Package ffx.potential.nonbonded.implicit

Class BornGradRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.implicit.BornGradRegion

public class BornGradRegion
extends ParallelRegion

Parallel computation of Born radii chain rule terms via the Grycuk method.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
protected Atom[]	atoms	An ordered array of atoms in the system.

Constructor Summary

Constructors

Constructor	Description
BornGradRegion(int nt, boolean neckCorrection, boolean tanhCorrection, boolean perfectHCTScale)	Compute the gradient due to changes in Born radii.

Method Summary

Modifier and Type	Method	Description
void	executeWith(ParallelTeam parallelTeam)	Execute the InitializationRegion with the passed ParallelTeam.
void	init(Atom[] atoms, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, double[] baseRadius, double[] descreenRadius, double[] overlapScale, double[] neckScale, double descreenOffset, double[] unscaledBornIntegral, boolean[] use, double cut2, boolean nativeEnvironmentApproximation, double[] born, AtomicDoubleArray3D grad, AtomicDoubleArray sharedBornGrad)
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, finish

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

Field Details

atoms

protected Atom[] atoms

An ordered array of atoms in the system.

Constructor Details

BornGradRegion

public BornGradRegion(int nt,
 boolean neckCorrection,
 boolean tanhCorrection,
 boolean perfectHCTScale)

Compute the gradient due to changes in Born radii.

Parameters:

nt - Number of threads.

neckCorrection - Include a neck correction.

tanhCorrection - Include a tanh correction.

perfectHCTScale - Use "perfect" HCT scale factors.

Method Details

executeWith

public void executeWith(ParallelTeam parallelTeam)

Execute the InitializationRegion with the passed ParallelTeam.

Parameters:

parallelTeam - The ParallelTeam instance to execute with.

init

public void init(Atom[] atoms,
 Crystal crystal,
 double[][][] sXYZ,
 int[][][] neighborLists,
 double[] baseRadius,
 double[] descreenRadius,
 double[] overlapScale,
 double[] neckScale,
 double descreenOffset,
 double[] unscaledBornIntegral,
 boolean[] use,
 double cut2,
 boolean nativeEnvironmentApproximation,
 double[] born,
 AtomicDoubleArray3D grad,
 AtomicDoubleArray sharedBornGrad)

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

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