Package ffx.potential.nonbonded.implicit

Class GKEnergyRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.implicit.GKEnergyRegion

public class GKEnergyRegion
extends ParallelRegion

Parallel calculation of the Generalized Kirkwood reaction field energy.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
protected final double	dOffset	Dielectric offset from:
protected final double	electric	Conversion from electron**2/Ang to kcal/mole.
protected final double	gkc	Empirical constant that controls the GK cross-term.
protected final GeneralizedKirkwood.NonPolarModel	nonPolarModel
protected static final double	oneThird	Constant factor used with quadrupoles.
protected final Polarization	polarization	Treatment of polarization.
protected final double	surfaceTension	Cavitation surface tension coefficient (kcal/mol/A^2).

Constructor Summary

Constructors

Constructor	Description
GKEnergyRegion(int nt, Polarization polarization, GeneralizedKirkwood.NonPolarModel nonPolarModel, double surfaceTension, double probe, double electric, double soluteDieletric, double solventDieletric, double gkc, boolean gkQI)

Method Summary

Modifier and Type	Method	Description
void	finish()	Perform finalization actions after parallel execution ends.
double	getEnergy()
int	getInteractions()
double	getPermanentEnergy()
double	getPolarizationEnergy()
AtomicDoubleArray	getSelfEnergy()
void	init(Atom[] atoms, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] baseRadius, double[] born, boolean gradient, ParallelTeam parallelTeam, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, 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

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

oneThird

protected static final double oneThird

Constant factor used with quadrupoles.

See Also:

• Constant Field Values

electric

protected final double electric

Conversion from electron**2/Ang to kcal/mole.

polarization

protected final Polarization polarization

Treatment of polarization.

nonPolarModel

protected final GeneralizedKirkwood.NonPolarModel nonPolarModel

dOffset

protected final double dOffset

Dielectric offset from:

W. C. Still, A. Tempczyk, R. C. Hawley and T. Hendrickson, "A Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics", J. Amer. Chem. Soc., 112, 6127-6129 (1990)

See Also:

• Constant Field Values

surfaceTension

protected final double surfaceTension

Cavitation surface tension coefficient (kcal/mol/A^2).

gkc

protected final double gkc

Empirical constant that controls the GK cross-term.

Constructor Details

GKEnergyRegion

public GKEnergyRegion(int nt,
 Polarization polarization,
 GeneralizedKirkwood.NonPolarModel nonPolarModel,
 double surfaceTension,
 double probe,
 double electric,
 double soluteDieletric,
 double solventDieletric,
 double gkc,
 boolean gkQI)

Method Details

getEnergy

public double getEnergy()

getPermanentEnergy

public double getPermanentEnergy()

getPolarizationEnergy

public double getPolarizationEnergy()

getSelfEnergy

public AtomicDoubleArray getSelfEnergy()

getInteractions

public int getInteractions()

init

public void init(Atom[] atoms,
 double[][][] globalMultipole,
 double[][][] inducedDipole,
 double[][][] inducedDipoleCR,
 Crystal crystal,
 double[][][] sXYZ,
 int[][][] neighborLists,
 boolean[] use,
 double cut2,
 double[] baseRadius,
 double[] born,
 boolean gradient,
 ParallelTeam parallelTeam,
 AtomicDoubleArray3D grad,
 AtomicDoubleArray3D torque,
 AtomicDoubleArray sharedBornGrad)

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

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