Class BornRadiiRegion

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

public class BornRadiiRegion extends ParallelRegion
Parallel computation of Born radii via the Grycuk method.
Since:
1.0
Author:
Michael J. Schnieders
  • Field Details

    • atoms

      protected Atom[] atoms
      An ordered array of atoms in the system.
  • Constructor Details

    • BornRadiiRegion

      public BornRadiiRegion(int nt, int nAtoms, ForceField forceField, boolean neckCorrection, boolean tanhCorrection, boolean perfectHCTScale)
      BornRadiiRegion Constructor.
      Parameters:
      nt - Number of threads.
      nAtoms - Number of atoms.
      forceField - The ForceField in use.
      neckCorrection - Perform a neck correction.
      tanhCorrection - Perform a tanh correction.
      perfectHCTScale - Use "perfect" HCT scale factors.
  • Method Details

    • getPerfectRadii

      public double[] getPerfectRadii()
      Return perfect Born radii read in as keywords, or base radii if perfect radii are not available.
      Returns:
      Array of perfect Born radii.
    • 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
    • init

      public void init(Atom[] atoms, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, double[] baseRadius, double[] descreenRadius, double[] overlapScale, double[] neckScale, double descreenOffset, boolean[] use, double cut2, boolean nativeEnvironmentApproximation, double[] born)
    • 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
    • getBorn

      public double[] getBorn()
    • getUnscaledBornIntegral

      public double[] getUnscaledBornIntegral()