Uses of Package
edu.rit.pj
Packages that use edu.rit.pj
Package
Description
The PJ package (Parallel Java) support shared memory, message passing and
hybrid shared memory/message passing parallelization in pure Java.
The Replica package provides replicated, shared reduction variables.
The Thermodynamics package computes free energy differences using Orthogonal Space Tempering
(OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
The Atomic package has implementations of a double array that can be safely operated on by
multiple threads.
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.
The Potential package implements molecular mechanics force fields with shared memory Parallel
Java and via OpenMM.
The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and
Particle Mesh Ewald electrostastics.
The Real Space package implements real space structure refinement.
The X-ray package implements support for X-ray and Neutron refinement.
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Classes in edu.rit.pj used by edu.rit.pjClassDescriptionClass BarrierAction is the abstract base class for an object containing code that is executed as part of a barrier wait.Class Comm provides a communicator for a PJ cluster parallel program.Class CommRequest provides an object for doing a non-blocking message passing operation in a PJ cluster parallel program.Class CommStatus provides the result of receiving a message from a communicator (class Comm).Class IntegerForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.Class IntegerSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.Class IntegerStrideForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.Class Lock provides an object used for synchronizing parallel team threads in a critical region.Class LongForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.Class LongSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.Class LongStrideForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.Class ParallelConstruct is the common base class for all parallel constructs that are executed by a ParallelTeam.Class ParallelForLoop is the abstract base class for a parallel for loop that is executed inside a ParallelRegion.Class ParallelIteration is the abstract base class for a parallel iteration that is executed inside a ParallelRegion.Class ParallelRegion is the abstract base class for a parallel region that is executed by a ParallelTeam of threads.Class ParallelSection is the abstract base class for a section of code to be executed in parallel.Class ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.Class Schedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.Class WorkerConstruct is the common base class for all worker constructs that are executed by a WorkerTeam.Class WorkerForLoop is the abstract base class for a worker for loop that is executed inside a WorkerRegion.Class WorkerIntegerForLoop is the abstract base class for one variation of a worker for loop that is executed inside a WorkerRegion.Class WorkerIntegerStrideForLoop is the abstract base class for one variation of a worker for loop that is executed inside a WorkerRegion.Class WorkerIteration is the abstract base class for a worker iteration that is executed inside a WorkerRegion.Class WorkerLongForLoop is the abstract base class for one variation of a worker for loop that is executed inside a WorkerRegion.Class WorkerLongStrideForLoop is the abstract base class for one variation of a worker for loop that is executed inside a WorkerRegion.Class WorkerRegion is the abstract base class for a worker region that is executed by a WorkerTeam of threads distributed across the processes of a cluster parallel program.Class WorkerTeam provides a team of threads, distributed across the processes of a cluster parallel program, for executing a WorkerRegion in parallel.
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Classes in edu.rit.pj used by edu.rit.pj.replica
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Classes in edu.rit.pj used by ffx.algorithms.optimize.manybodyClassDescriptionClass Comm provides a communicator for a PJ cluster parallel program.Class IntegerSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.Class ParallelConstruct is the common base class for all parallel constructs that are executed by a ParallelTeam.Class ParallelRegion is the abstract base class for a parallel region that is executed by a ParallelTeam of threads.Class WorkerConstruct is the common base class for all worker constructs that are executed by a WorkerTeam.Class WorkerRegion is the abstract base class for a worker region that is executed by a WorkerTeam of threads distributed across the processes of a cluster parallel program.
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Classes in edu.rit.pj used by ffx.algorithms.thermodynamics
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Classes in edu.rit.pj used by ffx.numerics.atomicClassDescriptionClass ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.
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Classes in edu.rit.pj used by ffx.numerics.fftClassDescriptionClass IntegerSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.Class ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.
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Classes in edu.rit.pj used by ffx.potentialClassDescriptionClass ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.
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Classes in edu.rit.pj used by ffx.potential.nonbondedClassDescriptionClass IntegerForLoop is the abstract base class for one variation of a parallel for loop that is executed inside a ParallelRegion.Class IntegerSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.Class ParallelConstruct is the common base class for all parallel constructs that are executed by a ParallelTeam.Class ParallelForLoop is the abstract base class for a parallel for loop that is executed inside a ParallelRegion.Class ParallelRegion is the abstract base class for a parallel region that is executed by a ParallelTeam of threads.Class ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.Class Schedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.
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Classes in edu.rit.pj used by ffx.potential.nonbonded.implicitClassDescriptionClass ParallelConstruct is the common base class for all parallel constructs that are executed by a ParallelTeam.Class ParallelRegion is the abstract base class for a parallel region that is executed by a ParallelTeam of threads.Class ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.
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Classes in edu.rit.pj used by ffx.potential.nonbonded.pmeClassDescriptionClass IntegerSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.Class ParallelConstruct is the common base class for all parallel constructs that are executed by a ParallelTeam.Class ParallelRegion is the abstract base class for a parallel region that is executed by a ParallelTeam of threads.Class ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.
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Classes in edu.rit.pj used by ffx.realspaceClassDescriptionClass ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.
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Classes in edu.rit.pj used by ffx.xrayClassDescriptionClass IntegerSchedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.Class ParallelConstruct is the common base class for all parallel constructs that are executed by a ParallelTeam.Class ParallelRegion is the abstract base class for a parallel region that is executed by a ParallelTeam of threads.Class ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.Class Schedule provides an object that determines how to schedule the iterations of a ParallelForLoop among the threads in a ParallelTeam.