Serialized Form

Package etomica

Class etomica.EtomicaInfo extends Object implements Serializable

Serialized Fields

description

String description

short_description

String short_description

enabled

boolean enabled

features

FeatureSet features

Package etomica.action

Class etomica.action.ActionGroupSeries extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

actions

IAction[] actions

Class etomica.action.ActionToggle extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

modifier

ModifierBoolean modifier

trueLabel

String trueLabel

falseLabel

String falseLabel

Class etomica.action.Activity extends Object implements Serializable

Serialized Fields

isActive

boolean isActive

haltRequested

boolean haltRequested

pauseRequested

boolean pauseRequested

isPaused

boolean isPaused

name

String name

Class etomica.action.AtomActionRandomizeVelocity extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

temperature

double temperature

random

IRandom random

Class etomica.action.AtomActionRotateBy extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

roll

double roll

pitch

double pitch

yaw

double yaw

Class etomica.action.AtomActionTranslateBy extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

translationVector

IVectorMutable translationVector

Class etomica.action.BoxActionAdapter extends Object implements Serializable

Serialized Fields

box

IBox box

Class etomica.action.BoxDeleteMolecules extends BoxActionAdapter implements Serializable

serialVersionUID: 1L

Serialized Fields

filter

AtomFilter filter

Class etomica.action.BoxImposePbc extends BoxActionAdapter implements Serializable

serialVersionUID: 1L

Serialized Fields

translator

AtomActionTranslateBy translator

moleculeTranslator

MoleculeChildAtomAction moleculeTranslator

space

ISpace space

positionDefinition

IAtomPositionDefinition positionDefinition

applyToMolecules

boolean applyToMolecules

Class etomica.action.BoxInflate extends BoxActionAdapter implements Serializable

serialVersionUID: 1L

Serialized Fields

translator

AtomActionTranslateBy translator

groupScaler

MoleculeChildAtomAction groupScaler

scaleVector

IVectorMutable scaleVector

dimVector

IVectorMutable dimVector

moleculeCenter

AtomPositionGeometricCenter moleculeCenter

Class etomica.action.BoxInflateDeformable extends BoxInflate implements Serializable

Serialized Fields

tempTens

Tensor tempTens

tempTensInv

Tensor tempTensInv

dimVector

IVectorMutable dimVector

Class etomica.action.BoxQuench extends BoxActionAdapter implements Serializable

serialVersionUID: 1L

Serialized Fields

temperature

double temperature

meterTemperature

MeterTemperature meterTemperature

dim

int dim

Class etomica.action.CalcVibrationalModes extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

modes

double[] modes

frequencies

double[] frequencies

positions

double[] positions

d

int[] d

dForces

double[][] dForces

prodFreq

double prodFreq

modeSigns

int[] modeSigns

fC

Jama.Matrix fC

mass

double mass

writeCount

int writeCount

ms

IMoleculeList ms

eigenDecomp

Jama.EigenvalueDecomposition eigenDecomp

cgd

CalcGradientDifferentiable cgd

Class etomica.action.ControllerActionAdapter extends Object implements Serializable

Serialized Fields

controller

IController controller

Class etomica.action.ControllerToggle extends ControllerActionAdapter implements Serializable

serialVersionUID: 1L

Class etomica.action.IntegratorActionAdapter extends Object implements Serializable

Serialized Fields

integrator

IIntegrator integrator

Class etomica.action.IntegratorDimerApproach extends IntegratorBox implements Serializable

serialVersionUID: 1L

Serialized Fields

space

ISpace space

atomActionTranslateBy

AtomActionTranslateBy atomActionTranslateBy

atomActionRotateBy

AtomActionRotateBy atomActionRotateBy

atomGroupActionRotateBy

MoleculeChildAtomAction atomGroupActionRotateBy

atomGroupActionTranslateBy

MoleculeChildAtomAction atomGroupActionTranslateBy

potentialMaster

IPotentialMaster potentialMaster

newOriginB

IVectorMutable newOriginB

translationVector

IVectorMutable translationVector

moleculeList

IMoleculeList moleculeList

atomSetA

IAtomList atomSetA

atomSetB

IAtomList atomSetB

monomerA

IMolecule monomerA

monomerB

IMolecule monomerB

r

double r

delta

double delta

route

int route

routeParams

double[][] routeParams

Class etomica.action.IntegratorReset extends IntegratorActionAdapter implements Serializable

serialVersionUID: 1L

Serialized Fields

ignoreOverlap

boolean ignoreOverlap

Class etomica.action.MoleculeActionTranslateTo extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

destination

IVectorMutable destination

atomPositionDefinition

IAtomPositionDefinition atomPositionDefinition

atomTranslator

MoleculeChildAtomAction atomTranslator

translationVector

IVectorMutable translationVector

Class etomica.action.MoleculeChildAtomAction extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

action

AtomAction action

Class etomica.action.PDBWriter extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

file

File file

elementCount

int elementCount

elementAtomType

LinkedList<E> elementAtomType

leafList

IAtomList leafList

Class etomica.action.ResetAccumulators extends DataStreamAction implements Serializable

serialVersionUID: 1L

Class etomica.action.ResetAccumulatorsAveraged extends ResetAccumulators implements Serializable

serialVersionUID: 1L

Class etomica.action.SimulationActionAdapter extends Object implements Serializable

Serialized Fields

simulation

ISimulation simulation

space

ISpace space

Class etomica.action.SimulationDataAction extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

dataStreamPumps

ArrayList<E> dataStreamPumps

streamAction

DataStreamAction streamAction

Class etomica.action.SimulationRestart extends SimulationActionAdapter implements Serializable

serialVersionUID: 1L

Serialized Fields

configuration

Configuration configuration

ignoreOverlap

boolean ignoreOverlap

accumulatorAction

SimulationDataAction accumulatorAction

controller

IController controller

Class etomica.action.XYZWriter extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

file

File file

elementCount

int elementCount

elementAtomType

LinkedList<E> elementAtomType

leafList

IAtomList leafList

doAppend

boolean doAppend

Package etomica.action.activity

Class etomica.action.activity.ActivityGroupParallel extends Activity implements Serializable

serialVersionUID: 1L

Serialized Fields

numActions

int numActions

actions

IAction[] actions

lastThread

etomica.action.activity.ActivityGroupParallel.MyThread lastThread

firstThread

etomica.action.activity.ActivityGroupParallel.MyThread firstThread

Class etomica.action.activity.ActivityGroupSeries extends Activity implements Serializable

serialVersionUID: 1L

Serialized Fields

currentAction

IAction currentAction

pauseAfterEachAction

boolean pauseAfterEachAction

numActions

int numActions

pendingActions

IAction[] pendingActions

completedActions

IAction[] completedActions

Class etomica.action.activity.ActivityIntegrate extends Activity implements Serializable

serialVersionUID: 1L

Serialized Fields

integrator

IIntegrator integrator

ignoreOverlap

boolean ignoreOverlap

sleepPeriod

int sleepPeriod

maxSteps

long maxSteps

stepCount

long stepCount

Class etomica.action.activity.Controller extends ActivityGroupSeries implements Serializable

serialVersionUID: 1L

Serialized Fields

eventManager

IEventManager eventManager

repeatCurrentAction

boolean repeatCurrentAction

urgentWaitObject

Controller.UrgentWaitObject urgentWaitObject

waitObject

Controller.WaitObject waitObject

actionStatusMap

HashMap<K,V> actionStatusMap

actionExceptionMap

HashMap<K,V> actionExceptionMap

Class etomica.action.activity.Controller.ActionStatus extends EnumeratedType implements Serializable

serialVersionUID: 1L

Serialization Methods

readResolve

private Object readResolve()

Required to guarantee singleton when deserializing.

Class etomica.action.activity.Controller.UrgentWaitObject extends Object implements Serializable

serialVersionUID: 1L

Class etomica.action.activity.Controller.WaitObject extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

currentActionDone

boolean currentActionDone

actionException

Throwable actionException

Class etomica.action.activity.ControllerEvent extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

controller

IController controller

type

ControllerEvent.Type type

action

IAction action

Class etomica.action.activity.ControllerEvent.Type extends EnumeratedType implements Serializable

Serialized Fields

index

int index

Class etomica.action.activity.ControllerEventManager extends EventManager implements Serializable

Package etomica.atom

Class etomica.atom.Atom extends Object implements Serializable

serialVersionUID: 3L

Serialized Fields

type

IAtomType type

index

int index

position

IVectorMutable position

parent

IMolecule parent

leafIndex

int leafIndex

Class etomica.atom.AtomFilterInShape extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

shape

Shape shape

positionDefinition

IAtomPositionDefinition positionDefinition

Class etomica.atom.AtomFilterStatic extends Object implements Serializable

serialVersionUID: 1L

Serialization Methods

readResolve

private Object readResolve()

Required to guarantee singleton when deserializing.

Serialized Fields

rv

boolean rv

Class etomica.atom.AtomGroupVelocityAverage extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

vectorSum

IVectorMutable vectorSum

Class etomica.atom.AtomLeafAgentManager extends BoxListenerAdapter implements Serializable

serialVersionUID: 1L

Serialized Fields

agentSource

AtomLeafAgentManager.AgentSource agentSource

agents

Object[] agents

box

IBox box

reservoirSize

int reservoirSize

Class etomica.atom.AtomLeafAgentManager.AgentIterator extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

agentManager

AtomLeafAgentManager agentManager

cursor

int cursor

agents

Object[] agents

Class etomica.atom.AtomLeafDynamic extends Atom implements Serializable

serialVersionUID: 1L

Serialized Fields

velocity

IVectorMutable velocity

Class etomica.atom.AtomListWrapper extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atoms

AtomArrayList atoms

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

iOrientation

IOrientation iOrientation

angularVelocity

IVectorMutable angularVelocity

Class etomica.atom.AtomPair extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atom0

IAtom atom0

atom1

IAtom atom1

Class etomica.atom.AtomPositionCOM extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

center

IVectorMutable center

Class etomica.atom.AtomPositionFirstAtom extends Object implements Serializable

serialVersionUID: 1L

Class etomica.atom.AtomPositionGeometricCenter extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

center

IVectorMutable center

Class etomica.atom.AtomPositionGeometricCenterPBC extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

center

IVectorMutable center

dr

IVectorMutable dr

boundary

IBoundary boundary

Class etomica.atom.AtomsetArray extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atoms

IAtom[] atoms

Class etomica.atom.AtomSetSinglet extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atom

IAtom atom

Class etomica.atom.AtomSourceRandomLeaf extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

list

IAtomList list

random

IRandom random

Class etomica.atom.AtomToAtomSetFixed extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atomArrayList

AtomArrayList atomArrayList

Class etomica.atom.AtomToIndexChild extends Object implements Serializable

serialVersionUID: 1L

Class etomica.atom.AtomToParentChildList extends Object implements Serializable

serialVersionUID: 1L

Class etomica.atom.AtomTypeAgentManager extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

agentSource

AtomTypeAgentManager.AgentSource agentSource

agents

Object[] agents

sim

ISimulation sim

Class etomica.atom.AtomTypeAgentManager.AgentIterator extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

agentManager

AtomTypeAgentManager agentManager

cursor

int cursor

agents

Object[] agents

Class etomica.atom.Molecule extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

index

int index

childList

AtomArrayList childList

species

ISpecies species

Class etomica.atom.MoleculeAgentManager extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

agentSource

MoleculeAgentManager.MoleculeAgentSource agentSource

agents

Object[][] agents

box

IBox box

sim

ISimulation sim

reservoirSize

int reservoirSize

Class etomica.atom.MoleculeAgentManager.AgentIterator extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

agentManager

MoleculeAgentManager agentManager

speciesCursor

int speciesCursor

moleculeCursor

int moleculeCursor

agents

Object[][] agents

speciesAgents

Object[] speciesAgents

Class etomica.atom.MoleculeListWrapper extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atoms

MoleculeArrayList atoms

Class etomica.atom.MoleculeOriented extends Molecule implements Serializable

serialVersionUID: 1L

Serialized Fields

orientation

IOrientation3D orientation

position

IVectorMutable position

Class etomica.atom.MoleculeOrientedDynamic extends MoleculeOriented implements Serializable

serialVersionUID: 1L

Serialized Fields

angularMomentum

IVectorMutable angularMomentum

velocity

IVectorMutable velocity

Class etomica.atom.MoleculePair extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atom0

IMolecule atom0

atom1

IMolecule atom1

Class etomica.atom.MoleculesetArray extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atoms

IMolecule[] atoms

Class etomica.atom.MoleculeSetSinglet extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atom

IMolecule atom

Class etomica.atom.MoleculeSourceRandomMolecule extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

random

IRandom random

Class etomica.atom.MoleculeToMoleculeListSpecies extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

moleculeList

IMoleculeList moleculeList

species

ISpecies species

Class etomica.atom.SpeciesAgentManager extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

agentSource

SpeciesAgentManager.AgentSource agentSource

agents

Object[] agents

sim

ISimulation sim

Class etomica.atom.SpeciesAgentManager.AgentIterator extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

agentManager

SpeciesAgentManager agentManager

cursor

int cursor

agents

Object[] agents

Package etomica.atom.iterator

Class etomica.atom.iterator.ApiInnerVariable extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

pair

AtomPair pair

aiInner

AtomIteratorAtomDependent aiInner

The iterators used to generate the sets of atoms.

aiOuter

AtomIterator aiOuter

doSwap

boolean doSwap

Class etomica.atom.iterator.ApiInterArrayList extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

outerList

IAtomList outerList

innerList

IAtomList innerList

outerIndex

int outerIndex

innerIndex

int innerIndex

atoms

AtomPair atoms

Class etomica.atom.iterator.ApiIntraArrayList extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

list

IAtomList list

outerIndex

int outerIndex

innerIndex

int innerIndex

atoms

AtomPair atoms

Class etomica.atom.iterator.ApiIntragroup extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

aiOuter

AtomsetIteratorBasisDependent aiOuter

targetAtom

IAtom targetAtom

direction

IteratorDirective.Direction direction

apiUp

ApiInnerVariable apiUp

apiDown

ApiInnerVariable apiDown

doGoDown

boolean doGoDown

upListNow

boolean upListNow

Class etomica.atom.iterator.ApiLeafAtoms extends ApiIntraArrayList implements Serializable

serialVersionUID: 1L

Class etomica.atom.iterator.AtomIteratorAllLeafType extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atomType

IAtomType[] atomType

box

IBox box

nextCursor

int nextCursor

next

AtomListWrapper next

Class etomica.atom.iterator.AtomIteratorArrayList extends AtomIteratorArrayListSimple implements Serializable

serialVersionUID: 1L

Serialized Fields

upListNow

boolean upListNow

numToSkip

int numToSkip

startAtom

IAtom startAtom

atomToIndex

AtomToIndex atomToIndex

atomToAtomSet

AtomToAtomLeafList atomToAtomSet

Class etomica.atom.iterator.AtomIteratorArrayListAdjacent extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

firstCursor

int firstCursor

direction

IteratorDirective.Direction direction

upListNow

boolean upListNow

dnListNow

boolean dnListNow

list

IAtomList list

atomToIndex

AtomToIndex atomToIndex

atomToAtomSet

AtomToAtomLeafList atomToAtomSet

atomSetSinglet

AtomSetSinglet atomSetSinglet

Class etomica.atom.iterator.AtomIteratorArrayListSimple extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

cursor

int cursor

Index of element to be returned by subsequent call to next.

list

IAtomList list

atomSetSinglet

AtomSetSinglet atomSetSinglet

Class etomica.atom.iterator.AtomIteratorBasis extends AtomIteratorArrayListSimple implements Serializable

serialVersionUID: 1L

Serialized Fields

littleList

AtomArrayList littleList

targetAtom

IAtom targetAtom

basis

IMolecule basis

myList

IAtomList myList

needSetupIterator

boolean needSetupIterator

Class etomica.atom.iterator.AtomIteratorBasisFilteredType extends AtomIteratorBasis implements Serializable

serialVersionUID: 1L

Serialized Fields

filteredType

IAtomType filteredType

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

IAtomType filteredType

Class etomica.atom.iterator.AtomIteratorNull extends Object implements Serializable

serialVersionUID: 1L

Class etomica.atom.iterator.AtomIteratorSinglet extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

hasNext

boolean hasNext

atom

IAtom atom

atomSetSinglet

AtomSetSinglet atomSetSinglet

Class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

next

AtomListWrapper next

basis

IMoleculeList basis

Class etomica.atom.iterator.IteratorDirective extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

includeLrc

boolean includeLrc

Flag indicating whether long-range correction contributions should be included in calculation. Default is true.

direction

IteratorDirective.Direction direction

potentialCriteriaHead

IteratorDirective.PotentialCriterion potentialCriteriaHead

targetAtom

IAtom targetAtom

targetMolecule

IMolecule targetMolecule

Class etomica.atom.iterator.IteratorDirective.Direction extends EnumeratedType implements Serializable

serialVersionUID: 1L

Serialization Methods

readResolve

private Object readResolve()

Required to guarantee singleton when deserializing.

Class etomica.atom.iterator.IteratorDirective.PotentialCriterion extends Object implements Serializable

Serialized Fields

nextCriterion

IteratorDirective.PotentialCriterion nextCriterion

Class etomica.atom.iterator.IteratorFactory extends Object implements Serializable

serialVersionUID: 1L

Class etomica.atom.iterator.MoleculeIteratorAll extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

species

ISpecies[] species

box

IBox box

nextCursor

int nextCursor

next

MoleculeListWrapper next

Class etomica.atom.iterator.MoleculeIteratorAllMolecules extends MoleculeIteratorArrayListSimple implements Serializable

serialVersionUID: 1L

Class etomica.atom.iterator.MoleculeIteratorArrayList extends MoleculeIteratorArrayListSimple implements Serializable

serialVersionUID: 1L

Serialized Fields

upListNow

boolean upListNow

numToSkip

int numToSkip

startAtom

IMolecule startAtom

atomToIndex

MoleculeToIndex atomToIndex

atomToAtomSet

MoleculeToMoleculeList atomToAtomSet

Class etomica.atom.iterator.MoleculeIteratorArrayListSimple extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

cursor

int cursor

Index of element to be returned by subsequent call to next.

list

IMoleculeList list

atomSetSinglet

MoleculeSetSinglet atomSetSinglet

Class etomica.atom.iterator.MoleculeIteratorMolecule extends MoleculeIteratorArrayListSimple implements Serializable

serialVersionUID: 1L

Serialized Fields

species

ISpecies species

littleList

MoleculeArrayList littleList

box

IBox box

targetAtom

IMolecule targetAtom

Class etomica.atom.iterator.MoleculeIteratorSinglet extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

hasNext

boolean hasNext

atom

IMolecule atom

atomSetSinglet

MoleculeSetSinglet atomSetSinglet

Class etomica.atom.iterator.MpiInnerFixed extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

pair

MoleculePair pair

aiInner

MoleculeIterator aiInner

aiOuter

MoleculeIterator aiOuter

doSwap

boolean doSwap

Class etomica.atom.iterator.MpiInnerVariable extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

pair

MoleculePair pair

aiInner

MoleculeIteratorMoleculeDependent aiInner

The iterators used to generate the sets of atoms.

aiOuter

MoleculeIterator aiOuter

doSwap

boolean doSwap

Class etomica.atom.iterator.MpiInterspecies1A extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

aiInner

MoleculeIteratorArrayListSimple aiInner

aiOuter

MoleculeIteratorSinglet aiOuter

species0

ISpecies species0

species1

ISpecies species1

apiUp

MpiInnerFixed apiUp

apiDown

MpiInnerFixed apiDown

iterator

MpiInnerFixed iterator

direction

IteratorDirective.Direction direction

allowedDirection

IteratorDirective.Direction allowedDirection

box

IBox box

targetMolecule

IMolecule targetMolecule

Class etomica.atom.iterator.MpiIntraspecies1A extends Object implements Serializable

serialVersionUID: 3L

Serialized Fields

aiOuter

MoleculeIteratorSinglet aiOuter

direction

IteratorDirective.Direction direction

apiUp

MpiInnerVariable apiUp

apiDown

MpiInnerVariable apiDown

doGoDown

boolean doGoDown

upListNow

boolean upListNow

species

ISpecies species

targetMolecule

IMolecule targetMolecule

box

IBox box

atomToAtomSet

MoleculeToMoleculeListSpecies atomToAtomSet

Class etomica.atom.iterator.MpiIntraspeciesAA extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

list

IMoleculeList list

outerIndex

int outerIndex

innerIndex

int innerIndex

atoms

MoleculePair atoms

species

ISpecies species

Class etomica.atom.iterator.MpiMolecule extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

iterator

MoleculesetIteratorBoxDependent iterator

api1A

MoleculesetIteratorPDT api1A

apiAA

MoleculesetIteratorBoxDependent apiAA

box

IBox box

Class etomica.atom.iterator.TripletInnerSequential extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

stateUpDown

int stateUpDown

doGoUp

boolean doGoUp

doGoDown

boolean doGoDown

childList

IAtomList childList

targetAtom

IAtom targetAtom

cursor

int cursor

next

AtomsetArray next

atomArray

IAtom[] atomArray

Package etomica.box

Class etomica.box.Box extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

leafList

AtomArrayList leafList

List of leaf atoms in box

indexReservoir

int[] indexReservoir

reservoirSize

int reservoirSize

reservoirCount

int reservoirCount

maxIndex

int maxIndex

boundary

IBoundary boundary

eventManager

BoxEventManager eventManager

moleculeLists

MoleculeArrayList[] moleculeLists

index

int index

space

ISpace space

allMoleculeList

AtomSetAllMolecules allMoleculeList

Class etomica.box.BoxAgentManager extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

agentSource

BoxAgentManager.BoxAgentSource agentSource

simEventManager

ISimulationEventManager simEventManager

agents

Object[] agents

Class etomica.box.BoxAgentSourceAtomManager extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atomAgentSource

AtomLeafAgentManager.AgentSource atomAgentSource

Class etomica.box.BoxAtomEvent extends BoxEvent implements Serializable

serialVersionUID: 1L

Serialized Fields

atom

IAtom atom

Class etomica.box.BoxAtomIndexEvent extends BoxAtomEvent implements Serializable

serialVersionUID: 1L

Serialized Fields

index

int index

Class etomica.box.BoxEvent extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

Class etomica.box.BoxEventManager extends Object implements Serializable

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

writeObject

private void writeObject(ObjectOutputStream out)
                  throws IOException

Throws:

IOException

Serialized Fields

box

IBox box

Class etomica.box.BoxGlobalAtomIndexEvent extends BoxEvent implements Serializable

serialVersionUID: 1L

Serialized Fields

maxIndex

int maxIndex

Class etomica.box.BoxIndexEvent extends BoxEvent implements Serializable

serialVersionUID: 1L

Serialized Fields

index

int index

Class etomica.box.BoxMoleculeAddedEvent extends BoxMoleculeEvent implements Serializable

serialVersionUID: 1L

Class etomica.box.BoxMoleculeCountEvent extends BoxEvent implements Serializable

Serialized Fields

count

int count

species

ISpecies species

Class etomica.box.BoxMoleculeEvent extends BoxEvent implements Serializable

serialVersionUID: 1L

Serialized Fields

molecule

IMolecule molecule

Class etomica.box.BoxMoleculeIndexEvent extends BoxMoleculeEvent implements Serializable

serialVersionUID: 1L

Serialized Fields

index

int index

Class etomica.box.BoxMoleculeRemovedEvent extends BoxMoleculeEvent implements Serializable

serialVersionUID: 1L

Package etomica.chem.electrostatics

Class etomica.chem.electrostatics.Charge extends 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 Object implements Serializable

Serialized Fields

symbol

String symbol

Class etomica.chem.elements.ElementChemical extends Element implements Serializable

Serialized Fields

mass

double mass

rm

double rm

atomicNumber

int atomicNumber

Class etomica.chem.elements.ElementSimple extends Element implements Serializable

serialVersionUID: 1L

Serialized Fields

rm

double rm

mass

double mass

Class etomica.chem.elements.Hydrogen extends ElementChemical implements Serializable

serialVersionUID: 1L

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

Package etomica.chem.models

Class etomica.chem.models.Model extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

species

ISpecies species

isDynamic

boolean isDynamic

potentialsAndIterators

Model.PotentialAndIterator[] potentialsAndIterators

Class etomica.chem.models.ModelChain extends Model implements Serializable

serialVersionUID: 1L

Serialized Fields

bondingPotential

Potential2 bondingPotential

numAtoms

int numAtoms

conformation

IConformation conformation

element

IElement element

speciesMade

boolean speciesMade

space

ISpace space

Package etomica.compatibility

Class etomica.compatibility.ClassRequirement extends Requirement implements Serializable

Serialized Fields

comparison

Feature comparison

Class etomica.compatibility.Feature extends Object implements Serializable

Serialized Fields

name

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 Object implements Serializable

Serialized Fields

list

HashMap<K,V> list

Class etomica.compatibility.NumericFeature extends Feature implements Serializable

Serialized Fields

value

double value

Class etomica.compatibility.Requirement extends Object implements Serializable

Class etomica.compatibility.RequirementSet extends Requirement implements Serializable

Serialized Fields

requirements

LinkedList<E> requirements

Class etomica.compatibility.StringFeature extends Feature implements Serializable

Serialized Fields

value

String value

Package etomica.config

Class etomica.config.ConfigurationFile extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

confName

String confName

Class etomica.config.ConfigurationLattice extends Object implements Serializable

serialVersionUID: 3L

Serialized Fields

lattice

SpaceLattice lattice

indexIterator

IndexIteratorSizable indexIterator

rescalingToFitVolume

boolean rescalingToFitVolume

atomActionTranslateTo

MoleculeActionTranslateTo atomActionTranslateTo

myLat

ConfigurationLattice.MyLattice myLat

boundaryPadding

double boundaryPadding

space

ISpace space

positionDefinition

IAtomPositionDefinition positionDefinition

Class etomica.config.ConfigurationLatticeSimple extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

lattice

SpaceLattice lattice

indexIterator

IndexIteratorSizable indexIterator

atomActionTranslateTo

MoleculeActionTranslateTo atomActionTranslateTo

space

ISpace space

Class etomica.config.ConfigurationLatticeWithPlane extends ConfigurationLattice implements Serializable

serialVersionUID: 2L

Serialized Fields

plane

Plane plane

species

ArrayList<E> species

allocation

HashMap<K,V> allocation

LEFT

int LEFT

RIGHT

int RIGHT

Class etomica.config.ConfigurationOrientedFile extends ConfigurationFile implements Serializable

serialVersionUID: 2L

Serialized Fields

direction

IVectorMutable direction

secondaryDirection

IVectorMutable secondaryDirection

Class etomica.config.ConfigurationZincblende extends ConfigurationLattice implements Serializable

serialVersionUID: 2L

Serialized Fields

translator0

MoleculeChildAtomAction translator0

translator1

MoleculeChildAtomAction translator1

species

ISpecies[] species

Class etomica.config.ConformationChain extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

space

ISpace space

Class etomica.config.ConformationChain2D extends ConformationChain implements Serializable

serialVersionUID: 1L

Serialized Fields

vectors

IVectorMutable[] vectors

tracker

int tracker

Class etomica.config.ConformationChain3D extends ConformationChain implements Serializable

serialVersionUID: 1L

Serialized Fields

vectors

IVectorMutable[] vectors

tracker

int tracker

Class etomica.config.ConformationChainZigZag extends ConformationChain implements Serializable

serialVersionUID: 1L

Serialized Fields

v1

IVectorMutable v1

v2

IVectorMutable v2

isVectorOne

boolean isVectorOne

Class etomica.config.ConformationChainZigZag2 extends ConformationChain implements Serializable

serialVersionUID: 1L

Serialized Fields

v1

IVectorMutable v1

v2

IVectorMutable v2

isVectorOne

boolean isVectorOne

Class etomica.config.ConformationLinear extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

space

ISpace space

bondLength

double bondLength

orientation

IVectorMutable orientation

angle

double[] angle

Class etomica.config.ConformationWater extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

bondLengthOH

double bondLengthOH

angleHOH

double angleHOH

space

ISpace space

Class etomica.config.GrainBoundaryConfiguration extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

latticeA

BravaisLatticeCrystal latticeA

latticeB

BravaisLatticeCrystal latticeB

speciesAFixed

ISpecies speciesAFixed

speciesBFixed

ISpecies speciesBFixed

speciesAMobile

ISpecies speciesAMobile

speciesBMobile

ISpecies speciesBMobile

indexIteratorA

IndexIteratorSizable indexIteratorA

indexIteratorB

IndexIteratorSizable indexIteratorB

atomActionTranslateTo

MoleculeActionTranslateTo atomActionTranslateTo

iteratorDimensionsA

int[] iteratorDimensionsA

iteratorDimensionsB

int[] iteratorDimensionsB

latticeDimensionsA

double[] latticeDimensionsA

latticeDimensionsB

double[] latticeDimensionsB

nCellsAx

int nCellsAx

nCellsAy

int nCellsAy

nCellsAz

int nCellsAz

nCellsBx

int nCellsBx

nCellsBy

int nCellsBy

nCellsBz

int nCellsBz

myLatA

etomica.config.GrainBoundaryConfiguration.MyLattice myLatA

myLatB

etomica.config.GrainBoundaryConfiguration.MyLattice myLatB

space

ISpace space

Package etomica.data

Class etomica.data.AccumulatorAverage extends DataAccumulator implements Serializable

serialVersionUID: 1L

Serialized Fields

mostRecent

IData mostRecent

average

IData average

error

IData error

standardDeviation

IData standardDeviation

blockCorrelation

IData blockCorrelation

dataGroup

DataGroup dataGroup

count

long count

blockCountDown

long blockCountDown

blockSize

long blockSize

mostRecentTag

DataTag mostRecentTag

averageTag

DataTag averageTag

errorTag

DataTag errorTag

standardDeviationTag

DataTag standardDeviationTag

blockCorrelationTag

DataTag blockCorrelationTag

Class etomica.data.AccumulatorAverage.StatType extends EnumeratedType implements Serializable

serialVersionUID: 1L

Serialized Fields

index

int index

Class etomica.data.AccumulatorAverageCollapsing extends AccumulatorAverage implements Serializable

serialVersionUID: 1L

Serialized Fields

maxBlocks

int maxBlocks

blockSums

double[] blockSums

currentBlockSum

double currentBlockSum

totalSumSquare

double totalSumSquare

totalSumBlockSq

double totalSumBlockSq

correlationSum

double correlationSum

totalBlockSum

double totalBlockSum

nominalBlockSize

long nominalBlockSize

Class etomica.data.AccumulatorAverageCollapsingLog extends DataAccumulator implements Serializable

serialVersionUID: 1L

Serialized Fields

count

long count

blockSums

double[] blockSums

sums

double[][] sums

lSums

double[][] lSums

averages

DataFunction averages

stdev

DataFunction stdev

avgDataInfo

DataFunction.DataInfoFunction avgDataInfo

nDataInfo

DataDoubleArray.DataInfoDoubleArray nDataInfo

nData

DataDoubleArray nData

nTag

DataTag nTag

rawData

double[] rawData

rawData2

double[] rawData2

rawData3

double[] rawData3

nRawData

int nRawData

rawDataBlockSize

int rawDataBlockSize

nRawDataDoubles

int nRawDataDoubles

intArrayList

ArrayList<E> intArrayList

random

IRandom random

Class etomica.data.AccumulatorAverageCovariance extends AccumulatorAverageFixed implements Serializable

serialVersionUID: 1L

Serialized Fields

covSum

DataDoubleArray covSum

blockCovSum

DataDoubleArray blockCovSum

covariance

DataDoubleArray covariance

blockCovariance

DataDoubleArray blockCovariance

Class etomica.data.AccumulatorAverageCovariance.StatType extends AccumulatorAverage.StatType implements Serializable

serialVersionUID: 1L

Class etomica.data.AccumulatorAverageFixed extends AccumulatorAverage implements Serializable

serialVersionUID: 1L

Serialized Fields

sum

IData sum

sumBlockSquare

IData sumBlockSquare

currentBlockSum

IData currentBlockSum

sumSquare

IData sumSquare

mostRecentBlock

IData mostRecentBlock

correlationSum

IData correlationSum

firstBlock

IData firstBlock

work

IData work

negativeChop

IFunction negativeChop

Class etomica.data.AccumulatorAverageFixedOutputFile extends AccumulatorAverage implements Serializable

serialVersionUID: 1L

Serialized Fields

sum

IData sum

sumBlockSquare

IData sumBlockSquare

currentBlockSum

IData currentBlockSum

sumSquare

IData sumSquare

mostRecentBlock

IData mostRecentBlock

correlationSum

IData correlationSum

firstBlock

IData firstBlock

work

IData work

negativeChop

IFunction negativeChop

fileWriter

FileWriter fileWriter

filename

String filename

toWriteFile

boolean toWriteFile

blockCounter

long blockCounter

Class etomica.data.AccumulatorCounter extends DataAccumulator implements Serializable

serialVersionUID: 1L

Serialized Fields

data

DataDouble data

Class etomica.data.AccumulatorHistogram extends DataAccumulator implements Serializable

serialVersionUID: 2L

Serialized Fields

histogram

Histogram histogram

xDataSource

DataSourceIndependentSimple xDataSource

data

DataFunction data

binnedDataInfo

IEtomicaDataInfo binnedDataInfo

nBins

int nBins

Class etomica.data.AccumulatorHistory extends DataAccumulator implements Serializable

serialVersionUID: 1L

Serialized Fields

history

History history

xDataSources

DataSourceIndependentSimple xDataSources

data

DataFunction data

nData

int nData

timeDataSource

DataSourceScalar timeDataSource

inputDataInfo

IEtomicaDataInfo inputDataInfo

Class etomica.data.AccumulatorHistory.DataSourceCount extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

count

int count

Class etomica.data.AccumulatorRatioAverage extends AccumulatorAverageFixed implements Serializable

serialVersionUID: 1L

Serialized Fields

ratio

IData ratio

ratioStandardDeviation

IData ratioStandardDeviation

ratioError

IData ratioError

ratioTag

DataTag ratioTag

ratioStandardDeviationTag

DataTag ratioStandardDeviationTag

ratioErrorTag

DataTag ratioErrorTag

Class etomica.data.AccumulatorRatioAverage.StatType extends AccumulatorAverage.StatType implements Serializable

serialVersionUID: 1L

Class etomica.data.DataAccumulator extends DataProcessorForked implements Serializable

serialVersionUID: 1L

Serialized Fields

putCount

int putCount

Counter that keeps track of the number of interval events received since last call to updateSums

pushInterval

int pushInterval

Accumulated data are pushed to the data sinks after every pushInterval calls

active

boolean active

Flag specifying whether the manager responds to integrator events

Class etomica.data.DataArrayWriter extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

fileWriter

FileWriter fileWriter

firstWrite

boolean firstWrite

dataInfo

IEtomicaDataInfo dataInfo

includeHeader

boolean includeHeader

Class etomica.data.DataFork extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

dataSinkList

etomica.data.DataFork.DataSinkWrapper[] dataSinkList

dataInfo

IEtomicaDataInfo dataInfo

tag

DataTag tag

Class etomica.data.DataGroupFilter extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

outputData

IData outputData

singleInstance

boolean singleInstance

indexes

int[] indexes

Class etomica.data.DataHistogram extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

histogram

Histogram histogram

xDataSource

DataSourceIndependentSimple xDataSource

data

DataFunction data

binnedDataInfo

IEtomicaDataInfo binnedDataInfo

nData

int nData

Class etomica.data.DataInfo extends Object implements Serializable

Serialized Fields

label

String label

dimension

Dimension dimension

tags

ArrayList<E> tags

tagArray

DataTag[] tagArray

Class etomica.data.DataInfoFactory extends Object implements Serializable

Serialized Fields

label

String label

dimension

Dimension dimension

tags

ArrayList<E> tags

Class etomica.data.DataLogger extends DataProcessor implements Serializable

serialVersionUID: 2L

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException

Throws:

IOException

ClassNotFoundException

Serialized Fields

count

int count

writeInterval

int writeInterval

fileName

String fileName

appending

boolean appending

fileNameSuffix

String fileNameSuffix

sameFileEachTime

boolean sameFileEachTime

closeFileEachTime

boolean closeFileEachTime

writeOnFinishSource

IEtomicaDataSource writeOnFinishSource

writeOnInterval

boolean writeOnInterval

Class etomica.data.DataProcessor extends Object implements Serializable

Serialized Fields

dataSink

IDataSink dataSink

trueDataSink

IDataSink trueDataSink

dataInfo

IEtomicaDataInfo dataInfo

tag

DataTag tag

Class etomica.data.DataProcessorChemicalPotential extends DataProcessor implements Serializable

Serialized Fields

densityProfileSource

IEtomicaDataSource densityProfileSource

data

DataFunction data

integrator

IntegratorBox integrator

Class etomica.data.DataProcessorForked extends DataProcessor implements Serializable

Serialized Fields

dataFork

DataFork dataFork

Class etomica.data.DataProcessorFunction extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

function

IFunction function

data

IData data

Class etomica.data.DataProcessorInterfacialTension extends DataProcessor implements Serializable

Serialized Fields

space

ISpace space

box

IBox box

data

DataDouble data

surfaceDim

int surfaceDim

Class etomica.data.DataPump extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

dataSourceInfo

IEtomicaDataInfo dataSourceInfo

dataSource

IEtomicaDataSource dataSource

Class etomica.data.DataPumpListener extends DataPump implements Serializable

serialVersionUID: 1L

Serialized Fields

interval

int interval

intervalCount

int intervalCount

Class etomica.data.DataSet extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

listeners

DataSetListener[] listeners

updatingOnAnyChange

boolean updatingOnAnyChange

dataChangedBits

int[] dataChangedBits

dataCasterJudge

DataSet.DataCasterJudge dataCasterJudge

psuedoSinks

DataSet.DataSetSink[] psuedoSinks

forwardDataMap

int[] forwardDataMap

backwardDataMap

int[] backwardDataMap

Class etomica.data.DataSinkConsole extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

out

PrintStream out

Class etomica.data.DataSinkTable extends DataSet implements Serializable

serialVersionUID: 1L

Serialized Fields

rowCount

int rowCount

Class etomica.data.DataSinkTable.DataCasterJudgeTable extends Object implements Serializable

serialVersionUID: 1L

Class etomica.data.DataSourceAcceptanceProbability extends DataSourceAcceptanceRatio implements Serializable

serialVersionUID: 1L

Class etomica.data.DataSourceAcceptanceRatio extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

move

MCMove move

Class etomica.data.DataSourceAtomDistance extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

space

ISpace space

vector

IVectorMutable vector

atom1

IAtom atom1

atom2

IAtom atom2

Class etomica.data.DataSourceCountCollisions extends DataSourceScalar implements Serializable

serialVersionUID: 2L

Serialized Fields

integrator

IntegratorHard integrator

Class etomica.data.DataSourceCountSteps extends DataSourceScalar implements Serializable

serialVersionUID: 2L

Serialized Fields

integrator

IIntegrator integrator

Class etomica.data.DataSourceCountTime extends DataSourceScalar implements Serializable

serialVersionUID: 2L

Serialized Fields

integrator

IntegratorMD integrator

Class etomica.data.DataSourceFunction extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

data

DataFunction data

dataInfo

IEtomicaDataInfo dataInfo

xSource

DataSourceUniform xSource

xData

DataDoubleArray xData

function

IFunction function

tag

DataTag tag

Class etomica.data.DataSourceGroup extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

dataSources

IEtomicaDataSource[] dataSources

latestData

IData[] latestData

data

DataGroup data

dataInfo

IEtomicaDataInfo dataInfo

tag

DataTag tag

Class etomica.data.DataSourceIndependentSimple extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

xData

DataDoubleArray[] xData

xDataInfo

DataDoubleArray.DataInfoDoubleArray[] xDataInfo

tag

DataTag tag

Class etomica.data.DataSourceRmsVelocity extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

iterator

AtomIterator iterator

atomData

DataDouble atomData

atomDataInfo

IEtomicaDataInfo atomDataInfo

dataInfo

IEtomicaDataInfo dataInfo

xData

DataDoubleArray xData

xDataInfo

DataDoubleArray.DataInfoDoubleArray xDataInfo

histogramRMS

Histogram histogramRMS

data

DataFunction data

tag

DataTag tag

xTag

DataTag xTag

Class etomica.data.DataSourceScalar extends Object implements Serializable

Serialized Fields

data

DataDouble data

dataInfo

IEtomicaDataInfo dataInfo

tag

DataTag tag

Class etomica.data.DataSourceTensorVirialHard extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

lastTime

double lastTime

integratorHard

IntegratorHard integratorHard

data

DataTensor data

work

Tensor work

dataInfo

DataTensor.DataInfoTensor dataInfo

tag

DataTag tag

Class etomica.data.DataSourceUniform extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

typeMin

DataSourceUniform.LimitType typeMin

typeMax

DataSourceUniform.LimitType typeMax

xMin

double xMin

xMax

double xMax

x

double[] x

data

DataDoubleArray data

dataInfo

DataDoubleArray.DataInfoDoubleArray dataInfo

dx

double dx

tag

DataTag tag

Class etomica.data.DataSourceUniform.LimitType extends EnumeratedType implements Serializable

serialVersionUID: 1L

Class etomica.data.DataStreamAction extends Object implements Serializable

Serialized Fields

start

Object start

Class etomica.data.DataTableAverages extends DataSinkTable implements Serializable

serialVersionUID: 1L

Serialized Fields

accumulators

AccumulatorAverage[] accumulators

types

AccumulatorAverage.StatType[] types

listenerGroup

IntegratorListenerGroupSeries listenerGroup

tableUpdateInterval

int tableUpdateInterval

accumulatorUpdateInterval

int accumulatorUpdateInterval

blockSize

int blockSize

integrator

IIntegrator integrator

Class etomica.data.DataTableWriter extends Object implements Serializable

serialVersionUID: 2L

Serialized Fields

firstWrite

boolean firstWrite

dataInfo

IEtomicaDataInfo dataInfo

includeHeader

boolean includeHeader

Class etomica.data.DataTag extends Object implements Serializable

serialVersionUID: 1L

Package etomica.data.meter

Class etomica.data.meter.MeterBondOrderParameterQ extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

Qreal

double[] Qreal

Qimag

double[] Qimag

L

int L

pairIterator

AtomsetIteratorBoxDependent pairIterator

r2Cut

double r2Cut

rThetaPhi

double[] rThetaPhi

coeff

double coeff

dr

IVectorMutable dr

Class etomica.data.meter.MeterDensity extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

species

ISpecies species

Class etomica.data.meter.MeterDihedralAngle extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

space

ISpace space

gSum

long[] gSum

data

DataFunction data

dataInfo

IEtomicaDataInfo dataInfo

phiData

DataDoubleArray phiData

iterator

AtomsetIteratorBoxDependent iterator

dr1

IVectorMutable dr1

dr2

IVectorMutable dr2

dr3

IVectorMutable dr3

boundary

IBoundary boundary

xDataSource

DataSourceUniform xDataSource

rMax

double rMax

name

String name

tag

DataTag tag

tetraNum

long tetraNum

Class etomica.data.meter.MeterEnergy extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

kinetic

DataSourceScalar kinetic

potential

DataSourceScalar potential

Class etomica.data.meter.MeterKineticEnergy extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

iterator

AtomIteratorBoxDependent iterator

box

IBox box

Class etomica.data.meter.MeterKineticEnergyFromIntegrator extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

integrator

IntegratorMD integrator

Class etomica.data.meter.MeterKineticEnergyRigid extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

sim

ISimulation sim

box

IBox box

angularVelocity

IVectorMutable angularVelocity

rotationTensor

RotationTensor3D rotationTensor

Class etomica.data.meter.MeterLocalDensity extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

iterator

AtomIteratorBoxDependent iterator

Class variable used to specify that all species are included in number-density calculation

shape

Polytope shape

Class etomica.data.meter.MeterLocalMoleFraction extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

species

ISpecies species

Class variable used to specify that all species are included in number-density calculation

iterator

AtomIteratorBoxDependent iterator

shape

Polytope shape

shapeOrigin

IVector shapeOrigin

tempVec

IVectorMutable tempVec

Class etomica.data.meter.MeterMeanSquareDisplacement extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

nAtoms

int nAtoms

iterator

AtomIteratorBoxDependent iterator

integrator

IntegratorBox integrator

rAccum

IVectorMutable[] rAccum

rLast

IVectorMutable[] rLast

space

ISpace space

Class etomica.data.meter.MeterMoleFraction extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

species

ISpecies species

box

IBox box

Class etomica.data.meter.MeterMomentumCOM extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

momentumSum

IVectorMutable momentumSum

data

DataVector data

dataInfo

DataInfo dataInfo

name

String name

tag

DataTag tag

Class etomica.data.meter.MeterNMolecules extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

species

ISpecies species

box

IBox box

Class etomica.data.meter.MeterPositionCOM extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

positionSum

IVectorMutable positionSum

data

DataVector data

dataInfo

DataInfo dataInfo

name

String name

tag

DataTag tag

Class etomica.data.meter.MeterPotentialEnergy extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

iteratorDirective

IteratorDirective iteratorDirective

energy

PotentialCalculationEnergySum energy

potential

IPotentialMaster potential

Class etomica.data.meter.MeterPotentialEnergyFromIntegrator extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

integrator

IntegratorBox integrator

Class etomica.data.meter.MeterPressure extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

integrator

IntegratorBox integrator

iteratorDirective

IteratorDirective iteratorDirective

virial

PotentialCalculationVirialSum virial

dim

int dim

Class etomica.data.meter.MeterPressureByVolumeChange extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

data

DataDoubleArray data

dataInfo

IEtomicaDataInfo dataInfo

tag

DataTag tag

dataArray

double[] dataArray

inflater

BoxInflate inflater

scale

IVectorMutable scale

inflateDimensions

boolean[] inflateDimensions

iteratorDirective

IteratorDirective iteratorDirective

energy

PotentialCalculationEnergySum energy

nDimension

int nDimension

space

ISpace space

xDataSource

DataSourceUniform xDataSource

vDataSource

MeterPressureByVolumeChange.DataSourceExp vDataSource

integrator

IntegratorBox integrator

Class etomica.data.meter.MeterPressureHard extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

virialSum

double virialSum

integratorHard

IntegratorHard integratorHard

lastTime

double lastTime

dim

int dim

Class etomica.data.meter.MeterPressureHardTensor extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

t0

double t0

v

Tensor v

integratorHard

IntegratorHard integratorHard

name

String name

box

IBox box

data

DataTensor data

dataInfo

IEtomicaDataInfo dataInfo

tag

DataTag tag

dim

int dim

Class etomica.data.meter.MeterPressureTensor extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

tag

DataTag tag

data

DataTensor data

dataInfo

DataInfo dataInfo

potentialMaster

IPotentialMaster potentialMaster

box

IBox box

iteratorDirective

IteratorDirective iteratorDirective

pc

PotentialCalculationPressureTensor pc

rD

double rD

Class etomica.data.meter.MeterPressureTensorFromIntegrator extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

integrator

IntegratorVelocityVerlet integrator

data

DataTensor data

dataInfo

DataInfo dataInfo

tag

DataTag tag

space

ISpace space

Class etomica.data.meter.MeterProfile extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

xDataSource

DataSourceUniform xDataSource

data

DataFunction data

dataInfo

IEtomicaDataInfo dataInfo

positionSource

RandomPositionSource positionSource

profileDim

int profileDim

Vector describing the orientation of the profile. For example, (1,0) is along the x-axis.

meter

DataSourcePositioned meter

Meter that defines the property being profiled.

tag

DataTag tag

Class etomica.data.meter.MeterProfileByAtoms extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

xDataSource

DataSourceUniform xDataSource

data

DataFunction data

positionDefinition

IAtomPositionDefinition positionDefinition

y

double[] y

nAtoms

int[] nAtoms

dataInfo

IEtomicaDataInfo dataInfo

profileDim

int profileDim

Vector describing the orientation of the profile. For example, (1,0) is along the x-axis.

position

IVectorMutable position

meter

DataSourceMolecular meter

Meter that defines the property being profiled.

tag

DataTag tag

species

ISpecies species

Class etomica.data.meter.MeterProfileByVolume extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

xDataSource

DataSourceUniform xDataSource

data

DataFunction data

dataInfo

IEtomicaDataInfo dataInfo

profileDim

int profileDim

Vector describing the orientation of the profile. For example, (1,0) is along the x-axis.

position

IVectorMutable position

meter

DataSourceMolecular meter

Meter that defines the property being profiled.

tag

DataTag tag

species

ISpecies species

positionDefinition

IAtomPositionDefinition positionDefinition

Class etomica.data.meter.MeterRadiusGyration extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

iterator

MoleculeIteratorAllMolecules iterator

cm

IVectorMutable cm

realPos

IVectorMutable realPos

dr

IVectorMutable dr

Class etomica.data.meter.MeterRDF extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

space

ISpace space

gSum

long[] gSum

data

DataFunction data

dataInfo

IEtomicaDataInfo dataInfo

rData

DataDoubleArray rData

iterator

AtomsetIteratorBoxDependent iterator

dr

IVectorMutable dr

boundary

IBoundary boundary

xDataSource

DataSourceUniform xDataSource

xMax

double xMax

name

String name

tag

DataTag tag

callCount

int callCount

Class etomica.data.meter.MeterStructureFactor extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

lattice

BravaisLatticeCrystal lattice

space

ISpace space

box

IBox box

struct

double[] struct

waveVec

IVectorMutable[] waveVec

moleculeList

IMoleculeList moleculeList

Class etomica.data.meter.MeterTemperature extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

meterKE

DataSourceScalar meterKE

sim

ISimulation sim

dim

int dim

Class etomica.data.meter.MeterTensorVelocity extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

name

String name

box

IBox box

data

DataTensor data

atomData

DataTensor atomData

dataInfo

DataTensor.DataInfoTensor dataInfo

tag

DataTag tag

Class etomica.data.meter.MeterVolume extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

Class etomica.data.meter.MeterWidomInsertion extends DataSourceScalar implements Serializable

serialVersionUID: 1L

Serialized Fields

integrator

IntegratorBox integrator

nInsert

int nInsert

Number of insertions attempted in each call to currentValue Default is 100

species

ISpecies species

testMolecule

IMolecule testMolecule

residual

boolean residual

atomTranslator

MoleculeActionTranslateTo atomTranslator

positionSource

RandomPositionSource positionSource

energyMeter

MeterPotentialEnergy energyMeter

Package etomica.data.types

Class etomica.data.types.CastGroupOfTablesToDataTable extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

outputData

DataTable outputData

outputDataInfo

DataTable.DataInfoTable outputDataInfo

Class etomica.data.types.CastGroupToDoubleArray extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

outputData

DataDoubleArray outputData

inputType

int inputType

Class etomica.data.types.CastToDouble extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

dataDouble

DataDouble dataDouble

inputType

int inputType

Class etomica.data.types.CastToDoubleArray extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

outputData

DataDoubleArray outputData

inputType

int inputType

Class etomica.data.types.CastToGroup extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

dataGroup

DataGroup dataGroup

inputType

int inputType

Class etomica.data.types.CastToTable extends DataProcessor implements Serializable

serialVersionUID: 1L

Serialized Fields

outputData

DataTable outputData

inputType

int inputType

xDataSource

DataSourceIndependent xDataSource

Class etomica.data.types.DataDouble extends 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 Object implements Serializable

serialVersionUID: 1L

Serialized Fields

x

double[] x

jumpCount

int[] jumpCount

arrayShape

int[] arrayShape

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.DataFunction extends DataDoubleArray implements Serializable

serialVersionUID: 1L

Class etomica.data.types.DataFunction.DataInfoFunction extends DataDoubleArray.DataInfoDoubleArray implements Serializable

serialVersionUID: 1L

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 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

IEtomicaDataInfo[] subDataInfo

Class etomica.data.types.DataGroup.DataInfoGroupFactory extends DataInfoFactory implements Serializable

serialVersionUID: 1L

Serialized Fields

subDataInfo

IEtomicaDataInfo[] 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

rowHeaders

String[] rowHeaders

nRows

int nRows

Class etomica.data.types.DataTable.DataInfoTableFactory extends DataGroup.DataInfoGroupFactory implements Serializable

serialVersionUID: 1L

Serialized Fields

columnInfoFactories

DataDoubleArray.DataInfoDoubleArrayFactory[] columnInfoFactories

rowHeaders

String[] rowHeaders

nRows

int nRows

Class etomica.data.types.DataTensor extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

x

Tensor x

The wrapped tensor data.

Class etomica.data.types.DataTensor.DataInfoTensor extends DataInfo implements Serializable

serialVersionUID: 1L

Serialized Fields

space

ISpace space

Class etomica.data.types.DataTensor.DataInfoTensorFactory extends DataInfoFactory implements Serializable

serialVersionUID: 1L

Serialized Fields

space

ISpace space

Class etomica.data.types.DataVector extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

x

IVectorMutable x

The wrapped vector data.

Class etomica.data.types.DataVector.DataInfoVector extends DataInfo implements Serializable

serialVersionUID: 1L

Serialized Fields

space

ISpace space

Class etomica.data.types.DataVector.DataInfoVectorFactory extends DataInfoFactory implements Serializable

serialVersionUID: 1L

Serialized Fields

space

ISpace space

Package etomica.exception

Class etomica.exception.AbnormalCompletionException extends RuntimeException implements Serializable

Class etomica.exception.ConfigurationOverlapException extends RuntimeException implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

Class etomica.exception.MethodNotImplementedException extends RuntimeException implements Serializable

Package etomica.graphics

Class etomica.graphics.AboutBoxWindow extends JDialog implements Serializable

Serialized Fields

eg

AboutBoxWindow.EtomicaGraphic eg

owner

Component owner

creationCredits

String[] creationCredits

softwareCredits

String[] softwareCredits

appName

String appName

ETOMICA_IMAGE

String ETOMICA_IMAGE

SUNY_TEXT

String SUNY_TEXT

CE_TEXT

String CE_TEXT

NSF_TEXT

String NSF_TEXT

WWW_TEXT

String WWW_TEXT

GRAPHIC_WIDTH

int GRAPHIC_WIDTH

GRAPHIC_HEIGHT

int GRAPHIC_HEIGHT

GRAPHIC_X

int GRAPHIC_X

GRAPHIC_Y

int GRAPHIC_Y

ABOUT_WIDTH

int ABOUT_WIDTH

ABOUT_HEIGHT

int ABOUT_HEIGHT

ABOUT_X

int ABOUT_X

ABOUT_Y

int ABOUT_Y

CREDIT_FONT_SIZE

int CREDIT_FONT_SIZE

Class etomica.graphics.AboutBoxWindow.EtomicaGraphic extends JPanel implements Serializable

Serialized Fields

etomicaImage

Icon etomicaImage

Class etomica.graphics.ActionGraphic extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

simulationAction

IAction simulationAction

Class etomica.graphics.BondListener extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

atomAgentManager

AtomLeafAgentManager atomAgentManager

bondIteratorsHash

HashMap<K,V> bondIteratorsHash

bondManager

BondManager bondManager

atomSetSinglet

MoleculeSetSinglet atomSetSinglet

Class etomica.graphics.ColorScheme extends Object implements Serializable

Serialized Fields

defaultColor

Color defaultColor

Class etomica.graphics.ColorScheme.Simple extends ColorScheme implements Serializable

serialVersionUID: 1L

Class etomica.graphics.ColorSchemeByType extends ColorScheme implements Serializable

Serialized Fields

colorMap

AtomTypeAgentManager colorMap

moreDefaultColors

Color[] moreDefaultColors

defaultColorsUsed

int defaultColorsUsed

Class etomica.graphics.ColorSchemeCell extends ColorScheme implements Serializable

serialVersionUID: 1L

Serialized Fields

hash

HashMap<K,V> hash

cellManager

NeighborCellManager cellManager

random

IRandom random

Class etomica.graphics.ColorSchemeCollectiveAgent extends ColorScheme implements Serializable

Serialized Fields

agentManager

AtomLeafAgentManager agentManager

Class etomica.graphics.ColorSchemeColliders extends ColorScheme implements Serializable

Serialized Fields

integrator

IntegratorHard integrator

colliderColor

Color colliderColor

Color applied to the downList atom of the colliding pair

partnerColor

Color partnerColor

Color applied to the upList atom of the colliding pair

Class etomica.graphics.ColorSchemeCoordination extends ColorSchemeCollectiveAgent implements Serializable

serialVersionUID: 1L

Serialized Fields

leafList

IAtomList leafList

colors

Color[] colors

nbrManager

NeighborListManager nbrManager

Class etomica.graphics.ColorSchemeNeighbor extends ColorSchemeCollectiveAgent implements Serializable

serialVersionUID: 1L

Serialized Fields

referenceAtom

IAtom referenceAtom

nbrIterator

Api1ACell nbrIterator

leafList

IAtomList leafList

typeColorScheme

ColorSchemeByType typeColorScheme

Class etomica.graphics.ColorSchemeNull extends ColorScheme implements Serializable

Class etomica.graphics.ColorSchemeRandom extends ColorScheme implements Serializable

serialVersionUID: 2L

Serialized Fields

agentManager

AtomLeafAgentManager agentManager

random

IRandom random

Class etomica.graphics.ColorSchemeRandomByMolecule extends ColorScheme implements Serializable

serialVersionUID: 2L

Serialized Fields

agentManager

MoleculeAgentManager agentManager

random

IRandom random

Class etomica.graphics.ColorSchemeTemperature extends ColorScheme implements Serializable

Serialized Fields

TLow

double TLow

THigh

double THigh

KEMin

double KEMin

KEMax

double KEMax

range

double range

Class etomica.graphics.DecimalSlider extends JSlider implements Serializable

Serialized Fields

labelTable

Hashtable<K,V> labelTable

maximum

int maximum

minimum

int minimum

precision

long precision

spacing

int spacing

halfSpacing

int halfSpacing

standardSpacingLabel

int standardSpacingLabel

Class etomica.graphics.DeviceBox.LabelType extends EnumeratedType implements Serializable

Class etomica.graphics.DeviceBoxValueChangedEvent extends AWTEvent implements Serializable

Serialized Fields

newValue

int newValue

Class etomica.graphics.DeviceSpinner.SpinnerListener extends Object implements Serializable

Class etomica.graphics.DeviceTableModelGeneric extends AbstractTableModel implements Serializable

Serialized Fields

columnNames

String[] columnNames

columnClasses

Class<T>[] columnClasses

data

Vector<E> data

numColumns

int numColumns

numRows

int numRows

Class etomica.graphics.DeviceTernarySelector.MyEventManager extends EventManager implements Serializable

Serialized Fields

triangle

etomica.graphics.DeviceTernarySelector.Triangle triangle

Class etomica.graphics.DimensionedDoubleEditor extends PropertyEditorSupport implements Serializable

Serialized Fields

valueEditor

PropertyEditor valueEditor

unit

PrefixedUnit unit

prefix

Prefix prefix

baseUnit

Unit baseUnit

availableUnits

Class<T>[] availableUnits

availableUnitNames

StringBuffer[] availableUnitNames

unitList

JComboBox unitList

Class etomica.graphics.DisplayBoxCanvas1D extends DisplayCanvas implements Serializable

Serialized Fields

scaleText

TextField scaleText

font

Font font

annotationHeight

int annotationHeight

shiftOrigin

int[] shiftOrigin

space

ISpace space

atomOrigin

int[] atomOrigin

Class etomica.graphics.DisplayBoxCanvas2D extends DisplayCanvas implements Serializable

Serialized Fields

scaleText

TextField scaleText

font

Font font

annotationHeight

int annotationHeight

shiftOrigin

int[] shiftOrigin

atomOrigin

int[] atomOrigin

boundingBox

IVectorMutable boundingBox

space

ISpace space

vec2

IVectorMutable vec2

Class etomica.graphics.DisplayBoxCanvasG3DSys extends DisplayCanvas implements Serializable

Serialized Fields

gsys

G3DSys gsys

coords

double[] coords

aam

AtomLeafAgentManager aam

oldPolytope

Polytope oldPolytope

polytopeLines

Line[] polytopeLines

boundaryDisplayed

boolean boundaryDisplayed

backgroundColor

Color backgroundColor

boundaryFrameColor

Color boundaryFrameColor

planeColor

Color planeColor

panel

Panel panel

initialOrient

boolean initialOrient

planes

Plane[] planes

planeTriangles

Triangle[][] planeTriangles

planeIntersections

IVectorMutable[] planeIntersections

work

IVectorMutable work

work2

IVectorMutable work2

work3

IVectorMutable work3

planeAngles

double[] planeAngles

space

ISpace space

pendingBonds

ArrayList<E> pendingBonds

Class etomica.graphics.DisplayBoxSpin2D extends DisplayBoxCanvas2D implements Serializable

Serialized Fields

spinWidth

int spinWidth

latticeIndex

int[] latticeIndex

neighborSiteManager

NeighborSiteManager neighborSiteManager

Class etomica.graphics.DisplayCanvas extends JPanel implements Serializable

Serialized Fields

offScreen

Image offScreen

osg

Graphics osg

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

resizable

boolean resizable

Flag to indicate if display can be resized

movable

boolean movable

Flag to indicate if display can be moved

writeScale

boolean writeScale

Flag to indicate if value of scale should be superimposed on image

pixel

Pixel pixel

controller

Controller controller

Class etomica.graphics.DisplayPlot.DataCasterJudgeFunction extends Object implements Serializable

Class etomica.graphics.DisplayPolytope.Applet extends 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

gsys

G3DSys gsys

polytopeLines

Line[] polytopeLines

backgroundColor

Color backgroundColor

boundaryFrameColor

Color boundaryFrameColor

panel

Panel panel

initialOrient

boolean initialOrient

displayPolytope

DisplayPolytope displayPolytope

Class etomica.graphics.DisplayTextBox.LabelType extends EnumeratedType implements Serializable

Class etomica.graphics.EtomicaPlot extends ptolemy.plot.Plot implements Serializable

Serialized Fields

displayPlot

DisplayPlot displayPlot

needUpdate

boolean needUpdate

Class etomica.graphics.PropertyText extends JTextField implements Serializable

Class etomica.graphics.SimulationPanel extends JPanel implements Serializable

Serialized Fields

toolbarPanel

JPanel toolbarPanel

controlPanel

JPanel controlPanel

graphicsPanel

JPanel graphicsPanel

footerPanel

JPanel footerPanel

plotPanel

JPanel plotPanel

metricPanel

JPanel metricPanel

tabbedPane

JTabbedPane tabbedPane

toolbar

DefaultToolbar toolbar

Package etomica.graphics2

Class etomica.graphics2.ColorSchemeByType extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

colormap

HashMap<K,V> colormap

colorindex

ArrayList<E> colorindex

position_in_list

int position_in_list

Class etomica.graphics2.ColorSchemeSimple extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

baseColor

Color baseColor

Package etomica.integrator

Class etomica.integrator.Integrator extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

initialized

boolean initialized

interval

int interval

iieCount

int iieCount

stepCount

long stepCount

eventManager

IntegratorEventManager eventManager

Class etomica.integrator.IntegratorAnalytic extends IntegratorMD implements Serializable

serialVersionUID: 1L

Serialized Fields

action

IntegratorAnalytic.AtomTimeAction action

Class etomica.integrator.IntegratorBox extends Integrator implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

temperature

double temperature

isothermal

boolean isothermal

meterPE

DataSourceScalar meterPE

currentPotentialEnergy

double currentPotentialEnergy

potentialMaster

IPotentialMaster potentialMaster

Class etomica.integrator.IntegratorConNVT extends IntegratorMD implements Serializable

serialVersionUID: 1L

Serialized Fields

forceSum

PotentialCalculationForceSum forceSum

allAtoms

IteratorDirective allAtoms

work

IVectorMutable work

work1

IVectorMutable work1

work2

IVectorMutable work2

work3

IVectorMutable work3

work4

IVectorMutable work4

halfTime

double halfTime

mass

double mass

agentManager

AtomLeafAgentManager agentManager

Temper

double Temper

Class etomica.integrator.IntegratorEvent extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

type

IntegratorEvent.Type type

source

IIntegrator source

Class etomica.integrator.IntegratorEvent.Type extends EnumeratedType implements Serializable

serialVersionUID: 1L

Class etomica.integrator.IntegratorEventManager extends Object implements Serializable

Serialized Fields

intervalListeners

LinkedList<E> intervalListeners

Class etomica.integrator.IntegratorGear4 extends IntegratorMD implements Serializable

serialVersionUID: 1L

Serialized Fields

forceSum

PotentialCalculationForceSum forceSum

allAtoms

IteratorDirective allAtoms

work1

IVectorMutable work1

work2

IVectorMutable work2

zeta

double zeta

chi

double chi

p1

double p1

p2

double p2

p3

double p3

p4

double p4

c0

double c0

c2

double c2

c3

double c3

c4

double c4

agentManager

AtomLeafAgentManager agentManager

Class etomica.integrator.IntegratorGear4NPH extends IntegratorGear4 implements Serializable

serialVersionUID: 1L

Serialized Fields

vol1

double vol1

vol2

double vol2

vol3

double vol3

vol4

double vol4

forceSumNPH

IntegratorGear4NPH.ForceSumNPH forceSumNPH

allAtoms

IteratorDirective allAtoms

inflate

BoxInflate inflate

targetH

double targetH

targetP

double targetP

targetT

double targetT

rrp

double rrp

rrh

double rrh

kp

double kp

kh

double kh

D

int D

meterTemperature

MeterTemperature meterTemperature

Class etomica.integrator.IntegratorGear4NPH.EnsembleToggler extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

integrator

IntegratorGear4NPH integrator

dim

int dim

Class etomica.integrator.IntegratorGear4NPH.MeterEnthalpy extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

data

DataDouble data

integrator

IntegratorGear4NPH integrator

dataInfo

IEtomicaDataInfo dataInfo

tag

DataTag tag

dim

int dim

Class etomica.integrator.IntegratorGEMC extends IntegratorManagerMC implements Serializable

serialVersionUID: 1L

Serialized Fields

volumeExchange

MCMoveVolumeExchange volumeExchange

moleculeExchange

MCMoveMoleculeExchange moleculeExchange

space

ISpace space

Class etomica.integrator.IntegratorHard extends IntegratorMD implements Serializable

serialVersionUID: 1L

Serialized Fields

colliderAgent

IntegratorHard.Agent colliderAgent

collisionListenerHead

etomica.integrator.IntegratorHard.CollisionListenerLinker collisionListenerHead

pair

AtomPair pair

singlet

AtomSetSinglet singlet

minDelta

double minDelta

debugPair

AtomPair debugPair

upList

IteratorDirective upList

downList

IteratorDirective downList

listToUpdate

AtomArrayList listToUpdate

eventList

TreeList eventList

reverseCollisionHandler

etomica.integrator.IntegratorHard.ReverseCollisionHandler reverseCollisionHandler

collisionHandlerUp

IntegratorHard.CollisionHandlerUp collisionHandlerUp

collisionHandlerDown

etomica.integrator.IntegratorHard.CollisionHandlerDown collisionHandlerDown

collisionTimeStep

double collisionTimeStep

collisionCount

int collisionCount

agentManager

AtomLeafAgentManager agentManager

nullPotentialManager

AtomTypeAgentManager nullPotentialManager

handlingEvent

int handlingEvent

Class etomica.integrator.IntegratorHard.Agent extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

atom

IAtom atom

collisionPartner

IAtom collisionPartner

collisionPotential

PotentialHard collisionPotential

eventLinker

TreeLinker eventLinker

nullPotential

PotentialHard nullPotential

atomSetSinglet

AtomSetSinglet atomSetSinglet

nullCollisionTime

double nullCollisionTime

integrator

IntegratorHard integrator

Class etomica.integrator.IntegratorHard.CollisionHandlerUp extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

minCollisionTime

double minCollisionTime

aia

IntegratorHard.Agent aia

atom1

IAtom atom1

collisionTimeStep

double collisionTimeStep

integratorAgentManager

AtomLeafAgentManager integratorAgentManager

Class etomica.integrator.IntegratorHardField extends IntegratorHard implements Serializable

serialVersionUID: 1L

Serialized Fields

forceSum

IntegratorHardField.PotentialCalculationForceSum forceSum

fieldsOnly

IteratorDirective fieldsOnly

noFieldsCriterion

IteratorDirective.PotentialCriterion noFieldsCriterion

Class etomica.integrator.IntegratorHardField.HardFieldAgent extends IntegratorHard.Agent implements Serializable

Serialized Fields

force

IVectorMutable force

forceFree

boolean forceFree

Class etomica.integrator.IntegratorManagerMC extends Integrator implements Serializable

serialVersionUID: 2L

Serialized Fields

globalMoveInterval

double globalMoveInterval

globalMoveProbability

double globalMoveProbability

moveManager

MCMoveManager moveManager

eventManager

IEventManager eventManager

integrators

IIntegrator[] integrators

nIntegrators

int nIntegrators

trialEvent

IEvent trialEvent

acceptedEvent

IEvent acceptedEvent

rejectedEvent

IEvent rejectedEvent

random

IRandom random

Class etomica.integrator.IntegratorMC extends IntegratorBox implements Serializable

serialVersionUID: 2L

Serialized Fields

random

IRandom random

moveManager

MCMoveManager moveManager

moveEventManager

IEventManager moveEventManager

trialEvent

IEvent trialEvent

acceptedEvent

IEvent acceptedEvent

rejectedEvent

IEvent rejectedEvent

Class etomica.integrator.IntegratorMD extends IntegratorBox implements Serializable

serialVersionUID: 2L

Serialized Fields

random

IRandom random

Elementary time step for the MD simulation

timeStep

double timeStep

currentKineticEnergy

double currentKineticEnergy

thermostat

IntegratorMD.ThermostatType thermostat

thermostatCount

int thermostatCount

thermostatInterval

int thermostatInterval

meterKE

DataSourceScalar meterKE

atomActionRandomizeVelocity

AtomActionRandomizeVelocity atomActionRandomizeVelocity

meterTemperature

MeterTemperature meterTemperature

momentum

IVectorMutable momentum

currentTime

double currentTime

space

ISpace space

Class etomica.integrator.IntegratorMD.ThermostatType extends EnumeratedType implements Serializable

serialVersionUID: 1L

Serialization Methods

readResolve

private Object readResolve()

Required to guarantee singleton when deserializing.

Class etomica.integrator.IntegratorNonintervalEvent extends IntegratorEvent implements Serializable

serialVersionUID: 1L

Class etomica.integrator.IntegratorNonintervalEvent.NonintervalEventType extends IntegratorEvent.Type implements Serializable

serialVersionUID: 1L

Class etomica.integrator.IntegratorPT extends IntegratorManagerMC implements Serializable

serialVersionUID: 1L

Serialized Fields

space

ISpace space

mcMoveSwapFactory

IntegratorPT.MCMoveSwapFactory mcMoveSwapFactory

Class etomica.integrator.IntegratorPT.BoxTracker extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

track

int[] track

dtrack

double[] dtrack

data

DataDoubleArray data

dataInfo

DataDoubleArray.DataInfoDoubleArray dataInfo

tag

DataTag tag

Class etomica.integrator.IntegratorRigidIterative extends IntegratorMD implements Serializable

serialVersionUID: 2L

Serialized Fields

torqueSum

PotentialCalculationTorqueSum torqueSum

allAtoms

IteratorDirective allAtoms

pressureTensor

Tensor pressureTensor

workTensor

Tensor workTensor

rotationTensor

RotationTensor3D rotationTensor

tempRotationTensor

RotationTensor3D tempRotationTensor

xWork

IVectorMutable xWork

typeAgentManager

SpeciesAgentManager typeAgentManager

tempAngularVelocity

IVectorMutable tempAngularVelocity

atomPositionCOM

AtomPositionCOM atomPositionCOM

translateBy

AtomActionTranslateBy translateBy

translator

MoleculeChildAtomAction translator

tempOrientation

OrientationFull3D tempOrientation

printInterval

int printInterval

maxIterations

int maxIterations

omegaTolerance

double omegaTolerance

storeAngularMomentum

boolean storeAngularMomentum

sim

ISimulation sim

leafAgentManager

AtomLeafAgentManager leafAgentManager

moleculeAgentManager

MoleculeAgentManager moleculeAgentManager

Class etomica.integrator.IntegratorRigidIterative.MoleculeAgent extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

torque

IVectorMutable torque

force

IVectorMutable force

Class etomica.integrator.IntegratorRigidMatrixIterative extends IntegratorMD implements Serializable

serialVersionUID: 2L

Serialized Fields

torqueSum

PotentialCalculationTorqueSum torqueSum

allAtoms

IteratorDirective allAtoms

pressureTensor

Tensor pressureTensor

workTensor

Tensor workTensor

rotationTensor

RotationTensor3D rotationTensor

xWork

IVectorMutable xWork

yWork

IVectorMutable yWork

typeAgentManager

SpeciesAgentManager typeAgentManager

tempAngularVelocity

IVectorMutable tempAngularVelocity

atomPositionCOM

AtomPositionCOM atomPositionCOM

translateBy

AtomActionTranslateBy translateBy

translator

MoleculeChildAtomAction translator

tempOrientation

OrientationFull3D tempOrientation

printInterval

int printInterval

maxIterations

int maxIterations

omegaTolerance

double omegaTolerance

rotationTolerance

double rotationTolerance

axesTensor

RotationTensor3D axesTensor

tempAxesTensor

RotationTensor3D tempAxesTensor

omegaTensor

Tensor omegaTensor

sim

ISimulation sim

leafAgentManager

AtomLeafAgentManager leafAgentManager

moleculeAgentManager

MoleculeAgentManager moleculeAgentManager

Class etomica.integrator.IntegratorRigidMatrixIterative.AtomAgent extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

force

IVectorMutable force

Class etomica.integrator.IntegratorRigidMatrixIterative.MoleculeAgent extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

torque

IVectorMutable torque

force

IVectorMutable force

Class etomica.integrator.IntegratorVelocityVerlet extends IntegratorMD implements Serializable

serialVersionUID: 2L

Serialized Fields

forceSum

PotentialCalculationForceSum forceSum

allAtoms

IteratorDirective allAtoms

pressureTensor

Tensor pressureTensor

workTensor

Tensor workTensor

agentManager

AtomLeafAgentManager agentManager

Class etomica.integrator.IntegratorVelocityVerlet.MyAgent extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

force

IVectorMutable force

Class etomica.integrator.IntegratorVelocityVerletRattle extends IntegratorVelocityVerletShake implements Serializable

serialVersionUID: 1L

Serialized Fields

dv

IVectorMutable dv

Class etomica.integrator.IntegratorVelocityVerletShake extends IntegratorMD implements Serializable

serialVersionUID: 2L

Serialized Fields

forceSum

PotentialCalculationForceSum forceSum

allAtoms

IteratorDirective allAtoms

shakeAgentManager

SpeciesAgentManager shakeAgentManager

agentManager

AtomLeafAgentManager agentManager

dr

IVectorMutable dr

shakeTol

double shakeTol

maxIterations

int maxIterations

moved

boolean[][] moved

drOld

IVectorMutable[] drOld

temp

IVectorMutable temp

printInterval

int printInterval

Class etomica.integrator.IntegratorVerlet extends IntegratorMD implements Serializable

serialVersionUID: 1L

Serialized Fields

forceSum

PotentialCalculationForcePressureSum forceSum

allAtoms

IteratorDirective allAtoms

t2

double t2

pressureTensor

Tensor pressureTensor

workTensor

Tensor workTensor

work

IVectorMutable work

agentManager

AtomLeafAgentManager agentManager

Package etomica.integrator.mcmove

Class etomica.integrator.mcmove.MCMove extends Object implements Serializable

Serialized Fields

potential

IPotentialMaster potential

nominalFrequency

int nominalFrequency

Value giving nominal frequency for performing this move. Default is 100, but may be given a different value by subclasses.

moveTracker

MCMoveTracker moveTracker

Class etomica.integrator.mcmove.MCMoveAtom extends MCMoveBoxStep implements Serializable

serialVersionUID: 2L

Serialized Fields

affectedAtomIterator

AtomIteratorSinglet affectedAtomIterator

energyMeter

MeterPotentialEnergy energyMeter

translationVector

IVectorRandom translationVector

atom

IAtom atom

uOld

double uOld

uNew

double uNew

atomSource

AtomSource atomSource

fixOverlap

boolean fixOverlap

random

IRandom random

space

ISpace space

Class etomica.integrator.mcmove.MCMoveBox extends MCMove implements Serializable

Serialized Fields

perParticleFrequency

boolean perParticleFrequency

Flag indicating whether nominal frequency is interpreted as a perParticleFrequency, or as a full frequency. Default is false, but may be given a different value by subclasses.

box

IBox box

Class etomica.integrator.mcmove.MCMoveBoxStep extends MCMoveBox implements Serializable

Serialized Fields

stepSize

double stepSize

stepSizeMax

double stepSizeMax

stepSizeMin

double stepSizeMin

Class etomica.integrator.mcmove.MCMoveDimer extends MCMoveBoxStep implements Serializable

serialVersionUID: 2L

Serialized Fields

affectedAtomIterator

AtomIteratorArrayListSimple affectedAtomIterator

affectedAtoms

AtomArrayList affectedAtoms

energyMeter

MeterPotentialEnergy energyMeter

translationVector

IVectorRandom translationVector

atom

IAtom atom

uOld

double uOld

uNew

double uNew

atomSource

AtomSource atomSource

fixOverlap

boolean fixOverlap

random

IRandom random

space

ISpace space

potentialMaster

PotentialMasterCell potentialMaster

neighborIterator

Api1ACell neighborIterator

dr

IVectorMutable dr

dimerPotential

IPotentialAtomic dimerPotential

atom1

IAtom atom1

Class etomica.integrator.mcmove.MCMoveDimerRotate extends MCMoveBoxStep implements Serializable

serialVersionUID: 2L

Serialized Fields

affectedAtomIterator

AtomIteratorArrayListSimple affectedAtomIterator

affectedAtoms

AtomArrayList affectedAtoms

energyMeter

MeterPotentialEnergy energyMeter

translationVector

IVectorRandom translationVector

atom

IAtom atom

uOld

double uOld

uNew

double uNew

atomSource

AtomSource atomSource

fixOverlap

boolean fixOverlap

random

IRandom random

space

ISpace space

potentialMaster

PotentialMasterCell potentialMaster

neighborIterator

Api1ACell neighborIterator

dr

IVectorMutable dr

dimerPotential

IPotentialAtomic dimerPotential

atom1

IAtom atom1

r0

IVectorMutable r0

Class etomica.integrator.mcmove.MCMoveEventManager extends EventManager implements Serializable

Class etomica.integrator.mcmove.MCMoveInsertDelete extends MCMoveBox implements Serializable

serialVersionUID: 2L

Serialized Fields

mu

double mu

energyMeter

MeterPotentialEnergy energyMeter

species

ISpecies species

affectedAtomIterator

AtomIteratorArrayListSimple affectedAtomIterator

testMolecule

IMolecule testMolecule

uOld

double uOld

uNew

double uNew

insert

boolean insert

reservoir

MoleculeArrayList reservoir

atomTranslator

MoleculeActionTranslateTo atomTranslator

moleculeList

IMoleculeList moleculeList

random

IRandom random

positionSource

RandomPositionSource positionSource

Class etomica.integrator.mcmove.MCMoveManager extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

box

IBox box

firstMoveLink

etomica.integrator.mcmove.MCMoveManager.MCMoveLinker firstMoveLink

lastMoveLink

etomica.integrator.mcmove.MCMoveManager.MCMoveLinker lastMoveLink

selectedLink

etomica.integrator.mcmove.MCMoveManager.MCMoveLinker selectedLink

frequencyTotal

int frequencyTotal

moveCount

int moveCount

isEquilibrating

boolean isEquilibrating

random

IRandom random

Class etomica.integrator.mcmove.MCMoveMolecule extends MCMoveBoxStep implements Serializable

serialVersionUID: 1L

Serialized Fields

affectedAtomIterator

AtomIteratorArrayListSimple affectedAtomIterator

energyMeter

MeterPotentialEnergy energyMeter

translationVector

IVectorRandom translationVector

uOld

double uOld

uNew

double uNew

random

IRandom random

space

ISpace space

moveMoleculeAction

MoleculeChildAtomAction moveMoleculeAction

groupTranslationVector

IVectorRandom groupTranslationVector

moleculeSource

MoleculeSource moleculeSource

molecule

IMolecule molecule

Class etomica.integrator.mcmove.MCMoveMoleculeExchange extends MCMove implements Serializable

serialVersionUID: 2L

Serialized Fields

box1

IBox box1

box2

IBox box2

integrator1

IntegratorBox integrator1

integrator2

IntegratorBox integrator2

energyMeter

MeterPotentialEnergy energyMeter

affectedAtomIterator

AtomIteratorArrayListSimple affectedAtomIterator

moleculeTranslator

MoleculeActionTranslateTo moleculeTranslator

moleculeReplacer

MoleculeChildAtomAction moleculeReplacer

translationVector

IVectorMutable translationVector

random

IRandom random

moleculeSource

MoleculeSource moleculeSource

positionSource

RandomPositionSource positionSource

Class etomica.integrator.mcmove.MCMoveRotate extends MCMoveAtom implements Serializable

serialVersionUID: 2L

Serialized Fields

oldOrientation

IOrientation oldOrientation

Class etomica.integrator.mcmove.MCMoveRotateMolecule3D extends MCMoveMolecule implements Serializable

serialVersionUID: 2L

Serialized Fields

positionDefinition

IAtomPositionDefinition positionDefinition

count

int count

count1

int count1

flag

boolean flag

flag1

boolean flag1

Class etomica.integrator.mcmove.MCMoveSemigrand extends MCMoveBox implements Serializable

serialVersionUID: 2L

Serialized Fields

speciesSet

ISpecies[] speciesSet

reservoirs

MoleculeArrayList[] reservoirs

fugacityFraction

double[] fugacityFraction

nSpecies

int nSpecies

affectedAtomIterator

AtomIteratorArrayListSimple affectedAtomIterator

energyMeter

MeterPotentialEnergy energyMeter

moleculeTranslator

MoleculeActionTranslateTo moleculeTranslator

atomPositionDefinition

IAtomPositionDefinition atomPositionDefinition

random

IRandom random

Class etomica.integrator.mcmove.MCMoveStep extends MCMove implements Serializable

Serialized Fields

stepSize

double stepSize

stepSizeMax

double stepSizeMax

stepSizeMin

double stepSizeMin

Class etomica.integrator.mcmove.MCMoveStepTracker extends MCMoveTracker implements Serializable

serialVersionUID: 1L

Serialized Fields

mcMove

MCMoveStepDependent mcMove

acceptanceTarget

double acceptanceTarget

adjustInterval

long adjustInterval

tunable

boolean tunable

lastAdjust

long lastAdjust

adjustStep

double adjustStep

defaultAdjustStep

double defaultAdjustStep

defaultAdjustInterval

long defaultAdjustInterval

noisyAdjustment

boolean noisyAdjustment

noReset

boolean noReset

Class etomica.integrator.mcmove.MCMoveSwapConfiguration extends MCMove implements Serializable

serialVersionUID: 1L

Serialized Fields

integrator1

IntegratorBox integrator1

integrator2

IntegratorBox integrator2

affectedAtomIterator

AtomIteratorLeafAtoms affectedAtomIterator

r

IVectorMutable r

u1

double u1

u2

double u2

temp1

double temp1

temp2

double temp2

deltaU1

double deltaU1

swappedBoxes

IBox[] swappedBoxes

Class etomica.integrator.mcmove.MCMoveSwapConfiguration.SwapFactory extends Object implements Serializable

serialVersionUID: 1L

Class etomica.integrator.mcmove.MCMoveTracker extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

nTrials

long nTrials

nAccept

long nAccept

chiSum

double chiSum

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

Class etomica.integrator.mcmove.MCMoveVolume extends MCMoveBoxStep implements Serializable

serialVersionUID: 2L

Serialized Fields

pressure

double pressure

energyMeter

MeterPotentialEnergy energyMeter

inflate

BoxInflate inflate

D

int D

random

IRandom random

affectedAtomIterator

AtomIteratorLeafAtoms affectedAtomIterator

Class etomica.integrator.mcmove.MCMoveVolumeExchange extends MCMoveStep implements Serializable

serialVersionUID: 1L

Serialized Fields

energyMeter

MeterPotentialEnergy energyMeter

firstBox

IBox firstBox

secondBox

IBox secondBox

integrator1

IntegratorBox integrator1

integrator2

IntegratorBox integrator2

inflate1

BoxInflate inflate1

inflate2

BoxInflate inflate2

ROOT

double ROOT

box1AtomIterator

AtomIteratorLeafAtoms box1AtomIterator

box2AtomIterator