Package ffx.openmm

Class Continuous3DFunction

java.lang.Object
ffx.openmm.TabulatedFunction
ffx.openmm.Continuous3DFunction
public class Continuous3DFunction extends TabulatedFunction
This is a TabulatedFunction that computes a continuous three dimensional function.

  • Field Summary

    Fields inherited from class ffx.openmm.TabulatedFunction

    pointer

  • Constructor Summary

    Constructors
    Constructor
    Description
    Continuous3DFunction(com.sun.jna.ptr.PointerByReference values, int xsize, int ysize, int zsize, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax, boolean periodic)
    Create a Continuous3DFunction f(x,y,z) based on a set of tabulated values.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    destroy()
    Destroy the continuous 3D function.
    void
    getFunctionParameters(com.sun.jna.ptr.PointerByReference values, com.sun.jna.ptr.IntByReference xsize, com.sun.jna.ptr.IntByReference ysize, com.sun.jna.ptr.IntByReference zsize, com.sun.jna.ptr.DoubleByReference xmin, com.sun.jna.ptr.DoubleByReference xmax, com.sun.jna.ptr.DoubleByReference ymin, com.sun.jna.ptr.DoubleByReference ymax, com.sun.jna.ptr.DoubleByReference zmin, com.sun.jna.ptr.DoubleByReference zmax)
    Get the parameters for the tabulated function.
    void
    setFunctionParameters(com.sun.jna.ptr.PointerByReference values, int xsize, int ysize, int zsize, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax)
    Set the parameters for the tabulated function.

    Methods inherited from class ffx.openmm.TabulatedFunction

    getPeriodic, getPointer, getUpdateCount

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • Continuous3DFunction

      public Continuous3DFunction(com.sun.jna.ptr.PointerByReference values, int xsize, int ysize, int zsize, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax, boolean periodic)
      Create a Continuous3DFunction f(x,y,z) based on a set of tabulated values.
      Parameters:
      values - the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax. A natural cubic spline is used to interpolate between the tabulated values. The function is assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize*zsize.
      xsize - the number of table elements along the x direction
      ysize - the number of table elements along the y direction
      zsize - the number of table elements along the z direction
      xmin - the value of x corresponding to the first element of values
      xmax - the value of x corresponding to the last element of values
      ymin - the value of y corresponding to the first element of values
      ymax - the value of y corresponding to the last element of values
      zmin - the value of z corresponding to the first element of values
      zmax - the value of z corresponding to the last element of values
      periodic - whether the interpolated function is periodic

  • Method Details

    • destroy

      public void destroy()
      Destroy the continuous 3D function.
      Specified by:
      destroy in class TabulatedFunction

    • getFunctionParameters

      public void getFunctionParameters(com.sun.jna.ptr.PointerByReference values, com.sun.jna.ptr.IntByReference xsize, com.sun.jna.ptr.IntByReference ysize, com.sun.jna.ptr.IntByReference zsize, com.sun.jna.ptr.DoubleByReference xmin, com.sun.jna.ptr.DoubleByReference xmax, com.sun.jna.ptr.DoubleByReference ymin, com.sun.jna.ptr.DoubleByReference ymax, com.sun.jna.ptr.DoubleByReference zmin, com.sun.jna.ptr.DoubleByReference zmax)
      Get the parameters for the tabulated function.
      Parameters:
      values - the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax. A natural cubic spline is used to interpolate between the tabulated values. The function is assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize*zsize.
      xsize - the number of table elements along the x direction
      ysize - the number of table elements along the y direction
      zsize - the number of table elements along the z direction
      xmin - the value of x corresponding to the first element of values
      xmax - the value of x corresponding to the last element of values
      ymin - the value of y corresponding to the first element of values
      ymax - the value of y corresponding to the last element of values
      zmin - the value of z corresponding to the first element of values
      zmax - the value of z corresponding to the last element of values

    • setFunctionParameters

      public void setFunctionParameters(com.sun.jna.ptr.PointerByReference values, int xsize, int ysize, int zsize, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax)
      Set the parameters for the tabulated function.
      Parameters:
      values - the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax. A natural cubic spline is used to interpolate between the tabulated values. The function is assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize*zsize.
      xsize - the number of table elements along the x direction
      ysize - the number of table elements along the y direction
      zsize - the number of table elements along the z direction
      xmin - the value of x corresponding to the first element of values
      xmax - the value of x corresponding to the last element of values
      ymin - the value of y corresponding to the first element of values
      ymax - the value of y corresponding to the last element of values
      zmin - the value of z corresponding to the first element of values
      zmax - the value of z corresponding to the last element of values