Uses of Class
edu.rit.pj.ParallelRegion

Packages that use ParallelRegion

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.algorithms.optimize.manybody	The manybody package implements many-body rotamer optimization infrastructure, including distance matrices, an energy expansion (self, two-body, three-body, and four-body), Dead-end elimination criteria, Goldstein elimination criteria, and supporting data structures for efficient optimization.
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.xray	The X-ray package implements support for X-ray and Neutron refinement.

Uses of ParallelRegion in edu.rit.pj

Subclasses of ParallelRegion in edu.rit.pj

Modifier and Type	Class	Description
class	KillRegion	Provides a mechanism to shut down a ParallelTeam's threads, enabling garbage collection.

Methods in edu.rit.pj that return ParallelRegion

Modifier and Type	Method	Description
final ParallelRegion	ParallelConstruct.region()	Returns the parallel region of code within which a parallel team is executing this parallel construct.
final ParallelRegion	ParallelTeam.region()	Returns the parallel region of code that this parallel team is executing.

Methods in edu.rit.pj with parameters of type ParallelRegion

Modifier and Type	Method	Description
final void	ParallelTeam.execute(ParallelRegion theRegion)	Execute the given parallel region.

Uses of ParallelRegion in ffx.algorithms.optimize.manybody

Subclasses of ParallelRegion in ffx.algorithms.optimize.manybody

Modifier and Type	Class	Description
class	DistanceRegion	Compute the minimum distance between each pair of residues for all rotamer permutations.
class	EnergyRegion
class	GoldsteinPairRegion

Uses of ParallelRegion in ffx.potential.nonbonded

Subclasses of ParallelRegion in ffx.potential.nonbonded

Modifier and Type	Class	Description
class	NeighborList	The NeighborList class builds Verlet lists in parallel via a spatial decomposition.
class	ReciprocalSpace.BSplineRegion	The class computes b-Splines that are used to spline multipoles and induced dipoles onto the PME grid.
class	RowRegion	The RowRegion class is used to parallelize placing onto a 3D grid
class	SliceRegion	The SliceLoop class is used to parallelize placing onto a 3D grid
class	SpatialDensityRegion	This class implements a spatial decomposition based on partitioning a grid into octants.

Uses of ParallelRegion in ffx.potential.nonbonded.implicit

Subclasses of ParallelRegion in ffx.potential.nonbonded.implicit

Modifier and Type	Class	Description
class	BornGradRegion	Parallel computation of Born radii chain rule terms via the Grycuk method.
class	BornRadiiRegion	Parallel computation of Born radii via the Grycuk method.
class	ConnollyRegion	ConnollyRegion uses the algorithms from the AMS/VAM programs of Michael Connolly to compute the analytical molecular surface area and volume of a collection of spherical atoms; thus it implements Fred Richards' molecular surface definition as a set of analytically defined spherical and toroidal polygons.
class	DispersionRegion	Parallel calculation of continuum dispersion energy via pairwise descreening.
class	GKEnergyRegion	Parallel calculation of the Generalized Kirkwood reaction field energy.
class	HydrophobicPMFRegion	Initial implementation of a Hydrophobic PMF.
class	InducedGKFieldRegion	Parallel calculation of the Generalized Kirkwood induced reaction field.
class	InitializationRegion	Parallel initialization of accumulation arrays for Generalized Kirkwood.
class	PermanentGKFieldRegion	Parallel computation of the Generalized Kirkwood permanent reaction field.
class	SurfaceAreaRegion	SurfaceAreaRegion performs an analytical computation of the weighted solvent accessible surface area of each atom and the first derivatives of the area with respect to Cartesian coordinates

Uses of ParallelRegion in ffx.potential.nonbonded.pme

Subclasses of ParallelRegion in ffx.potential.nonbonded.pme

Modifier and Type	Class	Description
class	DirectRegion	Parallel computation of induced dipoles due to the direct field.
class	ExpandInducedDipolesRegion	Parallel expansion of the asymmetric unit induced dipoles to symmetry mates by applying symmetry operator rotation matrices.
class	InducedDipoleFieldReduceRegion	Parallel summation and reduction of components of the induced dipole field at each atom.
class	InducedDipoleFieldRegion	Parallel calculation of the induced dipole field.
class	InitializationRegion	Parallel initialization of accumulation arrays, expand atomic coordinates and rotation of multipoles into the global frame.
class	OPTRegion	Parallel computation of the OPT induced dipoles.
class	PermanentFieldRegion	Parallel computation of the permanent field.
class	PolarizationEnergyRegion	Parallel computation of the polarization energy as sum over atomic contributions (-1/2 u.E).
class	RealSpaceEnergyRegion	Parallel evaluation of the PME real space energy and gradient.
class	ReciprocalEnergyRegion	Parallel evaluation of the PME reciprocal space energy and gradient.
class	ReduceRegion	Parallel conversion of torques into forces, and then reduce them.
class	SORRegion	Parallel successive over-relaxation (SOR) solver for the self-consistent field.

Uses of ParallelRegion in ffx.potential.terms

Subclasses of ParallelRegion in ffx.potential.terms

Modifier and Type	Class	Description
class	EnergyTermRegion

Uses of ParallelRegion in ffx.xray

Subclasses of ParallelRegion in ffx.xray

Modifier and Type	Class	Description
class	BulkSolventDensityRegion	This class implements a spatial decomposition based on partitioning a grid into octants.
class	BulkSolventList	The BulkSolventList class builds a list of atoms in symmetry mates that are within a cutoff distance of an atom in the asymmetric unit.
class	BulkSolventRowRegion	BulkSolventRowRegion class.
class	BulkSolventSliceRegion	This class implements a spatial decomposition based on partitioning a grid into octants.