Uses of Class
ffx.numerics.atomic.AtomicDoubleArray3D

Packages that use AtomicDoubleArray3D

Package	Description
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
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.
ffx.potential.nonbonded.pme	The pme package implements polarization and permanent electrostatics using Particle Mesh Ewald (PME).

Uses of AtomicDoubleArray3D in ffx.potential.bonded

Methods in ffx.potential.bonded with parameters of type AtomicDoubleArray3D

Modifier and Type	Method	Description
double	Angle.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	AngleTorsion.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	Bond.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
default double	BondedEnergy.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad)	energy.
double	BondedEnergy.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	ImproperTorsion.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	OutOfPlaneBend.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	PiOrbitalTorsion.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	RestrainDistance.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	RestrainPosition.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	Calculates energy and gradients for this coordinate restraint.
double	RestrainTorsion.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)
double	StretchBend.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	StretchTorsion.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	Torsion.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	TorsionTorsion.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
double	UreyBradley.energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.

Uses of AtomicDoubleArray3D in ffx.potential.nonbonded

Methods in ffx.potential.nonbonded that return AtomicDoubleArray3D

Modifier and Type	Method	Description
AtomicDoubleArray3D	GeneralizedKirkwood.getFieldGK()
AtomicDoubleArray3D	GeneralizedKirkwood.getFieldGKCR()
AtomicDoubleArray3D	GeneralizedKirkwood.getGrad()
AtomicDoubleArray3D	GeneralizedKirkwood.getTorque()

Methods in ffx.potential.nonbonded with parameters of type AtomicDoubleArray3D

Modifier and Type	Method	Description
void	GeneralizedKirkwood.reduce(AtomicDoubleArray3D g, AtomicDoubleArray3D t, AtomicDoubleArray3D lg, AtomicDoubleArray3D lt)

Uses of AtomicDoubleArray3D in ffx.potential.nonbonded.implicit

Methods in ffx.potential.nonbonded.implicit with parameters of type AtomicDoubleArray3D

Modifier and Type	Method	Description
double	ChandlerCavitation.energyAndGradient(double[][] positions, AtomicDoubleArray3D gradient)	Compute molecular volume and surface area.
double	ChandlerCavitation.energyAndGradientConnolly(AtomicDoubleArray3D gradient)	Compute the cavitation energy.
double	ChandlerCavitation.energyAndGradientGausVol(double[][] positions, AtomicDoubleArray3D gradient)	Compute molecular volume and surface area.
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	DispersionRegion.init(Atom[] atoms, Crystal crystal, boolean[] use, int[][][] neighborLists, double[] x, double[] y, double[] z, double cut2, boolean gradient, AtomicDoubleArray3D grad)	Initialize the DispersionRegion for energy calculation.
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	InducedGKFieldRegion.init(Atom[] atoms, double[][][] inducedDipole, double[][][] inducedDipoleCR, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] born, AtomicDoubleArray3D sharedGKField, AtomicDoubleArray3D sharedGKFieldCR)
void	InitializationRegion.init(GeneralizedKirkwood generalizedKirkwood, Atom[] atoms, boolean lambdaTerm, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray sharedBornGrad)
void	PermanentGKFieldRegion.init(Atom[] atoms, double[][][] globalMultipole, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] born, AtomicDoubleArray3D sharedGKField)

Constructors in ffx.potential.nonbonded.implicit with parameters of type AtomicDoubleArray3D

Modifier	Constructor	Description
	SurfaceAreaRegion(Atom[] atoms, double[] x, double[] y, double[] z, boolean[] use, int[][][] neighborLists, AtomicDoubleArray3D grad, int nt, double probe, double surfaceTension)	This class is a port of the Cavitation code in TINKER.

Uses of AtomicDoubleArray3D in ffx.potential.nonbonded.pme

Methods in ffx.potential.nonbonded.pme with parameters of type AtomicDoubleArray3D

Modifier and Type	Method	Description
void	DirectRegion.init(Atom[] atoms, double[] polarizability, double[][][] globalMultipole, double[][] cartMultipolePhi, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, boolean generalizedKirkwoodTerm, GeneralizedKirkwood generalizedKirkwood, EwaldParameters ewaldParameters, double soluteDielectric, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] directDipole, double[][] directDipoleCR, double[][] directField, double[][] directFieldCR)
void	InducedDipoleFieldReduceRegion.init(Atom[] atoms, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean generalizedKirkwoodTerm, GeneralizedKirkwood generalizedKirkwood, EwaldParameters ewaldParameters, double soluteDielectric, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR)
void	InducedDipoleFieldRegion.init(Atom[] atoms, Crystal crystal, boolean[] use, int[] molecule, double[] ipdamp, double[] thole, double[][][] coordinates, RealSpaceNeighborParameters realSpaceNeighborParameters, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean reciprocalSpaceTerm, ReciprocalSpace reciprocalSpace, LambdaMode lambdaMode, EwaldParameters ewaldParameters, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, PMETimings pmeTimings)
void	InitializationRegion.init(boolean lambdaTerm, AlchemicalParameters alchemicalParameters, ExtendedSystem esvSystem, Atom[] atoms, double[][][] coordinates, Crystal crystal, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, double[][][] globalMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[] polarizability, double[] titrationPolarizability, double[] tautomerPolarizability, double[] thole, double[] ipdamp, boolean[] use, int[][][] neighborLists, int[][][] realSpaceLists, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque)
void	OPTRegion.init(int currentOptOrder, Atom[] atoms, double[] polarizability, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, boolean generalizedKirkwoodTerm, GeneralizedKirkwood generalizedKirkwood, EwaldParameters ewaldParameters, double dielectric)
void	PCGSolver.init(Atom[] atoms, double[][][] coordinates, double[] polarizability, double[] ipdamp, double[] thole, boolean[] use, Crystal crystal, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] directDipole, double[][] directDipoleCR, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, EwaldParameters ewaldParameters, double dieletric, ParallelTeam parallelTeam, IntegerSchedule realSpaceSchedule, PMETimings pmeTimings)
void	PermanentFieldRegion.init(Atom[] atoms, Crystal crystal, double[][][] coordinates, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, int[][][] neighborLists, ScaleParameters scaleParameters, boolean[] use, int[] molecule, double[] ipdamp, double[] thole, int[][] ip11, int[][] mask12, int[][] mask13, int[][] mask14, LambdaMode lambdaMode, boolean reciprocalSpaceTerm, ReciprocalSpace reciprocalSpace, EwaldParameters ewaldParameters, PCGSolver pcgSolver, IntegerSchedule permanentSchedule, RealSpaceNeighborParameters realSpaceNeighborParameters, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR)
void	RealSpaceEnergyRegion.init(Atom[] atoms, Crystal crystal, ExtendedSystem extendedSystem, boolean esvTerm, double[][][] coordinates, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, double[][][] globalMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean[] use, int[] molecule, int[][] ip11, int[][] mask12, int[][] mask13, int[][] mask14, int[][] mask15, boolean[] isSoft, double[] ipdamp, double[] thole, RealSpaceNeighborParameters realSpaceNeighborParameters, boolean gradient, boolean lambdaTerm, boolean nnTerm, LambdaMode lambdaMode, Polarization polarization, EwaldParameters ewaldParameters, ScaleParameters scaleParameters, AlchemicalParameters alchemicalParameters, long[] realSpaceEnergyTime, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)
void	ReciprocalEnergyRegion.init(Atom[] atoms, Crystal crystal, boolean gradient, boolean lambdaTerm, boolean esvTerm, boolean[] use, double[][][] globalMultipole, double[][][] globalFracMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][] cartMultipolePhi, double[][] fracMultipolePhi, Polarization polarization, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, double[][] fracInducedDipolePhi, double[][] fracInducedDipolePhiCR, ReciprocalSpace reciprocalSpace, AlchemicalParameters alchemicalParameters, ExtendedSystem extendedSystem, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)
void	ReduceRegion.init(boolean lambdaTerm, boolean gradient, Atom[] atoms, double[][][] coordinates, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque)
void	SORRegion.init(Atom[] atoms, double[] polarizability, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] directDipole, double[][] directDipoleCR, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, boolean generalizedKirkwoodTerm, GeneralizedKirkwood generalizedKirkwood, EwaldParameters ewaldParameters)