Package ffx.xray

Class RefinementMinimize

java.lang.Object

ffx.xray.RefinementMinimize

All Implemented Interfaces:

Terminatable, OptimizationListener

public class RefinementMinimize
extends Object
implements OptimizationListener, Terminatable

Refinement minimization class using OptimizationListener interface, constructs a RefinementEnergy object for this purpose

Since:

1.0

Author:

Timothy D. Fenn

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	RefinementMinimize.RefinementMode	Different refinement mode selection types.

Field Summary

Fields

Modifier and Type	Field	Description
final RefinementEnergy	refinementEnergy

Constructor Summary

Constructors

Constructor	Description
RefinementMinimize(DataContainer data)	constructor for refinement, assumes coordinates and B factor optimization
RefinementMinimize(DataContainer data, RefinementMinimize.RefinementMode refinementmode)	constructor for refinement
RefinementMinimize(DataContainer data, RefinementMinimize.RefinementMode refinementMode, AlgorithmListener listener)	constructor for refinement

Method Summary

Modifier and Type	Method	Description
Double	getEps()	Getter for the field eps.
int	getNB()	get the number of B factor parameters being fit
int	getNOcc()	get the number of occupancy parameters being fit
int	getNXYZ()	get the number of xyz parameters being fit
RefinementEnergy	minimize()	minimize assuming an eps of 1.0 and Integer.MAX_VALUE cycles
RefinementEnergy	minimize(double eps)	minimize assuming Integer.MAX_VALUE cycles
RefinementEnergy	minimize(double eps, int maxiter)	minimize with input eps and cycles
RefinementEnergy	minimize(int maxiter)	minimize assuming an eps of 1.0 and limited cycles
RefinementEnergy	minimize(int m, double eps, int maxiter)	minimize with input cycles for matrix conditioning, eps and cycles
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.
static RefinementMinimize.RefinementMode	parseMode(String str)	Parse a string into a refinement mode.
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

refinementEnergy

public final RefinementEnergy refinementEnergy

Constructor Details

RefinementMinimize

public RefinementMinimize(DataContainer data)

constructor for refinement, assumes coordinates and B factor optimization

Parameters:

data - input DataContainer that will be used as the model, must contain a RefinementModel

RefinementMinimize

public RefinementMinimize(DataContainer data,
 RefinementMinimize.RefinementMode refinementmode)

constructor for refinement

Parameters:

data - input DataContainer that will be used as the model, must contain a RefinementModel and either DiffractionData or RealSpaceData

refinementmode - RefinementMinimize.RefinementMode for refinement

RefinementMinimize

public RefinementMinimize(DataContainer data,
 RefinementMinimize.RefinementMode refinementMode,
 AlgorithmListener listener)

constructor for refinement

Parameters:

data - input DataContainer that will be used as the model, must contain a RefinementModel and either DiffractionData or RealSpaceData

refinementMode - RefinementMinimize.RefinementMode for refinement

listener - AlgorithmListener a listener for updates

Method Details

parseMode

public static RefinementMinimize.RefinementMode parseMode(String str)

Parse a string into a refinement mode.

Parameters:

str - Refinement mode string.

Returns:

An instance of RefinementMode.

getEps

public Double getEps()

Getter for the field eps.

Returns:

a Double object.

getNB

public int getNB()

get the number of B factor parameters being fit

Returns:

the number of B factor parameters

getNOcc

public int getNOcc()

get the number of occupancy parameters being fit

Returns:

the number of occupancy parameters

getNXYZ

public int getNXYZ()

get the number of xyz parameters being fit

Returns:

the number of xyz parameters

minimize

public RefinementEnergy minimize()

minimize assuming an eps of 1.0 and Integer.MAX_VALUE cycles

Returns:

RefinementEnergy result

minimize

public RefinementEnergy minimize(double eps)

minimize assuming Integer.MAX_VALUE cycles

Parameters:

eps - input gradient rms desired

Returns:

RefinementEnergy result

minimize

public RefinementEnergy minimize(int maxiter)

minimize assuming an eps of 1.0 and limited cycles

Parameters:

maxiter - maximum iterations allowed

Returns:

RefinementEnergy result

minimize

public RefinementEnergy minimize(double eps,
 int maxiter)

minimize with input eps and cycles

Parameters:

eps - input gradient rms desired

maxiter - maximum iterations allowed

Returns:

RefinementEnergy result

minimize

public RefinementEnergy minimize(int m,
 double eps,
 int maxiter)

minimize with input cycles for matrix conditioning, eps and cycles

Parameters:

m - number of cycles of matrix updates

eps - input gradient rms desired

maxiter - maximum iterations allowed

Returns:

RefinementEnergy result

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