Package ffx.xray

Class BulkSolventSliceRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.SliceRegion

ffx.xray.BulkSolventSliceRegion

public class BulkSolventSliceRegion
extends SliceRegion

This class implements a spatial decomposition based on partitioning a grid into octants. The over-ridden "selectAtoms" method selects atoms that are not in the asymmetric unit, but are within the supplied cutoff radius.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
protected static final Logger	logger	Constant logger

Fields inherited from class ffx.potential.nonbonded.SliceRegion

buff, coordinates, select, sliceLoop

Constructor Summary

Constructors

Constructor	Description
BulkSolventSliceRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.

Method Summary

Modifier and Type	Method	Description
void	run()	Execute parallel code.
void	selectAtoms()	Select atoms that should be included.

Methods inherited from class ffx.potential.nonbonded.SliceRegion

finish, getGrid, getNatoms, getNsymm, setAtoms, setCrystal, setDensityLoop, setInitValue, start

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

logger

protected static final Logger logger

Constant logger

Constructor Details

BulkSolventSliceRegion

public BulkSolventSliceRegion(int gX,
 int gY,
 int gZ,
 double[] grid,
 int nSymm,
 int threadCount,
 Crystal crystal,
 Atom[] atoms,
 double[][][] coordinates,
 double cutoff,
 ParallelTeam parallelTeam)

Constructor for BulkSolventDensityRegion.

Parameters:

gX - a int.

gY - a int.

gZ - a int.

grid - an array of double.

nSymm - a int.

threadCount - a int.

crystal - a Crystal object.

atoms - an array of Atom objects.

coordinates - an array of double.

cutoff - a double.

parallelTeam - a ParallelTeam object.

Method Details

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.

Overrides:

run in class SliceRegion

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.

Overrides:

selectAtoms in class SliceRegion