Package ffx.xray

Class SigmaAMinimize

java.lang.Object

ffx.xray.SigmaAMinimize

All Implemented Interfaces:

Terminatable, OptimizationListener

public class SigmaAMinimize
extends Object
implements OptimizationListener, Terminatable

SigmaAMinimize class.

Since:

1.0

Author:

Timothy D. Fenn

Field Summary

Fields

Modifier and Type	Field	Description
protected final DiffractionRefinementData	refinementData

Method Summary

Modifier and Type	Method	Description
double	calculateLikelihoodFree()	calculateLikelihoodFree
double[]	getCoordinates(double[] x)	getCoordinates.
int	getNumberOfVariables()	getNumberOfVariables.
SigmaAEnergy	minimize()	minimize
SigmaAEnergy	minimize(double eps)	minimize
SigmaAEnergy	minimize(int m, double eps)	minimize
boolean	optimizationUpdate(int iter, int nBFGS, int nfun, double grms, double xrms, double f, double df, double angle, LineSearch.LineSearchResult info)	This method is called by the optimizer after each step.
void	terminate()	This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point.

Methods inherited from class java.lang.Object

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

Field Details

refinementData

protected final DiffractionRefinementData refinementData

Method Details

calculateLikelihoodFree

public double calculateLikelihoodFree()

calculateLikelihoodFree

Returns:

a double.

getCoordinates

public double[] getCoordinates(double[] x)

getCoordinates.

Parameters:

x - an array of

invalid reference

double

objects.

Returns:

an array of

invalid reference

double

objects.

getNumberOfVariables

public int getNumberOfVariables()

getNumberOfVariables.

Returns:

a int.

minimize

public SigmaAEnergy minimize()

minimize

Returns:

a SigmaAEnergy object.

minimize

public SigmaAEnergy minimize(double eps)

minimize

Parameters:

eps - a double.

Returns:

a SigmaAEnergy object.

minimize

public SigmaAEnergy minimize(int m,
 double eps)

minimize

Parameters:

m - a int.

eps - a double.

Returns:

a SigmaAEnergy object.

optimizationUpdate

public boolean optimizationUpdate(int iter,
 int nBFGS,
 int nfun,
 double grms,
 double xrms,
 double f,
 double df,
 double angle,
 LineSearch.LineSearchResult info)

This method is called by the optimizer after each step.

It can be used to log status messages, update the user interface, or gracefully terminate the optimizer.

Specified by:

optimizationUpdate in interface OptimizationListener

Parameters:

iter - Number of iterations.

nBFGS - Number of L-BFGS correction vectors.

nfun - Number of function evaluations.

grms - RMS gradient at current solution.

xrms - RMS coordinate change at current solution.

f - Function value at current solution.

df - Change in the function value compared to the previous solution.

angle - Current angle between gradient and search direction.

info - Result of the line search (null at iteration == 0).

Returns:

A return value of false will terminate the optimization.

terminate

public void terminate()

This should be implemented as a blocking interrupt; when the method returns the Terminatable algorithm has reached a clean termination point. For example, between minimize or molecular dynamics steps.

Specified by:

terminate in interface Terminatable