Package ffx.potential.nonbonded.implicit
Class GKEnergyRegion
java.lang.Object
edu.rit.pj.ParallelConstruct
edu.rit.pj.ParallelRegion
ffx.potential.nonbonded.implicit.GKEnergyRegion
Parallel calculation of the Generalized Kirkwood reaction field energy.
- Since:
- 1.0
- Author:
- Michael J. Schnieders
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Field Summary
Modifier and TypeFieldDescriptionprotected final double
Dielectric offset from:protected final double
Conversion from electron**2/Ang to kcal/mole.protected final double
Empirical constant that controls the GK cross-term.protected final GeneralizedKirkwood.NonPolarModel
protected static final double
Constant factor used with quadrupoles.protected final Polarization
Treatment of polarization.protected final double
Cavitation surface tension coefficient (kcal/mol/A^2). -
Constructor Summary
ConstructorDescriptionGKEnergyRegion
(int nt, Polarization polarization, GeneralizedKirkwood.NonPolarModel nonPolarModel, double surfaceTension, double probe, double electric, double soluteDieletric, double solventDieletric, double gkc, boolean gkQI) -
Method Summary
Modifier and TypeMethodDescriptionvoid
finish()
Perform finalization actions after parallel execution ends.double
int
double
double
void
init
(Atom[] atoms, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] baseRadius, double[] born, boolean gradient, ParallelTeam parallelTeam, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray sharedBornGrad) 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
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Field Details
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oneThird
protected static final double oneThirdConstant factor used with quadrupoles.- See Also:
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electric
protected final double electricConversion from electron**2/Ang to kcal/mole. -
polarization
Treatment of polarization. -
nonPolarModel
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dOffset
protected final double dOffsetDielectric offset from:W. C. Still, A. Tempczyk, R. C. Hawley and T. Hendrickson, "A Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics", J. Amer. Chem. Soc., 112, 6127-6129 (1990)
- See Also:
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surfaceTension
protected final double surfaceTensionCavitation surface tension coefficient (kcal/mol/A^2). -
gkc
protected final double gkcEmpirical constant that controls the GK cross-term.
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Constructor Details
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GKEnergyRegion
public GKEnergyRegion(int nt, Polarization polarization, GeneralizedKirkwood.NonPolarModel nonPolarModel, double surfaceTension, double probe, double electric, double soluteDieletric, double solventDieletric, double gkc, boolean gkQI)
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Method Details
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getEnergy
public double getEnergy() -
getPermanentEnergy
public double getPermanentEnergy() -
getPolarizationEnergy
public double getPolarizationEnergy() -
getSelfEnergy
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getInteractions
public int getInteractions() -
init
public void init(Atom[] atoms, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] baseRadius, double[] born, boolean gradient, ParallelTeam parallelTeam, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray sharedBornGrad) -
run
public void run()Description copied from class:ParallelRegion
Execute parallel code. All threads of the parallel team call therun()
method concurrently.The
run()
method must be implemented in a subclass.- Specified by:
run
in classParallelRegion
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start
public void start()Description copied from class:ParallelRegion
Perform initialization actions before parallel execution begins. Only one thread calls thestart()
method.The
start()
method may be overridden in a subclass. If not overridden, thestart()
method does nothing.- Overrides:
start
in classParallelRegion
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finish
public void finish()Description copied from class:ParallelRegion
Perform finalization actions after parallel execution ends. Only one thread calls thefinish()
method.The
finish()
method may be overridden in a subclass. If not overridden, thefinish()
method does nothing.- Overrides:
finish
in classParallelRegion
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