Package ffx.potential.nonbonded.implicit

Class DispersionRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.potential.nonbonded.implicit.DispersionRegion

public class DispersionRegion
extends ParallelRegion

Parallel calculation of continuum dispersion energy via pairwise descreening.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
protected Atom[]	atoms	An ordered array of atoms in the system.
static final double	DEFAULT_DISPERSION_OFFSET	The dispersion integral begins for each atom at: Rmin_ij + DISPERSION_OFFSET
static final double	DEFAULT_SOLUTE_OFFSET	Each solute atom blocks dispersion interactions with solvent: Rmin + SOLUTE_OFFSET

Constructor Summary

Constructors

Constructor	Description
DispersionRegion(int nt, Atom[] atoms, ForceField forceField)	DispersionRegion constructor.

Method Summary

Modifier and Type	Method	Description
void	allocate(Atom[] atoms)	Allocate storage given the Atom array.
double	getDispersionOffset()	The dispersion integral begins offset from the vdW radius.
double	getDispersionOverlapFactor()
double	getEnergy()
double	getSoluteOffset()
void	init(Atom[] atoms, Crystal crystal, boolean[] use, int[][][] neighborLists, double[] x, double[] y, double[] z, double cut2, boolean gradient, AtomicDoubleArray3D grad)	Initialize the DispersionRegion for energy calculation.
void	run()	Execute parallel code.
void	setDispersionOffest(double dispersionOffest)	The dispersion integral begins offset from the vdW radius.
void	setDispersionOverlapFactor(double dispersionOverlapFactor)	Set the dispersion overlap HCT scale factor.
void	setSoluteOffset(double soluteOffset)
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, finish

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

DEFAULT_DISPERSION_OFFSET

public static final double DEFAULT_DISPERSION_OFFSET

The dispersion integral begins for each atom at: Rmin_ij + DISPERSION_OFFSET

See Also:

• Constant Field Values

DEFAULT_SOLUTE_OFFSET

public static final double DEFAULT_SOLUTE_OFFSET

Each solute atom blocks dispersion interactions with solvent: Rmin + SOLUTE_OFFSET

See Also:

• Constant Field Values

atoms

protected Atom[] atoms

An ordered array of atoms in the system.

Constructor Details

DispersionRegion

public DispersionRegion(int nt,
 Atom[] atoms,
 ForceField forceField)

DispersionRegion constructor.

Parameters:

nt - Number of threads.

atoms - Atom array.

forceField - ForceField in use.

Method Details

allocate

public void allocate(Atom[] atoms)

Allocate storage given the Atom array.

Parameters:

atoms - Atom array in use.

setDispersionOffest

public void setDispersionOffest(double dispersionOffest)

The dispersion integral begins offset from the vdW radius.

Parameters:

dispersionOffest - The dispersion integral offset.

getDispersionOffset

public double getDispersionOffset()

The dispersion integral begins offset from the vdW radius.

Returns:

the dispersion integral offset.

getDispersionOverlapFactor

public double getDispersionOverlapFactor()

setDispersionOverlapFactor

public void setDispersionOverlapFactor(double dispersionOverlapFactor)

Set the dispersion overlap HCT scale factor.

Parameters:

dispersionOverlapFactor - The dispersion integral HCT scale factor.

getEnergy

public double getEnergy()

getSoluteOffset

public double getSoluteOffset()

setSoluteOffset

public void setSoluteOffset(double soluteOffset)

init

public void init(Atom[] atoms,
 Crystal crystal,
 boolean[] use,
 int[][][] neighborLists,
 double[] x,
 double[] y,
 double[] z,
 double cut2,
 boolean gradient,
 AtomicDoubleArray3D grad)

Initialize the DispersionRegion for energy calculation.

Parameters:

atoms - Atom array.

crystal - Crystal for periodic boundary conditions.

use - Flag to indicate an atom is to be used.

neighborLists - Neighbor-list for each atom.

x - X-coordinate array.

y - Y-coordinate array.

z - Z-coordinate array.

cut2 - The cut-off distance squared.

gradient - If true, compute the gradient.

grad - Array to store the gradient.

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.

Specified by:

run in class ParallelRegion

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.

Overrides:

start in class ParallelRegion