Package ffx.potential.nonbonded

Class SliceRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.SliceRegion

Direct Known Subclasses:

BulkSolventSliceRegion

public class SliceRegion
extends ParallelRegion

The SliceLoop class is used to parallelize placing onto a 3D grid

1) Multipoles using B-splines or

2) Diffraction form factors.

Each "slice" of the grid (i.e. a fixed value of the z-coordinate) is operated on by only a single thread to logically enforce atomic updates of grid magnitudes.

Author:

Armin Avdic

Field Summary

Fields

Modifier and Type	Field	Description
int	buff
protected double[][][]	coordinates
boolean[][]	select
protected SliceLoop[]	sliceLoop

Constructor Summary

Constructors

Constructor	Description
SliceRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Atom[] atoms, double[][][] coordinates)	Constructor for SliceRegion.

Method Summary

Modifier and Type	Method	Description
void	finish()	Perform finalization actions after parallel execution ends.
double[]	getGrid()	Getter for the field grid.
int	getNatoms()	getNatoms.
int	getNsymm()	getNsymm.
void	run()	Execute parallel code.
void	selectAtoms()	Select atoms that should be included.
void	setAtoms(Atom[] atoms)	Setter for the field atoms.
final void	setCrystal(Crystal crystal, int gX, int gY, int gZ)	Setter for the field crystal.
void	setDensityLoop(SliceLoop[] loops)	setDensityLoop.
void	setInitValue(double initValue)	Setter for the field initValue.
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

buff

public int buff

select

public boolean[][] select

sliceLoop

protected SliceLoop[] sliceLoop

coordinates

protected double[][][] coordinates

Constructor Details

SliceRegion

public SliceRegion(int gX,
 int gY,
 int gZ,
 double[] grid,
 int nSymm,
 int threadCount,
 Atom[] atoms,
 double[][][] coordinates)

Constructor for SliceRegion.

Parameters:

gX - a int.

gY - a int.

gZ - a int.

grid - the grid array.

nSymm - a int.

threadCount - a int.

atoms - an array of Atom objects.

coordinates - the atomic coordinate array.

Method Details

finish

public void finish()

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

getGrid

public double[] getGrid()

Getter for the field grid.

Returns:

return the grid array.

getNatoms

public int getNatoms()

getNatoms.

Returns:

a int.

getNsymm

public int getNsymm()

getNsymm.

Returns:

a int.

run

public void run()
         throws Exception

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.

selectAtoms

public void selectAtoms()

Select atoms that should be included. The default is to include all atoms, which is set up in the constructor. This function should be over-ridden by subclasses that want finer control.

setAtoms

public void setAtoms(Atom[] atoms)

Setter for the field atoms.

Parameters:

atoms - an array of Atom objects.

setCrystal

public final void setCrystal(Crystal crystal,
 int gX,
 int gY,
 int gZ)

Setter for the field crystal.

Parameters:

crystal - a Crystal object.

gX - a int.

gY - a int.

gZ - a int.

setDensityLoop

public void setDensityLoop(SliceLoop[] loops)

setDensityLoop.

Parameters:

loops - an array of SliceLoop objects.

setInitValue

public void setInitValue(double initValue)

Setter for the field initValue.

Parameters:

initValue - a double.

start

public void start()

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