Package etomica.models.nitrogen

Class CalcNumerical2ndDerivative

java.lang.Object

etomica.models.nitrogen.CalcNumerical2ndDerivative

public class CalcNumerical2ndDerivative
extends java.lang.Object

Determine the second derivative of the atomic/ molecular potential energy w.r.t. to its generalized coordinates, u, where u is defined as the relative deviation of the atom/ molecule from its nominal position The class use class SetToU method to put the atom/ molecule in space and the calculate the change in potential energy. Output is the second derivative of the energy, phi: d2_phi/du_i^2, or d2_phi/(du_i.du_j) For Hessian Matrix: d2_phi/(du_i.du_j) = d2_phi/(du_j.du_i) NOTE: fixedDeltaU in the field is the interval of change. It has to be CAREFULLY picked! Usually, start from a larger value (~0.1, e.g.) and the algorithm will reduce the value. One way to check is to compare d2f/(duiduj) and d2f/(dujdui), of course the smaller the value the better it is.

Field Summary

Fields

Modifier and Type	Field	Description
protected double[][]	a
protected Box	box
protected CoordinateDefinition	coordinateDefinition
protected double	deltaU
protected double	errt
protected double	fac
protected MeterPotentialEnergy	meterPotential

Constructor Summary

Constructors

Constructor	Description
CalcNumerical2ndDerivative(Box box, PotentialMaster potentialMaster, CoordinateDefinition coordinateDefinition)

Method Summary

Modifier and Type	Method	Description
double	computeA(int[] d, double[] u, double deltaU)
double	d2phi_du2(int[] d, double[] u)
double	dphi_du(int[] d, double[] u)
double	f(double[] newU)
double	getFixedDeltaU()
void	setFixedDeltaU(double fixedDeltaU)
void	setToInitialPosition()

Methods inherited from class java.lang.Object

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

Field Detail

coordinateDefinition

protected CoordinateDefinition coordinateDefinition

meterPotential

protected MeterPotentialEnergy meterPotential

box

protected Box box

deltaU

protected double deltaU

errt

protected double errt

fac

protected double fac

a

protected double[][] a

Constructor Detail

CalcNumerical2ndDerivative

public CalcNumerical2ndDerivative(Box box,
                                  PotentialMaster potentialMaster,
                                  CoordinateDefinition coordinateDefinition)

Method Detail

f

public double f(double[] newU)

dphi_du

public double dphi_du(int[] d,
                      double[] u)

d2phi_du2

public double d2phi_du2(int[] d,
                        double[] u)

computeA

public double computeA(int[] d,
                       double[] u,
                       double deltaU)

setToInitialPosition

public void setToInitialPosition()

getFixedDeltaU

public double getFixedDeltaU()

setFixedDeltaU

public void setFixedDeltaU(double fixedDeltaU)