Package ffx.potential.nonbonded.pme

Class RealSpaceEnergyRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.pme.RealSpaceEnergyRegion

All Implemented Interfaces:

MaskingInterface

public class RealSpaceEnergyRegion
extends ParallelRegion
implements MaskingInterface

Parallel evaluation of the PME real 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
protected int[][]	ip11	Polarization groups.

Constructor Summary

Constructors

Constructor	Description
RealSpaceEnergyRegion(ForceField.ELEC_FORM elecForm, int nt, ForceField forceField, boolean lambdaTerm, double electric)

Method Summary

Modifier and Type	Method	Description
void	applyMask(int i, boolean[] is14, double[]... masks)	Interactions with atom i that should not be included in the NeighborList should be set to 0.
void	executeWith(ParallelTeam parallelTeam)	Execute the RealSpaceEnergyRegion with the passed ParallelTeam.
void	finish()	Perform finalization actions after parallel execution ends.
int	getCount(int i)
int	getInteractions()
double	getPermanentEnergy()
double	getPolarizationEnergy()
void	init(Atom[] atoms, Crystal crystal, ExtendedSystem extendedSystem, boolean esvTerm, double[][][] coordinates, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, double[][][] globalMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean[] use, int[] molecule, int[][] ip11, int[][] mask12, int[][] mask13, int[][] mask14, int[][] mask15, boolean[] isSoft, double[] ipdamp, double[] thole, RealSpaceNeighborParameters realSpaceNeighborParameters, boolean gradient, boolean lambdaTerm, boolean nnTerm, LambdaMode lambdaMode, Polarization polarization, EwaldParameters ewaldParameters, ScaleParameters scaleParameters, AlchemicalParameters alchemicalParameters, long[] realSpaceEnergyTime, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)
void	removeMask(int i, boolean[] is14, double[]... masks)	After calling removeMask, all entries in the mask array should be 1 and is14 array false.
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

ip11

protected int[][] ip11

Polarization groups.

Constructor Details

RealSpaceEnergyRegion

public RealSpaceEnergyRegion(ForceField.ELEC_FORM elecForm,
 int nt,
 ForceField forceField,
 boolean lambdaTerm,
 double electric)

Method Details

applyMask

public void applyMask(int i,
 boolean[] is14,
 double[]... masks)

Description copied from interface: MaskingInterface

Interactions with atom i that should not be included in the NeighborList should be set to 0.

Specified by:

applyMask in interface MaskingInterface

Parameters:

i - The atom whose masking rules should be applied.

is14 - True if atom i and the current atom are 1-4 to each other.

masks - One or more masking arrays.

executeWith

public void executeWith(ParallelTeam parallelTeam)

Execute the RealSpaceEnergyRegion 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

getCount

public int getCount(int i)

getInteractions

public int getInteractions()

getPermanentEnergy

public double getPermanentEnergy()

getPolarizationEnergy

public double getPolarizationEnergy()

init

public void init(Atom[] atoms,
 Crystal crystal,
 ExtendedSystem extendedSystem,
 boolean esvTerm,
 double[][][] coordinates,
 MultipoleType.MultipoleFrameDefinition[] frame,
 int[][] axisAtom,
 double[][][] globalMultipole,
 double[][][] titrationMultipole,
 double[][][] tautomerMultipole,
 double[][][] inducedDipole,
 double[][][] inducedDipoleCR,
 boolean[] use,
 int[] molecule,
 int[][] ip11,
 int[][] mask12,
 int[][] mask13,
 int[][] mask14,
 int[][] mask15,
 boolean[] isSoft,
 double[] ipdamp,
 double[] thole,
 RealSpaceNeighborParameters realSpaceNeighborParameters,
 boolean gradient,
 boolean lambdaTerm,
 boolean nnTerm,
 LambdaMode lambdaMode,
 Polarization polarization,
 EwaldParameters ewaldParameters,
 ScaleParameters scaleParameters,
 AlchemicalParameters alchemicalParameters,
 long[] realSpaceEnergyTime,
 AtomicDoubleArray3D grad,
 AtomicDoubleArray3D torque,
 AtomicDoubleArray3D lambdaGrad,
 AtomicDoubleArray3D lambdaTorque,
 SharedDouble shareddEdLambda,
 SharedDouble sharedd2EdLambda2)

removeMask

public void removeMask(int i,
 boolean[] is14,
 double[]... masks)

Description copied from interface: MaskingInterface

After calling removeMask, all entries in the mask array should be 1 and is14 array false.

Specified by:

removeMask in interface MaskingInterface

Parameters:

i - The atom whose masking rules should be removed.

is14 - True if atom i and the current atom are 1-4 to each other.

masks - One or more masking arrays.

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