Package ffx.algorithms.optimize

Class PhMinimize

java.lang.Object

ffx.algorithms.optimize.PhMinimize

All Implemented Interfaces:

Terminatable, OptimizationListener

public class PhMinimize
extends Object
implements OptimizationListener, Terminatable

Minimize the potential energy of a system to an RMS gradient per atom convergence criteria.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
protected final AlgorithmListener	algorithmListener	The AlgorithmListener to update the UI.
protected boolean	done	A flag to indicate the algorithm is done.
protected double	energy	The final potential energy.
protected final ExtendedSystem	esvSystem	The extended system that contains the fictitious particle
protected final double[]	grad	The gradient.
protected double[]	gradESV	The gradient.
protected final MolecularAssembly	molecularAssembly	The MolecularAssembly being operated on.
protected final int	n	Number of variables.
protected final int	nESV	Number of Extended System variables.
protected int	nSteps	The number of optimization steps taken.
protected final Potential	potential	The potential energy to optimize.
protected final double[]	scaling	Scaling applied to each variable.
protected int	status	The return status of the optimization.
protected boolean	terminate	A flag to indicate the algorithm should be terminated.
protected double[]	theta	Current value of each Extended System variable.
protected long	time	Minimization time in nanoseconds.
protected final double[]	x	Current value of each variable.

Constructor Summary

Constructors

Constructor	Description
PhMinimize(MolecularAssembly molecularAssembly, AlgorithmListener algorithmListener, ExtendedSystem esvSystem)	Constructor for Minimize.
PhMinimize(MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, ExtendedSystem esvSystem)	Constructor for Minimize.

Method Summary

Modifier and Type	Method	Description
double	getEnergy()	Getter for the field energy.
double	getRMSGradient()	getRMSGradient.
int	getStatus()	Getter for the field status.
Potential	minimizeCoordinates()	minimize
Potential	minimizeCoordinates(double eps)	minimize
Potential	minimizeCoordinates(double eps, int maxIterations)	minimize
Potential	minimizeCoordinates(int m, double eps, int maxIterations)	minimize
Potential	minimizeTitration(double eps, int maxIterations)	minimize
Potential	minimizeTitration(int m, double eps, int maxIterations)	minimize
boolean	optimizationUpdate(int iteration, int nBFGS, int functionEvaluations, double rmsGradient, double rmsCoordinateChange, double energy, double energyChange, double angle, LineSearch.LineSearchResult lineSearchResult)	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

molecularAssembly

protected final MolecularAssembly molecularAssembly

The MolecularAssembly being operated on.

potential

protected final Potential potential

The potential energy to optimize.

esvSystem

protected final ExtendedSystem esvSystem

The extended system that contains the fictitious particle

algorithmListener

protected final AlgorithmListener algorithmListener

The AlgorithmListener to update the UI.

n

protected final int n

Number of variables.

nESV

protected final int nESV

Number of Extended System variables.

x

protected final double[] x

Current value of each variable.

theta

protected double[] theta

Current value of each Extended System variable.

grad

protected final double[] grad

The gradient.

gradESV

protected double[] gradESV

The gradient.

scaling

protected final double[] scaling

Scaling applied to each variable.

done

protected boolean done

A flag to indicate the algorithm is done.

terminate

protected boolean terminate

A flag to indicate the algorithm should be terminated.

time

protected long time

Minimization time in nanoseconds.

energy

protected double energy

The final potential energy.

status

protected int status

The return status of the optimization.

nSteps

protected int nSteps

The number of optimization steps taken.

Constructor Details

PhMinimize

public PhMinimize(MolecularAssembly molecularAssembly,
 Potential potential,
 AlgorithmListener algorithmListener,
 ExtendedSystem esvSystem)

Constructor for Minimize.

Parameters:

molecularAssembly - a MolecularAssembly object.

potential - a Potential object.

algorithmListener - a AlgorithmListener object.

PhMinimize

public PhMinimize(MolecularAssembly molecularAssembly,
 AlgorithmListener algorithmListener,
 ExtendedSystem esvSystem)

Constructor for Minimize.

Parameters:

molecularAssembly - a MolecularAssembly object.

algorithmListener - a AlgorithmListener object.

Method Details

getEnergy

public double getEnergy()

Getter for the field energy.

Returns:

a double.

getRMSGradient

public double getRMSGradient()

getRMSGradient.

Returns:

a double.

getStatus

public int getStatus()

Getter for the field status.

Returns:

The status of the optimization.

minimizeCoordinates

public Potential minimizeCoordinates()

minimize

Returns:

a Potential object.

minimizeCoordinates

public Potential minimizeCoordinates(double eps)

minimize

Parameters:

eps - The convergence criteria.

Returns:

a Potential object.

minimizeCoordinates

public Potential minimizeCoordinates(double eps,
 int maxIterations)

minimize

Parameters:

eps - The convergence criteria.

maxIterations - The maximum number of iterations.

Returns:

a Potential object.

minimizeCoordinates

public Potential minimizeCoordinates(int m,
 double eps,
 int maxIterations)

minimize

Parameters:

m - The number of previous steps used to estimate the Hessian.

eps - The convergence criteria.

maxIterations - The maximum number of iterations.

Returns:

a Potential object.

minimizeTitration

public Potential minimizeTitration(double eps,
 int maxIterations)

minimize

Parameters:

eps - The convergence criteria.

maxIterations - The maximum number of iterations.

Returns:

a Potential object.

minimizeTitration

public Potential minimizeTitration(int m,
 double eps,
 int maxIterations)

minimize

Parameters:

m - The number of previous steps used to estimate the Hessian.

eps - The convergence criteria.

maxIterations - The maximum number of iterations.

Returns:

a Potential object.

optimizationUpdate

public boolean optimizationUpdate(int iteration,
 int nBFGS,
 int functionEvaluations,
 double rmsGradient,
 double rmsCoordinateChange,
 double energy,
 double energyChange,
 double angle,
 LineSearch.LineSearchResult lineSearchResult)

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.

Implement the OptimizationListener interface.

Specified by:

optimizationUpdate in interface OptimizationListener

Parameters:

iteration - Number of iterations.

nBFGS - Number of L-BFGS correction vectors.

functionEvaluations - Number of function evaluations.

rmsGradient - RMS gradient at current solution.

rmsCoordinateChange - RMS coordinate change at current solution.

energy - Function value at current solution.

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

angle - Current angle between gradient and search direction.

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

Returns:

A return value of false will terminate the optimization.

Since:

1.0

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