Package ffx.algorithms.optimize.anneal

Class SimulatedAnnealing

java.lang.Object

ffx.algorithms.optimize.anneal.SimulatedAnnealing

All Implemented Interfaces:

Terminatable, Runnable

public class SimulatedAnnealing
extends Object
implements Runnable, Terminatable

Run NVT molecular dynamics at a series of temperatures to optimize a structure.

Since:

1.0

Author:

Michael J. Schnieders, Jacob M. Litman

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	SimulatedAnnealing.Schedules	Represents non-composite AnnealingSchedules known (i.e. not FlatEndAnnealSchedule).

Constructor Summary

Constructors

Constructor	Description
SimulatedAnnealing(MolecularAssembly molecularAssembly, Potential potentialEnergy, AlgorithmListener algorithmListener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator, AnnealingSchedule annealingSchedule, long mdSteps, double timeStep, boolean reInitVelocity, File dynFile)	Constructor for SimulatedAnnealing.

Method Summary

Modifier and Type	Method	Description
void	anneal()	anneal
double	getKineticEnergy()	getKineticEnergy.
double	getPotentialEnergy()	getPotentialEnergy.
double	getTemperature()	getTemperature.
double	getTotalEnergy()	getTotalEnergy.
void	run()
void	setPrintInterval(double printInterval)	Setter for the field printInterval.
void	setRestartFrequency(double restart)	Method to set the Restart Frequency.
void	setSaveFrequency(double save)	Sets the frequency of writing to the trajectory file.
void	setTrajectorySteps(int trajectorySteps)	Sets the number of steps to use per OpenMM cycle.
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

Constructor Details

SimulatedAnnealing

public SimulatedAnnealing(MolecularAssembly molecularAssembly,
 Potential potentialEnergy,
 AlgorithmListener algorithmListener,
 ThermostatEnum requestedThermostat,
 IntegratorEnum requestedIntegrator,
 AnnealingSchedule annealingSchedule,
 long mdSteps,
 double timeStep,
 boolean reInitVelocity,
 File dynFile)

Constructor for SimulatedAnnealing.

Parameters:

molecularAssembly - The Molecular Assembly to operate on.

potentialEnergy - The potential to anneal against.

algorithmListener - The algorithm listener is a callback to UI.

requestedThermostat - The requested thermostat.

requestedIntegrator - The requested integrator.

annealingSchedule - Schedule of temperatures to simulate at.

mdSteps - Steps per SA window.

timeStep - Time step for MD in psec.

reInitVelocity - Request velocities to be reinitialized.

dynFile - Dynamics restart file to begin from.

Method Details

anneal

public void anneal()

anneal

getKineticEnergy

public double getKineticEnergy()

getKineticEnergy.

Returns:

a double.

getPotentialEnergy

public double getPotentialEnergy()

getPotentialEnergy.

Returns:

a double.

getTemperature

public double getTemperature()

getTemperature.

Returns:

a double.

getTotalEnergy

public double getTotalEnergy()

getTotalEnergy.

Returns:

a double.

run

public void run()

This method should only be invoked within the SimulatedAnnealing instance.

Specified by:

run in interface Runnable

setPrintInterval

public void setPrintInterval(double printInterval)

Setter for the field printInterval.

Parameters:

printInterval - a double.

setRestartFrequency

public void setRestartFrequency(double restart)
                         throws IllegalArgumentException

Method to set the Restart Frequency.

Parameters:

restart - the time between writing restart files.

Throws:

IllegalArgumentException - If restart frequency is not a positive number

setSaveFrequency

public void setSaveFrequency(double save)

Sets the frequency of writing to the trajectory file.

Parameters:

save - Frequency (psec^-1) to write out the trajectory.

setTrajectorySteps

public void setTrajectorySteps(int trajectorySteps)

Sets the number of steps to use per OpenMM cycle.

Parameters:

trajectorySteps - Steps per OpenMM cycle.

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