Package ffx.realspace

Class RealSpaceEnergy

java.lang.Object

ffx.realspace.RealSpaceEnergy

All Implemented Interfaces:

CrystalPotential, OptimizationInterface, Potential, LambdaInterface

public class RealSpaceEnergy
extends Object
implements LambdaInterface, CrystalPotential

Combine the Real Space target and chemical potential energy.

Since:

1.0

Author:

Timothy D. Fenn, Michael J. Schnieders

Nested Class Summary

Nested classes/interfaces inherited from interface ffx.numerics.Potential

Potential.STATE, Potential.VARIABLE_TYPE

Field Summary

Fields

Modifier and Type	Field	Description
protected double	lambda	Value of the lambda state variable.

Constructor Summary

Constructors

Constructor	Description
RealSpaceEnergy(RealSpaceData realSpaceData, int nxyz, int nb, int nocc, RefinementMinimize.RefinementMode refinementMode)	Diffraction data energy target

Method Summary

Modifier and Type	Method	Description
boolean	destroy()	Destroys this Potential and frees up any associated resources, particularly worker Threads.
double	energy(double[] x)	The parameters passed in are only for "active" atoms.
double	energyAndGradient(double[] x, double[] g)	This method is called repeatedly to compute the function energy and gradient.
double[]	getAcceleration(double[] acceleration)	getAcceleration.
double[]	getCoordinates(double[] x)	Load the current value of the parameters.
Crystal	getCrystal()	Get the Crystal instance that specifies the periodic boundary conditions and symmetry.
double	getd2EdL2()	Get the 2nd partial derivative of the energy with respect to lambda.
double	getdEdL()	Get the partial derivative of the energy with respect to lambda.
void	getdEdXdL(double[] gradient)	Get the gradient of dEdL with respect to each parameter.
Potential.STATE	getEnergyTermState()	Get the Potential Energy terms that is active.
double	getLambda()	Get the current value of the state variable.
double[]	getMass()	Get the mass of each degree of freedom.
int	getNumberOfVariables()	Get the number of variables being operated on.
double[]	getPreviousAcceleration(double[] previousAcceleration)	getPreviousAcceleration.
RefinementMinimize.RefinementMode	getRefinementMode()	Getter for the field refinementMode.
double[]	getScaling()	Get the problem scaling.
double	getTotalEnergy()	Get the total energy of the system
Potential.VARIABLE_TYPE[]	getVariableTypes()	Get the type of all variables.
double[]	getVelocity(double[] velocity)	getVelocity.
void	setAcceleration(double[] acceleration)	setAcceleration.
void	setCoordinates(double[] x)	Set atomic coordinates positions.
void	setCrystal(Crystal crystal)	Set the Crystal instance that specifies the periodic boundary conditions and symmetry.
void	setEnergyTermState(Potential.STATE state)	Set the Potential Energy terms that should be active.
void	setLambda(double lambda)	Set the current value of the state variable.
void	setPreviousAcceleration(double[] previousAcceleration)	setPreviousAcceleration.
void	setRefinementMode(RefinementMinimize.RefinementMode refinementMode)	Setter for the field refinementMode.
void	setScaling(double[] scaling)	Scale the problem.
void	setVelocity(double[] velocity)	setVelocity.

Methods inherited from class java.lang.Object

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

Methods inherited from interface ffx.potential.bonded.LambdaInterface

dEdLZeroAtEnds

Methods inherited from interface ffx.numerics.OptimizationInterface

energy, energyAndGradient, getUnderlyingPotentials, scaleCoordinates, scaleCoordinatesAndGradient, unscaleCoordinates

Methods inherited from interface ffx.numerics.Potential

getConstraints, writeAdditionalRestartInfo

Field Details

lambda

protected double lambda

Value of the lambda state variable.

Constructor Details

RealSpaceEnergy

public RealSpaceEnergy(RealSpaceData realSpaceData,
 int nxyz,
 int nb,
 int nocc,
 RefinementMinimize.RefinementMode refinementMode)

Diffraction data energy target

Parameters:

realSpaceData - RealSpaceData object to associate with the target

nxyz - number of xyz parameters

nb - number of b factor parameters

nocc - number of occupancy parameters

refinementMode - the RefinementMinimize.RefinementMode type of refinement requested

Method Details

destroy

public boolean destroy()

Destroys this Potential and frees up any associated resources, particularly worker Threads. Default implementation is to return true (assume destruction successful).

Specified by:

destroy in interface OptimizationInterface

Returns:

If resource reclamation successful, or resources already reclaimed.

energy

public double energy(double[] x)

The parameters passed in are only for "active" atoms.

This method is called repeatedly to compute the function energy.

Specified by:

energy in interface OptimizationInterface

Parameters:

x - Input parameters.

Returns:

Function value at x.

energyAndGradient

public double energyAndGradient(double[] x,
 double[] g)

This method is called repeatedly to compute the function energy and gradient.

Specified by:

energyAndGradient in interface OptimizationInterface

Parameters:

x - Input parameters.

g - Output gradients with respect to each parameter.

Returns:

Function value at x.

getAcceleration

public double[] getAcceleration(double[] acceleration)

getAcceleration.

Specified by:

getAcceleration in interface Potential

Parameters:

acceleration - an array of double values.

Returns:

an array of double values.

getCoordinates

public double[] getCoordinates(double[] x)

Load the current value of the parameters. If the supplied array is null or not large enough, a new one should be created. The filled array is returned.

Specified by:

getCoordinates in interface OptimizationInterface

Parameters:

x - Supplied array.

Returns:

The array filled with parameter values.

getCrystal

public Crystal getCrystal()

Get the Crystal instance that specifies the periodic boundary conditions and symmetry.

Specified by:

getCrystal in interface CrystalPotential

Returns:

a Crystal instance.

setCrystal

public void setCrystal(Crystal crystal)

Set the Crystal instance that specifies the periodic boundary conditions and symmetry.

Specified by:

setCrystal in interface CrystalPotential

Parameters:

crystal - a Crystal instance.

getEnergyTermState

public Potential.STATE getEnergyTermState()

Get the Potential Energy terms that is active.

Specified by:

getEnergyTermState in interface Potential

Returns:

the STATE

setEnergyTermState

public void setEnergyTermState(Potential.STATE state)

Set the Potential Energy terms that should be active.

Specified by:

setEnergyTermState in interface Potential

Parameters:

state - include FAST varying energy terms, SLOW varying energy terms or BOTH.

getLambda

public double getLambda()

Get the current value of the state variable.

Specified by:

getLambda in interface LambdaInterface

Returns:

state

setLambda

public void setLambda(double lambda)

Set the current value of the state variable. May be ignored if lambda is not being applied.

Specified by:

setLambda in interface LambdaInterface

Parameters:

lambda - a double.

getMass

public double[] getMass()

Get the mass of each degree of freedom. This is required for molecular dynamics.

Specified by:

getMass in interface Potential

Returns:

The mass of each degree of freedom.

getNumberOfVariables

public int getNumberOfVariables()

Get the number of variables being operated on.

Specified by:

getNumberOfVariables in interface OptimizationInterface

Returns:

Number of variables.

getPreviousAcceleration

public double[] getPreviousAcceleration(double[] previousAcceleration)

getPreviousAcceleration.

Specified by:

getPreviousAcceleration in interface Potential

Parameters:

previousAcceleration - an array of double values.

Returns:

an array of double values.

getRefinementMode

public RefinementMinimize.RefinementMode getRefinementMode()

Getter for the field refinementMode.

Returns:

a RefinementMinimize.RefinementMode object.

setRefinementMode

public void setRefinementMode(RefinementMinimize.RefinementMode refinementMode)

Setter for the field refinementMode.

Parameters:

refinementMode - a RefinementMinimize.RefinementMode object.

getScaling

public double[] getScaling()

Get the problem scaling.

Specified by:

getScaling in interface OptimizationInterface

Returns:

The scaling value used for each variable.

setScaling

public void setScaling(double[] scaling)

Scale the problem. A good choice for optimization is the square root of the median eigenvalue of a typical Hessian.

Specified by:

setScaling in interface OptimizationInterface

Parameters:

scaling - The scaling value to use for each variable.

getTotalEnergy

public double getTotalEnergy()

Get the total energy of the system

Specified by:

getTotalEnergy in interface OptimizationInterface

Returns:

the total energy

getVariableTypes

public Potential.VARIABLE_TYPE[] getVariableTypes()

Get the type of all variables.

Return a reference to each variables type.

Specified by:

getVariableTypes in interface Potential

Returns:

The VARIABLE_TYPE of each variable.

getVelocity

public double[] getVelocity(double[] velocity)

getVelocity.

Specified by:

getVelocity in interface Potential

Parameters:

velocity - an array of double values.

Returns:

an array of double values.

getd2EdL2

public double getd2EdL2()

Get the 2nd partial derivative of the energy with respect to lambda.

Specified by:

getd2EdL2 in interface LambdaInterface

Returns:

d2EdL2

getdEdL

public double getdEdL()

Get the partial derivative of the energy with respect to lambda.

Specified by:

getdEdL in interface LambdaInterface

Returns:

dEdL

getdEdXdL

public void getdEdXdL(double[] gradient)

Get the gradient of dEdL with respect to each parameter.

Specified by:

getdEdXdL in interface LambdaInterface

Parameters:

gradient - - A double array of length the number of parameters in the model (commonly 3 * number of atoms).

setAcceleration

public void setAcceleration(double[] acceleration)

setAcceleration.

Specified by:

setAcceleration in interface Potential

Parameters:

acceleration - an array of double values.

setCoordinates

public void setCoordinates(double[] x)

Set atomic coordinates positions.

Specified by:

setCoordinates in interface OptimizationInterface

Parameters:

x - an array of coordinates for active atoms.

setPreviousAcceleration

public void setPreviousAcceleration(double[] previousAcceleration)

setPreviousAcceleration.

Specified by:

setPreviousAcceleration in interface Potential

Parameters:

previousAcceleration - an array of double values.

setVelocity

public void setVelocity(double[] velocity)

setVelocity.

Specified by:

setVelocity in interface Potential

Parameters:

velocity - an array of double values.