Package ffx.xray

Class XRayEnergy

java.lang.Object
ffx.xray.XRayEnergy
All Implemented Interfaces:
CrystalPotential, OptimizationInterface, Potential, LambdaInterface

public class XRayEnergy extends Object implements LambdaInterface, CrystalPotential
Combine the X-ray target and chemical potential energy.
Since:
1.0
Author:
Timothy D. Fenn, Michael J. Schnieders
  • Field Details

    • lambda

      protected double lambda
  • 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
      invalid reference
      double
      objects.
      Returns:
      an array of
      invalid reference
      double
      objects.
    • 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.
    • getCrystal

      public Crystal getCrystal()
      Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
      Specified by:
      getCrystal in interface CrystalPotential
      Returns:
      a Crystal instance.
    • setCrystal

      public void setCrystal(Crystal crystal)
      Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
      Specified by:
      setCrystal in interface CrystalPotential
      Parameters:
      crystal - a Crystal instance.
    • 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.
    • getLambda

      public double getLambda()
      Get the current value of the state variable.
      Specified by:
      getLambda in interface LambdaInterface
      Returns:
      state
    • setLambda

      public void setLambda(double lambda)
      Set the current value of the state variable. May be ignored if lambda is not being applied.
      Specified by:
      setLambda in interface LambdaInterface
      Parameters:
      lambda - a double.
    • 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.
    • getNB

      public int getNB()
      get the number of B factor parameters being fit
      Returns:
      the number of B factor parameters
    • setNB

      public void setNB(int nB)
      set the number of B factor parameters
      Parameters:
      nB - requested number of B factor parameters
    • getNOcc

      public int getNOcc()
      get the number of occupancy parameters being fit
      Returns:
      the number of occupancy parameters
    • setNOcc

      public void setNOcc(int nOCC)
      set the number of occupancy parameters
      Parameters:
      nOCC - requested number of occupancy parameters
    • getNXYZ

      public int getNXYZ()
      Get the number of xyz parameters being fit.
      Returns:
      the number of xyz parameters
    • setNXYZ

      public void setNXYZ(int nXYZ)
      set the number of xyz parameters
      Parameters:
      nXYZ - requested number of xyz parameters
    • 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
      invalid reference
      double
      objects.
      Returns:
      an array of
      invalid reference
      double
      objects.
    • getRefinementMode

      public RefinementMinimize.RefinementMode getRefinementMode()
      Getter for the field refinementMode.
      Returns:
      a RefinementMinimize.RefinementMode object.
    • setRefinementMode

      public void setRefinementMode(RefinementMinimize.RefinementMode refinementmode)
      Setter for the field refinementMode.
      Parameters:
      refinementmode - a RefinementMinimize.RefinementMode object.
    • 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.

      Return a reference to each variables type.

      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
      invalid reference
      double
      objects.
      Returns:
      an array of
      invalid reference
      double
      objects.
    • getd2EdL2

      public double getd2EdL2()
      Get the 2nd partial derivative of the energy with respect to lambda.
      Specified by:
      getd2EdL2 in interface LambdaInterface
      Returns:
      d2EdL2
    • getdEdL

      public double getdEdL()
      Get the partial derivative of the energy with respect to lambda.
      Specified by:
      getdEdL in interface LambdaInterface
      Returns:
      dEdL
    • getdEdXdL

      public void getdEdXdL(double[] gradient)
      Get the gradient of dEdL with respect to each parameter.
      Specified by:
      getdEdXdL in interface LambdaInterface
      Parameters:
      gradient - - A double array of length the number of parameters in the model (commonly 3 * number of atoms).
    • setAcceleration

      public void setAcceleration(double[] acceleration)
      setAcceleration.
      Specified by:
      setAcceleration in interface Potential
      Parameters:
      acceleration - an array of
      invalid reference
      double
      objects.
    • setCoordinates

      public void setCoordinates(double[] x)
      set atomic xyz coordinates based on current position
      Parameters:
      x - current parameters to set coordinates with
    • setOccupancies

      public void setOccupancies(double[] x)
      set atom occupancies based on current position
      Parameters:
      x - current parameters to set occupancies with
    • setPreviousAcceleration

      public void setPreviousAcceleration(double[] previousAcceleration)
      setPreviousAcceleration.
      Specified by:
      setPreviousAcceleration in interface Potential
      Parameters:
      previousAcceleration - an array of
      invalid reference
      double
      objects.
    • setVelocity

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