org.jmol.minimize.forcefield
Class Calculations
abstract
class
Calculations
extends Object
int[][] angles
int atomCount
int bondCount
Vector[] calculations
Vector constraints
static final int CALC_ANGLE
static final int CALC_DISTANCE
static final int CALC_ES
static final int CALC_MAX
static final int CALC_OOP
static final int CALC_TORSION
static final int CALC_VDW
final Vector3d da
final Vector3d db
final Vector3d dc
final Vector3d dd
public static final double DEG_TO_RAD
public Hashtable ffParams
boolean gradients
boolean havePartialCharges
int ia
int ib
int ic
int id
boolean isPreliminary
static final double KCAL_TO_KJ
StringBuffer logData
boolean logging
boolean loggingEnabled
double[] partialCharges
private static final double PI_OVER_2
public static final double RAD_TO_DEG
boolean silent
int[][] torsions
private static final double TWO_PI
final Vector3d v1
final Vector3d v2
final Vector3d v3
Calculations(
ForceField ff,
MinAtom[] minAtoms,
MinBond[] minBonds, int[][] angles, int[][] torsions, double[] partialCharges, Vector constraints)
void addForce(Vector3d v, int i, double dE)
void appendLogData(String s)
private double calc(int iType, boolean gradients)
abstract double compute(int iType, Object[] dataIn)
private double constrainQuadratic(double value, double targetValue, double k, int iType)
private double constraintEnergy(int iType)
double energyAngle(boolean gradients)
double energyBond(boolean gradients)
double energyES(boolean gradients)
double energyOOP(boolean gradients)
double energyStrBnd(boolean gradients)
double energyTorsion(boolean gradients)
double energyVDW(boolean gradients)
abstract String getAtomList(String title)
abstract String getDebugFooter(int iType, double energy)
abstract String getDebugHeader(int iType)
public String getLogData()
static
FFParam getParameter(String a, Hashtable ffParams)
abstract String getUnit()
boolean haveParams()
public void setConstraints(Vector constraints)
void setLoggingEnabled(boolean TF)
void setParams(Hashtable temp)
void setPreliminary(boolean TF)
public void setSilent(boolean TF)
abstract boolean setupCalculations()
abstract boolean setupElectrostatics()