Package ffx.potential.nonbonded

Class RowLoop

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelForLoop

edu.rit.pj.IntegerForLoop

ffx.potential.nonbonded.RowLoop

public abstract class RowLoop
extends IntegerForLoop

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

1) Multipoles using B-splines or

2) Diffraction form factors.

Each "row" of the grid (i.e. fixed values of the z and y-coordinates) 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 RowRegion	rowRegion

Constructor Summary

Constructors

Constructor	Description
RowLoop(int nAtoms, int nSymm, RowRegion rowRegion)	Constructor for RowLoop.

Method Summary

Modifier and Type	Method	Description
boolean	checkList(int[][][] zAtListBuild, int buff)	Check if the list is valid for the given zAtListBuild and buff.
abstract void	gridDensity(int iSymm, int iAtom, int lb, int ub)	Apply electron density "as normal" for an atom, but check that the y and z indeces are within the supplied bounds (inclusive).
void	run(int lb, int ub)	Execute one chunk of iterations of this parallel for loop.
void	saveZYValues(int[][][] zAtListBuild)	saveZYValues.
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

buildListA

protected ArrayList<Integer> buildListA

buildListS

protected ArrayList<Integer> buildListS

rowRegion

protected RowRegion rowRegion

rebuildList

protected boolean rebuildList

Constructor Details

RowLoop

public RowLoop(int nAtoms,
 int nSymm,
 RowRegion rowRegion)

Constructor for RowLoop.

Parameters:

nAtoms - a int.

nSymm - a int.

rowRegion - a RowRegion object.

Method Details

checkList

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

Check if the list is valid for the given zAtListBuild and buff.

Parameters:

zAtListBuild - the list of zAtListBuild.

buff - the buffer size.

Returns:

true if the list is valid, false otherwise.

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 y and z indeces are 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 for the y and z-axes.

ub - the upper bound for the y and z-axes.

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.

saveZYValues

public void saveZYValues(int[][][] zAtListBuild)

saveZYValues.

Parameters:

zAtListBuild - the list of zAtListBuild.

setNsymm

public void setNsymm(int nSymm)

setNsymm

Parameters:

nSymm - a int.