Package ffx.potential

Class ANIEnergy

java.lang.Object

ffx.potential.ANIEnergy

All Implemented Interfaces:

OptimizationInterface, Potential, LambdaInterface

public class ANIEnergy
extends Object
implements Potential, LambdaInterface

Nested Class Summary

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

Potential.STATE, Potential.VARIABLE_TYPE

Constructor Summary

Constructors

Constructor	Description
ANIEnergy(MolecularAssembly molecularAssembly)

Method Summary

Modifier and Type	Method	Description
double	energy(boolean gradient, boolean print)	Compute the ANI energy and gradint.
double	energy(double[] x)	This method is called repeatedly to compute the function energy.
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[] parameters)	Load the current value of the parameters.
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.
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	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	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

destroy, energy, energyAndGradient, getUnderlyingPotentials, scaleCoordinates, scaleCoordinatesAndGradient, unscaleCoordinates

Methods inherited from interface ffx.numerics.Potential

getConstraints, writeAdditionalRestartInfo

Constructor Details

ANIEnergy

public ANIEnergy(MolecularAssembly molecularAssembly)

Method Details

energy

public double energy(boolean gradient,
 boolean print)

Compute the ANI energy and gradint.

Parameters:

gradient - If true, compute the gradient.

print - If true, turn on extra printing.

Returns:

The ANI energy.

energy

public double energy(double[] x)

Description copied from interface: OptimizationInterface

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)

Description copied from interface: OptimizationInterface

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)

Description copied from interface: Potential

getAcceleration.

Specified by:

getAcceleration in interface Potential

Parameters:

acceleration - an array of

invalid reference

double

objects.

Returns:

an array of

invalid reference

double

objects.

getCoordinates

public double[] getCoordinates(double[] parameters)

Description copied from interface: OptimizationInterface

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:

parameters - Supplied array.

Returns:

The array filled with parameter values.

getEnergyTermState

public Potential.STATE getEnergyTermState()

Description copied from interface: Potential

Get the Potential Energy terms that is active.

Specified by:

getEnergyTermState in interface Potential

Returns:

the STATE

setEnergyTermState

public void setEnergyTermState(Potential.STATE state)

Description copied from interface: Potential

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.

getMass

public double[] getMass()

Description copied from interface: Potential

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()

Description copied from interface: OptimizationInterface

Get the number of variables being operated on.

Specified by:

getNumberOfVariables in interface OptimizationInterface

Returns:

Number of variables.

getPreviousAcceleration

public double[] getPreviousAcceleration(double[] previousAcceleration)

Description copied from interface: Potential

getPreviousAcceleration.

Specified by:

getPreviousAcceleration in interface Potential

Parameters:

previousAcceleration - an array of

invalid reference

double

objects.

Returns:

an array of

invalid reference

double

objects.

getScaling

public double[] getScaling()

Description copied from interface: OptimizationInterface

Get the problem scaling.

Specified by:

getScaling in interface OptimizationInterface

Returns:

The scaling value used for each variable.

setScaling

public void setScaling(double[] scaling)

Description copied from interface: OptimizationInterface

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()

Description copied from interface: OptimizationInterface

Get the total energy of the system

Specified by:

getTotalEnergy in interface OptimizationInterface

Returns:

the total energy

getVariableTypes

public Potential.VARIABLE_TYPE[] getVariableTypes()

Description copied from interface: Potential

Get the type of all variables.

Specified by:

getVariableTypes in interface Potential

Returns:

The VARIABLE_TYPE of each variable.

getVelocity

public double[] getVelocity(double[] velocity)

Description copied from interface: Potential

getVelocity.

Specified by:

getVelocity in interface Potential

Parameters:

velocity - an array of

invalid reference

double

objects.

Returns:

an array of

invalid reference

double

objects.

setAcceleration

public void setAcceleration(double[] acceleration)

Description copied from interface: Potential

setAcceleration.

Specified by:

setAcceleration in interface Potential

Parameters:

acceleration - an array of

invalid reference

double

objects.

setPreviousAcceleration

public void setPreviousAcceleration(double[] previousAcceleration)

Description copied from interface: Potential

setPreviousAcceleration.

Specified by:

setPreviousAcceleration in interface Potential

Parameters:

previousAcceleration - an array of

invalid reference

double

objects.

setVelocity

public void setVelocity(double[] velocity)

Description copied from interface: Potential

setVelocity.

Specified by:

setVelocity in interface Potential

Parameters:

velocity - an array of

invalid reference

double

objects.

getLambda

public double getLambda()

Description copied from interface: LambdaInterface

Get the current value of the state variable.

Specified by:

getLambda in interface LambdaInterface

Returns:

state

setLambda

public void setLambda(double lambda)

Description copied from interface: LambdaInterface

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.

getd2EdL2

public double getd2EdL2()

Description copied from interface: LambdaInterface

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

Specified by:

getd2EdL2 in interface LambdaInterface

Returns:

d2EdL2

getdEdL

public double getdEdL()

Description copied from interface: LambdaInterface

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)

Description copied from interface: LambdaInterface

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).