Uses of Class
edu.rit.pj.ParallelTeam

Packages that use ParallelTeam

Package	Description
edu.rit.pj	The PJ package (Parallel Java) support shared memory, message passing and hybrid shared memory/message passing parallelization in pure Java.
ffx.numerics.atomic	The Atomic package has implementations of a double array that can be safely operated on by multiple threads.
ffx.numerics.fft	The FFT package implements 1D and 3D FFTs of real or complex valued data, including SMP parallelization of 3D transforms and convolution using the Parallel Java library.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
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).
ffx.potential.terms	The terms package contains analytical potential energy terms and their gradients for bonded interactions (bond, angle, stretch-bend, torsions, impropers, Urey-Bradley) and restraint terms used by Force Field X.
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.

Uses of ParallelTeam in edu.rit.pj

Methods in edu.rit.pj that return ParallelTeam

Modifier and Type	Method	Description
final ParallelTeam	ParallelConstruct.team()	Returns the parallel team that is executing this parallel construct.

Uses of ParallelTeam in ffx.numerics.atomic

Methods in ffx.numerics.atomic with parameters of type ParallelTeam

Modifier and Type	Method	Description
void	AdderDoubleArray.reduce(ParallelTeam parallelTeam, int lb, int ub)	The AtomicDoubleArray handles the reduction automatically, so this method does nothing.
void	AtomicDoubleArray.reduce(ParallelTeam parallelTeam, int lowerBound, int upperBound)	Perform reduction between the given bounds using a ParallelTeam.
void	AtomicDoubleArray3D.reduce(ParallelTeam parallelTeam)	Perform a reduction on the entire array.
void	MultiDoubleArray.reduce(ParallelTeam parallelTeam, int lb, int ub)	Perform reduction between the given bounds using a ParallelTeam.
void	PJDoubleArray.reduce(ParallelTeam parallelTeam, int lowerBound, int upperBound)	Perform reduction between the given bounds using a ParallelTeam.
void	AdderDoubleArray.reset(ParallelTeam parallelTeam, int lb, int ub)	Reset the double array values to zero within the specified bounds using a ParallelTeam.
void	AtomicDoubleArray.reset(ParallelTeam parallelTeam, int lowerBound, int upperBound)	Reset the double array values to zero within the specified bounds using a ParallelTeam.
void	AtomicDoubleArray3D.reset(ParallelTeam parallelTeam)	Reset the double array to Zero.
void	MultiDoubleArray.reset(ParallelTeam parallelTeam, int lb, int ub)	Reset the double array values to zero within the specified bounds using a ParallelTeam.
void	PJDoubleArray.reset(ParallelTeam parallelTeam, int lowerBound, int upperBound)	Reset the double array values to zero within the specified bounds using a ParallelTeam.

Uses of ParallelTeam in ffx.numerics.fft

Methods in ffx.numerics.fft with parameters of type ParallelTeam

Modifier and Type	Method	Description
static double[]	Complex3DParallel.initRandomData(int dim, ParallelTeam parallelTeam)	Initialize a 3D data for testing purposes.

Constructors in ffx.numerics.fft with parameters of type ParallelTeam

Modifier	Constructor	Description
	Complex3DParallel(int nX, int nY, int nZ, ParallelTeam parallelTeam)	Initialize the 3D FFT for complex 3D matrix.
	Complex3DParallel(int nX, int nY, int nZ, ParallelTeam parallelTeam, IntegerSchedule integerSchedule)	Initialize the 3D FFT for complex 3D matrix.
	Complex3DParallel(int nX, int nY, int nZ, ParallelTeam parallelTeam, IntegerSchedule integerSchedule, DataLayout3D dataLayout)	Initialize the 3D FFT for complex 3D matrix.
	Complex3DParallel(int nX, int nY, int nZ, ParallelTeam parallelTeam, DataLayout3D dataLayout)	Initialize the 3D FFT for complex 3D matrix.
	Real3DParallel(int nX, int nY, int nZ, ParallelTeam parallelTeam)	Initialize the FFT for real input.
	Real3DParallel(int nX, int nY, int nZ, ParallelTeam parallelTeam, IntegerSchedule integerSchedule)	Initialize the FFT for real input.

Uses of ParallelTeam in ffx.potential

Methods in ffx.potential that return ParallelTeam

Modifier and Type	Method	Description
ParallelTeam	ForceFieldEnergy.getParallelTeam()	Getter for the field parallelTeam.
ParallelTeam	MolecularAssembly.getParallelTeam()	getParallelTeam.

Uses of ParallelTeam in ffx.potential.nonbonded

Constructors in ffx.potential.nonbonded with parameters of type ParallelTeam

Modifier	Constructor	Description
	GeneralizedKirkwood(ForceField forceField, Atom[] atoms, ParticleMeshEwald particleMeshEwald, Crystal crystal, ParallelTeam parallelTeam, double gkCutoff)	Constructor for GeneralizedKirkwood.
	NeighborList(Crystal crystal, Atom[] atoms, double cutoff, double buffer, ParallelTeam parallelTeam)	Constructor for the NeighborList class.
	ParticleMeshEwald(Atom[] atoms, int[] molecule, ForceField forceField, Crystal crystal, NeighborList neighborList, ForceField.ELEC_FORM elecForm, double ewaldCutoff, double gkCutoff, ParallelTeam parallelTeam)	ParticleMeshEwald constructor.
	ReciprocalSpace(ParticleMeshEwald particleMeshEwald, Crystal crystal, ForceField forceField, Atom[] atoms, double aewald, ParallelTeam fftTeam, ParallelTeam parallelTeam)	Reciprocal Space PME contribution.
	VanDerWaals(Atom[] atoms, int[] molecule, boolean[] neuralNetwork, Crystal crystal, ForceField forceField, ParallelTeam parallelTeam, double vdwCutoff, double neighborListCutoff)	The VanDerWaals class constructor.

Uses of ParallelTeam in ffx.potential.nonbonded.implicit

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

Modifier and Type	Method	Description
void	BornGradRegion.executeWith(ParallelTeam parallelTeam)	Execute the InitializationRegion with the passed ParallelTeam.
void	InitializationRegion.executeWith(ParallelTeam parallelTeam)	Execute the InitializationRegion with the passed ParallelTeam.
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)

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

Modifier	Constructor	Description
	GaussVol(Atom[] atoms, ForceField forceField, ParallelTeam parallelTeam)	Creates/Initializes a GaussVol instance.

Uses of ParallelTeam in ffx.potential.nonbonded.pme

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

Modifier and Type	Method	Description
void	DirectRegion.executeWith(ParallelTeam parallelTeam)	Execute the DirectRegion with the passed ParallelTeam.
void	ExpandInducedDipolesRegion.executeWith(ParallelTeam parallelTeam)	Execute the ExpandInducedDipolesRegion with the passed ParallelTeam.
void	InducedDipoleFieldReduceRegion.executeWith(ParallelTeam parallelTeam)	Execute the InducedDipoleFieldReduceRegion with the passed ParallelTeam.
void	InducedDipoleFieldRegion.executeWith(ParallelTeam sectionTeam)	Execute the InducedDipoleFieldRegion with the passed ParallelTeam.
void	InitializationRegion.executeWith(ParallelTeam parallelTeam)	Execute the InitializationRegion with the passed ParallelTeam.
void	RealSpaceEnergyRegion.executeWith(ParallelTeam parallelTeam)	Execute the RealSpaceEnergyRegion with the passed ParallelTeam.
void	ReciprocalEnergyRegion.executeWith(ParallelTeam parallelTeam)	Execute the ReciprocalEnergyRegion with the passed ParallelTeam.
void	ReduceRegion.executeWith(ParallelTeam parallelTeam)	Execute the ReduceRegion with the passed ParallelTeam.
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)

Constructors in ffx.potential.nonbonded.pme with parameters of type ParallelTeam

Modifier	Constructor	Description
	InducedDipoleFieldRegion(ParallelTeam parallelTeam, ForceField forceField, boolean lambdaTerm)
	PermanentFieldRegion(ParallelTeam pt, ForceField forceField, boolean lambdaTerm)

Uses of ParallelTeam in ffx.potential.terms

Constructors in ffx.potential.terms with parameters of type ParallelTeam

Modifier	Constructor	Description
	EnergyTermRegion(ParallelTeam parallelTeam, MolecularAssembly molecularAssembly, boolean lambdaTerm)	Constructor for BondedRegion.

Uses of ParallelTeam in ffx.realspace

Constructors in ffx.realspace with parameters of type ParallelTeam

Modifier	Constructor	Description
	RealSpaceData(MolecularAssembly[] molecularAssemblies, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, RealSpaceFile... dataFile)	Construct a real space data molecularAssemblies.
	RealSpaceData(MolecularAssembly[] molecularAssemblies, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, DiffractionData diffractionData)	Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecularAssemblies.
	RealSpaceData(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam)	Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecular molecularAssemblies.
	RealSpaceData(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, RealSpaceFile... datafile)	Construct a real space data molecularAssemblies.
	RealSpaceData(MolecularAssembly molecularAssembly, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, DiffractionData diffractionData)	Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecular molecularAssemblies.

Uses of ParallelTeam in ffx.xray

Methods in ffx.xray that return ParallelTeam

Modifier and Type	Method	Description
ParallelTeam	DiffractionData.getParallelTeam()	Getter for the field parallelTeam.

Constructors in ffx.xray with parameters of type ParallelTeam

Modifier	Constructor	Description
	BulkSolventDensityRegion(int gX, int gY, int gZ, double[] grid, int basisSize, int nSymm, int minWork, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.
	BulkSolventList(Crystal crystal, Atom[] atoms, double cutoff, ParallelTeam parallelTeam)	Constructor for the NeighborList class.
	BulkSolventRowRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.
	BulkSolventSliceRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.
	CrystalReciprocalSpace(ReflectionList reflectionList, Atom[] atoms, ParallelTeam fftTeam, ParallelTeam parallelTeam)	Crystal Reciprocal Space constructor, assumes this is not a bulk solvent mask and is not a neutron data set
	CrystalReciprocalSpace(ReflectionList reflectionList, Atom[] atoms, ParallelTeam fftTeam, ParallelTeam parallelTeam, boolean solventMask)	Crystal Reciprocal Space constructor, assumes this is not a neutron data set and implements a polynomial bulk solvent mask if needed
	CrystalReciprocalSpace(ReflectionList reflectionList, Atom[] atoms, ParallelTeam fftTeam, ParallelTeam parallelTeam, boolean solventMask, boolean neutron)	Crystal Reciprocal Space constructor, assumes a polynomial bulk solvent mask if needed
	CrystalReciprocalSpace(ReflectionList reflectionlist, Atom[] atoms, ParallelTeam fftTeam, ParallelTeam parallelTeam, boolean solventMask, boolean neutron, CrystalReciprocalSpace.SolventModel solventModel, CrystalReciprocalSpace.GridMethod gridMethod)	Crystal Reciprocal Space constructor, all parameters provided
	ScaleBulkMinimize(ReflectionList reflectionList, DiffractionRefinementData refinementData, CrystalReciprocalSpace crystalReciprocalSpace, ParallelTeam parallelTeam)	Constructor for ScaleBulkMinimize.