Package ffx.xray

Class ScaleBulkEnergy

java.lang.Object

ffx.xray.ScaleBulkEnergy

All Implemented Interfaces:

OptimizationInterface

public class ScaleBulkEnergy
extends Object
implements OptimizationInterface

Fit bulk solvent and aniso B scaling terms to correct calculated structure factors against data

Since:

1.0

Author:

Timothy D. Fenn

See Also:

• P. V. Afonine, R. W. Grosse-Kunstleve and P. D. Adams, Acta Cryst. (2005). D61, 850-855
• R. W. Grosse-Kunstleve and P. D. Adams, J. Appl. Cryst. (2002). 35, 477-480.
• J. A. Grant, B. T. Pickup, A. Nicholls, J. Comp. Chem. (2001). 22, 608-640
• J. S. Jiang, A. T. Brunger, JMB (1994) 243, 100-115.

Method Summary

Modifier and Type	Method	Description
boolean	destroy()	Destroys this Potential and frees up any associated resources, particularly worker Threads.
double	energy(double[] x)	This method is called repeatedly to compute the function energy.
double	energyAndGradient(double[] x, double[] g)	This method is called repeatedly to compute the function energy and gradient.
double[]	getCoordinates(double[] parameters)	Load the current value of the parameters.
int	getNumberOfVariables()	Get the number of variables being operated on.
double	getR()
double	getRfree()
double[]	getScaling()	Get the problem scaling.
double	getTotalEnergy()	Get the total energy of the system
void	setCoordinates(double[] parameters)	Set the current value of the parameters.
void	setScaling(double[] scaling)	Scale the problem.
double	target(double[] x, double[] g, boolean gradient, boolean print)	ScaleBulk target energy.

Methods inherited from class java.lang.Object

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

Methods inherited from interface ffx.numerics.OptimizationInterface

energy, energyAndGradient, getUnderlyingPotentials, scaleCoordinates, scaleCoordinatesAndGradient, unscaleCoordinates

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.

getR

public double getR()

getRfree

public double getRfree()

getCoordinates

public double[] getCoordinates(double[] parameters)

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:

parameters - Supplied array.

Returns:

The array filled with parameter values.

setCoordinates

public void setCoordinates(double[] parameters)

Set the current value of the parameters. If the supplied array is null or not large enough, no action is taken.

Specified by:

setCoordinates in interface OptimizationInterface

Parameters:

parameters - The array with parameter values.

getNumberOfVariables

public int getNumberOfVariables()

Get the number of variables being operated on.

Specified by:

getNumberOfVariables in interface OptimizationInterface

Returns:

Number of variables.

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(@Nullable
 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

target

public double target(double[] x,
 double[] g,
 boolean gradient,
 boolean print)

ScaleBulk target energy.

Parameters:

x - The parameter array.

g - The gradient of the parameter array.

gradient - If true, compute the gradient.

print - If true, enable verbose printing.

Returns:

The target energy.