Package ffx.potential.nonbonded.implicit

Class BornRadiiRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.implicit.BornRadiiRegion

public class BornRadiiRegion
extends ParallelRegion

Parallel computation of Born radii 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
BornRadiiRegion(int nt, int nAtoms, ForceField forceField, boolean neckCorrection, boolean tanhCorrection, boolean perfectHCTScale)	BornRadiiRegion Constructor.

Method Summary

Modifier and Type	Method	Description
void	finish()	Perform finalization actions after parallel execution ends.
double[]	getBorn()
double[]	getPerfectRadii()	Return perfect Born radii read in as keywords, or base radii if perfect radii are not available.
double[]	getUnscaledBornIntegral()
void	init(Atom[] atoms, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, double[] baseRadius, double[] descreenRadius, double[] overlapScale, double[] neckScale, double descreenOffset, boolean[] use, double cut2, boolean nativeEnvironmentApproximation, double[] born)
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

Field Details

atoms

protected Atom[] atoms

An ordered array of atoms in the system.

Constructor Details

BornRadiiRegion

public BornRadiiRegion(int nt,
 int nAtoms,
 ForceField forceField,
 boolean neckCorrection,
 boolean tanhCorrection,
 boolean perfectHCTScale)

BornRadiiRegion Constructor.

Parameters:

nt - Number of threads.

nAtoms - Number of atoms.

forceField - The ForceField in use.

neckCorrection - Perform a neck correction.

tanhCorrection - Perform a tanh correction.

perfectHCTScale - Use "perfect" HCT scale factors.

Method Details

getPerfectRadii

public double[] getPerfectRadii()

Return perfect Born radii read in as keywords, or base radii if perfect radii are not available.

Returns:

Array of perfect Born radii.

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

init

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

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

getBorn

public double[] getBorn()

getUnscaledBornIntegral

public double[] getUnscaledBornIntegral()