Package ffx.algorithms.optimize.manybody

Class GoldsteinPairRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.algorithms.optimize.manybody.GoldsteinPairRegion

public class GoldsteinPairRegion
extends ParallelRegion

Constructor Summary

Constructors

Constructor	Description
GoldsteinPairRegion(int nThreads)

Method Summary

Modifier and Type	Method	Description
void	finish()	Perform finalization actions after parallel execution ends.
ArrayList<Residue>	getMissedResidues()
double	getSumOverK()
void	init(Residue[] residues, int i, int riA, int riB, int j, int rjC, int rjD, int[][] bidiResNeighbors, RotamerOptimization rotamerOptimization)	Initializes a ParallelRegion to attempt the elimination of riA,rjC by riB,rjD.
void	run()	Execute parallel code.
void	start()	Perform initialization actions before parallel execution begins.

Methods inherited from class edu.rit.pj.ParallelRegion

barrier, barrier, critical, critical, criticalNonexclusive, criticalNonexclusive, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute

Methods inherited from class edu.rit.pj.ParallelConstruct

getThreadCount, getThreadIndex, isExecutingInParallel, region, team

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

GoldsteinPairRegion

public GoldsteinPairRegion(int nThreads)

Method Details

finish

public void finish()

Description copied from class: ParallelRegion

Perform finalization actions after parallel execution ends. Only one thread calls the finish() method.

The finish() method may be overridden in a subclass. If not overridden, the finish() method does nothing.

Overrides:

finish in class ParallelRegion

getMissedResidues

public ArrayList<Residue> getMissedResidues()

getSumOverK

public double getSumOverK()

init

public void init(Residue[] residues,
 int i,
 int riA,
 int riB,
 int j,
 int rjC,
 int rjD,
 int[][] bidiResNeighbors,
 RotamerOptimization rotamerOptimization)

Initializes a ParallelRegion to attempt the elimination of riA,rjC by riB,rjD.

Parameters:

residues - The residue array.

i - First residue of the pair.

riA - First member of the pair to attempt eliminating.

riB - First member of the pair to try eliminating by.

j - Second residue of the pair.

rjC - Second member of the pair to attempt eliminating.

rjD - Second member of the pair to try eliminating by.

bidiResNeighbors - All interaction partners of a Residue, including prior residues

rotamerOptimization - RotamerOptimization instance.

run

public void run()

Description copied from class: ParallelRegion

Execute parallel code. All threads of the parallel team call the run() method concurrently.

The run() method must be implemented in a subclass.

Specified by:

run in class ParallelRegion

start

public void start()

Description copied from class: ParallelRegion

Perform initialization actions before parallel execution begins. Only one thread calls the start() method.

The start() method may be overridden in a subclass. If not overridden, the start() method does nothing.

Overrides:

start in class ParallelRegion