Package ffx.potential

Class XtalEnergy

java.lang.Object
ffx.potential.XtalEnergy
All Implemented Interfaces:
OptimizationInterface, Potential
public class XtalEnergy extends Object implements Potential
This class computes the energy and Cartesian coordinate gradient, plus finite difference derivatives of lattice parameters.
Since:
1.0
Author:
Jooyeon Park

  • Constructor Details

  • Method Details

    • destroy

      public boolean destroy()
      Destroys this Potential and frees up any associated resources, particularly worker Threads. Default implementation is to return true (assume destruction successful).
      Specified by:
      destroy in interface OptimizationInterface
      Returns:
      If resource reclamation successful, or resources already reclaimed.

    • energy

      public double energy(double[] x)
      This method is called repeatedly to compute the function energy.
      Specified by:
      energy in interface OptimizationInterface
      Parameters:
      x - Input parameters.
      Returns:
      Function value at x.

    • energyAndGradient

      public double energyAndGradient(double[] x, double[] g)
      This method is called repeatedly to compute the function energy and gradient.
      Specified by:
      energyAndGradient in interface OptimizationInterface
      Parameters:
      x - Input parameters.
      g - Output gradients with respect to each parameter.
      Returns:
      Function value at x.

    • getAcceleration

      public double[] getAcceleration(double[] acceleration)
      getAcceleration.
      Specified by:
      getAcceleration in interface Potential
      Parameters:
      acceleration - an array of double values.
      Returns:
      an array of double values.

    • getCoordinates

      public double[] getCoordinates(double[] x)
      Load the current value of the parameters. If the supplied array is null or not large enough, a new one should be created. The filled array is returned.
      Specified by:
      getCoordinates in interface OptimizationInterface
      Parameters:
      x - Supplied array.
      Returns:
      The array filled with parameter values.

    • getEnergyTermState

      public Potential.STATE getEnergyTermState()
      Get the Potential Energy terms that is active.
      Specified by:
      getEnergyTermState in interface Potential
      Returns:
      the STATE

    • setEnergyTermState

      public void setEnergyTermState(Potential.STATE state)
      Set the Potential Energy terms that should be active.
      Specified by:
      setEnergyTermState in interface Potential
      Parameters:
      state - include FAST varying energy terms, SLOW varying energy terms or BOTH.

    • getMass

      public double[] getMass()
      Get the mass of each degree of freedom. This is required for molecular dynamics.
      Specified by:
      getMass in interface Potential
      Returns:
      The mass of each degree of freedom.

    • getNumberOfVariables

      public int getNumberOfVariables()
      Get the number of variables being operated on.
      Specified by:
      getNumberOfVariables in interface OptimizationInterface
      Returns:
      Number of variables.

    • getPreviousAcceleration

      public double[] getPreviousAcceleration(double[] previousAcceleration)
      getPreviousAcceleration.
      Specified by:
      getPreviousAcceleration in interface Potential
      Parameters:
      previousAcceleration - an array of double values.
      Returns:
      an array of double values.

    • getScaling

      public double[] getScaling()
      Get the problem scaling.
      Specified by:
      getScaling in interface OptimizationInterface
      Returns:
      The scaling value used for each variable.

    • setScaling

      public void setScaling(double[] scaling)
      Scale the problem. A good choice for optimization is the square root of the median eigenvalue of a typical Hessian.
      Specified by:
      setScaling in interface OptimizationInterface
      Parameters:
      scaling - The scaling value to use for each variable.

    • getTotalEnergy

      public double getTotalEnergy()
      Get the total energy of the system
      Specified by:
      getTotalEnergy in interface OptimizationInterface
      Returns:
      the total energy

    • getVariableTypes

      public Potential.VARIABLE_TYPE[] getVariableTypes()
      Get the type of all variables.
      Specified by:
      getVariableTypes in interface Potential
      Returns:
      The VARIABLE_TYPE of each variable.

    • getVelocity

      public double[] getVelocity(double[] velocity)
      getVelocity.
      Specified by:
      getVelocity in interface Potential
      Parameters:
      velocity - an array of double values.
      Returns:
      an array of double values.

    • setAcceleration

      public void setAcceleration(double[] acceleration)
      setAcceleration.
      Specified by:
      setAcceleration in interface Potential
      Parameters:
      acceleration - an array of double values.

    • setFractionalCoordinateMode

      public void setFractionalCoordinateMode(MolecularAssembly.FractionalMode fractionalMode)
      setFractionalCoordinateMode.
      Parameters:
      fractionalMode - a MolecularAssembly.FractionalMode object.

    • setPreviousAcceleration

      public void setPreviousAcceleration(double[] previousAcceleration)
      setPreviousAcceleration.
      Specified by:
      setPreviousAcceleration in interface Potential
      Parameters:
      previousAcceleration - an array of double values.

    • setVelocity

      public void setVelocity(double[] velocity)
      setVelocity.
      Specified by:
      setVelocity in interface Potential
      Parameters:
      velocity - an array of double values.

    • setCoordinates

      public void setCoordinates(double[] x)
      Sets atomic coordinates and lattice parameters.
      Specified by:
      setCoordinates in interface OptimizationInterface
      Parameters:
      x - First 3*nActive parameters are coordinates, next 6 are x parameters.