Package ffx.xray

Class BulkSolventDensityRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.SpatialDensityRegion

ffx.xray.BulkSolventDensityRegion

public class BulkSolventDensityRegion
extends SpatialDensityRegion

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 inherited from class ffx.potential.nonbonded.SpatialDensityRegion

actualCount, actualWork, coordinates, crystal, logger, nA, nAtoms, nB, nC, nSymm, nThreads, select, spatialDensityLoop

Constructor Summary

Constructors

Constructor	Description
BulkSolventDensityRegion(int gX, int gY, int gZ, double[] grid, int basisSize, int nSymm, int minWork, 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 assigned to cells.

Methods inherited from class ffx.potential.nonbonded.SpatialDensityRegion

assignAtomsToCells, getGrid, getNsymm, index, setAtoms, setCrystal, setDensityLoop, setInitValue

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

Constructor Details

BulkSolventDensityRegion

public BulkSolventDensityRegion(int gX,
 int gY,
 int gZ,
 double[] grid,
 int basisSize,
 int nSymm,
 int minWork,
 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.

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.

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 SpatialDensityRegion

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.

Overrides:

selectAtoms in class SpatialDensityRegion