.java
                    • MultiharmonicGraphicMC.java
                    • MeterUmbrella.java
                  • DataProcessorBias.java
                • materialfracture
                  • P1Tension.java
                  • StrainColorScheme.java
                  • MeterElongation.java
                  • MeterStress.java
                  • MeterLoad.java
                  • MeterStrain.java
                  • MaterialFractureGraphic.java
                  • MaterialFracture.java
                  • PotentialCalculationForceStress.java
                • pistoncylinder
                  • PistonCylinder.java
                  • MeterRDFCylinder.java
                  • ApiFilteredCylinder.java
                  • IntegratorHardPiston.java
                  • ModifierPistonPressure.java
                  • PistonPlane.java
                  • DataSourceWallPressure.java
                  • PistonCylinderGraphic.java
                  • ActionPistonUpdate.java
                  • BoundaryPistonCylinder.java
                • render
                  • RenderMD.java
                  • RenderMDGraphic.java
                  • ParseObj.java
                • adsorption
                  • VEOS3SW.java
                  • IntegratorHybrid.java
                  • MeterExcessAdsorbed.java
                  • ModifierPMu.java
                  • P1Wall.java
                  • DataSourceDensityFunction.java
                  • AdsorptionGraphic.java
                  • EOSSWPatel.java
                  • MeterProfileByVolumeAdsorption.java
                  • MyMCMove.java
                  • EOSSW.java
                  • Adsorption.java
                • joulethomson
                  • JouleThomsonSim.java
                  • IntegratorJT.java
                  • JouleThomson.java
                • chainequilibrium
                  • MolecularWeightAvg2.java
                  • ConfigurationLatticeRandom.java
                  • ChainEquilibriumGraphic.java
                  • ChainEquilibriumSim.java
                  • MeterConversion.java
                  • P2SquareWellBonded.java
                  • FreeRadicalPolymerizationGraphic.java
                  • AtomFilterChainLength.java
                  • ColorSchemeStepWise.java
                  • ConfigurationLatticeFreeRadical.java
                  • MolecularWeightAvg.java
                  • MeterChainLength.java
                  • P2SquareWellRadical.java
                  • ColorSchemeRadical.java
                  • FreeRadicalPolymerizationSim.java
                • ensembles
                  • LJMC.java
                  • LJMCGraphic.java
                • dcvgcmd
                  • SpeciesTube.java
                  • MeterFlux.java
                  • P1WCAWall.java
                  • IntegratorDCVGCMD.java
                  • ConformationTube.java
                  • DCVGCMDGraphic.java
                  • P1WCAPorousWall.java
                  • MyMCMove.java
                  • DCVGCMD.java
                  • ConfigurationLatticeTube.java
                • ljmd
                  • LjmdGraphic.java
                  • Ljmd.java
                • crystalviewer
                  • ColorSchemePlane.java
                  • CrystalViewer.java
                  • ClipPlaneEditor.java
                  • LatticeEditor.java
                • rheology
                  • MeterViscosity.java
                  • MeterNormalStress.java
                  • ConformationPolymer.java
                  • RheologyGraphic.java
                  • IntegratorPolymer.java
                  • MeterEndToEnd.java
                  • SimulationRheology.java
                • vle
                  • LJQB2.java
                  • VirialLJQB2.java
                  • MCMoveVolumeExchangeVLE.java
                  • VLE.java
                  • MCMoveMoleculeExchangeVLE.java
                  • VLESim.java
                  • MeterPressure2.java
                  • DeviceThermoSliderGEMC.java
                  • B2Fit.java
                • catalysis
                  • InteractionTracker.java
                  • CatalysisGraphic.java
                  • DataSourceWallPressureCatalysis.java
                  • P2SquareWellSurface.java
                  • Catalysis.java
                  • MeterDensityO2.java
                  • ReactionManagerCO.java
                  • MeterDensityCO.java
                  • MeterDensityCO2.java
                  • ConfigurationCatalysis.java
                  • ColorSchemeRadical.java
                  • P2SquareWellBondingCO.java
                  • P2SquareWellBonding.java
                • clustergenerator
                  • ClusterPanel.java
                  • MyApplet.java
                  • Plot.java
                • entropylottery
                  • ConfigurationZero.java
                  • MCMoveAtomAdjacent.java
                  • EntropyProcessor.java
                  • MeterEntropy.java
                  • DataSourceProbabilityDensity.java
                  • EntropyLottery.java
                  • DisplayBoxCanvas1DBins.java
                  • EntropyLotteryGraphic.java
                  • ModifierDimensions.java
                • sam
                  • SamGraphic.java
                  • MeterWallPressure.java
                  • IntegratorVelocityVerletSAM.java
                  • ConfigurationSAM.java
                  • PotentialCalculationForceSumWall.java
                  • P1WCAWall.java
                  • CriterionTether3.java
                  • Sam.java
                  • P1Sinusoidal.java
                  • SpeciesAlkaneThiol.java
                  • WallPlane.java
                  • MeterTilt.java
                • swmd
                  • Swmd.java
                  • SwmdGraphic.java
                • osmosis
                  • Osmosis.java
                  • OsmosisSim.java
                  • MeterOsmoticPressure.java
                  • P1HardWall.java
                • reactionequilibrium
                  • P2SquareWellBonded.java
                  • ReactionEquilibrium.java
                  • MeterDimerFraction.java
                  • ReactionEquilibriumGraphic.java
                • colloid
                  • MeterEnd2End.java
                  • P1Wall.java
                  • P2SquareWellMonomer.java
                  • NeighborListManagerColloid.java
                  • ColloidGraphic.java
                  • ConfigurationColloid.java
                  • ColloidSim.java
                  • P2HardSphereMC.java
                • droplet
                  • DropletGraphic.java
                  • ColorSchemeDropletSurface.java
                  • AtomFilterLiquid.java
                  • MeterDeformation.java
                  • DropletAtomic.java
                  • AtomFilterLiquidAtomic.java
                  • IntegratorDroplet.java
                  • P2Cohesion.java
                  • ConfigurationDroplet.java
                  • Droplet.java
                  • EllipseDisplayAction.java
                  • P1Smash.java
                  • ColorSchemeLiquidVapor.java
                  • DropletAtomicGraphic.java
                • mu
                  • P2SquareWellOneSide.java
                  • DataSourceWallPressureMu.java
                  • MeterDensitySides.java
                  • P1MagicWall.java
                  • MuGraphic.java
                  • Mu.java
                • interfacial
                  • DataSourceTensorVirialHardProfile.java
                  • DataProcessorInterfacialTensionProfile.java
                  • FitTanh.java
                  • InterfacialSWGraphic.java
                  • MeterOrientation.java
                  • InterfacialSW.java
        • test
          • java
            • etomica
              • crystalviewer
                • BLCPrimitiveHexagonalLatticePlaneTest.java
                • BLCPrimitiveMonoclinicLatticePlaneTest.java
                • BLCPrimitiveOrthorhombicLatticePlaneTest.java
                • BLCPrimitiveTriclinicLatticePlaneTest.java
                • LatticePlaneTestUtility.java
                • LatticeCubicSimpleLatticePlaneTest.java
                • BLCPrimitiveTetragonalLatticePlaneTest.java
    • README.md
    • benchmark.sh
    • settings.gradle
    • .gitignore
    • etomica-graphics3D
      • src
        • main
          • java
            • g3dsys
              • images
                • Line.java
                • Figure.java
                • ImageShell.java
                • Ellipse3D.java
                • Triangle.java
                • Ellipse.java
                • Axes.java
                • Bond.java
                • Ball.java
                • Box.java
              • control
                • FigureManager.java
                • G3DPanel.java
                • MouseManager.java
                • TransformManager.java
                • G3DSys.java
                • IndexIterator.java
                • KeyboardControl.java
            • org
              • jmol
                • script
                  • Token.java
                  • ScriptVariableInt.java
                  • ScriptVariable.java
                • viewer
                  • JmolConstants.java
                • constant
                  • EnumPalette.java
                  • StaticConstants.java
                  • EnumVdw.java
                  • EnumStereoMode.java
                • api
                  • ApiPlatform.java
                • util
                  • BitSetUtil.java
                  • Escape.java
                  • StringXBuilder.java
                  • AxisAngle4f.java
                  • Point4f.java
                  • Hermite.java
                  • Parser.java
                  • Elements.java
                  • JmolFont.java
                  • MeshSurface.java
                  • Int2IntHash.java
                  • TextFormat.java
                  • Normix.java
                  • ArrayUtil.java
                  • Shader.java
                  • Vector3f.java
                  • BitSet.java
                  • Point3f.java
                  • Measure.java
                  • Tuple3f.java
                  • Quadric.java
                  • Point3fi.java
                  • DefaultLogger.java
                  • Matrix4f.java
                  • ColorUtil.java
                  • Rgb16.java
                  • Quaternion.java
                  • Tuple4f.java
                  • GData.java
                  • Logger.java
                  • Geodesic.java
                  • Colix.java
                  • BoxInfo.java
                  • LoggerInterface.java
                  • Point3i.java
                  • Matrix3f.java
                  • TriangleData.java
                  • Eigen.java
                  • Tuple3i.java
                • awt
                  • Image.java
                  • Platform.java
                  • Display.java
                  • Font.java
                • g3d
                  • Pixelator.java
                  • TriangleRenderer.java
                  • CylinderRenderer.java
                  • TextSorter.java
                  • LineRenderer.java
                  • TextRenderer.java
                  • HermiteRenderer.java
                  • Graphics3D.java
                  • TextString.java
                  • ImageRenderer.java
                  • SphereRenderer.java
                  • CircleRenderer.java
                  • PixelatorShaded.java
                  • Platform3D.java
                • LICENSE.txt
        • test