Package ffx.algorithms.mc

Class MDMove

java.lang.Object

ffx.algorithms.mc.MDMove

All Implemented Interfaces:

MCMove

public class MDMove
extends Object
implements MCMove

Use MD as a coordinate based MC move.

Author:

Mallory R. Tollefson

Constructor Summary

Constructors

Constructor	Description
MDMove(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, DynamicsOptions dynamics, long stepsPerCycle, File dynRestartFile)	Constructor for MDMove.

Method Summary

Modifier and Type	Method	Description
double	getEnergyChange()	Get the total energy change for the current move.
double	getInitialKinetic()
double	getInitialPotential()
double	getInitialTotal()
double	getKineticEnergy()	getKineticEnergy.
MolecularDynamics	getMD()
double	getPotentialEnergy()	getPotentialEnergy.
void	move()	Performs the move associated with this MCMove.
void	move(MDVerbosity verbosityLevel)	Performs an MDMove.
void	revertMove()	Reverts the last applied move() call.
void	setMDIntervalSteps(int intervalSteps)
EnumSet<MDWriteAction>	writeFilesForStep(long mdStep, boolean trySnapshot, boolean tryRestart)	Write restart and trajectory files if the provided step matches the frequency.

Methods inherited from class java.lang.Object

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

Constructor Details

MDMove

public MDMove(MolecularAssembly assembly,
 Potential potentialEnergy,
 AlgorithmListener listener,
 DynamicsOptions dynamics,
 long stepsPerCycle,
 @Nullable
 File dynRestartFile)

Constructor for MDMove.

Parameters:

assembly - a MolecularAssembly object.

potentialEnergy - a Potential object.

listener - a AlgorithmListener object.

dynamics - CLI object containing key MD information.

stepsPerCycle - Number of MD steps per MC cycle.

dynRestartFile - File to read restart from.

Method Details

getEnergyChange

public double getEnergyChange()

Get the total energy change for the current move.

Returns:

Total energy change.

getInitialKinetic

public double getInitialKinetic()

getInitialPotential

public double getInitialPotential()

getInitialTotal

public double getInitialTotal()

getKineticEnergy

public double getKineticEnergy()

getKineticEnergy.

Returns:

a double.

getMD

public MolecularDynamics getMD()

getPotentialEnergy

public double getPotentialEnergy()

getPotentialEnergy.

Returns:

a double.

move

public void move()

Performs the move associated with this MCMove.

Specified by:

move in interface MCMove

move

public void move(MDVerbosity verbosityLevel)

Performs an MDMove.

Parameters:

verbosityLevel - How verbose to be.

revertMove

public void revertMove()

Reverts the last applied move() call. Returns the same energy change as described above (with the same sign).

Specified by:

revertMove in interface MCMove

setMDIntervalSteps

public void setMDIntervalSteps(int intervalSteps)

writeFilesForStep

public EnumSet<MDWriteAction> writeFilesForStep(long mdStep,
 boolean trySnapshot,
 boolean tryRestart)

Write restart and trajectory files if the provided step matches the frequency.

Parameters:

mdStep - MD step (not MC cycle number) to write files (if any) for.

trySnapshot - If false, do not write snapshot even if the time step is correct.

tryRestart - If false, do not write a restart file even if the time step is correct.

Returns:

Returns the write actions.