Package ffx.potential.nonbonded.pme

Class ReciprocalEnergyRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.pme.ReciprocalEnergyRegion

public class ReciprocalEnergyRegion
extends ParallelRegion

Parallel evaluation of the PME reciprocal space energy and gradient.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
double[][][]	inducedDipole	Dimensions of [nsymm][nAtoms][3]
double[][][]	inducedDipoleCR

Constructor Summary

Constructors

Constructor	Description
ReciprocalEnergyRegion(int nt, double aewald, double electric)

Method Summary

Modifier and Type	Method	Description
void	executeWith(ParallelTeam parallelTeam)	Execute the ReciprocalEnergyRegion with the passed ParallelTeam.
void	finish()	Perform finalization actions after parallel execution ends.
double	getInducedDipoleReciprocalEnergy()
double	getInducedDipoleSelfEnergy()
double	getPermanentReciprocalEnergy()
double	getPermanentSelfEnergy()
void	init(Atom[] atoms, Crystal crystal, boolean gradient, boolean lambdaTerm, boolean esvTerm, boolean[] use, double[][][] globalMultipole, double[][][] globalFracMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][] cartMultipolePhi, double[][] fracMultipolePhi, Polarization polarization, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, double[][] fracInducedDipolePhi, double[][] fracInducedDipolePhiCR, ReciprocalSpace reciprocalSpace, AlchemicalParameters alchemicalParameters, ExtendedSystem extendedSystem, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)
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

inducedDipole

public double[][][] inducedDipole

Dimensions of [nsymm][nAtoms][3]

inducedDipoleCR

public double[][][] inducedDipoleCR

Constructor Details

ReciprocalEnergyRegion

public ReciprocalEnergyRegion(int nt,
 double aewald,
 double electric)

Method Details

executeWith

public void executeWith(ParallelTeam parallelTeam)

Execute the ReciprocalEnergyRegion with the passed ParallelTeam.

Parameters:

parallelTeam - The ParallelTeam instance to execute with.

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

getInducedDipoleReciprocalEnergy

public double getInducedDipoleReciprocalEnergy()

getInducedDipoleSelfEnergy

public double getInducedDipoleSelfEnergy()

getPermanentReciprocalEnergy

public double getPermanentReciprocalEnergy()

getPermanentSelfEnergy

public double getPermanentSelfEnergy()

init

public void init(Atom[] atoms,
 Crystal crystal,
 boolean gradient,
 boolean lambdaTerm,
 boolean esvTerm,
 boolean[] use,
 double[][][] globalMultipole,
 double[][][] globalFracMultipole,
 double[][][] titrationMultipole,
 double[][][] tautomerMultipole,
 double[][] cartMultipolePhi,
 double[][] fracMultipolePhi,
 Polarization polarization,
 double[][][] inducedDipole,
 double[][][] inducedDipoleCR,
 double[][] cartesianDipolePhi,
 double[][] cartesianDipolePhiCR,
 double[][] fracInducedDipolePhi,
 double[][] fracInducedDipolePhiCR,
 ReciprocalSpace reciprocalSpace,
 AlchemicalParameters alchemicalParameters,
 ExtendedSystem extendedSystem,
 AtomicDoubleArray3D grad,
 AtomicDoubleArray3D torque,
 AtomicDoubleArray3D lambdaGrad,
 AtomicDoubleArray3D lambdaTorque,
 SharedDouble shareddEdLambda,
 SharedDouble sharedd2EdLambda2)

run

public void run()
         throws Exception

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

Throws:

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

Exception - if any.

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