Package ffx.algorithms.optimize.manybody

Class TwoBodyEnergyRegion

java.lang.Object

edu.rit.pj.WorkerConstruct

edu.rit.pj.WorkerRegion

ffx.algorithms.optimize.manybody.TwoBodyEnergyRegion

public class TwoBodyEnergyRegion
extends WorkerRegion

Compute 2-Body energy values in parallel across nodes.

Constructor Summary

Constructors

Constructor	Description
TwoBodyEnergyRegion(RotamerOptimization rotamerOptimization, DistanceMatrix dM, EnergyExpansion eE, EliminatedRotamers eR, Residue[] residues, List<Residue> allResiduesList, BufferedWriter energyWriter, Comm world, int numProc, boolean prunePairClashes, double superpositionThreshold, boolean master, int rank, boolean verbose, boolean writeEnergyRestart, boolean printFiles)

Method Summary

Modifier and Type	Method	Description
void	finish()	Perform finalization actions after parallel execution ends.
void	run()	Execute parallel code.
void	start()	Perform initialization actions before parallel execution begins.

Methods inherited from class edu.rit.pj.WorkerRegion

execute, execute, execute, execute, execute, execute, execute

Methods inherited from class edu.rit.pj.WorkerConstruct

getThreadCount, getThreadIndex, getTotalThreadCount, isExecutingInParallel, isMasterThread, region, team

Methods inherited from class java.lang.Object

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

Constructor Details

TwoBodyEnergyRegion

public TwoBodyEnergyRegion(RotamerOptimization rotamerOptimization,
 DistanceMatrix dM,
 EnergyExpansion eE,
 EliminatedRotamers eR,
 Residue[] residues,
 List<Residue> allResiduesList,
 BufferedWriter energyWriter,
 Comm world,
 int numProc,
 boolean prunePairClashes,
 double superpositionThreshold,
 boolean master,
 int rank,
 boolean verbose,
 boolean writeEnergyRestart,
 boolean printFiles)

Method Details

finish

public void finish()

Description copied from class: WorkerRegion

Perform finalization actions after parallel execution ends. Only one thread in each process 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 WorkerRegion

run

public void run()
         throws Exception

Description copied from class: WorkerRegion

Execute parallel code. All threads of the worker team in each process call the run() method concurrently.

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

Specified by:

run in class WorkerRegion

Throws:

Exception - The run() method may throw any exception.

Exception - if any.

start

public void start()

Description copied from class: WorkerRegion

Perform initialization actions before parallel execution begins. Only one thread in each process 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 WorkerRegion