Package ffx.potential.nonbonded.pme

Class PermanentFieldRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.pme.PermanentFieldRegion

All Implemented Interfaces:

MaskingInterface

public class PermanentFieldRegion
extends ParallelRegion
implements MaskingInterface

Parallel computation of the permanent field.

This class can be executed by a ParallelTeam with exactly 2 threads.

The Real Space and Reciprocal Space Sections will be run concurrently, each with the number of threads defined by their respective ParallelTeam instances.

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
PermanentFieldRegion(ParallelTeam pt, ForceField forceField, boolean lambdaTerm)

Method Summary

Modifier and Type	Method	Description
void	applyMask(int i, boolean[] is14, double[]... masks)	Apply permanent field masking rules.
long	getInitTime(int threadId)
long	getPermTime(int threadId)
long	getRealSpacePermTime()
void	init(Atom[] atoms, Crystal crystal, double[][][] coordinates, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, int[][][] neighborLists, ScaleParameters scaleParameters, boolean[] use, int[] molecule, double[] ipdamp, double[] thole, int[][] ip11, int[][] mask12, int[][] mask13, int[][] mask14, LambdaMode lambdaMode, boolean reciprocalSpaceTerm, ReciprocalSpace reciprocalSpace, EwaldParameters ewaldParameters, PCGSolver pcgSolver, IntegerSchedule permanentSchedule, RealSpaceNeighborParameters realSpaceNeighborParameters, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR)
void	initTimings()
void	removeMask(int i, boolean[] is14, double[]... masks)	Remove permanent field masking rules.
void	run()	Execute parallel code.

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, start

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

PermanentFieldRegion

public PermanentFieldRegion(ParallelTeam pt,
 ForceField forceField,
 boolean lambdaTerm)

Method Details

applyMask

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

Apply permanent field masking rules.

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.

initTimings

public void initTimings()

getRealSpacePermTime

public long getRealSpacePermTime()

getInitTime

public long getInitTime(int threadId)

getPermTime

public long getPermTime(int threadId)

init

public void init(Atom[] atoms,
 Crystal crystal,
 double[][][] coordinates,
 double[][][] globalMultipole,
 double[][][] inducedDipole,
 double[][][] inducedDipoleCR,
 int[][][] neighborLists,
 ScaleParameters scaleParameters,
 boolean[] use,
 int[] molecule,
 double[] ipdamp,
 double[] thole,
 int[][] ip11,
 int[][] mask12,
 int[][] mask13,
 int[][] mask14,
 LambdaMode lambdaMode,
 boolean reciprocalSpaceTerm,
 ReciprocalSpace reciprocalSpace,
 EwaldParameters ewaldParameters,
 PCGSolver pcgSolver,
 IntegerSchedule permanentSchedule,
 RealSpaceNeighborParameters realSpaceNeighborParameters,
 AtomicDoubleArray3D field,
 AtomicDoubleArray3D fieldCR)

removeMask

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

Remove permanent field masking rules.

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