Serialized Form

Package etomica.action
- Class etomica.action.ActionToggle extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - falseLabel
```
java.lang.String falseLabel
```
    - modifier
```
ModifierBoolean modifier
```
    - trueLabel
```
java.lang.String trueLabel
```
- Class etomica.action.AtomActionRandomizeVelocity extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - random
```
IRandom random
```
    - temperature
```
double temperature
```
- Class etomica.action.AtomActionRotateBy extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pitch
```
double pitch
```
    - roll
```
double roll
```
    - yaw
```
double yaw
```
- Class etomica.action.AtomActionTranslateBy extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - translationVector
```
Vector translationVector
```
- Class etomica.action.BoxActionAdapter extends java.lang.Object implements Serializable
  - Serialized Fields
    - box
```
Box box
```
- Class etomica.action.BoxDeleteMolecules extends BoxActionAdapter implements Serializable
  - Serialized Fields
    - filter
```
java.util.function.Predicate<T extends java.lang.Object> filter
```
- Class etomica.action.BoxImposePbc extends BoxActionAdapter implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - applyToMolecules
```
boolean applyToMolecules
```
    - moleculeTranslator
```
MoleculeChildAtomAction moleculeTranslator
```
    - positionDefinition
```
IMoleculePositionDefinition positionDefinition
```
    - space
```
Space space
```
    - translator
```
AtomActionTranslateBy translator
```
- Class etomica.action.BoxInflate extends BoxActionAdapter implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - dimVector
```
Vector dimVector
```
    - groupScaler
```
MoleculeChildAtomAction groupScaler
```
    - moleculeCenter
```
MoleculePositionGeometricCenter moleculeCenter
```
    - scaleVector
```
Vector scaleVector
```
    - translator
```
AtomActionTranslateBy translator
```
- Class etomica.action.BoxInflateAnisotropic extends BoxInflate implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cVector
```
Vector cVector
```
    - cVectorOld
```
Vector cVectorOld
```
    - deltaX
```
double[] deltaX
```
    - translationVector
```
Vector translationVector
```
- Class etomica.action.BoxInflateDeformable extends BoxInflate implements Serializable
  - Serialized Fields
    - tempTens
```
Tensor tempTens
```
    - tempTensInv
```
Tensor tempTensInv
```
- Class etomica.action.BoxQuench extends BoxActionAdapter implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - dim
```
int dim
```
    - meterTemperature
```
MeterTemperature meterTemperature
```
    - temperature
```
double temperature
```
- Class etomica.action.CalcVibrationalModes extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cgd
```
CalcGradientDifferentiable cgd
```
    - d
```
int[] d
```
    - dForces
```
double[][] dForces
```
    - eigenDecomp
```
Jama.EigenvalueDecomposition eigenDecomp
```
    - fC
```
Jama.Matrix fC
```
    - frequencies
```
double[] frequencies
```
    - mass
```
double mass
```
    - modes
```
double[] modes
```
    - modeSigns
```
int[] modeSigns
```
    - ms
```
IMoleculeList ms
```
    - positions
```
double[] positions
```
    - prodFreq
```
double prodFreq
```
    - writeCount
```
int writeCount
```
- Class etomica.action.IntegratorActionAdapter extends java.lang.Object implements Serializable
  - Serialized Fields
    - integrator
```
Integrator integrator
```
- Class etomica.action.IntegratorReset extends IntegratorActionAdapter implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ignoreOverlap
```
boolean ignoreOverlap
```
- Class etomica.action.MoleculeActionTranslateTo extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomPositionDefinition
```
IMoleculePositionDefinition atomPositionDefinition
```
    - atomTranslator
```
MoleculeChildAtomAction atomTranslator
```
    - destination
```
Vector destination
```
    - translationVector
```
Vector translationVector
```
- Class etomica.action.MoleculeChildAtomAction extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - action
```
AtomAction action
```
- Class etomica.action.ResetAccumulators extends DataStreamAction implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.action.ResetAccumulatorsAveraged extends ResetAccumulators implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.action.SimulationDataAction extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - dataStreamPumps
```
java.util.ArrayList<E extends java.lang.Object> dataStreamPumps
```
    - streamAction
```
DataStreamAction streamAction
```
- Class etomica.action.XYZWriter extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - doAppend
```
boolean doAppend
```
    - elementAtomType
```
java.util.LinkedList<E extends java.lang.Object> elementAtomType
```
    - elementCount
```
int elementCount
```
    - file
```
java.io.File file
```
    - leafList
```
IAtomList leafList
```
Package etomica.AlkaneEH
- Class etomica.AlkaneEH.ConformationAlkaneEH extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angleCCC
```
double angleCCC
```
    - angleCCC_half
```
double angleCCC_half
```
    - angleCCH
```
double angleCCH
```
    - angleHCH
```
double angleHCH
```
    - angleHCH_half
```
double angleHCH_half
```
    - CCbondL
```
double CCbondL
```
    - CHbondL
```
double CHbondL
```
    - numCarbons
```
int numCarbons
```
    - numCH2
```
int numCH2
```
    - numH
```
int numH
```
    - space
```
Space space
```
Package etomica.association
- Class etomica.association.AtomSourceRandomMonomer extends AtomSourceRandomLeaf implements Serializable
  - Serialized Fields
    - associationManager
```
AssociationManager associationManager
```
- Class etomica.association.BiasVolume extends java.lang.Object implements Serializable
  - Serialized Fields
    - space
```
Space space
```
- Class etomica.association.BiasVolumeAceticAcid extends BiasVolumeMolecule implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - boundary
```
Boundary boundary
```
    - C1CH31
```
Vector C1CH31
```
    - C1DBO1
```
Vector C1DBO1
```
    - C1SBO1
```
Vector C1SBO1
```
    - C2C1
```
Vector C2C1
```
    - C2CH32
```
Vector C2CH32
```
    - C2DBO2
```
Vector C2DBO2
```
    - C2SBO2
```
Vector C2SBO2
```
    - dv
```
Vector dv
```
    - groupTranslationVector
```
Vector groupTranslationVector
```
    - H1O2
```
Vector H1O2
```
    - H2O1
```
Vector H2O1
```
    - innerRadius
```
double innerRadius
```
    - maxCosPhi
```
double maxCosPhi
```
    - maxCosTheta
```
double maxCosTheta
```
    - moveMoleculeAction
```
MoleculeChildAtomAction moveMoleculeAction
```
    - newPositionC
```
Vector newPositionC
```
    - OO1
```
Vector OO1
```
    - OO2
```
Vector OO2
```
    - pair
```
MoleculePair pair
```
    - radius
```
double radius
```
    - random
```
IRandom random
```
    - rotationTensor
```
RotationTensor3D rotationTensor
```
    - secondAxis
```
Vector secondAxis
```
    - thirdAxis
```
Vector thirdAxis
```
    - work1
```
Vector work1
```
    - work2
```
Vector work2
```
- Class etomica.association.BiasVolumeCube extends BiasVolume implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - boundary
```
Boundary boundary
```
    - dimensions
```
Vector dimensions
```
    - random
```
IRandom random
```
    - work
```
Vector work
```
- Class etomica.association.BiasVolumeMolecule extends java.lang.Object implements Serializable
  - Serialized Fields
    - space
```
Space space
```
- Class etomica.association.BiasVolumeSphere extends BiasVolume implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - boundary
```
Boundary boundary
```
    - innerRadius
```
double innerRadius
```
    - radius
```
double radius
```
    - random
```
IRandom random
```
    - work
```
Vector work
```
- Class etomica.association.BiasVolumeSphereOriented extends BiasVolume implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - boundary
```
Boundary boundary
```
    - ec1
```
double ec1
```
    - ec2
```
double ec2
```
    - innerRadius
```
double innerRadius
```
    - radius
```
double radius
```
    - random
```
IRandom random
```
    - work
```
Vector work
```
- Class etomica.association.BiasVolumeSphereOrientedDoubleSites extends BiasVolume implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - boundary
```
Boundary boundary
```
    - direction
```
Vector direction
```
    - ec1
```
double ec1
```
    - ec2
```
double ec2
```
    - innerRadius
```
double innerRadius
```
    - radius
```
double radius
```
    - random
```
IRandom random
```
    - work
```
Vector work
```
- Class etomica.association.MoleculeSourceRandomMonomer extends MoleculeSourceRandomMolecule implements Serializable
  - Serialized Fields
    - associationManager
```
AssociationManagerMolecule associationManager
```
Package etomica.atom
- Class etomica.atom.Atom extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  3L
  - Serialized Fields
    - index
```
int index
```
    - leafIndex
```
int leafIndex
```
    - parent
```
IMolecule parent
```
    - position
```
Vector position
```
    - type
```
AtomType type
```
- Class etomica.atom.AtomGroupVelocityAverage extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - vectorSum
```
Vector vectorSum
```
- Class etomica.atom.AtomHydrogen extends AtomOriented implements Serializable
  - Serialized Fields
    - bondLength
```
double bondLength
```
- Class etomica.atom.AtomLeafDynamic extends Atom implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - velocity
```
Vector velocity
```
- Class etomica.atom.AtomOriented extends Atom implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - iOrientation
```
IOrientation iOrientation
```
- Class etomica.atom.AtomOrientedDynamic extends AtomLeafDynamic implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angularVelocity
```
Vector angularVelocity
```
    - iOrientation
```
IOrientation iOrientation
```
- Class etomica.atom.AtomOrientedQuaternion extends Atom implements Serializable
  - Serialized Fields
    - quaternion
```
VectorND quaternion
```
- Class etomica.atom.AtomSourceRandomLeaf extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - list
```
IAtomList list
```
    - random
```
IRandom random
```
- Class etomica.atom.AtomToAtomSetFixed extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomArrayList
```
AtomArrayList atomArrayList
```
- Class etomica.atom.AtomToIndexChild extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.atom.AtomToParentChildList extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.atom.iterator
- Class etomica.atom.iterator.ApiInnerVariable extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - aiInner
```
AtomIteratorAtomDependent aiInner
```
      The iterators used to generate the sets of atoms.
    - aiOuter
```
AtomIterator aiOuter
```
    - doSwap
```
boolean doSwap
```
    - pair
```
AtomPair pair
```
- Class etomica.atom.iterator.ApiInterArrayList extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atoms
```
AtomPair atoms
```
    - innerIndex
```
int innerIndex
```
    - innerList
```
IAtomList innerList
```
    - outerIndex
```
int outerIndex
```
    - outerList
```
IAtomList outerList
```
- Class etomica.atom.iterator.ApiIntraArrayList extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atoms
```
AtomPair atoms
```
    - innerIndex
```
int innerIndex
```
    - list
```
IAtomList list
```
    - outerIndex
```
int outerIndex
```
- Class etomica.atom.iterator.ApiIntragroup extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - aiOuter
```
AtomsetIteratorBasisDependent aiOuter
```
    - apiDown
```
ApiInnerVariable apiDown
```
    - apiUp
```
ApiInnerVariable apiUp
```
    - direction
```
IteratorDirective.Direction direction
```
    - doGoDown
```
boolean doGoDown
```
    - targetAtom
```
IAtom targetAtom
```
    - upListNow
```
boolean upListNow
```
- Class etomica.atom.iterator.ApiLeafAtoms extends ApiIntraArrayList implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.atom.iterator.AtomIteratorArrayList extends AtomIteratorArrayListSimple implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomToAtomSet
```
AtomToAtomLeafList atomToAtomSet
```
    - atomToIndex
```
AtomToIndex atomToIndex
```
    - numToSkip
```
int numToSkip
```
    - startAtom
```
IAtom startAtom
```
    - upListNow
```
boolean upListNow
```
- Class etomica.atom.iterator.AtomIteratorArrayListAdjacent extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomSetSinglet
```
AtomSetSinglet atomSetSinglet
```
    - atomToAtomSet
```
AtomToAtomLeafList atomToAtomSet
```
    - atomToIndex
```
AtomToIndex atomToIndex
```
    - direction
```
IteratorDirective.Direction direction
```
    - dnListNow
```
boolean dnListNow
```
    - firstCursor
```
int firstCursor
```
    - list
```
IAtomList list
```
    - upListNow
```
boolean upListNow
```
- Class etomica.atom.iterator.AtomIteratorArrayListSimple extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - atomSetSinglet
```
AtomSetSinglet atomSetSinglet
```
    - cursor
```
int cursor
```
      Index of element to be returned by subsequent call to next.
    - list
```
IAtomList list
```
- Class etomica.atom.iterator.AtomIteratorBasis extends AtomIteratorArrayListSimple implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - basis
```
IMolecule basis
```
    - littleList
```
AtomArrayList littleList
```
    - myList
```
IAtomList myList
```
    - needSetupIterator
```
boolean needSetupIterator
```
    - targetAtom
```
IAtom targetAtom
```
- Class etomica.atom.iterator.AtomIteratorBasisAdjustableStart extends AtomIteratorArrayList implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - basis
```
IMolecule basis
```
    - littleList
```
AtomArrayList littleList
```
    - myList
```
IAtomList myList
```
    - needSetupIterator
```
boolean needSetupIterator
```
    - targetAtom
```
IAtom targetAtom
```
- Class etomica.atom.iterator.AtomIteratorBasisFilteredType extends AtomIteratorBasis implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - filteredType
```
AtomType filteredType
```
- Class etomica.atom.iterator.AtomIteratorBasisFilteredType2 extends AtomIteratorBasis implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - filteredType1
```
AtomType filteredType1
```
    - filteredType2
```
AtomType filteredType2
```
- Class etomica.atom.iterator.AtomIteratorLeafAtoms extends AtomIteratorArrayListSimple implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.atom.iterator.AtomIteratorLeafFilteredType extends AtomIteratorLeafAtoms implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - filteredType
```
AtomType filteredType
```
- Class etomica.atom.iterator.AtomIteratorNull extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.atom.iterator.AtomIteratorSinglet extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atom
```
IAtom atom
```
    - atomSetSinglet
```
AtomSetSinglet atomSetSinglet
```
    - hasNext
```
boolean hasNext
```
Package etomica.chem.electrostatics
- Class etomica.chem.electrostatics.Charge extends java.lang.Object implements Serializable
  - Serialized Fields
    - q
```
double q
```
Package etomica.chem.elements
- Class etomica.chem.elements.Argon extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Carbon extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Chlorine extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Copper extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Element extends java.lang.Object implements Serializable
  - Serialized Fields
    - symbol
```
java.lang.String symbol
```
- Class etomica.chem.elements.ElementChemical extends Element implements Serializable
  - Serialized Fields
    - atomicNumber
```
int atomicNumber
```
    - mass
```
double mass
```
    - rm
```
double rm
```
- Class etomica.chem.elements.ElementSimple extends Element implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mass
```
double mass
```
    - rm
```
double rm
```
- Class etomica.chem.elements.Fluorine extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Helium extends ElementChemical implements Serializable
- Class etomica.chem.elements.Hydrogen extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Iron extends ElementChemical implements Serializable
- Class etomica.chem.elements.Nitrogen extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Oxygen extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Silver extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Sodium extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Sulfur extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Tin extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.chem.elements.Tungsten extends ElementChemical implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.compatibility
- Class etomica.compatibility.ClassRequirement extends Requirement implements Serializable
  - Serialized Fields
    - comparison
```
Feature comparison
```
- Class etomica.compatibility.Feature extends java.lang.Object implements Serializable
  - Serialized Fields
    - name
```
java.lang.String name
```
- Class etomica.compatibility.FeatureRequirement extends Requirement implements Serializable
  - Serialized Fields
    - expected_result
```
int expected_result
```
    - reference
```
Feature reference
```
- Class etomica.compatibility.FeatureSet extends java.lang.Object implements Serializable
  - Serialized Fields
    - list
```
java.util.HashMap<K extends java.lang.Object,V extends java.lang.Object> list
```
- Class etomica.compatibility.NumericFeature extends Feature implements Serializable
  - Serialized Fields
    - value
```
double value
```
- Class etomica.compatibility.Requirement extends java.lang.Object implements Serializable
- Class etomica.compatibility.RequirementSet extends Requirement implements Serializable
  - Serialized Fields
    - requirements
```
java.util.LinkedList<E extends java.lang.Object> requirements
```
- Class etomica.compatibility.StringFeature extends Feature implements Serializable
  - Serialized Fields
    - value
```
java.lang.String value
```
Package etomica.config
- Class etomica.config.ConfigurationFile extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - confName
```
java.lang.String confName
```
- Class etomica.config.ConfigurationLattice extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  3L
  - Serialized Fields
    - atomActionTranslateTo
```
MoleculeActionTranslateTo atomActionTranslateTo
```
    - boundaryPadding
```
double boundaryPadding
```
    - indexIterator
```
IndexIteratorSizable indexIterator
```
    - lattice
```
SpaceLattice lattice
```
    - myLat
```
ConfigurationLattice.MyLattice myLat
```
    - positionDefinition
```
IMoleculePositionDefinition positionDefinition
```
    - rescalingToFitVolume
```
boolean rescalingToFitVolume
```
    - space
```
Space space
```
- Class etomica.config.ConfigurationLatticeRandom extends ConfigurationLattice implements Serializable
  - Serialized Fields
    - random
```
IRandom random
```
- Class etomica.config.ConfigurationLatticeSimple extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - atomActionTranslateTo
```
MoleculeActionTranslateTo atomActionTranslateTo
```
    - indexIterator
```
IndexIteratorSizable indexIterator
```
    - lattice
```
SpaceLattice lattice
```
    - space
```
Space space
```
- Class etomica.config.ConfigurationLatticeWithPlane extends ConfigurationLattice implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - allocation
```
java.util.HashMap<K extends java.lang.Object,V extends java.lang.Object> allocation
```
    - LEFT
```
int LEFT
```
    - plane
```
Plane plane
```
    - RIGHT
```
int RIGHT
```
    - species
```
java.util.ArrayList<E extends java.lang.Object> species
```
- Class etomica.config.ConfigurationOrientedFile extends ConfigurationFile implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - direction
```
Vector direction
```
    - secondaryDirection
```
Vector secondaryDirection
```
- Class etomica.config.ConfigurationZincblende extends ConfigurationLattice implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - species
```
ISpecies[] species
```
    - translator0
```
MoleculeChildAtomAction translator0
```
    - translator1
```
MoleculeChildAtomAction translator1
```
- Class etomica.config.ConformationChain extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
- Class etomica.config.ConformationChain2D extends ConformationChain implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - tracker
```
int tracker
```
    - vectors
```
Vector[] vectors
```
- Class etomica.config.ConformationChain3D extends ConformationChain implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - tracker
```
int tracker
```
    - vectors
```
Vector[] vectors
```
- Class etomica.config.ConformationChainZigZag extends ConformationChain implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - isVectorOne
```
boolean isVectorOne
```
    - v1
```
Vector v1
```
    - v2
```
Vector v2
```
- Class etomica.config.ConformationChainZigZag2 extends ConformationChain implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - isVectorOne
```
boolean isVectorOne
```
    - v1
```
Vector v1
```
    - v2
```
Vector v2
```
- Class etomica.config.ConformationLinear extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angle
```
double[] angle
```
    - bondLength
```
double bondLength
```
    - orientation
```
Vector orientation
```
    - space
```
Space space
```
- Class etomica.config.ConformationWater extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angleHOH
```
double angleHOH
```
    - bondLengthOH
```
double bondLengthOH
```
    - space
```
Space space
```
- Class etomica.config.GrainBoundaryConfiguration extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - atomActionTranslateTo
```
MoleculeActionTranslateTo atomActionTranslateTo
```
    - indexIteratorA
```
IndexIteratorSizable indexIteratorA
```
    - indexIteratorB
```
IndexIteratorSizable indexIteratorB
```
    - iteratorDimensionsA
```
int[] iteratorDimensionsA
```
    - iteratorDimensionsB
```
int[] iteratorDimensionsB
```
    - latticeA
```
BravaisLatticeCrystal latticeA
```
    - latticeB
```
BravaisLatticeCrystal latticeB
```
    - latticeDimensionsA
```
double[] latticeDimensionsA
```
    - latticeDimensionsB
```
double[] latticeDimensionsB
```
    - myLatA
```
etomica.config.GrainBoundaryConfiguration.MyLattice myLatA
```
    - myLatB
```
etomica.config.GrainBoundaryConfiguration.MyLattice myLatB
```
    - nCellsAx
```
int nCellsAx
```
    - nCellsAy
```
int nCellsAy
```
    - nCellsAz
```
int nCellsAz
```
    - nCellsBx
```
int nCellsBx
```
    - nCellsBy
```
int nCellsBy
```
    - nCellsBz
```
int nCellsBz
```
    - space
```
Space space
```
    - speciesAFixed
```
ISpecies speciesAFixed
```
    - speciesAMobile
```
ISpecies speciesAMobile
```
    - speciesBFixed
```
ISpecies speciesBFixed
```
    - speciesBMobile
```
ISpecies speciesBMobile
```
Package etomica.data
- Class etomica.data.DataInfo extends java.lang.Object implements Serializable
  - Serialized Fields
    - dimension
```
Dimension dimension
```
    - label
```
java.lang.String label
```
    - tagArray
```
DataTag[] tagArray
```
    - tags
```
java.util.List<E extends java.lang.Object> tags
```
- Class etomica.data.DataInfoFactory extends java.lang.Object implements Serializable
  - Serialized Fields
    - dimension
```
Dimension dimension
```
    - label
```
java.lang.String label
```
    - tags
```
java.util.ArrayList<E extends java.lang.Object> tags
```
- Class etomica.data.DataSinkConsole extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - out
```
java.io.PrintStream out
```
- Class etomica.data.DataSourceCountSteps extends DataSourceScalar implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - integrator
```
Integrator integrator
```
- Class etomica.data.DataSourceFunction extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
DataFunction data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - function
```
IFunction function
```
    - tag
```
DataTag tag
```
    - xData
```
DataDoubleArray xData
```
    - xSource
```
DataSourceUniform xSource
```
- Class etomica.data.DataSourceGroup extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
DataGroup data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - dataSources
```
IDataSource[] dataSources
```
    - latestData
```
IData[] latestData
```
    - tag
```
DataTag tag
```
- Class etomica.data.DataSourceRmsVelocity extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomData
```
DataDouble atomData
```
    - atomDataInfo
```
IDataInfo atomDataInfo
```
    - data
```
DataFunction data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - histogramRMS
```
Histogram histogramRMS
```
    - iterator
```
AtomIterator iterator
```
    - tag
```
DataTag tag
```
    - xData
```
DataDoubleArray xData
```
    - xDataInfo
```
DataDoubleArray.DataInfoDoubleArray xDataInfo
```
    - xTag
```
DataTag xTag
```
- Class etomica.data.DataSourceTensorVirialHard extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
DataTensor data
```
    - dataInfo
```
DataTensor.DataInfoTensor dataInfo
```
    - integratorHard
```
IntegratorHard integratorHard
```
    - lastTime
```
double lastTime
```
    - tag
```
DataTag tag
```
    - work
```
Tensor work
```
- Class etomica.data.DataSourceUniform extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
DataDoubleArray data
```
    - dataInfo
```
DataDoubleArray.DataInfoDoubleArray dataInfo
```
    - doEnforceBounds
```
boolean doEnforceBounds
```
    - dx
```
double dx
```
    - tag
```
DataTag tag
```
    - typeMax
```
DataSourceUniform.LimitType typeMax
```
    - typeMin
```
DataSourceUniform.LimitType typeMin
```
    - x
```
double[] x
```
    - xMax
```
double xMax
```
    - xMin
```
double xMin
```
- Class etomica.data.DataStreamAction extends java.lang.Object implements Serializable
  - Serialized Fields
    - start
```
java.lang.Object start
```
Package etomica.data.histogram
- Class etomica.data.histogram.HistogramCollapsing extends HistogramSimple implements Serializable
  - Serialized Fields
    - firstValue
```
double firstValue
```
    - firstValueCount
```
long firstValueCount
```
- Class etomica.data.histogram.HistogramExpanding extends HistogramSimple implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.data.histogram.HistogramNotSoSimple extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - count
```
long count
```
    - counts
```
int[] counts
```
    - deltaX
```
double deltaX
```
    - doAveraging
```
boolean doAveraging
```
    - histogram
```
double[] histogram
```
    - nBins
```
int nBins
```
    - sums
```
double[] sums
```
    - totalSum
```
double totalSum
```
    - xMax
```
double xMax
```
    - xMin
```
double xMin
```
    - xValues
```
double[] xValues
```
- Class etomica.data.histogram.HistogramReweightedData extends java.lang.Object implements Serializable
  - Serialized Fields
    - deltaX
```
double deltaX
```
    - histogram
```
double[] histogram
```
    - nBins
```
int nBins
```
    - sum
```
long sum
```
    - sums
```
double[] sums
```
    - weightSum
```
double weightSum
```
    - xMax
```
double xMax
```
    - xMin
```
double xMin
```
    - xValues
```
double[] xValues
```
- Class etomica.data.histogram.HistogramSimple extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - counts
```
long[] counts
```
    - deltaX
```
double deltaX
```
    - histogram
```
double[] histogram
```
    - nBins
```
int nBins
```
    - sum
```
long sum
```
    - xMax
```
double xMax
```
    - xMin
```
double xMin
```
    - xValues
```
double[] xValues
```
Package etomica.data.history
- Class etomica.data.history.HistoryScrolling extends java.lang.Object implements Serializable
  - Serialized Fields
    - cursor
```
int cursor
```
    - full
```
boolean full
```
    - history
```
double[] history
```
    - tempX
```
double[] tempX
```
    - tempY
```
double[] tempY
```
    - xValues
```
double[] xValues
```
Package etomica.data.meter
- Class etomica.data.meter.MeterDihedralAngle extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - boundary
```
Boundary boundary
```
    - box
```
Box box
```
    - data
```
DataFunction data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - dr1
```
Vector dr1
```
    - dr2
```
Vector dr2
```
    - dr3
```
Vector dr3
```
    - gSum
```
long[] gSum
```
    - iterator
```
AtomsetIteratorBoxDependent iterator
```
    - name
```
java.lang.String name
```
    - phiData
```
DataDoubleArray phiData
```
    - rMax
```
double rMax
```
    - space
```
Space space
```
    - tag
```
DataTag tag
```
    - tetraNum
```
long tetraNum
```
    - xDataSource
```
DataSourceUniform xDataSource
```
- Class etomica.data.meter.MeterMomentumCOM extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - data
```
DataVector data
```
    - dataInfo
```
DataInfo dataInfo
```
    - momentumSum
```
Vector momentumSum
```
    - name
```
java.lang.String name
```
    - tag
```
DataTag tag
```
- Class etomica.data.meter.MeterPositionCOM extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - data
```
DataVector data
```
    - dataInfo
```
DataInfo dataInfo
```
    - name
```
java.lang.String name
```
    - positionSum
```
Vector positionSum
```
    - tag
```
DataTag tag
```
- Class etomica.data.meter.MeterPressureByVolumeChange extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
DataDoubleArray data
```
    - dataArray
```
double[] dataArray
```
    - dataInfo
```
IDataInfo dataInfo
```
    - energy
```
PotentialCalculationEnergySum energy
```
    - inflateDimensions
```
boolean[] inflateDimensions
```
    - inflater
```
BoxInflate inflater
```
    - integrator
```
IntegratorBox integrator
```
    - iteratorDirective
```
IteratorDirective iteratorDirective
```
    - nDimension
```
int nDimension
```
    - scale
```
Vector scale
```
    - space
```
Space space
```
    - tag
```
DataTag tag
```
    - vDataSource
```
MeterPressureByVolumeChange.DataSourceExp vDataSource
```
    - xDataSource
```
DataSourceUniform xDataSource
```
- Class etomica.data.meter.MeterPressureTensorFromIntegrator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
DataTensor data
```
    - dataInfo
```
DataInfo dataInfo
```
    - integrator
```
IntegratorVelocityVerlet integrator
```
    - space
```
Space space
```
    - tag
```
DataTag tag
```
- Class etomica.data.meter.MeterProfile extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - data
```
DataFunction data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - meter
```
DataSourcePositioned meter
```
      Meter that defines the property being profiled.
    - positionSource
```
RandomPositionSource positionSource
```
    - profileDim
```
int profileDim
```
      Vector describing the orientation of the profile. For example, (1,0) is along the x-axis.
    - tag
```
DataTag tag
```
    - xDataSource
```
DataSourceUniform xDataSource
```
- Class etomica.data.meter.MeterProfileByAtoms extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - data
```
DataFunction data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - meter
```
DataSourceMolecular meter
```
      Meter that defines the property being profiled.
    - nAtoms
```
int[] nAtoms
```
    - position
```
Vector position
```
    - positionDefinition
```
IMoleculePositionDefinition positionDefinition
```
    - profileDim
```
int profileDim
```
      Vector describing the orientation of the profile. For example, (1,0) is along the x-axis.
    - species
```
ISpecies species
```
    - tag
```
DataTag tag
```
    - xDataSource
```
DataSourceUniform xDataSource
```
    - y
```
double[] y
```
- Class etomica.data.meter.MeterProfileByVolume extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - data
```
DataFunction data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - dV
```
double dV
```
    - meter
```
DataSourceMolecular meter
```
      Meter that defines the property being profiled.
    - position
```
Vector position
```
    - positionDefinition
```
IMoleculePositionDefinition positionDefinition
```
    - profileDim
```
int profileDim
```
      Vector describing the orientation of the profile. For example, (1,0) is along the x-axis.
    - species
```
ISpecies species
```
    - tag
```
DataTag tag
```
    - xDataSource
```
DataSourceUniform xDataSource
```
- Class etomica.data.meter.MeterTensorVelocity extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomData
```
DataTensor atomData
```
    - box
```
Box box
```
    - data
```
DataTensor data
```
    - dataInfo
```
DataTensor.DataInfoTensor dataInfo
```
    - name
```
java.lang.String name
```
    - tag
```
DataTag tag
```
Package etomica.data.types
- Class etomica.data.types.CastToTable extends DataProcessor implements Serializable
  - Serialized Fields
    - inputType
```
int inputType
```
    - outputData
```
DataTable outputData
```
    - xDataSource
```
DataSourceIndependent xDataSource
```
- Class etomica.data.types.DataDouble extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
double x
```
      The wrapped data value held by this object.
- Class etomica.data.types.DataDouble.DataInfoDouble extends DataInfo implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.data.types.DataDouble.DataInfoDoubleFactory extends DataInfoFactory implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.data.types.DataDoubleArray extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayShape
```
int[] arrayShape
```
    - jumpCount
```
int[] jumpCount
```
    - x
```
double[] x
```
- Class etomica.data.types.DataDoubleArray.DataInfoDoubleArray extends DataInfo implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayShape
```
int[] arrayShape
```
- Class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory extends DataInfoFactory implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayShape
```
int[] arrayShape
```
- Class etomica.data.types.DataDoubleBDArray extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayShape
```
int[] arrayShape
```
    - jumpCount
```
int[] jumpCount
```
    - mc
```
java.math.MathContext mc
```
    - x
```
java.math.BigDecimal[] x
```
- Class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray extends DataInfo implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayShape
```
int[] arrayShape
```
    - precision
```
int precision
```
- Class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory extends DataInfoFactory implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - arrayShape
```
int[] arrayShape
```
    - precision
```
int precision
```
- Class etomica.data.types.DataFunction extends DataDoubleArray implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.data.types.DataFunction.DataInfoFunction extends DataDoubleArray.DataInfoDoubleArray implements Serializable
  - Serialized Fields
    - xDataSource
```
DataSourceIndependent xDataSource
```
- Class etomica.data.types.DataFunction.DataInfoFunctionFactory extends DataDoubleArray.DataInfoDoubleArrayFactory implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - xDataSource
```
DataSourceIndependent xDataSource
```
- Class etomica.data.types.DataGroup extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
IData[] data
```
- Class etomica.data.types.DataGroup.DataInfoGroup extends DataInfo implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - subDataInfo
```
IDataInfo[] subDataInfo
```
- Class etomica.data.types.DataGroup.DataInfoGroupFactory extends DataInfoFactory implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - subDataInfo
```
IDataInfo[] subDataInfo
```
- Class etomica.data.types.DataTable extends DataGroup implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.data.types.DataTable.DataInfoTable extends DataGroup.DataInfoGroup implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - nRows
```
int nRows
```
    - rowHeaders
```
java.lang.String[] rowHeaders
```
- Class etomica.data.types.DataTable.DataInfoTableFactory extends DataGroup.DataInfoGroupFactory implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - columnInfoFactories
```
DataDoubleArray.DataInfoDoubleArrayFactory[] columnInfoFactories
```
    - nRows
```
int nRows
```
    - rowHeaders
```
java.lang.String[] rowHeaders
```
- Class etomica.data.types.DataTensor.DataInfoTensor extends DataInfo implements Serializable
  - Serialized Fields
    - space
```
Space space
```
- Class etomica.data.types.DataTensor.DataInfoTensorFactory extends DataInfoFactory implements Serializable
  - Serialized Fields
    - space
```
Space space
```
- Class etomica.data.types.DataVector extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
Vector x
```
      The wrapped vector data.
- Class etomica.data.types.DataVector.DataInfoVector extends DataInfo implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
- Class etomica.data.types.DataVector.DataInfoVectorFactory extends DataInfoFactory implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
Package etomica.eam
- Class etomica.eam.PotentialCalculationEnergySumEAM extends PotentialCalculationEnergySum implements Serializable
  - Serialized Fields
    - p2
```
P2EAM p2
```
    - sum
```
double sum
```
Package etomica.eigenstuff
- Class etomica.eigenstuff.MyEigenvalueDecomposition extends java.lang.Object implements Serializable
  - Serialized Fields
    - d
```
double[] d
```
      Arrays for internal storage of eigenvalues.
      
      internal storage of eigenvalues.
    - e
```
double[] e
```
      Arrays for internal storage of eigenvalues.
      
      internal storage of eigenvalues.
    - H
```
double[][] H
```
      Array for internal storage of nonsymmetric Hessenberg form.
      
      internal storage of nonsymmetric Hessenberg form.
    - issymmetric
```
boolean issymmetric
```
      Symmetry flag.
      
      internal symmetry flag.
    - n
```
int n
```
      Row and column dimension (square matrix).
      
      matrix dimension.
    - ort
```
double[] ort
```
      Working storage for nonsymmetric algorithm.
      
      working storage for nonsymmetric algorithm.
    - V
```
double[][] V
```
      Array for internal storage of eigenvectors.
      
      internal storage of eigenvectors.
Package etomica.exception
- Class etomica.exception.AbnormalCompletionException extends java.lang.RuntimeException implements Serializable
- Class etomica.exception.ConfigurationOverlapException extends java.lang.RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
- Class etomica.exception.MethodNotImplementedException extends java.lang.RuntimeException implements Serializable
Package etomica.freeenergy.npath
- Class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies extends PotentialCalculationEnergySum implements Serializable
  - Serialized Fields
    - sum1
```
double sum1
```
    - sum2
```
double sum2
```
- Class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergiesEAM extends DataSourceEnergies.PotentialCalculationEnergies implements Serializable
  - Serialized Fields
    - p2
```
P2EAM p2
```
Package etomica.graph.engine
- Class etomica.graph.engine.ConsoleUI extends javax.swing.JTextArea implements Serializable
  
  serialVersionUID:
  
  8775341949270012136L
  - Serialized Fields
    - buffer
```
java.lang.StringBuffer buffer
```
    - lineStart
```
int lineStart
```
    - reader
```
ConsoleReader reader
```
- Class etomica.graph.engine.Interpreter.InterpreterException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  -4211862381484158892L
- Class etomica.graph.engine.Launcher.ConsoleWindow extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  -3245527931727439689L
  - Serialized Fields
    - console
```
ConsoleUI console
```
- Class etomica.graph.engine.Parser.ParserException extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  941457687073478706L
Package etomica.graph.view.rasterizer
- Class etomica.graph.view.rasterizer.SVGConverterException extends java.lang.Exception implements Serializable
  - Serialized Fields
    - errorCode
```
java.lang.String errorCode
```
      Error code
    - errorInfo
```
java.lang.Object[] errorInfo
```
      Additional information about the error condition
    - isFatal
```
boolean isFatal
```
      Defines whether or not this is a fatal error condition
Package etomica.graph.viewer
- Class etomica.graph.viewer.ClusterViewer extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  4330455556112932184L
  - Serialized Fields
    - mainPanel
```
javax.swing.JPanel mainPanel
```
    - name
```
java.lang.String name
```
Package etomica.graphics
- Class etomica.graphics.AboutBoxWindow extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - creationCredits
```
java.lang.String[] creationCredits
```
    - owner
```
java.awt.Component owner
```
    - softwareCredits
```
java.lang.String[] softwareCredits
```
- Class etomica.graphics.ActionGraphic extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - simulationAction
```
IAction simulationAction
```
- Class etomica.graphics.DecimalSlider extends javax.swing.JSlider implements Serializable
  - Serialized Fields
    - halfSpacing
```
int halfSpacing
```
    - labelTable
```
java.util.Hashtable<K extends java.lang.Object,V extends java.lang.Object> labelTable
```
    - maximum
```
int maximum
```
    - minimum
```
int minimum
```
    - precision
```
long precision
```
    - spacing
```
int spacing
```
    - standardSpacingLabel
```
int standardSpacingLabel
```
- Class etomica.graphics.DeviceBoxValueChangedEvent extends java.awt.AWTEvent implements Serializable
  - Serialized Fields
    - newValue
```
int newValue
```
- Class etomica.graphics.DeviceSpinner.SpinnerListener extends java.lang.Object implements Serializable
- Class etomica.graphics.DeviceTableModelGeneric extends javax.swing.table.AbstractTableModel implements Serializable
  - Serialized Fields
    - columnClasses
```
java.lang.Class<T extends java.lang.Object>[] columnClasses
```
    - columnNames
```
java.lang.String[] columnNames
```
    - data
```
java.util.Vector<E extends java.lang.Object> data
```
    - numColumns
```
int numColumns
```
    - numRows
```
int numRows
```
- Class etomica.graphics.DimensionedDoubleEditor extends java.beans.PropertyEditorSupport implements Serializable
  - Serialized Fields
    - availableUnitNames
```
java.lang.StringBuffer[] availableUnitNames
```
    - availableUnits
```
java.lang.Class<T extends java.lang.Object>[] availableUnits
```
    - baseUnit
```
Unit baseUnit
```
    - prefix
```
Prefix prefix
```
    - unit
```
PrefixedUnit unit
```
    - unitList
```
javax.swing.JComboBox<E extends java.lang.Object> unitList
```
    - valueEditor
```
java.beans.PropertyEditor valueEditor
```
- Class etomica.graphics.DisplayBoxCanvas1D extends DisplayCanvas implements Serializable
  - Serialized Fields
    - annotationHeight
```
int annotationHeight
```
    - atomOrigin
```
int[] atomOrigin
```
    - font
```
java.awt.Font font
```
    - scaleText
```
java.awt.TextField scaleText
```
    - shiftOrigin
```
int[] shiftOrigin
```
    - space
```
Space space
```
- Class etomica.graphics.DisplayBoxCanvas2D extends DisplayCanvas implements Serializable
  - Serialized Fields
    - annotationHeight
```
int annotationHeight
```
    - atomOrigin
```
int[] atomOrigin
```
    - boundingBox
```
Vector boundingBox
```
    - font
```
java.awt.Font font
```
    - orientationColor
```
java.awt.Color orientationColor
```
    - orientationLength
```
double orientationLength
```
    - shiftOrigin
```
int[] shiftOrigin
```
    - space
```
Space space
```
- Class etomica.graphics.DisplayBoxCanvasG3DSys extends DisplayCanvas implements Serializable
  - Serialized Fields
    - aam
```
AtomLeafAgentManager<E> aam
```
    - aamOriented
```
AtomLeafAgentManager<E> aamOriented
```
    - atomTypeOrientedManager
```
java.util.Map<K extends java.lang.Object,V extends java.lang.Object> atomTypeOrientedManager
```
    - backgroundColor
```
java.awt.Color backgroundColor
```
    - boundaryDisplayed
```
boolean boundaryDisplayed
```
    - boundaryFrameColor
```
java.awt.Color boundaryFrameColor
```
    - coords
```
double[] coords
```
    - gsys
```
G3DSys gsys
```
    - initialOrient
```
boolean initialOrient
```
    - lineFigures
```
Line[] lineFigures
```
    - lines
```
LineSegment[] lines
```
    - oldPolytope
```
Polytope oldPolytope
```
    - panel
```
java.awt.Panel panel
```
    - pendingBonds
```
java.util.ArrayList<E extends java.lang.Object> pendingBonds
```
    - planeAngles
```
double[] planeAngles
```
    - planeColor
```
java.awt.Color planeColor
```
    - planeIntersections
```
Vector[] planeIntersections
```
    - planes
```
Plane[] planes
```
    - planeTriangles
```
Triangle[][] planeTriangles
```
    - polytopeLines
```
Line[] polytopeLines
```
    - rMax
```
Vector rMax
```
    - rMin
```
Vector rMin
```
    - space
```
Space space
```
    - work
```
Vector work
```
    - work2
```
Vector work2
```
    - work3
```
Vector work3
```
- Class etomica.graphics.DisplayBoxSpin2D extends DisplayBoxCanvas2D implements Serializable
  - Serialized Fields
    - latticeIndex
```
int[] latticeIndex
```
    - neighborSiteManager
```
NeighborSiteManager neighborSiteManager
```
    - spinWidth
```
int spinWidth
```
- Class etomica.graphics.DisplayCanvas extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - controller
```
Controller controller
```
    - displayBox
```
DisplayBox displayBox
```
    - drawBoundary
```
int drawBoundary
```
      Variable specifying whether a line tracing the boundary of the display should be drawn Default value is BOUNDARY_OUTLINE
    - movable
```
boolean movable
```
      Flag to indicate if display can be moved
    - offScreen
```
java.awt.Image offScreen
```
    - osg
```
java.awt.Graphics osg
```
    - pixel
```
Pixel pixel
```
    - resizable
```
boolean resizable
```
      Flag to indicate if display can be resized
    - writeScale
```
boolean writeScale
```
      Flag to indicate if value of scale should be superimposed on image
- Class etomica.graphics.DisplayPolytope.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.graphics.DisplayPolytopeCanvas2D extends DisplayCanvas implements Serializable
  - Serialized Fields
    - displayPolytope
```
DisplayPolytope displayPolytope
```
- Class etomica.graphics.DisplayPolytopeCanvasG3DSys extends DisplayCanvas implements Serializable
  - Serialized Fields
    - backgroundColor
```
java.awt.Color backgroundColor
```
    - boundaryFrameColor
```
java.awt.Color boundaryFrameColor
```
    - displayPolytope
```
DisplayPolytope displayPolytope
```
    - gsys
```
G3DSys gsys
```
    - initialOrient
```
boolean initialOrient
```
    - panel
```
java.awt.Panel panel
```
    - polytopeLines
```
Line[] polytopeLines
```
- Class etomica.graphics.EtomicaPlot extends ptolemy.plot.Plot implements Serializable
  - Serialized Fields
    - displayPlot
```
DisplayPlot displayPlot
```
    - needUpdate
```
boolean needUpdate
```
- Class etomica.graphics.PropertyText extends javax.swing.JTextField implements Serializable
- Class etomica.graphics.SimulationPanel extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - controlPanel
```
javax.swing.JPanel controlPanel
```
    - footerPanel
```
javax.swing.JPanel footerPanel
```
    - graphicsPanel
```
javax.swing.JPanel graphicsPanel
```
    - metricPanel
```
javax.swing.JPanel metricPanel
```
    - plotPanel
```
javax.swing.JPanel plotPanel
```
    - tabbedPane
```
javax.swing.JTabbedPane tabbedPane
```
    - toolbar
```
DefaultToolbar toolbar
```
    - toolbarPanel
```
javax.swing.JPanel toolbarPanel
```
Package etomica.integrator
- Class etomica.integrator.IntegratorPT.BoxTracker extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - data
```
DataDoubleArray data
```
    - dataInfo
```
DataDoubleArray.DataInfoDoubleArray dataInfo
```
    - dtrack
```
double[] dtrack
```
    - tag
```
DataTag tag
```
    - track
```
int[] track
```
- Class etomica.integrator.IntegratorRigidIterative.AtomForceAgent extends java.lang.Object implements Serializable
  - Serialized Fields
    - force
```
Vector force
```
- Class etomica.integrator.IntegratorRigidIterative.MoleculeAgent extends java.lang.Object implements Serializable
  - Serialized Fields
    - force
```
Vector force
```
    - torque
```
Vector torque
```
Package etomica.integrator.mcmove
- Class etomica.integrator.mcmove.MCMoveSwapConfiguration.SwapFactory extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.integrator.mcmove.MCMoveTrialCompletedEvent extends MCMoveEvent implements Serializable
  - Serialized Fields
    - isAccepted
```
boolean isAccepted
```
    - moveManager
```
MCMoveManager moveManager
```
- Class etomica.integrator.mcmove.MCMoveTrialInitiatedEvent extends MCMoveEvent implements Serializable
  - Serialized Fields
    - moveManager
```
MCMoveManager moveManager
```
Package etomica.lattice
- Class etomica.lattice.BravaisLattice extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - latticeVector
```
Vector latticeVector
```
    - primitive
```
Primitive primitive
```
- Class etomica.lattice.BravaisLatticeCrystal extends BravaisLattice implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - basis
```
Basis basis
```
    - crystalIndex
```
int[] crystalIndex
```
    - D
```
int D
```
    - position
```
Vector position
```
- Class etomica.lattice.CellLattice.NeighborIterator extends RectangularLatticeNbrIteratorSquare implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - idx
```
int[] idx
```
    - neighborDistance
```
double neighborDistance
```
    - previousDimensions
```
Vector previousDimensions
```
- Class etomica.lattice.IndexIteratorRectangular extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - count
```
int count
```
    - D
```
int D
```
    - index
```
int[] index
```
    - indexCopy
```
int[] indexCopy
```
    - maxCount
```
int maxCount
```
    - size
```
int[] size
```
- Class etomica.lattice.IndexIteratorTriangular extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - allowEqualElements
```
boolean allowEqualElements
```
    - D
```
int D
```
    - hasNext
```
boolean hasNext
```
    - index
```
int[] index
```
    - indexCopy
```
int[] indexCopy
```
    - maxElement
```
int maxElement
```
    - maxElementMin
```
int maxElementMin
```
- Class etomica.lattice.IndexIteratorTriangularPermutations extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - coreIterator
```
IndexIteratorTriangular coreIterator
```
    - counts
```
int[] counts
```
    - D
```
int D
```
    - hasNext
```
boolean hasNext
```
    - nextIterate
```
int[] nextIterate
```
    - permutationIterator
```
PermutationDegenerateIterator permutationIterator
```
    - permute
```
int[] permute
```
    - vals
```
int[] vals
```
- Class etomica.lattice.LatticeCubicBcc extends BravaisLatticeCrystal implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.LatticeCubicDiamond extends BravaisLatticeCrystal implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.LatticeCubicFcc extends BravaisLatticeCrystal implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.LatticeCubicSimple extends BravaisLattice implements Serializable
  - Serialized Fields
    - primitive
```
PrimitiveCubic primitive
```
- Class etomica.lattice.LatticeHcp extends BravaisLatticeCrystal implements Serializable
- Class etomica.lattice.LatticeHcp4 extends BravaisLatticeCrystal implements Serializable
- Class etomica.lattice.LatticeOrthorhombicHexagonal extends BravaisLatticeCrystal implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.LatticePlane extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - delta
```
Vector delta
```
    - millerIndices
```
int[] millerIndices
```
    - normal
```
Vector normal
```
    - origin
```
Vector origin
```
    - plane
```
Plane plane
```
    - primitive
```
Primitive primitive
```
    - space
```
Space space
```
- Class etomica.lattice.LatticeSumCrystal.DataGroupLSC extends DataGroup implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.RectangularLattice.Iterator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cursor
```
int cursor
```
    - idx
```
int[] idx
```
    - lattice
```
RectangularLattice lattice
```
    - size
```
int size
```
- Class etomica.lattice.RectangularLatticeNbrIterator extends java.lang.Object implements Serializable
  - Serialized Fields
    - centralSite
```
int[] centralSite
```
    - cursor
```
int cursor
```
    - D
```
int D
```
    - direction
```
IteratorDirective.Direction direction
```
    - doDown
```
boolean doDown
```
    - doUp
```
boolean doUp
```
    - isPeriodic
```
boolean[] isPeriodic
```
    - lattice
```
RectangularLattice lattice
```
    - latticeIndex
```
int[] latticeIndex
```
    - needNeighborUpdate
```
boolean needNeighborUpdate
```
    - neighborCount
```
int neighborCount
```
    - neighbors
```
int[] neighbors
```
- Class etomica.lattice.RectangularLatticeNbrIteratorAdjacent extends RectangularLatticeNbrIterator implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.RectangularLatticeNbrIteratorSquare extends RectangularLatticeNbrIterator implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - furthestNeighborDelta
```
int furthestNeighborDelta
```
    - halfNeighborCount
```
int halfNeighborCount
```
    - range
```
int[] range
```
Package etomica.lattice.crystal
- Class etomica.lattice.crystal.Basis extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - scaledCoordinates
```
Vector[] scaledCoordinates
```
- Class etomica.lattice.crystal.BasisBetaSnA5 extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.BasisCubicBcc extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.BasisCubicDiamond extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.BasisCubicFcc extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.BasisCubicFccDiamond extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.BasisHcp extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.BasisHcp4 extends Basis implements Serializable
- Class etomica.lattice.crystal.BasisHcpBaseCentered extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.BasisMonatomic extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.BasisOrthorhombicHexagonal extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.Primitive extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angle
```
double[] angle
```
    - D
```
int D
```
    - idx
```
int[] idx
```
    - latticeVectors
```
Vector[] latticeVectors
```
    - size
```
double[] size
```
    - space
```
Space space
```
- Class etomica.lattice.crystal.PrimitiveBcc extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cubicSize
```
double cubicSize
```
    - unitVectors
```
Vector[] unitVectors
```
- Class etomica.lattice.crystal.PrimitiveCubic extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - aBC
```
double aBC
```
- Class etomica.lattice.crystal.PrimitiveFcc extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cubicSize
```
double cubicSize
```
    - unitVectors
```
Vector[] unitVectors
```
- Class etomica.lattice.crystal.PrimitiveGeneral extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.PrimitiveHCP4 extends PrimitiveOrthorhombic implements Serializable
- Class etomica.lattice.crystal.PrimitiveHexagonal extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ab
```
double ab
```
- Class etomica.lattice.crystal.PrimitiveHexagonal.PrimitiveHexagonalReciprocal extends PrimitiveHexagonal implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.PrimitiveHexagonal2D extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ab
```
double ab
```
- Class etomica.lattice.crystal.PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal extends PrimitiveHexagonal2D implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.PrimitiveMonoclinic extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal extends PrimitiveMonoclinic implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.PrimitiveOrthorhombic extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.PrimitiveTetragonal extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - ab
```
double ab
```
- Class etomica.lattice.crystal.PrimitiveTriclinic extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.lattice.crystal.PrimitiveTrigonal extends Primitive implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.math
- Class etomica.math.DoubleRange extends java.lang.Object implements Serializable
  - Serialized Fields
    - max
```
double max
```
    - min
```
double min
```
Package etomica.math.discrete
- Class etomica.math.discrete.CombinationIterator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - index
```
int[] index
```
    - indexCopy
```
int[] indexCopy
```
    - k
```
int k
```
    - k0unset
```
boolean k0unset
```
    - n
```
int n
```
- Class etomica.math.discrete.PermutationDegenerateIterator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - degeneracy
```
int[] degeneracy
```
    - element
```
int element
```
    - hasNext
```
boolean hasNext
```
    - iLast
```
int[] iLast
```
    - indexIterator
```
IndexIteratorTriangular indexIterator
```
    - n
```
int n
```
    - nextIndex
```
int[] nextIndex
```
    - subIndex
```
int[] subIndex
```
    - subPermutation
```
PermutationDegenerateIterator subPermutation
```
    - zero
```
int[] zero
```
- Class etomica.math.discrete.PermutationIterator extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - hasNext
```
boolean hasNext
```
    - iLast
```
int iLast
```
    - n
```
int n
```
    - subIndex
```
int[] subIndex
```
    - subPermutation
```
PermutationIterator subPermutation
```
Package etomica.math.function
- Class etomica.math.function.Function.Abs extends java.lang.Object implements Serializable
- Class etomica.math.function.Function.Chop extends java.lang.Object implements Serializable
  - Serialized Fields
    - eps
```
double eps
```
- Class etomica.math.function.Function.Constant extends java.lang.Object implements Serializable
  - Serialized Fields
    - c
```
double c
```
- Class etomica.math.function.Function.Exp extends java.lang.Object implements Serializable
- Class etomica.math.function.Function.Identity extends java.lang.Object implements Serializable
- Class etomica.math.function.Function.Linear extends java.lang.Object implements Serializable
  - Serialized Fields
    - a
```
double a
```
    - b
```
double b
```
    - ra
```
double ra
```
- Class etomica.math.function.Function.Log extends java.lang.Object implements Serializable
- Class etomica.math.function.Function.Reciprocal extends java.lang.Object implements Serializable
- Class etomica.math.function.Function.Sqrt extends java.lang.Object implements Serializable
- Class etomica.math.function.FunctionChain extends java.lang.Object implements Serializable
  - Serialized Fields
    - head
```
FunctionChain.Link head
```
    - tail
```
FunctionChain.Link tail
```
- Class etomica.math.function.FunctionChain.Link extends java.lang.Object implements Serializable
  - Serialized Fields
    - function
```
IFunction function
```
    - next
```
FunctionChain.Link next
```
    - previous
```
FunctionChain.Link previous
```
Package etomica.math.geometry
- Class etomica.math.geometry.Circle extends Hypersphere implements Serializable
- Class etomica.math.geometry.Cube extends Hexahedron implements Serializable
  - Serialized Fields
    - edgeLength
```
double edgeLength
```
    - n
```
double n
```
    - p
```
double p
```
- Class etomica.math.geometry.Cuboid extends Hexahedron implements Serializable
  - Serialized Fields
    - edgeLengths
```
Vector edgeLengths
```
    - pa
```
double pa
```
    - pb
```
double pb
```
    - pc
```
double pc
```
- Class etomica.math.geometry.Hexahedron extends Polyhedron implements Serializable
- Class etomica.math.geometry.Hypersphere extends java.lang.Object implements Serializable
  - Serialized Fields
    - D
```
int D
```
    - position
```
Vector position
```
    - radius
```
double radius
```
- Class etomica.math.geometry.LineSegment extends Polytope implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - edges
```
LineSegment[] edges
```
- Class etomica.math.geometry.Parallelepiped extends Hexahedron implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - a
```
Vector a
```
    - b
```
Vector b
```
    - c
```
Vector c
```
    - work
```
Vector work
```
- Class etomica.math.geometry.Parallelogram extends Polygon implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - a
```
Vector a
```
    - b
```
Vector b
```
- Class etomica.math.geometry.Plane extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - a
```
double a
```
    - b
```
double b
```
    - c
```
double c
```
    - d
```
double d
```
    - epsilon
```
double epsilon
```
      Tolerance used to judge if a given point is in the plane. Method inPlane is true if the point given to is at a distance from the plane less than this value. Default is 1e-5.
    - inPlane
```
Vector[] inPlane
```
    - space
```
Space space
```
    - work0
```
Vector work0
```
    - work1
```
Vector work1
```
- Class etomica.math.geometry.Point extends Polytope implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.math.geometry.Polygon extends Polytope implements Serializable
  - Serialized Fields
    - edges
```
LineSegment[] edges
```
- Class etomica.math.geometry.PolygonGeneral extends Polygon implements Serializable
- Class etomica.math.geometry.Polyhedron extends Polytope implements Serializable
  - Serialized Fields
    - edges
```
LineSegment[] edges
```
    - faces
```
Polygon[] faces
```
- Class etomica.math.geometry.PolyhedronGeneral extends Polyhedron implements Serializable
- Class etomica.math.geometry.Polytope extends java.lang.Object implements Serializable
  - Serialized Fields
    - D
```
int D
```
    - embeddedSpace
```
Space embeddedSpace
```
    - hyperPlanes
```
Polytope[] hyperPlanes
```
    - noTranslation
```
boolean noTranslation
```
    - position
```
Vector position
```
    - vertices
```
Vector[] vertices
```
      These vertices are used in all external representations of the polygon. Changes to them do not necessarily change the state of the polygon.
- Class etomica.math.geometry.Rectangle extends Polygon implements Serializable
  - Serialized Fields
    - edgeLengths
```
Vector2D edgeLengths
```
    - nX
```
double nX
```
    - nY
```
double nY
```
    - pX
```
double pX
```
    - pY
```
double pY
```
- Class etomica.math.geometry.Sphere extends Hypersphere implements Serializable
- Class etomica.math.geometry.Square extends Polygon implements Serializable
  - Serialized Fields
    - edgeLength
```
double edgeLength
```
    - n
```
double n
```
    - p
```
double p
```
- Class etomica.math.geometry.TruncatedOctahedron extends Polyhedron implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - edgeLength
```
double edgeLength
```
Package etomica.math.numerical
- Class etomica.math.numerical.AkimaSplineSmootherApp.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.math.numerical.AkimaSplineSmootherDyApp.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.math.numerical.FastFourierTransform extends java.lang.Object implements Serializable
  - Serialized Fields
    - imaginary
```
double[] imaginary
```
    - length
```
int length
```
    - real
```
double[] real
```
Package etomica.meta.serializers
- Class etomica.meta.serializers.VectorSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<Vector> implements Serializable
Package etomica.models.co2
- Class etomica.models.co2.ConformationCO2 extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
    - vector
```
Vector vector
```
Package etomica.models.nitrogen
- Class etomica.models.nitrogen.ConformationNitrogen extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
    - vector
```
Vector vector
```
- Class etomica.models.nitrogen.ConformationNitrogenShellModel extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
    - vector
```
Vector vector
```
- Class etomica.models.nitrogen.CoordinateDefinitionNitrogen extends CoordinateDefinitionMolecule implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomGroupAction
```
MoleculeChildAtomAction atomGroupAction
```
    - atomGroupActionTranslate
```
MoleculeChildAtomAction atomGroupActionTranslate
```
    - axis
```
Vector axis
```
    - configuration
```
Configuration configuration
```
    - isAlpha
```
boolean isAlpha
```
    - isBeta
```
boolean isBeta
```
    - isBetaHCP
```
boolean isBetaHCP
```
    - isBetaLatticeSum
```
boolean isBetaLatticeSum
```
    - isDoLatticeSum
```
boolean isDoLatticeSum
```
    - isGamma
```
boolean isGamma
```
    - orientationManager
```
MoleculeAgentManager<E> orientationManager
```
    - orientVector
```
Vector orientVector
```
    - positionVector
```
Vector[] positionVector
```
    - random
```
IRandom random
```
    - rotationTensor
```
RotationTensor3D rotationTensor
```
    - rotDim
```
int rotDim
```
    - tensor
```
Tensor3D tensor
```
    - translateBy
```
AtomActionTranslateBy translateBy
```
    - xzOrientationTensor
```
Tensor[] xzOrientationTensor
```
    - yOrientationTensor
```
Tensor[] yOrientationTensor
```
- Class etomica.models.nitrogen.CoordinateDefinitionNitrogen.OrientationAgentSource extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox extends CoordinateDefinitionMolecule implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomGroupAction
```
MoleculeChildAtomAction atomGroupAction
```
    - axis
```
Vector axis
```
    - configuration
```
Configuration configuration
```
    - innersegment
```
int[][] innersegment
```
    - isAlpha
```
boolean isAlpha
```
    - isGamma
```
boolean isGamma
```
    - orientationManager
```
MoleculeAgentManager<E> orientationManager
```
    - random
```
IRandom random
```
    - rotationTensor
```
RotationTensor3D rotationTensor
```
    - segment
```
int[] segment
```
    - speciesA
```
ISpecies speciesA
```
    - speciesB
```
ISpecies speciesB
```
    - tensor
```
Tensor3D tensor
```
    - xzOrientationTensor
```
Tensor[] xzOrientationTensor
```
    - yOrientationTensor
```
Tensor[] yOrientationTensor
```
- Class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.models.nitrogen.LatticeSumCrystalMolecular.DataGroupLSC extends DataGroup implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.models.nitrogen.MeterNormalizedCoord extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - coordinateDefinition
```
CoordinateDefinition coordinateDefinition
```
    - data
```
DataGroup data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - dof
```
int dof
```
    - histogramU
```
HistogramExpanding[] histogramU
```
    - isVolFluctuation
```
boolean isVolFluctuation
```
    - name
```
java.lang.String name
```
    - tag
```
DataTag tag
```
    - uDistributions
```
DataDoubleArray[] uDistributions
```
    - uDistributionsInfo
```
DataDoubleArray.DataInfoDoubleArray[] uDistributionsInfo
```
- Class etomica.models.nitrogen.MeterNormalizedCoordBeta extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - coordinateDefinition
```
CoordinateDefinition coordinateDefinition
```
    - data
```
DataGroup data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - dof
```
int dof
```
    - histogramU
```
HistogramExpanding[] histogramU
```
    - tag
```
DataTag tag
```
    - uDistributions
```
DataDoubleArray[] uDistributions
```
    - uDistributionsInfo
```
DataDoubleArray.DataInfoDoubleArray[] uDistributionsInfo
```
- Class etomica.models.nitrogen.MeterOrientationDistribution extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angle
```
double[] angle
```
    - axes
```
Vector[] axes
```
    - b
```
Vector b
```
    - c
```
Vector c
```
    - coordinateDefinition
```
CoordinateDefinitionNitrogen coordinateDefinition
```
    - data
```
DataGroup data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - dof
```
int dof
```
    - histogramU
```
HistogramExpanding[] histogramU
```
    - molAxis
```
Vector molAxis
```
    - tag
```
DataTag tag
```
    - temp
```
Vector temp
```
    - uDistributions
```
DataDoubleArray[] uDistributions
```
    - uDistributionsInfo
```
DataDoubleArray.DataInfoDoubleArray[] uDistributionsInfo
```
- Class etomica.models.nitrogen.MeterRotationDistributionGroup extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angle
```
double angle
```
    - coordinateDefinition
```
CoordinateDefinitionNitrogen coordinateDefinition
```
    - data
```
DataGroup data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - histogramExpanding
```
HistogramExpanding histogramExpanding
```
    - histogramNotSimple
```
HistogramNotSoSimple histogramNotSimple
```
    - initOrient
```
Vector initOrient
```
    - molAxis
```
Vector molAxis
```
    - tag
```
DataTag tag
```
    - uDistributions
```
DataDoubleArray[] uDistributions
```
    - uDistributionsInfo
```
DataDoubleArray.DataInfoDoubleArray[] uDistributionsInfo
```
Package etomica.models.traPPE
- Class etomica.models.traPPE.SpeciesFactoryMethanol extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.models.water
- Class etomica.models.water.ConfigurationFileTIP4P extends ConfigurationFile implements Serializable
  - Serialized Fields
    - isIce
```
boolean isIce
```
    - space
```
Space space
```
- Class etomica.models.water.ConformationWaterGCPM extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angleHOH
```
double angleHOH
```
    - bondLengthOH
```
double bondLengthOH
```
    - rOM
```
double rOM
```
    - space
```
Space space
```
- Class etomica.models.water.ConformationWaterGCPMCOM extends ConformationWaterGCPM implements Serializable
- Class etomica.models.water.ConformationWaterTIP4P extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
- Class etomica.models.water.OrientationCalcWater3P extends ConformationWater3P implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomPositionCOM
```
MoleculePositionCOM atomPositionCOM
```
    - com0
```
Vector com0
```
    - initialized
```
boolean initialized
```
    - previousTensor
```
RotationTensor previousTensor
```
    - rotationTensor
```
RotationTensor3D rotationTensor
```
    - workTensor
```
RotationTensor workTensor
```
    - xWork
```
Vector xWork
```
    - yWork
```
Vector yWork
```
    - zWork
```
Vector zWork
```
- Class etomica.models.water.OrientationCalcWater4P extends ConformationWaterTIP4P implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomPositionCOM
```
MoleculePositionCOM atomPositionCOM
```
    - com0
```
Vector com0
```
    - initialized
```
boolean initialized
```
    - previousTensor
```
RotationTensor previousTensor
```
    - rotationTensor
```
RotationTensor3D rotationTensor
```
    - workTensor
```
RotationTensor workTensor
```
    - xWork
```
Vector xWork
```
    - yWork
```
Vector yWork
```
    - zWork
```
Vector zWork
```
Package etomica.modifier
- Class etomica.modifier.ModifierFunctionWrapper extends ModifierGeneral implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - function
```
FunctionInvertible function
```
- Class etomica.modifier.ModifierGeneral extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readObject
```
private void readObject(java.io.ObjectInputStream s)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException
```
      Throws:
      
      java.io.IOException
      
      java.lang.ClassNotFoundException
  - Serialized Fields
    - dimension
```
Dimension dimension
```
    - label
```
java.lang.String label
```
    - nObjects
```
int nObjects
```
    - object
```
java.lang.Object[] object
```
    - property
```
java.lang.String property
```
- Class etomica.modifier.ModifierNMolecule extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - species
```
ISpecies species
```
- Class etomica.modifier.ModifyAction extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - modifier
```
Modifier modifier
```
    - value
```
double value
```
Package etomica.modules
- Class etomica.modules.ModuleLauncher extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - argsField
```
javax.swing.JTextField argsField
```
    - currentModule
```
EtomicaModuleInfo currentModule
```
    - descriptionPane
```
javax.swing.JTextPane descriptionPane
```
Package etomica.modules.adsorption
- Class etomica.modules.adsorption.AdsorptionGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.modules.adsorption.MeterProfileByVolumeAdsorption extends MeterProfileByVolume implements Serializable
  - Serialized Fields
    - xMax
```
double xMax
```
    - xMin
```
double xMin
```
Package etomica.modules.catalysis
- Class etomica.modules.catalysis.CatalysisGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.modules.catalysis.ConfigurationCatalysis.BasisOrthorhombicHexagonal3D extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.chainequilibrium
- Class etomica.modules.chainequilibrium.ChainEquilibriumGraphic.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical extends ConfigurationLattice implements Serializable
  
  serialVersionUID:
  
  3L
  - Serialized Fields
    - random
```
IRandom random
```
    - speciesInitiator
```
ISpecies speciesInitiator
```
    - speciesMonomer
```
ISpecies speciesMonomer
```
- Class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.modules.chainequilibrium.MeterChainLength extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - agentManager
```
AtomLeafAgentManager<E> agentManager
```
    - box
```
Box box
```
    - data
```
DataFunction data
```
    - dataInfo
```
DataFunction.DataInfoFunction dataInfo
```
    - ignoredAtomType
```
AtomType ignoredAtomType
```
    - tag
```
DataTag tag
```
    - tagManager
```
AtomLeafAgentManager<E> tagManager
```
    - xData
```
DataDoubleArray xData
```
    - xDataInfo
```
DataDoubleArray.DataInfoDoubleArray xDataInfo
```
    - xTag
```
DataTag xTag
```

Package etomica.modules.clustergenerator

Class etomica.modules.clustergenerator.ClusterPanel extends Plot implements Serializable
- Serialized Fields
  - cluster
```
ClusterDiagram cluster
```
  - drawNumbersBlack
```
boolean drawNumbersBlack
```
  - drawNumbersWhite
```
boolean drawNumbersWhite
```
  - drawPoints
```
boolean drawPoints
```
  - eBonds
```
boolean eBonds
```
  - fBonds
```
boolean fBonds
```
  - x
```
double[] x
```
  - y
```
double[] y
```

Class etomica.modules.clustergenerator.MyApplet extends javax.swing.JApplet implements Serializable

Serialized Fields

allPermutations
```
boolean allPermutations
```
allPermutationsCB
```
java.awt.Checkbox allPermutationsCB
```

bondTypeToggler

MyApplet.BondTypeToggler bondTypeToggler

checkBox
```
java.awt.Checkbox checkBox
```
checkBox1
```
java.awt.Checkbox checkBox1
```
checkBox2
```
java.awt.Checkbox checkBox2
```
cluster
```
ClusterDiagram cluster
```
displayPanel
```
javax.swing.JTabbedPane displayPanel
```
eDrawBondsCB
```
java.awt.Checkbox eDrawBondsCB
```

excludeArticulationPairCB

java.awt.Checkbox excludeArticulationPairCB

excludeArticulationPointCB

java.awt.Checkbox excludeArticulationPointCB

excludeNodalPointCB
```
java.awt.Checkbox excludeNodalPointCB
```
fDrawBondsCB
```
java.awt.Checkbox fDrawBondsCB
```
firstTimeDrawn
```
boolean firstTimeDrawn
```
gbConst
```
java.awt.GridBagConstraints gbConst
```
gbLayout
```
java.awt.GridBagLayout gbLayout
```
generateGraphicsCB
```
java.awt.Checkbox generateGraphicsCB
```
generator
```
ClusterGenerator generator
```
goButton
```
javax.swing.JButton goButton
```
graphicOut
```
javax.swing.JScrollPane graphicOut
```
graphicOut2
```
javax.swing.JPanel graphicOut2
```
graphicPanel
```
javax.swing.JPanel graphicPanel
```

graphicsToggler

MyApplet.GraphicsToggler graphicsToggler

managerPanel
```
javax.swing.JPanel managerPanel
```
myPanel
```
javax.swing.JPanel myPanel
```
nBody
```
int nBody
```
nBodyField
```
java.awt.TextField nBodyField
```
nRootField
```
java.awt.TextField nRootField
```
onlyDoublyConnectedCB
```
java.awt.Checkbox onlyDoublyConnectedCB
```
onlySinglyConnectedCB
```
java.awt.Checkbox onlySinglyConnectedCB
```
output
```
java.awt.TextArea output
```
radioB
```
javax.swing.JRadioButton radioB
```
radioB1
```
javax.swing.JRadioButton radioB1
```
reeHooverCB
```
java.awt.Checkbox reeHooverCB
```
running
```
boolean running
```
starter
```
MyApplet.Starter starter
```
stopNow
```
boolean stopNow
```
stopper
```
MyApplet.Stopper stopper
```
textAreaForBonds
```
java.awt.TextArea textAreaForBonds
```
totalNCluster
```
javax.swing.JTextField totalNCluster
```

Class etomica.modules.clustergenerator.Plot extends java.awt.Component implements Serializable

Serialized Fields

awtColor
```
java.awt.Color[] awtColor
```
awtColorString
```
java.lang.String[] awtColorString
```

colorTable

java.util.Hashtable<K extends java.lang.Object,V extends java.lang.Object> colorTable

osg
```
java.awt.Graphics osg
```
umax
```
int umax
```
umin
```
int umin
```
vmax
```
int vmax
```
vmin
```
int vmin
```
xmax_
```
double xmax_
```
xmin_
```
double xmin_
```
xPixels
```
int xPixels
```
ymax_
```
double ymax_
```
ymin_
```
double ymin_
```
yPixels
```
int yPixels
```

Package etomica.modules.colloid
- Class etomica.modules.colloid.ColloidGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.crystalviewer
- Class etomica.modules.crystalviewer.CrystalViewer extends SimulationPanel implements Serializable
  - Serialized Fields
    - boundary
```
BoundaryDeformableLattice boundary
```
    - box
```
Box box
```
    - center
```
Vector center
```
    - clipPlaneEditor
```
ClipPlaneEditor clipPlaneEditor
```
    - displayBox
```
DisplayBox displayBox
```
    - latticeEditor
```
LatticeEditor latticeEditor
```
    - latticePlane
```
LatticePlane latticePlane
```
    - sim
```
Simulation sim
```
    - species
```
SpeciesGeneral species
```
- Class etomica.modules.crystalviewer.CrystalViewer.Applet extends javax.swing.JApplet implements Serializable
Package etomica.modules.dcvgcmd
- Class etomica.modules.dcvgcmd.ConfigurationLatticeTube extends ConfigurationLattice implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomActionTranslateTo
```
MoleculeActionTranslateTo atomActionTranslateTo
```
    - indexIterator
```
IndexIteratorSizable indexIterator
```
    - length
```
double length
```
    - speciesSpheres
```
SpeciesGeneral[] speciesSpheres
```
    - speciesTube
```
SpeciesGeneral speciesTube
```
- Class etomica.modules.dcvgcmd.DCVGCMDGraphic.Applet extends javax.swing.JApplet implements Serializable
Package etomica.modules.droplet
- Class etomica.modules.droplet.DropletAtomicGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.modules.droplet.DropletGraphic.Applet extends javax.swing.JApplet implements Serializable
Package etomica.modules.ensembles
- Class etomica.modules.ensembles.LJMCGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.glass
- Class etomica.modules.glass.DisplayBoxCanvas2DGlass extends DisplayBoxCanvas2D implements Serializable
  - Serialized Fields
    - configIndex
```
int configIndex
```
    - configStorage
```
ConfigurationStorage configStorage
```
    - dr
```
Vector dr
```
    - drawDisplacement
```
boolean drawDisplacement
```
    - flipDisplacement
```
boolean flipDisplacement
```
- Class etomica.modules.glass.DisplayBoxCanvas3DGlass extends DisplayBoxCanvasG3DSys implements Serializable
  - Serialized Fields
    - bonds
```
Bond[] bonds
```
    - configIndex
```
int configIndex
```
    - configStorage
```
ConfigurationStorage configStorage
```
    - dr
```
Vector dr
```
    - drawDisplacement
```
boolean drawDisplacement
```
    - flipDisplacement
```
boolean flipDisplacement
```
    - oldBalls
```
Ball[] oldBalls
```
Package etomica.modules.insertion
- Class etomica.modules.insertion.InsertionGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.interfacial
- Class etomica.modules.interfacial.DataSourceTensorVirialHardProfile extends DataSourceTensorVirialHard implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - binSize
```
double binSize
```
    - halfL
```
double halfL
```
    - L
```
double L
```
    - lastProfileTime
```
double lastProfileTime
```
    - Li
```
double Li
```
    - nBins
```
int nBins
```
    - profileData
```
DataGroup profileData
```
    - profileDataInfo
```
DataGroup.DataInfoGroup profileDataInfo
```
    - virialProfile
```
double[][] virialProfile
```
    - virialProfileWork
```
double[][] virialProfileWork
```
    - xData
```
DataDoubleArray xData
```
    - xDataInfo
```
DataDoubleArray.DataInfoDoubleArray xDataInfo
```
    - xTag
```
DataTag xTag
```
- Class etomica.modules.interfacial.InterfacialSWGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.ljmd
- Class etomica.modules.ljmd.LjmdGraphic.Applet extends javax.swing.JApplet implements Serializable
Package etomica.modules.materialfracture
- Class etomica.modules.materialfracture.MaterialFractureGraphic.Applet extends javax.swing.JApplet implements Serializable
Package etomica.modules.mu
- Class etomica.modules.mu.MuGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.multiharmonic
- Class etomica.modules.multiharmonic.MultiharmonicGraphic.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.modules.multiharmonic.MultiharmonicGraphicMC.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.multiharmonic.mbar
- Class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.multiharmonic.overlap
- Class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.multiharmonic.umbrella
- Class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.pistoncylinder
- Class etomica.modules.pistoncylinder.ApiFilteredCylinder extends ApiLeafAtoms implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - filter
```
ApiFilteredCylinder.AtomFilterInCylinder filter
```
- Class etomica.modules.pistoncylinder.PistonCylinderGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.modules.pistoncylinder.PistonPlane extends Plane implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pistonPotential
```
P1HardMovingBoundary pistonPotential
```
Package etomica.modules.reactionequilibrium
- Class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MassEditor extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - mass
```
DeviceBox mass
```
- Class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MySpeciesEditor extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - nSlider
```
DeviceNSelector nSlider
```
Package etomica.modules.rheology
- Class etomica.modules.rheology.RheologyGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.rosmosis
- Class etomica.modules.rosmosis.ReverseOsmosisGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.sam
- Class etomica.modules.sam.SamGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.modules.sam.WallPlane extends Plane implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - wallPotential
```
P1WCAWall wallPotential
```
Package etomica.modules.statistics
- Class etomica.modules.statistics.HistoryStatistics extends HistoryScrolling implements Serializable
Package etomica.modules.swmd
- Class etomica.modules.swmd.SwmdGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.modules.vle
- Class etomica.modules.vle.B2Fit extends SimulationPanel implements Serializable
  - Serialized Fields
    - dPlot
```
DevicePlotPoints dPlot
```
- Class etomica.modules.vle.B2Fit.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.modules.vle.VLE.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.molecule
- Class etomica.molecule.Molecule extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - childList
```
AtomArrayList childList
```
    - index
```
int index
```
    - species
```
ISpecies species
```
- Class etomica.molecule.MoleculeOriented extends Molecule implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - orientation
```
IOrientation3D orientation
```
    - position
```
Vector position
```
- Class etomica.molecule.MoleculeOrientedDynamic extends MoleculeOriented implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angularMomentum
```
Vector angularMomentum
```
    - velocity
```
Vector velocity
```
- Class etomica.molecule.MoleculePositionCOM extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - center
```
Vector center
```
- Class etomica.molecule.MoleculePositionFirstAtom extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.molecule.MoleculePositionGeometricCenter extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - center
```
Vector center
```
- Class etomica.molecule.MoleculePositionGeometricCenterAlkaneEH extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - center
```
Vector center
```
    - speciesAlkane
```
ISpecies speciesAlkane
```
- Class etomica.molecule.MoleculePositionGeometricCenterPBC extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - boundary
```
Boundary boundary
```
    - center
```
Vector center
```
    - dr
```
Vector dr
```
- Class etomica.molecule.MoleculeSourceRandomMolecule extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - random
```
IRandom random
```
- Class etomica.molecule.MoleculeToMoleculeListSpecies extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - moleculeList
```
IMoleculeList moleculeList
```
    - species
```
ISpecies species
```
- Class etomica.molecule.MoleculeToMoleculeSetFixed extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - moleculeArrayList
```
MoleculeArrayList moleculeArrayList
```
Package etomica.molecule.iterator
- Class etomica.molecule.iterator.IteratorFactory extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.molecule.iterator.MoleculeIteratorAll extends java.lang.Object implements Serializable
  - Serialized Fields
    - box
```
Box box
```
    - next
```
MoleculeArrayList next
```
    - nextCursor
```
int nextCursor
```
    - oneIterate
```
boolean oneIterate
```
    - species
```
ISpecies[] species
```
- Class etomica.molecule.iterator.MoleculeIteratorAllMolecules extends MoleculeIteratorArrayListSimple implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.molecule.iterator.MoleculeIteratorArrayList extends MoleculeIteratorArrayListSimple implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomToAtomSet
```
MoleculeToMoleculeList atomToAtomSet
```
    - atomToIndex
```
MoleculeToIndex atomToIndex
```
    - numToSkip
```
int numToSkip
```
    - startAtom
```
IMolecule startAtom
```
    - upListNow
```
boolean upListNow
```
- Class etomica.molecule.iterator.MoleculeIteratorArrayListSimple extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - atomSetSinglet
```
MoleculeSetSinglet atomSetSinglet
```
    - cursor
```
int cursor
```
      Index of element to be returned by subsequent call to next.
    - list
```
IMoleculeList list
```
- Class etomica.molecule.iterator.MoleculeIteratorMolecule extends MoleculeIteratorArrayListSimple implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - littleList
```
MoleculeArrayList littleList
```
    - species
```
ISpecies species
```
    - targetAtom
```
IMolecule targetAtom
```
- Class etomica.molecule.iterator.MoleculeIteratorSinglet extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atom
```
IMolecule atom
```
    - atomSetSinglet
```
MoleculeSetSinglet atomSetSinglet
```
    - hasNext
```
boolean hasNext
```
- Class etomica.molecule.iterator.MpiInnerFixed extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - aiInner
```
MoleculeIterator aiInner
```
    - aiOuter
```
MoleculeIterator aiOuter
```
    - doSwap
```
boolean doSwap
```
    - pair
```
MoleculePair pair
```
- Class etomica.molecule.iterator.MpiInnerVariable extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - aiInner
```
MoleculeIteratorMoleculeDependent aiInner
```
      The iterators used to generate the sets of atoms.
    - aiOuter
```
MoleculeIterator aiOuter
```
    - doSwap
```
boolean doSwap
```
    - pair
```
MoleculePair pair
```
- Class etomica.molecule.iterator.MpiInterArrayList extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - innerIndex
```
int innerIndex
```
    - innerList
```
IMoleculeList innerList
```
    - molecules
```
MoleculePair molecules
```
    - outerIndex
```
int outerIndex
```
    - outerList
```
IMoleculeList outerList
```
- Class etomica.molecule.iterator.MpiInterspecies1A extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - aiInner
```
MoleculeIteratorArrayListSimple aiInner
```
    - aiOuter
```
MoleculeIteratorSinglet aiOuter
```
    - allowedDirection
```
IteratorDirective.Direction allowedDirection
```
    - apiDown
```
MpiInnerFixed apiDown
```
    - apiUp
```
MpiInnerFixed apiUp
```
    - box
```
Box box
```
    - direction
```
IteratorDirective.Direction direction
```
    - iterator
```
MpiInnerFixed iterator
```
    - species0
```
ISpecies species0
```
    - species1
```
ISpecies species1
```
    - targetMolecule
```
IMolecule targetMolecule
```
- Class etomica.molecule.iterator.MpiIntraArrayList extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - innerIndex
```
int innerIndex
```
    - list
```
IMoleculeList list
```
    - molecules
```
MoleculePair molecules
```
    - outerIndex
```
int outerIndex
```
- Class etomica.molecule.iterator.MpiIntraspecies1A extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  3L
  - Serialized Fields
    - aiOuter
```
MoleculeIteratorSinglet aiOuter
```
    - apiDown
```
MpiInnerVariable apiDown
```
    - apiUp
```
MpiInnerVariable apiUp
```
    - atomToAtomSet
```
MoleculeToMoleculeListSpecies atomToAtomSet
```
    - box
```
Box box
```
    - direction
```
IteratorDirective.Direction direction
```
    - doGoDown
```
boolean doGoDown
```
    - species
```
ISpecies species
```
    - targetMolecule
```
IMolecule targetMolecule
```
    - upListNow
```
boolean upListNow
```
- Class etomica.molecule.iterator.MpiIntraspeciesAA extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atoms
```
MoleculePair atoms
```
    - innerIndex
```
int innerIndex
```
    - list
```
IMoleculeList list
```
    - outerIndex
```
int outerIndex
```
    - species
```
ISpecies species
```
- Class etomica.molecule.iterator.MpiMolecule extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - api1A
```
MoleculesetIteratorPDT api1A
```
    - apiAA
```
MoleculesetIteratorBoxDependent apiAA
```
    - box
```
Box box
```
    - iterator
```
MoleculesetIteratorBoxDependent iterator
```
Package etomica.nbr
- Class etomica.nbr.CriterionAdapter extends java.lang.Object implements Serializable
  - Serialized Fields
    - subCriterion
```
NeighborCriterion subCriterion
```
- Class etomica.nbr.CriterionBondedSimple extends CriterionAdapter implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - isBonded
```
boolean isBonded
```
- Class etomica.nbr.CriterionInterMolecular extends CriterionAdapter implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - intraCriterion
```
NeighborCriterion intraCriterion
```
    - intraMolecularOnly
```
boolean intraMolecularOnly
```
Package etomica.nbr.cell
- Class etomica.nbr.cell.Cell extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - latticeArrayIndex
```
int latticeArrayIndex
```
    - occupants
```
AtomArrayList occupants
```
- Class etomica.nbr.cell.Cell.CellFactory extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.nbr.cell.molecule
- Class etomica.nbr.cell.molecule.CellMolecular extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - latticeArrayIndex
```
int latticeArrayIndex
```
    - occupants
```
MoleculeArrayList occupants
```
- Class etomica.nbr.cell.molecule.CellMolecular.CellFactory extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.nbr.cell.molecule.Mpi1ACell extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - aiInner
```
MoleculeIterator aiInner
```
    - aiSeq
```
MoleculeIteratorArrayListSimple aiSeq
```
    - aiSeqDirectableDn
```
MoleculeIteratorArrayList aiSeqDirectableDn
```
    - aiSeqDirectableUp
```
MoleculeIteratorArrayList aiSeqDirectableUp
```
    - boxAgentManager
```
BoxAgentManager<E> boxAgentManager
```
    - cellManager
```
NeighborCellManagerMolecular cellManager
```
    - direction
```
IteratorDirective.Direction direction
```
    - doGoDown
```
boolean doGoDown
```
    - inCentralCell
```
boolean inCentralCell
```
    - lattice
```
CellLattice lattice
```
    - latticeIndex
```
int[] latticeIndex
```
    - molToMolSetFixed
```
MoleculeToMoleculeSetFixed molToMolSetFixed
```
    - neighborIterator
```
CellLattice.NeighborIterator neighborIterator
```
    - pair
```
MoleculePair pair
```
    - periodicity
```
boolean[] periodicity
```
    - targetMolecule
```
IMolecule targetMolecule
```
    - upListNow
```
boolean upListNow
```
- Class etomica.nbr.cell.molecule.MpiAACell extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - cellIterator
```
RectangularLattice.Iterator cellIterator
```
    - interListIterator
```
MpiInterArrayList interListIterator
```
    - intraListIterator
```
MpiIntraArrayList intraListIterator
```
    - listIterator
```
MoleculesetIterator listIterator
```
    - neighborIterator
```
CellLattice.NeighborIterator neighborIterator
```
    - periodicity
```
boolean[] periodicity
```
- Class etomica.nbr.cell.molecule.NeighborCellManagerMolecular extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - agentManager
```
MoleculeAgentManager<E> agentManager
```
    - box
```
Box box
```
    - cellRange
```
int cellRange
```
    - doApplyPBC
```
boolean doApplyPBC
```
    - lattice
```
CellLattice lattice
```
    - moleculeSite
```
IMoleculePositionDefinition moleculeSite
```
    - numCells
```
int[] numCells
```
    - positionDefinition
```
IMoleculePositionDefinition positionDefinition
```
    - range
```
double range
```
    - sim
```
Simulation sim
```
    - space
```
Space space
```
    - v
```
Vector v
```
Package etomica.nbr.list.molecule
- Class etomica.nbr.list.molecule.MoleculeNeighborLists extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - downList
```
MoleculeArrayList[] downList
```
    - upList
```
MoleculeArrayList[] upList
```
- Class etomica.nbr.list.molecule.MoleculePotentialList extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - isInteractingList
```
boolean[] isInteractingList
```
- Class etomica.nbr.list.molecule.NeighborCellManagerListMolecular extends NeighborCellManagerMolecular implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - potentialMaster
```
PotentialMasterListMolecular potentialMaster
```
- Class etomica.nbr.list.molecule.NeighborListManagerMolecular extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - agentManager1Body
```
MoleculeAgentManager<E> agentManager1Body
```
    - agentManager2Body
```
MoleculeAgentManager<E> agentManager2Body
```
    - box
```
Box box
```
    - cell1ANbrIterator
```
Mpi1ACell cell1ANbrIterator
```
    - cellNbrIterator
```
MpiAACell cellNbrIterator
```
    - doApplyPBC
```
boolean doApplyPBC
```
    - eventManager
```
NeighborListEventManagerMolecular eventManager
```
    - iieCount
```
int iieCount
```
    - initialized
```
boolean initialized
```
    - moleculeSetSinglet
```
MoleculeSetSinglet moleculeSetSinglet
```
    - oldCriteria
```
NeighborCriterionMolecular[] oldCriteria
```
    - pbcEnforcer
```
BoxImposePbc pbcEnforcer
```
    - potentialMaster
```
PotentialMasterListMolecular potentialMaster
```
    - quiet
```
boolean quiet
```
    - updateInterval
```
int updateInterval
```
- Class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - potentialMaster
```
PotentialMasterListMolecular potentialMaster
```
- Class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular extends NeighborListManagerMolecular implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - pair
```
MoleculePair pair
```
Package etomica.nbr.molecule
- Class etomica.nbr.molecule.CriterionAdapterMolecular extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - subCriterion
```
NeighborCriterionMolecular subCriterion
```
- Class etomica.nbr.molecule.CriterionAllMolecular extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.nbr.molecule.CriterionSpecies extends CriterionAdapterMolecular implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - species
```
ISpecies species
```
- Class etomica.nbr.molecule.CriterionSpeciesPair extends CriterionAdapterMolecular implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - species0
```
ISpecies species0
```
    - species1
```
ISpecies species1
```

Package etomica.nbr.site

Class etomica.nbr.site.Api1ASite extends java.lang.Object implements Serializable

serialVersionUID:: 1L

Serialized Fields

boxAgentManager
```
BoxAgentManager<E> boxAgentManager
```
direction
```
IteratorDirective.Direction direction
```
doGoDown
```
boolean doGoDown
```
lattice
```
CellLattice lattice
```
latticeIndex
```
int[] latticeIndex
```

neighborIterator

RectangularLatticeNbrIterator neighborIterator

neighborSiteManager
```
NeighborSiteManager neighborSiteManager
```
pair
```
AtomPair pair
```
periodicity
```
boolean[] periodicity
```
targetAtom
```
IAtom targetAtom
```
upListNow
```
boolean upListNow
```

Package etomica.normalmode
- Class etomica.normalmode.BasisBigCell extends Basis implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.normalmode.ConformationHSDimer extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - L
```
double L
```
    - orientationX
```
IOrientation orientationX
```
    - space
```
Space space
```
- Class etomica.normalmode.CoordinateDefinition.BasisCell extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cellPosition
```
Vector cellPosition
```
    - molecules
```
IMoleculeList molecules
```
- Class etomica.normalmode.CoordinateDefinitionHSDimer extends CoordinateDefinitionMolecule implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atomGroupAction
```
MoleculeChildAtomAction atomGroupAction
```
    - axes
```
Vector[][] axes
```
    - axis
```
Vector axis
```
    - configuration
```
Configuration configuration
```
    - cosTheta
```
double[] cosTheta
```
    - orientation
```
IOrientation orientation
```
    - orientationSelector
```
CoordinateDefinitionHSDimer.IntegerFunction orientationSelector
```
- Class etomica.normalmode.CoordinateDefinitionLeaf extends CoordinateDefinition implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - u
```
double[] u
```
    - workVector
```
Vector workVector
```
- Class etomica.normalmode.CoordinateDefinitionLeafSuperBox extends CoordinateDefinitionLeaf implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - is864
```
boolean is864
```
    - speciesA
```
ISpecies speciesA
```
    - speciesB
```
ISpecies speciesB
```
- Class etomica.normalmode.CoordinateDefinitionMolecule extends CoordinateDefinition implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - inflate
```
BoxInflate inflate
```
    - initVolume
```
Vector initVolume
```
    - moleculeSiteManager
```
MoleculeAgentManager<E> moleculeSiteManager
```
    - positionDefinition
```
IMoleculePositionDefinition positionDefinition
```
    - rScale
```
double rScale
```
    - sim
```
Simulation sim
```
    - u
```
double[] u
```
    - work1
```
Vector work1
```
- Class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - positionDefinition
```
IMoleculePositionDefinition positionDefinition
```
    - space
```
Space space
```
- Class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation extends CoordinateDefinition implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - inflate
```
BoxInflate inflate
```
    - initVolume
```
Vector initVolume
```
    - moleculeSiteManager
```
MoleculeAgentManager<E> moleculeSiteManager
```
    - positionDefinition
```
IMoleculePositionDefinition positionDefinition
```
    - rScale
```
double rScale
```
    - sim
```
Simulation sim
```
    - u
```
double[] u
```
    - work1
```
Vector work1
```
- Class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - positionDefinition
```
IMoleculePositionDefinition positionDefinition
```
    - space
```
Space space
```
- Class etomica.normalmode.HTTPSoftSphereApplet.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.normalmode.MeterNormalMode extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - callCount
```
int callCount
```
    - coordinateDefinition
```
CoordinateDefinition coordinateDefinition
```
    - data
```
DataGroup data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - imaginaryT
```
double[] imaginaryT
```
    - name
```
java.lang.String name
```
    - numWaveVectors
```
int numWaveVectors
```
    - realT
```
double[] realT
```
    - tag
```
DataTag tag
```
    - waveVectorFactory
```
WaveVectorFactory waveVectorFactory
```
    - waveVectors
```
Vector[] waveVectors
```
- Class etomica.normalmode.ModifierCells3D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - mostRecentValue
```
int mostRecentValue
```
    - previousValue
```
int previousValue
```
    - species
```
ISpecies species
```
- Class etomica.normalmode.ModifierXCells2D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - mostRecentValue
```
int mostRecentValue
```
    - previousValue
```
int previousValue
```
    - species
```
ISpecies species
```
    - yCell
```
int yCell
```
- Class etomica.normalmode.ModifierYCells2D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
Box box
```
    - mostRecentValue
```
int mostRecentValue
```
    - previousValue
```
int previousValue
```
    - species
```
ISpecies species
```
    - xCell
```
int xCell
```
- Class etomica.normalmode.NormalModeAnalysisDisplay1D.Applet extends javax.swing.JApplet implements Serializable
  - Serialized Fields
    - density
```
double density
```
    - numAtoms
```
int numAtoms
```
    - temperature
```
double temperature
```
- Class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.normalmode.NormalModeAnalysisDisplay3D.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.normalmode.SimLJVacancy.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.normalmode.SoftSphereSolidEOSCalculator extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - bAField
```
javax.swing.JFormattedTextField bAField
```
    - bAFormat
```
java.text.NumberFormat bAFormat
```
    - bALabel
```
javax.swing.JLabel bALabel
```
    - bUField
```
javax.swing.JFormattedTextField bUField
```
    - bUFormat
```
java.text.NumberFormat bUFormat
```
    - bULabel
```
javax.swing.JLabel bULabel
```
    - c
```
double[][][] c
```
    - density
```
double density
```
    - densityField
```
javax.swing.JFormattedTextField densityField
```
    - densityFormat
```
java.text.NumberFormat densityFormat
```
    - densityLabel
```
javax.swing.JLabel densityLabel
```
    - epsilon
```
double epsilon
```
    - n
```
int n
```
    - sigma
```
double sigma
```
    - temperature
```
double temperature
```
    - temperatureField
```
javax.swing.JFormattedTextField temperatureField
```
    - temperatureFormat
```
java.text.NumberFormat temperatureFormat
```
    - temperatureLabel
```
javax.swing.JLabel temperatureLabel
```
    - ulat0
```
double[][] ulat0
```
    - vib0
```
double[][] vib0
```
    - ZField
```
javax.swing.JFormattedTextField ZField
```
    - ZFormat
```
java.text.NumberFormat ZFormat
```
    - ZLabel
```
javax.swing.JLabel ZLabel
```
- Class etomica.normalmode.WaveVectorFactory1D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - coefficients
```
double[] coefficients
```
    - waveVectors
```
Vector[] waveVectors
```
- Class etomica.normalmode.WaveVectorFactory2D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - coefficients
```
double[] coefficients
```
    - primitive
```
Primitive primitive
```
    - space
```
Space space
```
    - waveVectors
```
Vector[] waveVectors
```
- Class etomica.normalmode.WaveVectorFactoryFcc extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - coefficients
```
double[] coefficients
```
    - dim
```
int dim
```
    - primitive
```
PrimitiveFcc primitive
```
    - waveVectors
```
Vector3D[] waveVectors
```
- Class etomica.normalmode.WaveVectorFactorySimple extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - coefficients
```
double[] coefficients
```
    - primitive
```
Primitive primitive
```
    - space
```
Space space
```
    - waveVectors
```
Vector[] waveVectors
```
- Class etomica.normalmode.WaveVectorFactorySuperBox extends WaveVectorFactorySimple implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.normalmode.nptdemo
- Class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling extends DisplayBoxCanvas2D implements Serializable
  - Serialized Fields
    - coordinateDefinition
```
CoordinateDefinition coordinateDefinition
```
    - displayDensity
```
double displayDensity
```
    - p
```
Vector p
```
    - pressure
```
double pressure
```
Package etomica.potential
- Class etomica.potential.PotentialArray extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - criteria
```
NeighborCriterion[] criteria
```
    - mostRecentIndex
```
int mostRecentIndex
```
    - potentials
```
IPotential[] potentials
```
- Class etomica.potential.PotentialArrayByType extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mostRecentIndex
```
int mostRecentIndex
```
    - potentials
```
IPotential[] potentials
```
    - types
```
AtomType[] types
```
- Class etomica.potential.PotentialArrayMolecular extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - criteria
```
NeighborCriterionMolecular[] criteria
```
    - mostRecentIndex
```
int mostRecentIndex
```
    - potentials
```
IPotentialMolecular[] potentials
```
- Class etomica.potential.PotentialCalculationEnergySum extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - sum
```
double sum
```
- Class etomica.potential.PotentialCalculationEnergySumBigDecimal extends PotentialCalculationEnergySum implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mc
```
java.math.MathContext mc
```
    - precision
```
int precision
```
    - sum
```
java.math.BigDecimal sum
```
- Class etomica.potential.PotentialGroup.PotentialLinker extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - enabled
```
boolean enabled
```
    - iterator
```
AtomsetIteratorBasisDependent iterator
```
    - next
```
PotentialGroup.PotentialLinker next
```
    - potential
```
IPotentialAtomic potential
```
    - types
```
AtomType[] types
```
- Class etomica.potential.PotentialReactive.BondChangeData extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atom
```
IAtom atom
```
    - newPartners
```
IAtom[] newPartners
```
    - oldPartners
```
IAtom[] oldPartners
```
Package etomica.rotation
- Class etomica.rotation.ConfigurationWater108 extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
- Class etomica.rotation.ConfigurationWater108TIP4P extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
- Class etomica.rotation.ConfigurationWater256 extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
- Class etomica.rotation.ConfigurationWater3 extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
- Class etomica.rotation.ConfigurationWater3_3P extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
- Class etomica.rotation.DipoleBox.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.DipoleBoxMatrix.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.IntegratorVelocityVerletQuaternion.MoleculeAgent extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - force
```
Vector force
```
    - quat
```
double[] quat
```
    - torque
```
Vector torque
```
- Class etomica.rotation.IntegratorVelocityVerletQuaternion.MyTypeAgent extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - calcer
```
OrientationCalcQuaternion calcer
```
- Class etomica.rotation.SingleDipole.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.SingleDumbellRattle.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.SingleDumbellShake.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.SingleWater.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.SingleWaterMatrix.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.SingleWaterRattle.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.SingleWaterShake.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.WaterBox.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.WaterDroplet.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.WaterDropletMatrix.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.WaterDropletRattle.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.WaterDropletShake.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.WaterTrimer.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.WaterTrimerRattle.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.rotation.WaterTrimerShake.Applet extends javax.swing.JApplet implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.server.dao
- Class etomica.server.dao.DataStreamStore extends java.util.concurrent.ConcurrentHashMap<java.util.UUID,DataStreamStore.DataPlumbing> implements Serializable
- Class etomica.server.dao.SimulationStore extends java.util.concurrent.ConcurrentHashMap<java.util.UUID,SimulationModel> implements Serializable
Package etomica.server.serializers
- Class etomica.server.serializers.DataSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<IData> implements Serializable
- Class etomica.server.serializers.PropertySerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<Property> implements Serializable
- Class etomica.server.serializers.WrapperSerializer extends com.fasterxml.jackson.databind.ser.std.StdSerializer<Wrapper<?>> implements Serializable
Package etomica.simulation.prototypes
- Class etomica.simulation.prototypes.LJMD3D.Applet extends javax.swing.JApplet implements Serializable
- Class etomica.simulation.prototypes.LJMD3DNbr.Applet extends javax.swing.JApplet implements Serializable
Package etomica.space
- Class etomica.space.Space extends java.lang.Object implements Serializable
Package etomica.space1d
- Class etomica.space1d.RotationTensor1D extends Tensor1D implements Serializable
- Class etomica.space1d.Space1D extends Space implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      Required to guarantee singleton when deserializing.
- Class etomica.space1d.Tensor1D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - xx
```
double xx
```
- Class etomica.space1d.Vector1D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
double x
```
Package etomica.space2d
- Class etomica.space2d.Orientation2D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - angle
```
double angle
```
    - direction
```
Vector direction
```
- Class etomica.space2d.RotationTensor2D extends Tensor2D implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.space2d.Space2D extends Space implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      Required to guarantee singleton when deserializing.
- Class etomica.space2d.Tensor2D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - xx
```
double xx
```
    - xy
```
double xy
```
    - yx
```
double yx
```
    - yy
```
double yy
```
- Class etomica.space2d.Vector2D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
double x
```
    - y
```
double y
```
Package etomica.space3d
- Class etomica.space3d.Orientation3D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - direction
```
Vector direction
```
    - temp
```
Vector temp
```
    - temp2
```
Vector temp2
```
- Class etomica.space3d.OrientationFull3D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - direction
```
Vector direction
```
    - rotationTensor
```
Tensor3D rotationTensor
```
    - secondaryDirection
```
Vector secondaryDirection
```
    - v2
```
Vector v2
```
    - v3
```
Vector v3
```
- Class etomica.space3d.RotationTensor3D extends Tensor3D implements Serializable
  - Serialized Fields
    - work
```
Vector3D work
```
- Class etomica.space3d.Space3D extends Space implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
```
      Required to guarantee singleton when deserializing.
- Class etomica.space3d.Tensor3D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - xx
```
double xx
```
    - xy
```
double xy
```
    - xz
```
double xz
```
    - yx
```
double yx
```
    - yy
```
double yy
```
    - yz
```
double yz
```
    - zx
```
double zx
```
    - zy
```
double zy
```
    - zz
```
double zz
```
- Class etomica.space3d.Vector3D extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
double x
```
    - y
```
double y
```
    - z
```
double z
```
Package etomica.spaceNd
- Class etomica.spaceNd.VectorND extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
double[] x
```
Package etomica.spin.ising
- Class etomica.spin.ising.ConfigurationAligned extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L

Package etomica.starpolymer

Class etomica.starpolymer.MeterBondLength extends java.lang.Object implements Serializable

serialVersionUID:: 1L

Serialized Fields

box
```
Box box
```
callCount
```
long callCount
```
data
```
DataFunction data
```
dataInfo
```
IDataInfo dataInfo
```
dr
```
Vector dr
```
f
```
int f
```
gSum
```
long[] gSum
```
hist
```
Histogram hist
```
l
```
int l
```
name
```
java.lang.String name
```
rData
```
DataDoubleArray rData
```
space
```
Space space
```
tag
```
DataTag tag
```
type1
```
AtomType type1
```
type2
```
AtomType type2
```
xDataSource
```
DataSourceUniform xDataSource
```
xMax
```
double xMax
```

Package etomica.statmech
- Class etomica.statmech.MaxwellBoltzmann.Distribution extends java.lang.Object implements Serializable
  - Serialized Fields
    - a
```
double a
```
    - c
```
double c
```
    - mass
```
double mass
```
    - space
```
Space space
```
    - temperature
```
double temperature
```
Package etomica.units.dimensions
- Class etomica.units.dimensions.Angle extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Area extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Charge extends Dimension implements Serializable
- Class etomica.units.dimensions.CompoundDimension extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - dimensions
```
Dimension[] dimensions
```
    - exponents
```
double[] exponents
```
- Class etomica.units.dimensions.Current extends Dimension implements Serializable
- Class etomica.units.dimensions.Dimension extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - name
```
java.lang.String name
```
    - signature
```
double[] signature
```
- Class etomica.units.dimensions.DimensionRatio extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - dDimension
```
Dimension dDimension
```
    - nDimension
```
Dimension nDimension
```
- Class etomica.units.dimensions.Dipole extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.ElectricPotential extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Energy extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Force extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Fraction extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Frequency extends Dimension implements Serializable
- Class etomica.units.dimensions.Length extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.LuminousIntensity extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Mass extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Momentum extends Dimension implements Serializable
- Class etomica.units.dimensions.Null extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Power extends Dimension implements Serializable
- Class etomica.units.dimensions.Pressure extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Pressure2D extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Quantity extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Temperature extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Time extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Undefined extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Velocity extends Dimension implements Serializable
- Class etomica.units.dimensions.Viscosity extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Volume extends Dimension implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialization Methods
    - readResolve
```
private java.lang.Object readResolve()
                              throws java.io.ObjectStreamException
```
      Required to guarantee singleton when deserializing.
      
      Throws:
      
      java.io.ObjectStreamException
- Class etomica.units.dimensions.Wavenumber extends Dimension implements Serializable
Package etomica.util
- Class etomica.util.Grabber.ImagePanel extends java.awt.Component implements Serializable
  - Serialized Fields
    - myImage
```
java.awt.Image myImage
```
    - osg
```
java.awt.Graphics osg
```
- Class etomica.util.ReadParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - fields
```
java.lang.reflect.Field[] fields
```
    - fileName
```
java.lang.String fileName
```
    - wrapper
```
ParameterBase wrapper
```
- Class etomica.util.ScientificFormat extends java.text.NumberFormat implements Serializable
  - Serialized Fields
    - decmode
```
boolean decmode
```
    - dfmt
```
java.text.DecimalFormat dfmt
```
    - efmt
```
java.text.DecimalFormat efmt
```
    - expmode
```
boolean expmode
```
    - flexmode
```
boolean flexmode
```
    - maxwidth
```
int maxwidth
```
    - parseMatissaOnly
```
boolean parseMatissaOnly
```
- Class etomica.util.TreeList extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - head
```
TreeLinker head
```
- Class etomica.util.WriteParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - fileName
```
java.lang.String fileName
```
    - wrapper
```
ParameterBase wrapper
```
Package etomica.virial
- Class etomica.virial.AtomPairSet extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - aPairs
```
MoleculePair[][] aPairs
```
- Class etomica.virial.ClusterBonds extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - bondIndexArray
```
int[][] bondIndexArray
```
    - nPermutations
```
int nPermutations
```
    - nPoints
```
int nPoints
```
    - permutations
```
int[][] permutations
```
    - rPermutations
```
double rPermutations
```
    - usePermutations
```
boolean usePermutations
```
- Class etomica.virial.ClusterBondsNonAdditive extends ClusterBonds implements Serializable
  - Serialized Fields
    - multiBonds
```
int[][] multiBonds
```
- Class etomica.virial.ClusterSum extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - beta
```
double beta
```
    - clusters
```
ClusterBonds[] clusters
```
    - clusterWeights
```
double[] clusterWeights
```
    - cPairID
```
long cPairID
```
    - doCaching
```
boolean doCaching
```
    - f
```
MayerFunction[] f
```
    - fOld
```
double[][] fOld
```
    - fullBondIndexArray
```
int[][][] fullBondIndexArray
```
    - fValues
```
double[][][] fValues
```
    - lastCPairID
```
long lastCPairID
```
    - lastValue
```
double lastValue
```
    - value
```
double value
```
- Class etomica.virial.ClusterSumAssociation extends ClusterSum implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - clusterCriteria
```
ClusterSumAssociation.ClusterCriteria clusterCriteria
```
- Class etomica.virial.ClusterSumEF extends ClusterSum implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - numF
```
int numF
```
- Class etomica.virial.ClusterSumExternalField extends ClusterSum implements Serializable
  - Serialized Fields
    - meterPE
```
MeterPotentialEnergy meterPE
```
- Class etomica.virial.ClusterSumHS extends ClusterSum implements Serializable
  - Serialized Fields
    - cliqueCount
```
int cliqueCount
```
    - cliqueList
```
int[] cliqueList
```
    - cliqueSet
```
boolean[] cliqueSet
```
    - eCliqueCount
```
int eCliqueCount
```
    - eCliqueList
```
int[] eCliqueList
```
    - edgeCount
```
int edgeCount
```
    - fA
```
double[] fA
```
    - fB
```
double[] fB
```
    - fC
```
double[] fC
```
    - fQ
```
double[] fQ
```
    - fullBondMask
```
int[] fullBondMask
```
    - n
```
int n
```
    - outDegree
```
byte[] outDegree
```
    - precalcQ
```
boolean precalcQ
```
- Class etomica.virial.ClusterSumIC extends ClusterSum implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - f12
```
MayerFunction[] f12
```
    - lastSubClusterValues
```
double[] lastSubClusterValues
```
    - subClusterValues
```
double[] subClusterValues
```
- Class etomica.virial.ClusterSumMultibody extends ClusterSum implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - fNonAdditive
```
MayerFunctionNonAdditive[] fNonAdditive
```
    - fNonAdditiveNeeded
```
int[][] fNonAdditiveNeeded
```
    - fNonAdditiveValues
```
double[][] fNonAdditiveValues
```
    - moleculeList
```
MoleculeArrayList moleculeList
```
    - numNonAdditiveNeeded
```
int[] numNonAdditiveNeeded
```
    - pushR2
```
double pushR2
```
    - r2
```
double[] r2
```
- Class etomica.virial.ClusterSumMultibodyShell extends ClusterSumMultibody implements Serializable
  - Serialized Fields
    - coreCluster
```
ClusterSumMultibody coreCluster
```
- Class etomica.virial.ClusterSumNonAdditiveTrimerEnergy extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - atoms
```
AtomArrayList atoms
```
    - beta
```
double beta
```
    - clusters
```
ClusterBonds[] clusters
```
    - clusterWeights
```
double[] clusterWeights
```
    - cPairID
```
long cPairID
```
    - deltaCut2
```
double deltaCut2
```
    - f
```
MayerFunction[] f
```
    - fValues
```
double[][][] fValues
```
    - lastCPairID
```
long lastCPairID
```
    - lastValue
```
double lastValue
```
    - no72B2B3NonAdd
```
boolean no72B2B3NonAdd
```
    - p3NonAdd
```
Potential p3NonAdd
```
    - pushR2
```
double pushR2
```
    - value
```
double value
```
- Class etomica.virial.ClusterSumPolarizable extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - beta
```
double beta
```
    - clusters
```
ClusterBonds[] clusters
```
    - clusterWeights
```
double[] clusterWeights
```
    - cPairID
```
long cPairID
```
    - deltaCut2
```
double deltaCut2
```
    - doCaching
```
boolean doCaching
```
    - f
```
MayerFunction[] f
```
    - fValues
```
double[][][] fValues
```
    - lastCPairID
```
long lastCPairID
```
    - lastValue
```
double lastValue
```
    - pushR2
```
double pushR2
```
    - scfAtoms
```
MoleculeArrayList scfAtoms
```
    - uijPol
```
double[][] uijPol
```
    - value
```
double value
```
- Class etomica.virial.ClusterSumPolarizableWertheimProduct extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - beta
```
double beta
```
    - clusters
```
ClusterBonds[] clusters
```
    - clusterWeights
```
double[] clusterWeights
```
    - cPairID
```
long cPairID
```
    - deltaCut2
```
double deltaCut2
```
    - f
```
MayerFunction[] f
```
    - fOld
```
double[][] fOld
```
    - fullBondIndexArray
```
int[][][] fullBondIndexArray
```
    - fValues
```
double[][][] fValues
```
    - lastCPairID
```
long lastCPairID
```
    - lastValue
```
double lastValue
```
    - oldDirtyAtom
```
int oldDirtyAtom
```
    - pushR2
```
double pushR2
```
    - scfAtoms
```
MoleculeArrayList scfAtoms
```
    - uijPol
```
double[][] uijPol
```
    - value
```
double value
```
- Class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - beta
```
double beta
```
    - clusters
```
ClusterBonds[] clusters
```
    - clusterWeights
```
double[] clusterWeights
```
    - cPairID
```
long cPairID
```
    - deltaCut2
```
double deltaCut2
```
    - doCaching
```
boolean doCaching
```
    - f
```
MayerFunction[] f
```
    - fOld
```
double[][] fOld
```
    - fullBondIndexArray
```
int[][][] fullBondIndexArray
```
    - fValues
```
double[][][] fValues
```
    - lastCPairID
```
long lastCPairID
```
    - lastValue
```
double lastValue
```
    - oldDirtyAtom
```
int oldDirtyAtom
```
    - pushR2
```
double pushR2
```
    - scfAtoms
```
MoleculeArrayList scfAtoms
```
    - uijPol
```
double[][] uijPol
```
    - value
```
double value
```
- Class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - beta
```
double beta
```
    - clusters
```
ClusterBonds[] clusters
```
    - clusterWeights
```
double[] clusterWeights
```
    - cPairID
```
long cPairID
```
    - deltaCut2
```
double deltaCut2
```
    - doCaching
```
boolean doCaching
```
    - f
```
MayerFunction[] f
```
    - fOld
```
double[][] fOld
```
    - fullBondIndexArray
```
int[][][] fullBondIndexArray
```
    - fValues
```
double[][][] fValues
```
    - lastCPairID
```
long lastCPairID
```
    - lastValue
```
double lastValue
```
    - oldDirtyAtom
```
int oldDirtyAtom
```
    - pushR2
```
double pushR2
```
    - scfAtoms
```
MoleculeArrayList scfAtoms
```
    - uijPol
```
double[][] uijPol
```
    - value
```
double value
```
- Class etomica.virial.ClusterSumShell extends ClusterSum implements Serializable
  - Serialized Fields
    - coreCluster
```
ClusterSum coreCluster
```
- Class etomica.virial.ClusterSumStickyEF extends ClusterSumEF implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - clusterBuddies
```
ClusterSumStickyEF[] clusterBuddies
```
    - iDiagram
```
int iDiagram
```
    - isTrial
```
boolean isTrial
```
    - numDiagrams
```
int numDiagrams
```
    - oldDiagram
```
int oldDiagram
```
    - random
```
IRandom random
```
- Class etomica.virial.ClusterWeightAbs extends java.lang.Object implements Serializable
  - Serialized Fields
    - doAbs
```
boolean doAbs
```
    - weightCluster
```
ClusterAbstract weightCluster
```
- Class etomica.virial.ClusterWeightUmbrella extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - clusterArray
```
ClusterAbstract[] clusterArray
```
    - weightCoefficients
```
double[] weightCoefficients
```
- Class etomica.virial.ConfigurationCluster extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  3L
  - Serialized Fields
    - space
```
Space space
```
- Class etomica.virial.ConfigurationClusterAceticAcid extends ConfigurationCluster implements Serializable
  - Serialized Fields
    - f
```
MayerFunction f
```
    - f2
```
MayerFunction f2
```
    - f3
```
MayerFunction f3
```
    - random
```
IRandom random
```
- Class etomica.virial.ConfigurationClusterChain extends ConfigurationCluster implements Serializable
- Class etomica.virial.ConfigurationClusterChainFourSites extends ConfigurationCluster implements Serializable
- Class etomica.virial.ConfigurationClusterMove extends ConfigurationCluster implements Serializable
  - Serialized Fields
    - distance
```
double distance
```
    - random
```
IRandom random
```
- Class etomica.virial.ConfigurationClusterWertheimGCPM extends ConfigurationCluster implements Serializable
  - Serialized Fields
    - associationPotential
```
PNWaterGCPMThreeSite associationPotential
```
    - associationPotential2
```
PNWaterGCPMThreeSite associationPotential2
```
    - associationPotential3
```
PNWaterGCPMThreeSite associationPotential3
```
    - diagramIndex
```
double diagramIndex
```
    - nonAssociationPotential
```
PNWaterGCPMThreeSite nonAssociationPotential
```
    - random
```
IRandom random
```
- Class etomica.virial.ConfigurationClusterWertheimGCPM4Pt extends ConfigurationCluster implements Serializable
  - Serialized Fields
    - associationPotential
```
PNWaterGCPMThreeSite associationPotential
```
    - associationPotential2
```
PNWaterGCPMThreeSite associationPotential2
```
    - associationPotential3
```
PNWaterGCPMThreeSite associationPotential3
```
    - diagramIndex
```
double diagramIndex
```
    - nonAssociationPotential
```
PNWaterGCPMThreeSite nonAssociationPotential
```
    - random
```
IRandom random
```
- Class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling extends ConfigurationCluster implements Serializable
  - Serialized Fields
    - associationPotential
```
PNWaterGCPMThreeSite associationPotential
```
    - associationPotential2
```
PNWaterGCPMThreeSite associationPotential2
```
    - associationPotential3
```
PNWaterGCPMThreeSite associationPotential3
```
    - diagramIndex
```
double diagramIndex
```
    - nonAssociationPotential
```
PNWaterGCPMThreeSite nonAssociationPotential
```
    - random
```
IRandom random
```
- Class etomica.virial.Conformation7SiteRigidSF6 extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - bondL
```
double bondL
```
    - space
```
Space space
```
    - vector
```
Vector vector
```
- Class etomica.virial.ConformationAnthracene3site extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
    - vector
```
Vector vector
```
- Class etomica.virial.ConformationAnthraceneTraPPE extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
    - vector
```
Vector vector
```
- Class etomica.virial.ConformationNaphthaleneTraPPE extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
    - vector
```
Vector vector
```
- Class etomica.virial.ConformationPh3site extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
    - vector
```
Vector vector
```
- Class etomica.virial.ConformationPhenanthreneTraPPE extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - space
```
Space space
```
    - vector
```
Vector vector
```
- Class etomica.virial.MayerEGeneral extends java.lang.Object implements Serializable
  - Serialized Fields
    - potential
```
IPotentialMolecular potential
```
- Class etomica.virial.MayerENonGeneral extends java.lang.Object implements Serializable
  - Serialized Fields
    - potential
```
IPotentialMolecular potential
```
    - pU
```
double pU
```
- Class etomica.virial.MayerPUGeneral extends java.lang.Object implements Serializable
  - Serialized Fields
    - dr
```
Vector dr
```
    - mu
```
double mu
```
      Constructor Mayer function using given potential.
    - potential
```
IPotentialMolecular potential
```
    - sigmaHS
```
double sigmaHS
```
- Class etomica.virial.MeterSamplingWeight extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - data
```
DataDoubleArray data
```
    - dataDistance
```
DataSourceAtomDistance dataDistance
```
    - dataInfo
```
IDataInfo dataInfo
```
    - tag
```
DataTag tag
```
- Class etomica.virial.MeterVirial extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - clusters
```
ClusterAbstract[] clusters
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - tag
```
DataTag tag
```
- Class etomica.virial.MeterVirialExternalField extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - cluster
```
ClusterAbstract cluster
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - tag
```
DataTag tag
```
    - wallPosition
```
double[] wallPosition
```
- Class etomica.virial.MeterVirialExternalFieldConfined extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - cluster
```
ClusterAbstract cluster
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - tag
```
DataTag tag
```
    - wallDistance
```
double[] wallDistance
```
    - wallPosition
```
double[] wallPosition
```
- Class etomica.virial.MeterVirialExternalFieldOverlapConfined extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - clusters
```
java.util.List<E extends java.lang.Object> clusters
```
    - comparator
```
MeterVirialExternalFieldOverlapConfined.RangeComparator comparator
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - listsPoint
```
java.util.List<E extends java.lang.Object> listsPoint
```
    - tag
```
DataTag tag
```
    - temperature
```
double temperature
```
    - wallDistance
```
double[] wallDistance
```
- Class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - clusters
```
java.util.List<E extends java.lang.Object> clusters
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - epsilonWF
```
double epsilonWF
```
    - lambdaWF
```
double lambdaWF
```
    - listsPoint
```
java.util.List<E extends java.lang.Object> listsPoint
```
    - tag
```
DataTag tag
```
    - temperature
```
double temperature
```
    - walldistance
```
double walldistance
```
    - wallPosition
```
double[] wallPosition
```
- Class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - clusters
```
java.util.List<E extends java.lang.Object> clusters
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - epsilonWF
```
double epsilonWF
```
    - lambdaWF
```
double lambdaWF
```
    - listsPoint
```
java.util.List<E extends java.lang.Object> listsPoint
```
    - tag
```
DataTag tag
```
    - temperature
```
double temperature
```
    - wallDistance
```
double[] wallDistance
```
- Class etomica.virial.MeterVirialExternalFieldOverlapRho extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - clusters
```
java.util.List<E extends java.lang.Object> clusters
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - listsPoint
```
java.util.List<E extends java.lang.Object> listsPoint
```
    - tag
```
DataTag tag
```
    - wallPosition
```
double[] wallPosition
```
- Class etomica.virial.MeterVirialExternalFieldRho extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - clusters
```
java.util.List<E extends java.lang.Object> clusters
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - listsPoint
```
java.util.List<E extends java.lang.Object> listsPoint
```
    - tag
```
DataTag tag
```
    - wallPosition
```
double[] wallPosition
```
- Class etomica.virial.MeterVirialExternalFieldSW extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - cluster
```
ClusterAbstract cluster
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - epsilonWF
```
double epsilonWF
```
    - lambdaWF
```
double lambdaWF
```
    - tag
```
DataTag tag
```
    - temperature
```
double temperature
```
    - wallPosition
```
double[] wallPosition
```
- Class etomica.virial.MeterVirialIC extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - box
```
BoxCluster box
```
    - data
```
DataDoubleArray data
```
    - dataInfo
```
IDataInfo dataInfo
```
    - tag
```
DataTag tag
```
    - targetCluster
```
ClusterSumIC targetCluster
```
- Class etomica.virial.MuFGeneral extends java.lang.Object implements Serializable
  - Serialized Fields
    - mu
```
double mu
```
    - potential
```
IPotentialMolecular potential
```
- Class etomica.virial.MuGeneral extends java.lang.Object implements Serializable
  - Serialized Fields
    - mu
```
double mu
```
    - potential
```
IPotentialMolecular potential
```
- Class etomica.virial.SpeciesFactorySpheres extends java.lang.Object implements Serializable
- Class etomica.virial.SpeciesFactoryWaterGCPM extends java.lang.Object implements Serializable
Package etomica.virial.cluster
- Class etomica.virial.cluster.Chain extends ClusterBonds implements Serializable
- Class etomica.virial.cluster.ClusterDiagram extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - mConnections
```
int[][] mConnections
```
    - mIsRootPoint
```
boolean[] mIsRootPoint
```
    - mNumBody
```
int mNumBody
```
    - mNumConnections
```
int mNumConnections
```
    - mNumIdenticalPermutations
```
int mNumIdenticalPermutations
```
    - mNumRootPoints
```
int mNumRootPoints
```
    - mReeHooverFactor
```
int mReeHooverFactor
```
    - mRootPoints
```
int[] mRootPoints
```
    - weight
```
Rational weight
```
- Class etomica.virial.cluster.ClusterDiagramTree extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - currentNode
```
ClusterTreeNode[] currentNode
```
    - doDiagramSampling
```
boolean doDiagramSampling
```
    - fValue
```
double[] fValue
```
    - histogramming
```
boolean histogramming
```
    - iBond
```
int[] iBond
```
    - mNumBody
```
int mNumBody
```
    - mNumBondTypes
```
int mNumBondTypes
```
    - mRootNode
```
ClusterTreeNode mRootNode
```
    - numDiagrams
```
int numDiagrams
```
    - pickedDiagram
```
int pickedDiagram
```
    - prefactor
```
double prefactor
```
    - random
```
IRandom random
```
    - values
```
double[] values
```
- Class etomica.virial.cluster.ClusterGenerator extends java.lang.Object implements Serializable
  - Serialized Fields
    - excludeRootPermutations
```
boolean excludeRootPermutations
```
    - mAllPermutations
```
boolean mAllPermutations
```
    - mCluster
```
ClusterDiagram mCluster
```
    - mClusterCopy
```
ClusterDiagram mClusterCopy
```
    - mConnectList
```
int[][] mConnectList
```
    - mConnectStack
```
int[] mConnectStack
```
    - mConnectStackLen
```
int mConnectStackLen
```
    - mCurrentConnection
```
int mCurrentConnection
```
    - mExcludeArticulationPair
```
boolean mExcludeArticulationPair
```
    - mExcludeArticulationPoint
```
boolean mExcludeArticulationPoint
```
    - mExcludeNodalPoint
```
boolean mExcludeNodalPoint
```
    - mMarked
```
boolean[] mMarked
```
    - mOnlyConnected
```
boolean mOnlyConnected
```
    - mOnlyDoublyConnected
```
boolean mOnlyDoublyConnected
```
    - mReeHoover
```
boolean mReeHoover
```
    - mReeHooverGenerator
```
ClusterGenerator mReeHooverGenerator
```
    - mStack
```
int[] mStack
```
    - mStartConnection
```
int mStartConnection
```
    - mStopConnection
```
int mStopConnection
```
    - mTotalNumConnections
```
int mTotalNumConnections
```
- Class etomica.virial.cluster.Full extends ClusterBonds implements Serializable
- Class etomica.virial.cluster.Ring extends ClusterBonds implements Serializable
Package etomica.virial.GUI.components
- Class etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - indexSelectedSpecies
```
int indexSelectedSpecies
```
- Class etomica.virial.GUI.components.ExceptionSameSpeciesSamePotential extends java.lang.Exception implements Serializable
  - Serialized Fields
    - message
```
java.lang.String message
```
- Class etomica.virial.GUI.components.ExceptionSingleSiteAtomicPotential extends java.lang.Exception implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.virial.GUI.containers
- Class etomica.virial.GUI.containers.AppFrameMixtureBuilder extends javax.swing.JFrame implements Serializable
  
  serialVersionUID:
  
  1L
- Class etomica.virial.GUI.containers.PanelMainFrame extends javax.swing.JPanel implements Serializable
  
  serialVersionUID:
  
  1L

Package etomica.virial.GUI.models

Class etomica.virial.GUI.models.ModelMoleculeListDisplayTable extends javax.swing.table.AbstractTableModel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - columnNames
```
java.lang.String[] columnNames
```
  - data
```
java.lang.Object[][] data
```
Class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new extends javax.swing.table.AbstractTableModel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - columnNames
```
java.lang.String[] columnNames
```
  - data
```
java.lang.Object[][] data
```
Class etomica.virial.GUI.models.ModelPotParamDisplayTable extends javax.swing.table.AbstractTableModel implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - columnNames
```
java.lang.String[] columnNames
```
  - data
```
java.lang.Object[][] data
```

Class etomica.virial.GUI.models.ViewSpeciesSelection extends javax.swing.JPanel implements Serializable

serialVersionUID:: 1L

Serialized Fields

AddAnotherSpecies
```
javax.swing.JButton AddAnotherSpecies
```
AddPotential
```
javax.swing.JButton AddPotential
```
AddSameSpecies
```
javax.swing.JButton AddSameSpecies
```
AddSpecies
```
javax.swing.JButton AddSpecies
```
addSpecies1
```
javax.swing.JButton addSpecies1
```
addSpecies2
```
javax.swing.JButton addSpecies2
```
addSpecies3
```
javax.swing.JButton addSpecies3
```
AlterSimEnv
```
javax.swing.JButton AlterSimEnv
```
Description
```
javax.swing.JTextArea Description
```
EditVariables
```
javax.swing.JButton EditVariables
```

modelSelectedSpecies

ModelSelectedSpecies modelSelectedSpecies

modelSpeciesSelection

ModelSpeciesSelection modelSpeciesSelection

moleculeListDisplayLSM

javax.swing.ListSelectionModel moleculeListDisplayLSM

moleculeListDisplayLSMListener

javax.swing.event.ListSelectionListener moleculeListDisplayLSMListener

moleculeListDisplayTable

javax.swing.JTable moleculeListDisplayTable

moleculeListDisplayTM

ModelMoleculeListDisplayTable_new moleculeListDisplayTM

moleculeListDisplayTMListener

javax.swing.event.TableModelListener moleculeListDisplayTMListener

potentialJList

javax.swing.JList<E extends java.lang.Object> potentialJList

potentialJListListener

javax.swing.event.ListSelectionListener potentialJListListener

potentialListDisplayLSM

javax.swing.ListSelectionModel potentialListDisplayLSM

potentialParamDispayTable

javax.swing.JTable potentialParamDispayTable

potentialParamDisplayLSM

javax.swing.ListSelectionModel potentialParamDisplayLSM

potentialParamDisplayLSMListener

javax.swing.event.ListSelectionListener potentialParamDisplayLSMListener

potentialParamDisplayTM

ModelPotParamDisplayTable potentialParamDisplayTM

potentialParamDisplayTMListener

javax.swing.event.TableModelListener potentialParamDisplayTMListener

Remove
```
javax.swing.JButton Remove
```
removeSpecies1
```
javax.swing.JButton removeSpecies1
```
removeSpecies2
```
javax.swing.JButton removeSpecies2
```
removeSpecies3
```
javax.swing.JButton removeSpecies3
```
Reset
```
javax.swing.JButton Reset
```
Run
```
javax.swing.JButton Run
```
speciesCount1
```
javax.swing.JTextField speciesCount1
```
speciesCount2
```
javax.swing.JTextField speciesCount2
```
speciesCount3
```
javax.swing.JTextField speciesCount3
```

speciesJList

javax.swing.JList<E extends java.lang.Object> speciesJList

speciesJListListener

javax.swing.event.ListSelectionListener speciesJListListener

speciesListDisplayLSM

javax.swing.ListSelectionModel speciesListDisplayLSM

Package etomica.virial.GUI.views

Class etomica.virial.GUI.views.ViewAlertMsgBox extends javax.swing.JFrame implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - CloseWindow
```
javax.swing.JButton CloseWindow
```
  - Message
```
javax.swing.JTextArea Message
```
Class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval extends javax.swing.JFrame implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - Message
```
javax.swing.JLabel Message
```
  - noDoNotRemoveSpeciesButton
```
javax.swing.JButton noDoNotRemoveSpeciesButton
```
  - yesRemoveSpeciesButton
```
javax.swing.JButton yesRemoveSpeciesButton
```
Class etomica.virial.GUI.views.ViewAlkaneLengthSelection extends javax.swing.JFrame implements Serializable

serialVersionUID:

1L
- Serialized Fields
  - alkaneSpherePanel
```
javax.swing.JPanel alkaneSpherePanel
```
  - closeWindow
```
javax.swing.JButton closeWindow
```
  - NoOfSpheres
```
javax.swing.JTextField NoOfSpheres
```
  - saveValues
```
javax.swing.JButton saveValues
```

Class etomica.virial.GUI.views.ViewSimEnvironmentSelection extends javax.swing.JFrame implements Serializable

Serialized Fields

closeWindow
```
javax.swing.JButton closeWindow
```
message
```
javax.swing.JLabel message
```
noOfStepsField
```
javax.swing.JTextField noOfStepsField
```
saveValues
```
javax.swing.JButton saveValues
```

sigmaHSRefBorder

javax.swing.border.Border[] sigmaHSRefBorder

sigmaHSRefField

javax.swing.JTextField[] sigmaHSRefField

sigmaHSRefFieldA
```
javax.swing.JTextField sigmaHSRefFieldA
```
sigmaHSRefFieldB
```
javax.swing.JTextField sigmaHSRefFieldB
```
sigmaHSRefFieldC
```
javax.swing.JTextField sigmaHSRefFieldC
```
sigmaHSRefLabel
```
javax.swing.JLabel[] sigmaHSRefLabel
```
SimEnvParamPanel
```
javax.swing.JPanel SimEnvParamPanel
```
temperatureField
```
javax.swing.JTextField temperatureField
```

Class etomica.virial.GUI.views.ViewSpeciesSelection extends javax.swing.JPanel implements Serializable

serialVersionUID:: 1L

Serialized Fields

AddPotential
```
javax.swing.JButton AddPotential
```

alertMsgBoxSpeciesRemoval

ViewAlertMsgBoxSpeciesRemoval alertMsgBoxSpeciesRemoval

AlterSimEnv
```
javax.swing.JButton AlterSimEnv
```
countOfSpecies
```
javax.swing.JSpinner[] countOfSpecies
```

countOfSpeciesSLM

javax.swing.SpinnerListModel[] countOfSpeciesSLM

countOfSpeciesSLMListener

javax.swing.event.ChangeListener[] countOfSpeciesSLMListener

Description
```
javax.swing.JTextArea Description
```
EditVariables
```
javax.swing.JButton EditVariables
```

modelSelectedSpecies

ModelSelectedSpecies modelSelectedSpecies

modelSpeciesSelection

ModelSpeciesSelection modelSpeciesSelection

moleculeListDisplayLSM

javax.swing.ListSelectionModel moleculeListDisplayLSM

moleculeListDisplayLSMListener

javax.swing.event.ListSelectionListener moleculeListDisplayLSMListener

moleculeListDisplayTable

javax.swing.JTable moleculeListDisplayTable

moleculeListDisplayTM

ModelMoleculeListDisplayTable_new moleculeListDisplayTM

moleculeListDisplayTMListener

javax.swing.event.TableModelListener moleculeListDisplayTMListener

potentialJList

javax.swing.JList<E extends java.lang.Object> potentialJList

potentialJListListener

javax.swing.event.ListSelectionListener potentialJListListener

potentialListDisplayLSM

javax.swing.ListSelectionModel potentialListDisplayLSM

potentialParamDispayTable

javax.swing.JTable potentialParamDispayTable

potentialParamDisplayLSM

javax.swing.ListSelectionModel potentialParamDisplayLSM

potentialParamDisplayLSMListener

javax.swing.event.ListSelectionListener potentialParamDisplayLSMListener

potentialParamDisplayTM

ModelPotParamDisplayTable potentialParamDisplayTM

potentialParamDisplayTMListener

javax.swing.event.TableModelListener potentialParamDisplayTMListener

Reset
```
javax.swing.JButton Reset
```
Run
```
javax.swing.JButton Run
```

speciesJList

javax.swing.JList<E extends java.lang.Object> speciesJList

speciesJListListener

javax.swing.event.ListSelectionListener speciesJListListener

speciesListDisplayLSM

javax.swing.ListSelectionModel speciesListDisplayLSM

speciesRemovalMsgBox

javax.swing.JOptionPane speciesRemovalMsgBox

spinnerPanel
```
javax.swing.JPanel spinnerPanel
```

Package etomica.virial.paralleltempering
- Class etomica.virial.paralleltempering.MCMoveSwapCluster.SwapFactory extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
Package etomica.virial.simulations
- Class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.MuDeltaEBond extends java.lang.Object implements Serializable
  - Serialized Fields
    - groupTranslationVector
```
Vector groupTranslationVector
```
    - O1O2
```
Vector O1O2
```
    - potentialWater
```
P2WaterTIP4PHardCore potentialWater
```
    - potentialWaterDHS
```
VirialB2WaterTIP4P_DHS_difference.P2WaterDHS potentialWaterDHS
```
    - space
```
Space space
```
- Class etomica.virial.simulations.VirialB3C2TIP4Pwater.fPlusBetaEU extends java.lang.Object implements Serializable
  - Serialized Fields
    - potentialWater
```
P2WaterTIP4PHardCore potentialWater
```
    - space
```
Space space
```
- Class etomica.virial.simulations.VirialB3C2TIP4Pwater.MuProduct extends java.lang.Object implements Serializable
  - Serialized Fields
    - potentialWater
```
P2WaterTIP4PHardCore potentialWater
```
Package etomica.zeolite
- Class etomica.zeolite.ConfigurationFileXYZ extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  2L
  - Serialized Fields
    - confName
```
java.lang.String confName
```
    - dim
```
Vector dim
```
    - max
```
Vector max
```
    - min
```
Vector min
```
    - nAtomsList
```
int[] nAtomsList
```
    - space
```
Space space
```
    - updatedDimensions
```
Vector updatedDimensions
```
- Class etomica.zeolite.ZeoliteSimStart extends IntegratorActionAdapter implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - filename
```
java.lang.String filename
```
    - graphic
```
zeoliteSimGraphic graphic
```
    - ignoreOverlap
```
boolean ignoreOverlap
```
    - interval
```
int interval
```
    - sim
```
ZeoliteSimulation sim
```
    - sp
```
SpeciesGeneral sp
```
Package org.jmol.util
- Class org.jmol.util.AxisAngle4f extends java.lang.Object implements Serializable
  - Serialized Fields
    - angle
```
float angle
```
      The angle.
    - x
```
float x
```
      The x coordinate.
    - y
```
float y
```
      The y coordinate.
    - z
```
float z
```
      The z coordinate.
- Class org.jmol.util.Matrix3f extends java.lang.Object implements Serializable
  - Serialized Fields
    - m00
```
float m00
```
      The first element of the first row.
    - m01
```
float m01
```
      The second element of the first row.
    - m02
```
float m02
```
      third element of the first row.
    - m10
```
float m10
```
      The first element of the second row.
    - m11
```
float m11
```
      The second element of the second row.
    - m12
```
float m12
```
      The third element of the second row.
    - m20
```
float m20
```
      The first element of the third row.
    - m21
```
float m21
```
      The second element of the third row.
    - m22
```
float m22
```
      The third element of the third row.
- Class org.jmol.util.Matrix4f extends java.lang.Object implements Serializable
  - Serialized Fields
    - m00
```
float m00
```
      The first element of the first row.
    - m01
```
float m01
```
      The second element of the first row.
    - m02
```
float m02
```
      third element of the first row.
    - m03
```
float m03
```
      The fourth element of the first row.
    - m10
```
float m10
```
      The first element of the second row.
    - m11
```
float m11
```
      The second element of the second row.
    - m12
```
float m12
```
      The third element of the second row.
    - m13
```
float m13
```
      The fourth element of the second row.
    - m20
```
float m20
```
      The first element of the third row.
    - m21
```
float m21
```
      The second element of the third row.
    - m22
```
float m22
```
      The third element of the third row.
    - m23
```
float m23
```
      The fourth element of the third row.
    - m30
```
float m30
```
      The first element of the fourth row.
    - m31
```
float m31
```
      The second element of the fourth row.
    - m32
```
float m32
```
      The third element of the fourth row.
    - m33
```
float m33
```
      The fourth element of the fourth row.
- Class org.jmol.util.Point3f extends Tuple3f implements Serializable
- Class org.jmol.util.Point3fi extends Point3f implements Serializable
  - Serialized Fields
    - index
```
int index
```
    - modelIndex
```
short modelIndex
```
    - screenDiameter
```
short screenDiameter
```
    - screenX
```
int screenX
```
    - screenY
```
int screenY
```
    - screenZ
```
int screenZ
```
- Class org.jmol.util.Point3i extends Tuple3i implements Serializable
- Class org.jmol.util.Point4f extends Tuple4f implements Serializable
- Class org.jmol.util.Tuple3f extends java.lang.Object implements Serializable
  - Serialized Fields
    - x
```
float x
```
      The x coordinate.
    - y
```
float y
```
      The y coordinate.
    - z
```
float z
```
      The z coordinate.
- Class org.jmol.util.Tuple3i extends java.lang.Object implements Serializable
  - Serialized Fields
    - x
```
int x
```
      The x coordinate.
    - y
```
int y
```
      The y coordinate.
    - z
```
int z
```
      The z coordinate.
- Class org.jmol.util.Tuple4f extends java.lang.Object implements Serializable
  - Serialized Fields
    - w
```
float w
```
      The w coordinate.
    - x
```
float x
```
      The x coordinate.
    - y
```
float y
```
      The y coordinate.
    - z
```
float z
```
      The z coordinate.
- Class org.jmol.util.Vector3f extends Tuple3f implements Serializable

Serialized Form

Package etomica.action

Class etomica.action.ActionToggle extends java.lang.Object implements Serializable

Serialized Fields

falseLabel

modifier

trueLabel

Class etomica.action.AtomActionRandomizeVelocity extends java.lang.Object implements Serializable

Serialized Fields

random

temperature

Class etomica.action.AtomActionRotateBy extends java.lang.Object implements Serializable

Serialized Fields

pitch

roll

yaw

Class etomica.action.AtomActionTranslateBy extends java.lang.Object implements Serializable

Serialized Fields

translationVector

Class etomica.action.BoxActionAdapter extends java.lang.Object implements Serializable

Serialized Fields

box

Class etomica.action.BoxDeleteMolecules extends BoxActionAdapter implements Serializable

Serialized Fields

filter

Class etomica.action.BoxImposePbc extends BoxActionAdapter implements Serializable

Serialized Fields

applyToMolecules

moleculeTranslator

positionDefinition

space

translator

Class etomica.action.BoxInflate extends BoxActionAdapter implements Serializable

Serialized Fields

dimVector

groupScaler

moleculeCenter

scaleVector

translator

Class etomica.action.BoxInflateAnisotropic extends BoxInflate implements Serializable

Serialized Fields

cVector

cVectorOld

deltaX

translationVector

Class etomica.action.BoxInflateDeformable extends BoxInflate implements Serializable

Serialized Fields

tempTens

tempTensInv

Class etomica.action.BoxQuench extends BoxActionAdapter implements Serializable

Serialized Fields

dim

meterTemperature

temperature

Class etomica.action.CalcVibrationalModes extends java.lang.Object implements Serializable

Serialized Fields

cgd

d

dForces

eigenDecomp

fC

frequencies

mass

modes

modeSigns

ms

positions

prodFreq

writeCount

Class etomica.action.IntegratorActionAdapter extends java.lang.Object implements Serializable

Serialized Fields

integrator

Class etomica.action.IntegratorReset extends IntegratorActionAdapter implements Serializable

Serialized Fields

ignoreOverlap

Class etomica.action.MoleculeActionTranslateTo extends java.lang.Object implements Serializable

Serialized Fields

atomPositionDefinition

atomTranslator

destination