Class ChandlerCavitation

java.lang.Object
ffx.potential.nonbonded.implicit.ChandlerCavitation

public class ChandlerCavitation extends Object
The ChandlerCavitation class smoothly switches between a volume based dependence for small solutes to a surface area dependence for large solutes.
Since:
1.0
Author:
Michael J. Schnieders
  • Constructor Details

  • Method Details

    • energyAndGradient

      public double energyAndGradient(double[][] positions, AtomicDoubleArray3D gradient)
      Compute molecular volume and surface area.
      Parameters:
      positions - Atomic positions to use.
      gradient - Atomic coordinate gradient.
      Returns:
      The cavitation energy.
    • energyAndGradientConnolly

      public double energyAndGradientConnolly(AtomicDoubleArray3D gradient)
      Compute the cavitation energy.
      Parameters:
      gradient - Add the gradient to this AtomicDoubleArray3D.
      Returns:
      Returns the cavitation energy.
    • energyAndGradientGausVol

      public double energyAndGradientGausVol(double[][] positions, AtomicDoubleArray3D gradient)
      Compute molecular volume and surface area.
      Parameters:
      positions - Atomic positions to use.
      gradient - Atomic coordinate gradient.
      Returns:
      The cavitation energy.
    • getConnollyRegion

      public ConnollyRegion getConnollyRegion()
    • getCrossOver

      public double getCrossOver()
    • setCrossOver

      public void setCrossOver(double crossOver)
    • getEffectiveRadius

      public double getEffectiveRadius()
    • getEnergy

      public double getEnergy()
    • getGaussVol

      public GaussVol getGaussVol()
    • getSolventPressure

      public double getSolventPressure()
    • setSolventPressure

      public void setSolventPressure(double solventPressure)
    • getSurfaceArea

      public double getSurfaceArea()
      Return Surface Area (A^2).
      Returns:
      Surface Area (A^2).
    • getSurfaceAreaEnergy

      public double getSurfaceAreaEnergy()
      Return Surface Area based cavitation energy.
      Returns:
      Surface Area based cavitation energy.
    • getSurfaceTension

      public double getSurfaceTension()
    • setSurfaceTension

      public void setSurfaceTension(double surfaceTension)
    • getVolume

      public double getVolume()
      Return Volume (A^3).
      Returns:
      Volume (A^3).
    • getVolumeEnergy

      public double getVolumeEnergy()
      Return Volume based cavitation energy.
      Returns:
      Volume based cavitation energy.