Hierarchy For Package etomica.normalmode

Package Hierarchies:

• All Packages

Class Hierarchy

• java.lang.Object
  • etomica.normalmode.ArrayA2B
  • etomica.normalmode.ArrayB2A
  • etomica.normalmode.ArrayReader1D
  • etomica.normalmode.ArrayReader2D
  • etomica.lattice.crystal.Basis (implements java.io.Serializable)
    • etomica.normalmode.BasisBigCell
  • etomica.normalmode.CalcHarmonicA
  • etomica.normalmode.CalcJacobian
  • etomica.graphics.ColorScheme
    • etomica.normalmode.HSNPT.ColorSchemeDisplacement
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • etomica.normalmode.SoftSphereSolidEOSCalculator (implements java.beans.PropertyChangeListener)
      • java.awt.Panel (implements javax.accessibility.Accessible)
        • java.applet.Applet
          • javax.swing.JApplet (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer)
            • etomica.normalmode.HTTPSoftSphereApplet.Applet
            • etomica.normalmode.NormalModeAnalysisDisplay1D.Applet
            • etomica.normalmode.NormalModeAnalysisDisplay1DGraphic.Applet
            • etomica.normalmode.NormalModeAnalysisDisplay2DGraphic.Applet
            • etomica.normalmode.NormalModeAnalysisDisplay3D.Applet
            • etomica.normalmode.NormalModeAnalysisDisplay3DGraphic.Applet
            • etomica.normalmode.SimLJVacancy.Applet
  • etomica.normalmode.ConformationHSDimer (implements etomica.config.IConformationOriented, java.io.Serializable)
  • etomica.normalmode.CoordinateDefinition
    • etomica.normalmode.CoordinateDefinitionLeaf (implements java.io.Serializable)
      • etomica.normalmode.CoordinateDefinitionLeafSuperBox
    • etomica.normalmode.CoordinateDefinitionMolecule (implements java.io.Serializable)
      • etomica.normalmode.CoordinateDefinitionHSDimer (implements java.io.Serializable)
    • etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation (implements java.io.Serializable)
  • etomica.normalmode.CoordinateDefinition.BasisCell (implements java.io.Serializable)
  • etomica.normalmode.CoordinateDefinition.SiteSource (implements etomica.atom.AtomLeafAgentManager.AgentSource<E>)
  • etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource (implements etomica.molecule.MoleculeAgentManager.MoleculeAgentSource<E>, java.io.Serializable)
  • etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource (implements etomica.molecule.MoleculeAgentManager.MoleculeAgentSource<E>, java.io.Serializable)
  • etomica.data.DataProcessor (implements etomica.data.DataPipe)
    • etomica.normalmode.BoltzmannProcessor
    • etomica.normalmode.DataProcessorBoltzmannFactor
    • etomica.normalmode.DataProcessorSum
  • etomica.normalmode.DataSourceFE (implements etomica.data.DataSourceIndependent, etomica.data.IDataSource)
  • etomica.normalmode.DataSourceFEHistogram (implements etomica.data.DataSourceIndependent, etomica.data.IDataSource)
  • etomica.normalmode.DataSourceImposedFEFit (implements etomica.data.DataSourceIndependent, etomica.data.IDataSource)
  • etomica.normalmode.DataSourceImposedFEHistogram (implements etomica.data.DataSourceIndependent, etomica.data.IDataSource)
  • etomica.normalmode.DataSourcePMu (implements etomica.data.DataSourceIndependent, etomica.data.IDataSource)
  • etomica.normalmode.DataSourcePN (implements etomica.data.DataSourceIndependent, etomica.data.IDataSource)
  • etomica.data.DataSourceScalar (implements etomica.data.IDataSource)
    • etomica.normalmode.DataSourceAvgPressure
    • etomica.normalmode.DataSourceAvgPressure2
    • etomica.normalmode.DataSourceMuRoot
    • etomica.normalmode.DataSourceMuRoot.DataSourceMuRootDPressure
    • etomica.normalmode.DataSourceMuRoot.DataSourceMuRootDU
    • etomica.normalmode.DataSourceMuRoot.DataSourceMuRootPressure
    • etomica.normalmode.DataSourceMuRoot.DataSourceMuRootVacancyConcentration
    • etomica.normalmode.DataSourceMuRoot1
    • etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootPressure
    • etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootVacancyConcentration
    • etomica.normalmode.DataSourceMuRootPMatch
    • etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootPressure
    • etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration
    • etomica.normalmode.MeterAPIPotentialEnergy
    • etomica.normalmode.MeterDisplacementMoleculeRMS
    • etomica.normalmode.MeterDisplacementRMS
    • etomica.normalmode.MeterHarmonicCoordinate
    • etomica.normalmode.MeterHarmonicEnergy
    • etomica.normalmode.MeterHarmonicEnergyFromMove
    • etomica.normalmode.MeterJacobian
    • etomica.normalmode.MeterMaxExpansion
    • etomica.normalmode.MeterPhiDeviation
    • etomica.data.meter.MeterPotentialEnergy
      • etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
      • etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
      • etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
      • etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
    • etomica.normalmode.MeterPressureSuperBox
    • etomica.normalmode.MeterThetaDeviation
    • etomica.normalmode.SimOverlapLJModule.MeterPotentialEnergyDifference
  • etomica.graphics.Device
    • etomica.normalmode.DeviceCellNum3DSlider
    • etomica.normalmode.DeviceCellNumXYSlider
    • etomica.normalmode.DeviceEigenvaluesSlider
    • etomica.normalmode.DeviceWaveVectorSlider
  • etomica.normalmode.HarmonicCrystal
  • etomica.normalmode.HarmonicCrystalSoftSphereBCC
  • etomica.normalmode.HarmonicCrystalSoftSphereFCC
  • etomica.normalmode.HarmonicCrystalSoftSphereHCP
  • etomica.normalmode.HarmonicCrystalSsFccNxy
  • etomica.normalmode.HessianFromFile
  • etomica.normalmode.HSNPT.ActionSummer (implements etomica.atom.AtomLeafAgentManager.AgentSource<E>, etomica.action.IAction)
  • etomica.normalmode.HSNPT.MyAgent
  • etomica.integrator.Integrator
    • etomica.integrator.IntegratorBox
      • etomica.integrator.IntegratorMD (implements etomica.box.BoxEventListener)
        • etomica.integrator.IntegratorHard (implements etomica.atom.AtomLeafAgentManager.AgentSource<E>, etomica.nbr.list.INeighborListListener)
          • etomica.normalmode.IntegratorHardMDMC
        • etomica.normalmode.IntegratorHarmonic
  • etomica.normalmode.LatticeSumMolecularCrystal
  • etomica.integrator.mcmove.MCMove
    • etomica.integrator.mcmove.MCMoveBox
      • etomica.integrator.mcmove.MCMoveBoxStep (implements etomica.integrator.mcmove.MCMoveStepDependent)
        • etomica.normalmode.MCMoveAtomCoupled
        • etomica.normalmode.MCMoveAtomCoupledBennet
        • etomica.normalmode.MCMoveAtomCoupledUmbrella
        • etomica.normalmode.MCMoveAtomSuperBox
        • etomica.normalmode.MCMoveHarmonicStep
        • etomica.integrator.mcmove.MCMoveMolecule (implements etomica.integrator.mcmove.MCMoveMolecular)
          • etomica.integrator.mcmove.MCMoveRotateMolecule3D
            • etomica.normalmode.MCMoveRotateMoleculePhiTheta
        • etomica.normalmode.MCMoveMoleculeCoupled
        • etomica.normalmode.MCMovePhaseAngle
        • etomica.normalmode.MCMoveSingleMode
        • etomica.normalmode.MCMoveVolumeMonoclinic
        • etomica.normalmode.MCMoveVolumeMonoclinicAngle
        • etomica.normalmode.MCMoveVolumeMonoclinicScaled
        • etomica.normalmode.MCMoveVolumeSolid
        • etomica.normalmode.MCMoveVolumeSolidNPTMolecular
          • etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
        • etomica.normalmode.MCMoveWV
      • etomica.normalmode.MCMoveEinsteinCrystal
      • etomica.normalmode.MCMoveHarmonic
        • etomica.normalmode.MCMoveHarmonicEin
  • etomica.normalmode.MeterAtomicDisplacement (implements etomica.data.DataSourceIndependent, etomica.action.IAction, etomica.data.IDataSource)
  • etomica.normalmode.MeterBoltzmann (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterBoltzmannHarmonic (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterBoltzmannHTTP (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterBoltzmannTarget (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterDADB (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterDDP (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterDirectSamplingHarmonic (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterDirectSamplingTarget (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterDP (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterHarmonicSingleEnergy (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterNormalMode (implements etomica.action.IAction, etomica.data.IDataSource, java.io.Serializable)
  • etomica.normalmode.MeterOverlapSwitch (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterPlaneSlip (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterSamplingHarmonic (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterSamplingTarget (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterSolidDA (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterSolidDACut (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterSolidMirror (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterSolidProps (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterSolidPropsLJ (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterTargetTP (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterTilt (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterTiltHistogram (implements etomica.data.DataSourceIndependent, etomica.action.IAction, etomica.data.IDataSource)
  • etomica.normalmode.MeterTiltRotation (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterTiltRotationHistogram (implements etomica.action.IAction, etomica.data.IDataSource)
  • etomica.normalmode.MeterTiltRotationStdev (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkBennetHarmonic (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkBennetTarget (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkHarmonicBennet (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkHarmonicPhaseSpace (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkHarmonicTargetandReweighting (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkHarmonicUmbrella (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkTargetBennet (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkTargetHarmonicandReweighting (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkTargetPhaseSpace (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkTargetUmbrella (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkUmbrellaHarmonic (implements etomica.data.IDataSource)
  • etomica.normalmode.MeterWorkUmbrellaTarget (implements etomica.data.IDataSource)
  • etomica.normalmode.ModifierCells3D (implements etomica.modifier.Modifier, java.io.Serializable)
  • etomica.normalmode.ModifierXCells2D (implements etomica.modifier.Modifier, java.io.Serializable)
  • etomica.normalmode.ModifierYCells2D (implements etomica.modifier.Modifier, java.io.Serializable)
  • etomica.normalmode.NormalModeEigenGetter
  • etomica.normalmode.NormalModes1DHR (implements etomica.normalmode.NormalModes)
  • etomica.normalmode.NormalModes2D (implements etomica.normalmode.NormalModes)
  • etomica.normalmode.NormalModes3D (implements etomica.normalmode.NormalModes)
  • etomica.normalmode.NormalModesFromFile (implements etomica.normalmode.NormalModes)
  • etomica.normalmode.NormalModesMolecular (implements etomica.normalmode.NormalModes)
  • etomica.normalmode.NormalModesPotential (implements etomica.normalmode.NormalModes)
  • etomica.normalmode.NormalModesSoftSpherical (implements etomica.normalmode.NormalModes)
  • etomica.normalmode.NormalModesVariable
  • etomica.normalmode.P1ConstraintNbr (implements etomica.potential.IPotentialAtomic)
  • etomica.normalmode.P1ConstraintNbrHcp (implements etomica.potential.IPotentialAtomic)
  • etomica.util.ParameterBase
    • etomica.normalmode.HarmonicCrystalSsFccNxy.Params
    • etomica.normalmode.HSDimerNPT.HSMD3DParameters
    • etomica.normalmode.HSNPT.HSMD3DParameters
    • etomica.normalmode.HTTPSoftSphereApplet.SimOverlapTPSSParams
    • etomica.normalmode.LJVacancyMin.SimOverlapParam
    • etomica.normalmode.MinimizeHCP.SimOverlapParam
    • etomica.normalmode.SimBennet.SimBennetParam
    • etomica.normalmode.SimEinStep1.SimOverlapParam
    • etomica.normalmode.SimEinStep1HCP.SimOverlapParam
    • etomica.normalmode.SimEinStep2.SimOverlapParam
    • etomica.normalmode.SimEinStep2HCP.SimOverlapParam
    • etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
    • etomica.normalmode.SimHSMDVacancy.HSMDVParams
    • etomica.normalmode.SimLJHTTISuper.SimOverlapParam
    • etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
    • etomica.normalmode.SimLJHTTISuperHCP2.SimOverlapParam
    • etomica.normalmode.SimLJHTTISuperSFMD.SimOverlapParam
    • etomica.normalmode.SimLJVacancy.LJParams
    • etomica.normalmode.SimOverlap.SimOverlapParam
    • etomica.normalmode.SimOverlapLJ.SimOverlapParam
    • etomica.normalmode.SimOverlapLJModule.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
    • etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
    • etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
    • etomica.normalmode.SimTargetUmbrella.SimBennetParam
    • etomica.normalmode.SimUmbrella.SimBennetParam
    • etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
  • etomica.potential.Potential (implements etomica.potential.IPotentialAtomic)
    • etomica.potential.Potential1
      • etomica.normalmode.P1Constraint
    • etomica.potential.Potential2
      • etomica.normalmode.P2XOrder (implements etomica.potential.Potential2Spherical, etomica.potential.PotentialHard)
  • etomica.normalmode.PotentialCalculationEFSSP (implements etomica.potential.PotentialCalculation)
  • etomica.normalmode.PotentialCalculationLJSP (implements etomica.potential.PotentialCalculation)
  • etomica.normalmode.PotentialCalculationSolidSuper (implements etomica.potential.PotentialCalculation)
  • etomica.normalmode.PotentialCalculationSolidSuperCut (implements etomica.potential.PotentialCalculation)
    • etomica.normalmode.PotentialCalculationSolidSuperCutLS
  • etomica.normalmode.SimOverlapLJModule
  • etomica.normalmode.SimOverlapLJModule.APIPotentialReference (implements etomica.normalmode.IAPIPotential)
  • etomica.normalmode.SimOverlapLJModule.APIPotentialTarget (implements etomica.normalmode.IAPIPotential)
  • etomica.normalmode.SimOverlapModule
  • etomica.simulation.Simulation
    • etomica.normalmode.HessianDB
    • etomica.normalmode.HSDimerNPT
    • etomica.normalmode.HSNPT
    • etomica.normalmode.HTTPSoftSphereSim
    • etomica.normalmode.LJVacancyMin
    • etomica.normalmode.MinimizeHCP
    • etomica.normalmode.NormalModeAnalysisDisplay1D
    • etomica.normalmode.NormalModeAnalysisDisplay2D
    • etomica.normalmode.NormalModeAnalysisDisplay3D
    • etomica.normalmode.SimBennet
    • etomica.normalmode.SimCalcJ
    • etomica.normalmode.SimCalcS
    • etomica.normalmode.SimCalcSLJ
    • etomica.normalmode.SimCalcSMorse
    • etomica.normalmode.SimCalcSSoftSphere2D
    • etomica.normalmode.SimCalcSSoftSphereFCC
    • etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
    • etomica.normalmode.SimEinStep1
    • etomica.normalmode.SimEinStep1HCP
    • etomica.normalmode.SimEinStep2
    • etomica.normalmode.SimEinStep2HCP
    • etomica.normalmode.SimFluidSoftSphere
    • etomica.normalmode.SimHarmonic
    • etomica.normalmode.SimHarmonicUmbrella
    • etomica.normalmode.SimHSMDVacancy
    • etomica.normalmode.SimLJHTTISuper
    • etomica.normalmode.SimLJHTTISuperHCP
    • etomica.normalmode.SimLJHTTISuperHCP2
    • etomica.normalmode.SimLJHTTISuperSFMD
    • etomica.normalmode.SimLJVacancy
    • etomica.normalmode.SimModesJ
    • etomica.normalmode.SimOverlap
    • etomica.normalmode.SimOverlapLJ
    • etomica.normalmode.SimOverlapSoftSphere
    • etomica.normalmode.SimOverlapSoftSphereDP
    • etomica.normalmode.SimOverlapSoftSphereEin
    • etomica.normalmode.SimOverlapSoftSphereEinHarm
    • etomica.normalmode.SimOverlapSoftSphereHCP
    • etomica.normalmode.SimOverlapSoftSphereReweighting
    • etomica.normalmode.SimOverlapSoftSphereSoftness
    • etomica.normalmode.SimOverlapSoftSphereSuperBox
    • etomica.normalmode.SimOverlapSoftSphereTP
    • etomica.normalmode.SimOverlapSoftSphereTPHCP
    • etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
    • etomica.normalmode.SimOverlapSSnxy
    • etomica.normalmode.SimTarget
    • etomica.normalmode.SimTargetUmbrella
    • etomica.normalmode.SimUmbrella
    • etomica.normalmode.SimUmbrellaSoftSphere
  • etomica.graphics.SimulationGraphic (implements etomica.simulation.SimulationContainer)
    • etomica.normalmode.HTTPSoftSphereApplet
    • etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
    • etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
    • etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
  • etomica.normalmode.SoftSphereSolidEOS
  • etomica.normalmode.SpeciesHSDimer
  • etomica.normalmode.WaveVectorFactory1D (implements java.io.Serializable, etomica.normalmode.WaveVectorFactory)
  • etomica.normalmode.WaveVectorFactory2D (implements java.io.Serializable, etomica.normalmode.WaveVectorFactory)
  • etomica.normalmode.WaveVectorFactoryFcc (implements java.io.Serializable, etomica.normalmode.WaveVectorFactory)
  • etomica.normalmode.WaveVectorFactoryFromFile (implements etomica.normalmode.WaveVectorFactory)
  • etomica.normalmode.WaveVectorFactorySimple (implements java.io.Serializable, etomica.normalmode.WaveVectorFactory)
    • etomica.normalmode.WaveVectorFactorySuperBox
  • etomica.normalmode.WriteS (implements etomica.action.IAction)

Interface Hierarchy

• etomica.normalmode.CoordinateDefinitionHSDimer.IntegerFunction
• etomica.normalmode.IAPIPotential
• etomica.normalmode.LatticeSumMolecularCrystal.AtomicTensorAtomicPair
• etomica.normalmode.NormalModes
• etomica.normalmode.WaveVectorFactory