org.jmol.minimize.forcefield

Class Calculations

abstract class Calculations extends Object

Field Summary
int[][]angles
intatomCount
MinAtom[]atoms
intbondCount
MinBond[]bonds
Vector[]calculations
Vectorconstraints
static intCALC_ANGLE
static intCALC_DISTANCE
static intCALC_ES
static intCALC_MAX
static intCALC_OOP
static intCALC_TORSION
static intCALC_VDW
Vector3dda
Vector3ddb
Vector3ddc
Vector3ddd
static doubleDEG_TO_RAD
ForceFieldff
HashtableffParams
booleangradients
booleanhavePartialCharges
intia
intib
intic
intid
booleanisPreliminary
static doubleKCAL_TO_KJ
StringBufferlogData
booleanlogging
booleanloggingEnabled
double[]partialCharges
static doublePI_OVER_2
static doubleRAD_TO_DEG
booleansilent
int[][]torsions
static doubleTWO_PI
Vector3dv1
Vector3dv2
Vector3dv3
Constructor Summary
Calculations(ForceField ff, MinAtom[] minAtoms, MinBond[] minBonds, int[][] angles, int[][] torsions, double[] partialCharges, Vector constraints)
Method Summary
voidaddForce(Vector3d v, int i, double dE)
voidappendLogData(String s)
doublecalc(int iType, boolean gradients)
abstract doublecompute(int iType, Object[] dataIn)
doubleconstrainQuadratic(double value, double targetValue, double k, int iType)
doubleconstraintEnergy(int iType)
doubleenergyAngle(boolean gradients)
doubleenergyBond(boolean gradients)
doubleenergyES(boolean gradients)
doubleenergyOOP(boolean gradients)
doubleenergyStrBnd(boolean gradients)
doubleenergyTorsion(boolean gradients)
doubleenergyVDW(boolean gradients)
abstract StringgetAtomList(String title)
abstract StringgetDebugFooter(int iType, double energy)
abstract StringgetDebugHeader(int iType)
StringgetLogData()
static FFParamgetParameter(String a, Hashtable ffParams)
abstract StringgetUnit()
booleanhaveParams()
voidsetConstraints(Vector constraints)
voidsetLoggingEnabled(boolean TF)
voidsetParams(Hashtable temp)
voidsetPreliminary(boolean TF)
voidsetSilent(boolean TF)
abstract booleansetupCalculations()
abstract booleansetupElectrostatics()

Field Detail

angles

int[][] angles

atomCount

int atomCount

atoms

MinAtom[] atoms

bondCount

int bondCount

bonds

MinBond[] bonds

calculations

Vector[] calculations

constraints

Vector constraints

CALC_ANGLE

static final int CALC_ANGLE

CALC_DISTANCE

static final int CALC_DISTANCE

CALC_ES

static final int CALC_ES

CALC_MAX

static final int CALC_MAX

CALC_OOP

static final int CALC_OOP

CALC_TORSION

static final int CALC_TORSION

CALC_VDW

static final int CALC_VDW

da

final Vector3d da

db

final Vector3d db

dc

final Vector3d dc

dd

final Vector3d dd

DEG_TO_RAD

public static final double DEG_TO_RAD

ff

ForceField ff

ffParams

public Hashtable ffParams

gradients

boolean gradients

havePartialCharges

boolean havePartialCharges

ia

int ia

ib

int ib

ic

int ic

id

int id

isPreliminary

boolean isPreliminary

KCAL_TO_KJ

static final double KCAL_TO_KJ

logData

StringBuffer logData

logging

boolean logging

loggingEnabled

boolean loggingEnabled

partialCharges

double[] partialCharges

PI_OVER_2

private static final double PI_OVER_2

RAD_TO_DEG

public static final double RAD_TO_DEG

silent

boolean silent

torsions

int[][] torsions

TWO_PI

private static final double TWO_PI

v1

final Vector3d v1

v2

final Vector3d v2

v3

final Vector3d v3

Constructor Detail

Calculations

Calculations(ForceField ff, MinAtom[] minAtoms, MinBond[] minBonds, int[][] angles, int[][] torsions, double[] partialCharges, Vector constraints)

Method Detail

addForce

void addForce(Vector3d v, int i, double dE)

appendLogData

void appendLogData(String s)

calc

private double calc(int iType, boolean gradients)

compute

abstract double compute(int iType, Object[] dataIn)

constrainQuadratic

private double constrainQuadratic(double value, double targetValue, double k, int iType)

constraintEnergy

private double constraintEnergy(int iType)

energyAngle

double energyAngle(boolean gradients)

energyBond

double energyBond(boolean gradients)

energyES

double energyES(boolean gradients)

energyOOP

double energyOOP(boolean gradients)

energyStrBnd

double energyStrBnd(boolean gradients)

energyTorsion

double energyTorsion(boolean gradients)

energyVDW

double energyVDW(boolean gradients)

getAtomList

abstract String getAtomList(String title)

getDebugFooter

abstract String getDebugFooter(int iType, double energy)

getDebugHeader

abstract String getDebugHeader(int iType)

getLogData

public String getLogData()

getParameter

static FFParam getParameter(String a, Hashtable ffParams)

getUnit

abstract String getUnit()

haveParams

boolean haveParams()

setConstraints

public void setConstraints(Vector constraints)

setLoggingEnabled

void setLoggingEnabled(boolean TF)

setParams

void setParams(Hashtable temp)

setPreliminary

void setPreliminary(boolean TF)

setSilent

public void setSilent(boolean TF)

setupCalculations

abstract boolean setupCalculations()

setupElectrostatics

abstract boolean setupElectrostatics()