Package etomica.models.nitrogen

Class CalcNumerical2ndDerivativeNitrogen

java.lang.Object

etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen

public class CalcNumerical2ndDerivativeNitrogen
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 MoleculeChildAtomAction	atomGroupActionTranslate
protected Box	box
protected CoordinateDefinitionNitrogen	coordinateDefinition
protected double[]	deltaU
protected Vector	destination
protected boolean	doLatticeSum
protected double	errt
protected double	fac
protected double[][]	generalizedCoord
protected Vector	lsPosition
protected MoleculePositionGeometricCenter	pos
protected P2Nitrogen	potential
protected double	rC
protected AtomActionTranslateBy	translateBy
protected MoleculeActionTranslateTo	translator
protected double	xVecBox
protected double	yVecBox
protected double	zVecBox

Constructor Summary

Constructors

Constructor	Description
CalcNumerical2ndDerivativeNitrogen(Box box, P2Nitrogen potential, CoordinateDefinitionNitrogen coordinateDefinition)
CalcNumerical2ndDerivativeNitrogen(Box box, P2Nitrogen potential, CoordinateDefinitionNitrogen coordinateDefinition, boolean doLatticeSum, double rC)

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

box

protected Box box

pos

protected MoleculePositionGeometricCenter pos

translator

protected MoleculeActionTranslateTo translator

coordinateDefinition

protected CoordinateDefinitionNitrogen coordinateDefinition

potential

protected P2Nitrogen potential

translateBy

protected AtomActionTranslateBy translateBy

atomGroupActionTranslate

protected MoleculeChildAtomAction atomGroupActionTranslate

lsPosition

protected Vector lsPosition

destination

protected Vector destination

errt

protected double errt

fac

protected double fac

xVecBox

protected double xVecBox

yVecBox

protected double yVecBox

zVecBox

protected double zVecBox

rC

protected double rC

deltaU

protected double[] deltaU

a

protected double[][] a

generalizedCoord

protected double[][] generalizedCoord

doLatticeSum

protected boolean doLatticeSum

Constructor Detail

CalcNumerical2ndDerivativeNitrogen

public CalcNumerical2ndDerivativeNitrogen(Box box,
                                          P2Nitrogen potential,
                                          CoordinateDefinitionNitrogen coordinateDefinition)

CalcNumerical2ndDerivativeNitrogen

public CalcNumerical2ndDerivativeNitrogen(Box box,
                                          P2Nitrogen potential,
                                          CoordinateDefinitionNitrogen coordinateDefinition,
                                          boolean doLatticeSum,
                                          double rC)

Method Detail

f

public double f(int[] moleculei,
                double[][] newU)

d2phi_du2

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

computeA

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

setToInitialPosition

public void setToInitialPosition(int[] moleculei)

getFixedDeltaU

public double getFixedDeltaU()

setFixedDeltaU

public void setFixedDeltaU(double fixedDeltaU)