Package ffx.xray

Class BulkSolventList

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.xray.BulkSolventList

public class BulkSolventList
extends ParallelRegion

The BulkSolventList class builds a list of atoms in symmetry mates that are within a cutoff distance of an atom in the asymmetric unit. This is done in parallel via a spatial decomposition.

1. The unit cell is partitioned into nA * nB * nC smaller axis-aligned cells, where nA, nB and nC are chosen as large as possible subject to the criteria that the length of each side of a sub-volume (rCellA, rCellB, rCellC) multiplied by (nEdgeA, nEdgeB, nEdgeC), respectively, must be greater than the cutoff distance Rcut plus a buffer distance delta:
   rCellA * nEdgeA .GE. (Rcut + delta)
rCellB * nEdgeB .GE. (Rcut + delta)
rCellC * nEdgeC .GE. (Rcut + delta) All neighbors of an atom are in a block of (2*nEdgeA+1)(2*nEdgeB+1)(2*nEdgeC+1) neighborCells.

Since:

1.0

Author:

Michael J. Schnieders

Constructor Summary

Constructors

Constructor	Description
BulkSolventList(Crystal crystal, Atom[] atoms, double cutoff, ParallelTeam parallelTeam)	Constructor for the NeighborList class.

Method Summary

Modifier and Type	Method	Description
void	buildList(double[][][] coordinates, boolean[][] selected, boolean log)	This method can be called as necessary to build/rebuild the neighbor lists.
void	finish()	Perform finalization actions after parallel execution ends.
void	run()	Execute parallel code.
void	start()	Perform initialization actions before parallel execution begins.

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

Constructor Details

BulkSolventList

public BulkSolventList(Crystal crystal,
 Atom[] atoms,
 double cutoff,
 ParallelTeam parallelTeam)

Constructor for the NeighborList class.

Parameters:

crystal - Definition of the unit cell and space group.

atoms - The atoms to generate Verlet lists for.

cutoff - The cutoff distance.

parallelTeam - Specifies the parallel environment.

Since:

1.0

Method Details

buildList

public void buildList(double[][][] coordinates,
 boolean[][] selected,
 boolean log)

This method can be called as necessary to build/rebuild the neighbor lists.

Parameters:

coordinates - The coordinates of each atom [nSymm][nAtoms*3].

selected - The list of selected atoms [nSymm][nAtoms].

log - a boolean.

Since:

1.0

finish

public void finish()

Perform finalization actions after parallel execution ends. Only one thread calls the finish() method.

The finish() method may be overridden in a subclass. If not overridden, the finish() method does nothing.

This is method should not be called; it is invoked by Parallel Java.

since 0.1

Overrides:

finish in class ParallelRegion

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.

This is method should not be called; it is invoked by Parallel Java.

Specified by:

run in class ParallelRegion

Since:

1.0

start

public void start()

Perform initialization actions before parallel execution begins. Only one thread calls the start() method.

The start() method may be overridden in a subclass. If not overridden, the start() method does nothing.

This is method should not be called; it is invoked by Parallel Java.

Overrides:

start in class ParallelRegion

Since:

1.0