Class GKEnergyRegion

java.lang.Object
edu.rit.pj.ParallelConstruct
edu.rit.pj.ParallelRegion
ffx.potential.nonbonded.implicit.GKEnergyRegion

public class GKEnergyRegion extends ParallelRegion
Parallel calculation of the Generalized Kirkwood reaction field energy.
Since:
1.0
Author:
Michael J. Schnieders
  • Field Details

    • oneThird

      protected static final double oneThird
      Constant factor used with quadrupoles.
      See Also:
    • electric

      protected final double electric
      Conversion from electron**2/Ang to kcal/mole.
    • polarization

      protected final Polarization polarization
      Treatment of polarization.
    • nonPolarModel

      protected final GeneralizedKirkwood.NonPolarModel nonPolarModel
    • dOffset

      protected final double dOffset
      Dielectric 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:
    • surfaceTension

      protected final double surfaceTension
      Cavitation surface tension coefficient (kcal/mol/A^2).
    • gkc

      protected final double gkc
      Empirical constant that controls the GK cross-term.
  • Constructor Details

    • GKEnergyRegion

      public GKEnergyRegion(int nt, Polarization polarization, GeneralizedKirkwood.NonPolarModel nonPolarModel, double surfaceTension, double probe, double electric, double soluteDieletric, double solventDieletric, double gkc, boolean gkQI)
  • Method Details

    • getEnergy

      public double getEnergy()
    • getPermanentEnergy

      public double getPermanentEnergy()
    • getPolarizationEnergy

      public double getPolarizationEnergy()
    • getSelfEnergy

      public AtomicDoubleArray getSelfEnergy()
    • 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 the run() method concurrently.

      The run() method must be implemented in a subclass.

      Specified by:
      run in class ParallelRegion
    • start

      public void start()
      Description copied from class: ParallelRegion
      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
    • finish

      public void finish()
      Description copied from class: ParallelRegion
      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.

      Overrides:
      finish in class ParallelRegion