Package ffx.potential.nonbonded

Class SpatialDensityRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.SpatialDensityRegion

Direct Known Subclasses:

BulkSolventDensityRegion

public class SpatialDensityRegion
extends ParallelRegion

This class implements a spatial decomposition based on partitioning a grid into octants.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
int[]	actualCount
protected int	actualWork	Number of octant work cells with at least one atom (actualWork is less than or equal to nWork).
protected double[][][]	coordinates
protected Crystal	crystal
protected static final Logger	logger	Constant logger
protected int	nA	The number of divisions along the A-axis.
int	nAtoms
protected int	nB	The number of divisions along the B-axis.
protected int	nC	The number of divisions along the C-Axis.
protected final int	nSymm
final int	nThreads
protected boolean[][]	select
protected SpatialDensityLoop[]	spatialDensityLoop

Constructor Summary

Constructors

Constructor	Description
SpatialDensityRegion(int gX, int gY, int gZ, double[] grid, int basisSize, int nSymm, int minWork, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates)	Constructor for SpatialDensityRegion.

Method Summary

Modifier and Type	Method	Description
void	assignAtomsToCells()	Assign asymmetric and symmetry mate atoms to cells.
double[]	getGrid()	Getter for the field grid.
int	getNsymm()	getNsymm
int	index(int ia, int ib, int ic)	index
void	run()	Execute parallel code.
void	selectAtoms()	Select atoms that should be assigned to cells.
void	setAtoms(Atom[] atoms)	setAtoms.
final void	setCrystal(Crystal crystal, int gX, int gY, int gZ)	Setter for the field crystal.
void	setDensityLoop(SpatialDensityLoop[] loops)	setDensityLoop
void	setInitValue(double initValue)	Setter for the field initValue.

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

logger

protected static final Logger logger

Constant logger

nThreads

public final int nThreads

nSymm

protected final int nSymm

actualCount

public int[] actualCount

nAtoms

public int nAtoms

nA

protected int nA

The number of divisions along the A-axis.

nB

protected int nB

The number of divisions along the B-axis.

nC

protected int nC

The number of divisions along the C-Axis.

actualWork

protected int actualWork

Number of octant work cells with at least one atom (actualWork is less than or equal to nWork).

coordinates

protected double[][][] coordinates

select

protected boolean[][] select

crystal

protected Crystal crystal

spatialDensityLoop

protected SpatialDensityLoop[] spatialDensityLoop

Constructor Details

SpatialDensityRegion

public SpatialDensityRegion(int gX,
 int gY,
 int gZ,
 double[] grid,
 int basisSize,
 int nSymm,
 int minWork,
 int threadCount,
 Crystal crystal,
 Atom[] atoms,
 double[][][] coordinates)

Constructor for SpatialDensityRegion.

Parameters:

gX - a int.

gY - a int.

gZ - a int.

grid - an array of double.

basisSize - a int.

nSymm - a int.

minWork - a int.

threadCount - a int.

crystal - a Crystal object.

atoms - an array of Atom objects.

coordinates - an array of double.

Method Details

assignAtomsToCells

public void assignAtomsToCells()

Assign asymmetric and symmetry mate atoms to cells. This is very fast; there is little to be gained from parallelization at this point.

getGrid

public double[] getGrid()

Getter for the field grid.

Returns:

an array of double.

getNsymm

public int getNsymm()

getNsymm

Returns:

a int.

index

public int index(int ia,
 int ib,
 int ic)

index

Parameters:

ia - a int.

ib - a int.

ic - a int.

Returns:

a int.

run

public void run()

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

selectAtoms

public void selectAtoms()

Select atoms that should be assigned to cells. 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)

setAtoms.

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(SpatialDensityLoop[] loops)

setDensityLoop

Parameters:

loops - an array of SpatialDensityLoop objects.

setInitValue

public void setInitValue(double initValue)

Setter for the field initValue.

Parameters:

initValue - a double.