Uses of Interface
ffx.numerics.atomic.AtomicDoubleArray

Packages that use AtomicDoubleArray

Package	Description
ffx.numerics.atomic	The Atomic package has implementations of a double array that can be safely operated on by multiple threads.
ffx.potential.nonbonded	The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.implicit	The implicit package implements implicit solvent models and related terms, including Generalized Kirkwood (GK) electrostatics, surface area terms, dispersion/cavitation contributions, and supporting parallel regions for Born radii and field evaluation.

Uses of AtomicDoubleArray in ffx.numerics.atomic

Classes in ffx.numerics.atomic that implement AtomicDoubleArray

Modifier and Type	Class	Description
class	AdderDoubleArray	AdderDoubleArray implements the AtomicDoubleArray interface using an array of java.util.concurrent.atomic.DoubleAdder.
class	MultiDoubleArray	The MultiDoubleArray avoids the need for Atomic variables, but at the cost of storing a full size double array for each thread.
class	PJDoubleArray	PJDoubleArray implements the AtomicDoubleArray interface using the Parallel Java class SharedDoubleArray.

Methods in ffx.numerics.atomic that return AtomicDoubleArray

Modifier and Type	Method	Description
abstract AtomicDoubleArray	AtomicDoubleArray.AtomicDoubleArrayImpl.createInstance(int threads, int size)	Factory method to create an AtomicDoubleArray instance.

Constructors in ffx.numerics.atomic with parameters of type AtomicDoubleArray

Modifier	Constructor	Description
	AtomicDoubleArray3D(AtomicDoubleArray x, AtomicDoubleArray y, AtomicDoubleArray z)	Construct an atomic 3D double array using the specified AtomicDoubleArray instances.

Uses of AtomicDoubleArray in ffx.potential.nonbonded

Methods in ffx.potential.nonbonded that return AtomicDoubleArray

Modifier and Type	Method	Description
AtomicDoubleArray	GeneralizedKirkwood.getSelfEnergy()

Uses of AtomicDoubleArray in ffx.potential.nonbonded.implicit

Methods in ffx.potential.nonbonded.implicit that return AtomicDoubleArray

Modifier and Type	Method	Description
AtomicDoubleArray	GKEnergyRegion.getSelfEnergy()

Methods in ffx.potential.nonbonded.implicit with parameters of type AtomicDoubleArray

Modifier and Type	Method	Description
void	BornGradRegion.init(Atom[] atoms, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, double[] baseRadius, double[] descreenRadius, double[] overlapScale, double[] neckScale, double descreenOffset, double[] unscaledBornIntegral, boolean[] use, double cut2, boolean nativeEnvironmentApproximation, double[] born, AtomicDoubleArray3D grad, AtomicDoubleArray sharedBornGrad)
void	GKEnergyRegion.init(Atom[] atoms, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] baseRadius, double[] born, boolean gradient, ParallelTeam parallelTeam, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray sharedBornGrad)
void	InitializationRegion.init(GeneralizedKirkwood generalizedKirkwood, Atom[] atoms, boolean lambdaTerm, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray sharedBornGrad)