etomica.normalmode

Interfaces

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

Classes

• ArrayA2B
• ArrayB2A
• ArrayReader1D
• ArrayReader2D
• BasisBigCell
• BoltzmannProcessor
• CalcHarmonicA
• CalcJacobian
• ConformationHSDimer
• CoordinateDefinition
• CoordinateDefinition.BasisCell
• CoordinateDefinition.SiteSource
• CoordinateDefinitionHSDimer
• CoordinateDefinitionLeaf
• CoordinateDefinitionLeafSuperBox
• CoordinateDefinitionMolecule
• CoordinateDefinitionMolecule.MoleculeSiteSource
• CoordinateDefinitionMoleculeVolumeFluctuation
• CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
• DataProcessorBoltzmannFactor
• DataProcessorSum
• DataSourceAvgPressure
• DataSourceAvgPressure2
• DataSourceFE
• DataSourceFEHistogram
• DataSourceImposedFEFit
• DataSourceImposedFEHistogram
• DataSourceMuRoot
• DataSourceMuRoot1
• DataSourceMuRootPMatch
• DataSourcePMu
• DataSourcePN
• DeviceCellNum3DSlider
• DeviceCellNumXYSlider
• DeviceEigenvaluesSlider
• DeviceWaveVectorSlider
• HarmonicCrystal
• HarmonicCrystalSoftSphereBCC
• HarmonicCrystalSoftSphereFCC
• HarmonicCrystalSoftSphereHCP
• HarmonicCrystalSsFccNxy
• HarmonicCrystalSsFccNxy.Params
• HessianDB
• HessianFromFile
• HSDimerNPT
• HSDimerNPT.HSMD3DParameters
• HSNPT
• HSNPT.ActionSummer
• HSNPT.ColorSchemeDisplacement
• HSNPT.HSMD3DParameters
• HSNPT.MyAgent
• HTTPSoftSphereApplet
• HTTPSoftSphereApplet.Applet
• HTTPSoftSphereApplet.SimOverlapTPSSParams
• HTTPSoftSphereSim
• IntegratorHardMDMC
• IntegratorHarmonic
• LatticeSumMolecularCrystal
• LJVacancyMin
• LJVacancyMin.SimOverlapParam
• MCMoveAtomCoupled
• MCMoveAtomCoupledBennet
• MCMoveAtomCoupledUmbrella
• MCMoveAtomSuperBox
• MCMoveEinsteinCrystal
• MCMoveHarmonic
• MCMoveHarmonicEin
• MCMoveHarmonicStep
• MCMoveMoleculeCoupled
• MCMovePhaseAngle
• MCMoveRotateMoleculePhiTheta
• MCMoveSingleMode
• MCMoveVolumeMonoclinic
• MCMoveVolumeMonoclinicAngle
• MCMoveVolumeMonoclinicScaled
• MCMoveVolumeSolid
• MCMoveVolumeSolidNPTMolecular
• MCMoveVolumeSolidNPTMolecularOriented
• MCMoveWV
• MeterAPIPotentialEnergy
• MeterAtomicDisplacement
• MeterBoltzmann
• MeterBoltzmannHarmonic
• MeterBoltzmannHTTP
• MeterBoltzmannTarget
• MeterDADB
• MeterDDP
• MeterDirectSamplingHarmonic
• MeterDirectSamplingTarget
• MeterDisplacementMoleculeRMS
• MeterDisplacementRMS
• MeterDP
• MeterHarmonicCoordinate
• MeterHarmonicEnergy
• MeterHarmonicEnergyFromMove
• MeterHarmonicSingleEnergy
• MeterJacobian
• MeterMaxExpansion
• MeterNormalMode
• MeterOverlapSwitch
• MeterPhiDeviation
• MeterPlaneSlip
• MeterPressureSuperBox
• MeterSamplingHarmonic
• MeterSamplingTarget
• MeterSolidDA
• MeterSolidDACut
• MeterSolidMirror
• MeterSolidProps
• MeterSolidPropsLJ
• MeterTargetTP
• MeterThetaDeviation
• MeterTilt
• MeterTiltHistogram
• MeterTiltRotation
• MeterTiltRotationHistogram
• MeterTiltRotationStdev
• MeterWorkBennetHarmonic
• MeterWorkBennetTarget
• MeterWorkHarmonicBennet
• MeterWorkHarmonicPhaseSpace
• MeterWorkHarmonicTargetandReweighting
• MeterWorkHarmonicUmbrella
• MeterWorkTargetBennet
• MeterWorkTargetHarmonicandReweighting
• MeterWorkTargetPhaseSpace
• MeterWorkTargetUmbrella
• MeterWorkUmbrellaHarmonic
• MeterWorkUmbrellaTarget
• MinimizeHCP
• MinimizeHCP.SimOverlapParam
• ModifierCells3D
• ModifierXCells2D
• ModifierYCells2D
• NormalModeAnalysisDisplay1D
• NormalModeAnalysisDisplay1D.Applet
• NormalModeAnalysisDisplay1DGraphic
• NormalModeAnalysisDisplay1DGraphic.Applet
• NormalModeAnalysisDisplay2D
• NormalModeAnalysisDisplay2DGraphic
• NormalModeAnalysisDisplay2DGraphic.Applet
• NormalModeAnalysisDisplay3D
• NormalModeAnalysisDisplay3D.Applet
• NormalModeAnalysisDisplay3DGraphic
• NormalModeAnalysisDisplay3DGraphic.Applet
• NormalModeEigenGetter
• NormalModes1DHR
• NormalModes2D
• NormalModes3D
• NormalModesFromFile
• NormalModesMolecular
• NormalModesPotential
• NormalModesSoftSpherical
• NormalModesVariable
• P1Constraint
• P1ConstraintNbr
• P1ConstraintNbrHcp
• P2XOrder
• PotentialCalculationEFSSP
• PotentialCalculationLJSP
• PotentialCalculationSolidSuper
• PotentialCalculationSolidSuperCut
• PotentialCalculationSolidSuperCutLS
• SimBennet
• SimBennet.SimBennetParam
• SimCalcJ
• SimCalcS
• SimCalcSLJ
• SimCalcSMorse
• SimCalcSSoftSphere2D
• SimCalcSSoftSphereFCC
• SimCalcSSoftSphereFCCSuperBox
• SimEinStep1
• SimEinStep1.SimOverlapParam
• SimEinStep1HCP
• SimEinStep1HCP.SimOverlapParam
• SimEinStep2
• SimEinStep2.MeterPotentialEnergyComposite
• SimEinStep2.SimOverlapParam
• SimEinStep2HCP
• SimEinStep2HCP.MeterPotentialEnergyComposite
• SimEinStep2HCP.SimOverlapParam
• SimFluidSoftSphere
• SimHarmonic
• SimHarmonicUmbrella
• SimHarmonicUmbrella.SimBennetParam
• SimHSMDVacancy
• SimHSMDVacancy.HSMDVParams
• SimLJHTTISuper
• SimLJHTTISuper.SimOverlapParam
• SimLJHTTISuperHCP
• SimLJHTTISuperHCP.SimOverlapParam
• SimLJHTTISuperHCP2
• SimLJHTTISuperHCP2.SimOverlapParam
• SimLJHTTISuperSFMD
• SimLJHTTISuperSFMD.SimOverlapParam
• SimLJVacancy
• SimLJVacancy.Applet
• SimLJVacancy.LJParams
• SimModesJ
• SimOverlap
• SimOverlap.SimOverlapParam
• SimOverlapLJ
• SimOverlapLJ.SimOverlapParam
• SimOverlapLJModule
• SimOverlapLJModule.APIPotentialReference
• SimOverlapLJModule.APIPotentialTarget
• SimOverlapLJModule.MeterPotentialEnergyDifference
• SimOverlapLJModule.SimOverlapParam
• SimOverlapModule
• SimOverlapSoftSphere
• SimOverlapSoftSphere.SimOverlapParam
• SimOverlapSoftSphereDP
• SimOverlapSoftSphereDP.SimOverlapParam
• SimOverlapSoftSphereEin
• SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
• SimOverlapSoftSphereEin.SimOverlapParam
• SimOverlapSoftSphereEinHarm
• SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
• SimOverlapSoftSphereEinHarm.SimOverlapParam
• SimOverlapSoftSphereHCP
• SimOverlapSoftSphereHCP.SimOverlapParam
• SimOverlapSoftSphereReweighting
• SimOverlapSoftSphereReweighting.SimOverlapParam
• SimOverlapSoftSphereSoftness
• SimOverlapSoftSphereSoftness.SimOverlapParam
• SimOverlapSoftSphereSuperBox
• SimOverlapSoftSphereSuperBox.SimOverlapParam
• SimOverlapSoftSphereTP
• SimOverlapSoftSphereTP.SimOverlapParam
• SimOverlapSoftSphereTPHCP
• SimOverlapSoftSphereTPHCP.SimOverlapParam
• SimOverlapSoftSphereTPSlantedBox
• SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
• SimOverlapSSnxy
• SimOverlapSSnxy.SimOverlapParam
• SimTarget
• SimTargetUmbrella
• SimTargetUmbrella.SimBennetParam
• SimUmbrella
• SimUmbrella.SimBennetParam
• SimUmbrellaSoftSphere
• SimUmbrellaSoftSphere.SimBennetParam
• SoftSphereSolidEOS
• SoftSphereSolidEOSCalculator
• SpeciesHSDimer
• WaveVectorFactory1D
• WaveVectorFactory2D
• WaveVectorFactoryFcc
• WaveVectorFactoryFromFile
• WaveVectorFactorySimple
• WaveVectorFactorySuperBox
• WriteS