Package ffx.potential.nonbonded

Class SliceLoop

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelForLoop

edu.rit.pj.IntegerForLoop

ffx.potential.nonbonded.SliceLoop

public abstract class SliceLoop
extends IntegerForLoop

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
protected ArrayList<Integer>	buildListA
protected ArrayList<Integer>	buildListS
protected boolean	rebuildList
protected SliceRegion	sliceRegion

Constructor Summary

Constructors

Constructor	Description
SliceLoop(int nAtoms, int nSymm, SliceRegion sliceRegion)	Constructor for SliceLoop.

Method Summary

Modifier and Type	Method	Description
boolean	checkList(int[][] zAtListBuild, int buff)	checkList.
abstract void	gridDensity(int iSymm, int iAtom, int lb, int ub)	Apply electron density "as normal" for an atom, but check that the z index is within the supplied bounds (inclusive).
void	run(int lb, int ub)	Execute one chunk of iterations of this parallel for loop.
void	saveZValues(int[][] zAtListBuild)	saveZValues.
void	setNsymm(int nSymm)	setNsymm

Methods inherited from class edu.rit.pj.IntegerForLoop

finish, ordered, schedule, start, stopLoop

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

rebuildList

protected boolean rebuildList

buildListA

protected ArrayList<Integer> buildListA

buildListS

protected ArrayList<Integer> buildListS

sliceRegion

protected SliceRegion sliceRegion

Constructor Details

SliceLoop

public SliceLoop(int nAtoms,
 int nSymm,
 SliceRegion sliceRegion)

Constructor for SliceLoop.

Parameters:

nAtoms - a int.

nSymm - a int.

sliceRegion - a SliceRegion object.

Method Details

checkList

public boolean checkList(int[][] zAtListBuild,
 int buff)

checkList.

Parameters:

zAtListBuild - an array of

invalid reference

int

objects.

buff - a int.

Returns:

a boolean.

gridDensity

public abstract void gridDensity(int iSymm,
 int iAtom,
 int lb,
 int ub)

Apply electron density "as normal" for an atom, but check that the z index is within the supplied bounds (inclusive).

Parameters:

iSymm - the SymOp to apply.

iAtom - the index of the Atom to put onto the grid.

lb - the lower bound along the z-axis.

ub - the upper bound along the z-axis.

run

public void run(int lb,
 int ub)
         throws Exception

Execute one chunk of iterations of this parallel for loop. The run() method must perform the loop body for indexes first through last inclusive, increasing the loop index by +1 after each iteration.

The run() method must be overridden in a subclass.

Specified by:

run in class IntegerForLoop

Parameters:

lb - First loop index.

ub - Last loop index.

Throws:

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

Exception - if any.

saveZValues

public void saveZValues(int[][] zAtListBuild)

saveZValues.

Parameters:

zAtListBuild - an array of

invalid reference

int

objects.

setNsymm

public void setNsymm(int nSymm)

setNsymm

Parameters:

nSymm - a int.