Package ffx.algorithms.mc

Class MolecularMC

java.lang.Object

ffx.algorithms.mc.BoltzmannMC

ffx.algorithms.mc.MolecularMC

All Implemented Interfaces:

MetropolisMC

public class MolecularMC
extends BoltzmannMC

The MolecularMC class is a framework to take Monte Carlo steps on a molecular system. It does not implement an MC algorithm, nor does it implement move sets; it is used to evaluate a single MC step with movements defined by implementations of MCMove.

Since:

1.0

Author:

Michael J. Schnieders, Jacob M. Litman

Field Summary

Fields inherited from class ffx.algorithms.mc.BoltzmannMC

random

Constructor Summary

Constructors

Constructor	Description
MolecularMC(MolecularAssembly molecularAssembly)	Constructs a DefaultMC instance with a molecular assembly and its PotentialEnergy.
MolecularMC(MolecularAssembly molecularAssembly, Potential potential)	Constructs a DefaultMC instance with a molecular assembly and a specific Potential.

Method Summary

Modifier and Type	Method	Description
protected double	currentEnergy()	Must return the current energy of the system.
MolecularAssembly	getMolecularAssembly()	Returns the associated MolecularAssembly.
Potential	getPotential()	Returns the associated Potential.
void	revertStep()	If possible, reverts the last successful Monte Carlo step taken.
protected void	storeState()	Store the state for reverting a move.
String	toString()

Methods inherited from class ffx.algorithms.mc.BoltzmannMC

acceptChance, evaluateMove, evaluateMove, getAccept, getE1, getE2, getTemperature, lastEnergy, mcStep, mcStep, mcStep, mcStep, setPrint, setRandomSeed, setTemperature

Methods inherited from class java.lang.Object

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

Constructor Details

MolecularMC

public MolecularMC(MolecularAssembly molecularAssembly)

Constructs a DefaultMC instance with a molecular assembly and its PotentialEnergy. Fancy footwork will be required if we ever need to use multiple assemblies at once.

Parameters:

molecularAssembly - MolecularAssembly to operate on.

MolecularMC

public MolecularMC(MolecularAssembly molecularAssembly,
 Potential potential)

Constructs a DefaultMC instance with a molecular assembly and a specific Potential.

Parameters:

molecularAssembly - MolecularAssembly to operate on.

potential - a Potential object.

Method Details

getMolecularAssembly

public MolecularAssembly getMolecularAssembly()

Returns the associated MolecularAssembly.

Returns:

MolecularAssembly

getPotential

public Potential getPotential()

Returns the associated Potential.

Returns:

Potential.

revertStep

public void revertStep()

If possible, reverts the last successful Monte Carlo step taken.

toString

public String toString()

Overrides:

toString in class Object

currentEnergy

protected double currentEnergy()

Must return the current energy of the system.

Calculates the energy at the current state; identical to RotamerOptimization method of same name.

Specified by:

currentEnergy in class BoltzmannMC

Returns:

Current system energy

storeState

protected void storeState()

Store the state for reverting a move. Must be properly implemented for revertStep() to function properly; otherwise, the implementation of revertStep() should throw an OperationNotSupportedException.

Specified by:

storeState in class BoltzmannMC