public abstract class ForceField
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
(package private) int |
atomCount |
(package private) MinAtom[] |
atoms |
(package private) int |
bondCount |
(package private) MinBond[] |
bonds |
(package private) java.util.BitSet |
bsFixed |
(package private) Calculations |
calc |
private double[][] |
coordSaved |
private double |
criterion |
(package private) int |
currentStep |
private double |
dE |
private double |
e0 |
(package private) static int |
EANGLE |
(package private) static int |
EBOND |
(package private) static int |
EELECTROSTATIC |
(package private) static int |
ENERGY |
(package private) static int |
EOOP |
(package private) static int |
ESTRBND |
(package private) static int |
ETORSION |
(package private) static int |
EVDW |
(package private) Minimizer |
minimizer |
private int |
stepMax |
Constructor and Description |
---|
ForceField() |
Modifier and Type | Method and Description |
---|---|
private void |
clearForces() |
boolean |
detectExplosion() |
(package private) double |
energyAngle(boolean gradients) |
(package private) double |
energyBond(boolean gradients) |
(package private) double |
energyES(boolean gradients) |
double |
energyFull(boolean gradients,
boolean isSilent) |
(package private) double |
energyOOP(boolean gradients) |
(package private) double |
energyStrBnd(boolean gradients) |
(package private) double |
energyTorsion(boolean gradients) |
(package private) double |
energyVDW(boolean gradients) |
java.lang.String |
getAtomList(java.lang.String title) |
abstract java.util.List |
getAtomTypes() |
int |
getCurrentStep() |
private double |
getDE(MinAtom atom,
int terms,
int i,
double delta) |
double |
getEnergy() |
private double |
getEnergy(int terms,
boolean gradients) |
double |
getEnergyDiff() |
protected abstract java.util.Hashtable |
getFFParameters() |
java.lang.String |
getLogData() |
(package private) double |
getNormalizedDE() |
private java.lang.String |
getUnits() |
private void |
linearSearch() |
private void |
restoreCoordinates() |
private void |
saveCoordinates() |
void |
setConstraints(Minimizer m) |
private void |
setForcesUsingNumericalDerivative(MinAtom atom,
int terms) |
void |
setModel(Minimizer m) |
boolean |
setup() |
void |
steepestDescentInitialize(int stepMax,
double criterion) |
boolean |
steepestDescentTakeNSteps(int n) |
static final int ENERGY
static final int EBOND
static final int EANGLE
static final int ESTRBND
static final int ETORSION
static final int EOOP
static final int EVDW
static final int EELECTROSTATIC
Calculations calc
private double criterion
private double e0
private double dE
int currentStep
private int stepMax
private double[][] coordSaved
int atomCount
int bondCount
MinAtom[] atoms
MinBond[] bonds
java.util.BitSet bsFixed
Minimizer minimizer
private java.lang.String getUnits()
public abstract java.util.List getAtomTypes()
protected abstract java.util.Hashtable getFFParameters()
public void setModel(Minimizer m)
public void setConstraints(Minimizer m)
public boolean setup()
public void steepestDescentInitialize(int stepMax, double criterion)
private void clearForces()
public boolean steepestDescentTakeNSteps(int n)
private double getEnergy(int terms, boolean gradients)
private void setForcesUsingNumericalDerivative(MinAtom atom, int terms)
private double getDE(MinAtom atom, int terms, int i, double delta)
public double energyFull(boolean gradients, boolean isSilent)
double energyStrBnd(boolean gradients)
double energyBond(boolean gradients)
double energyAngle(boolean gradients)
double energyTorsion(boolean gradients)
double energyOOP(boolean gradients)
double energyVDW(boolean gradients)
double energyES(boolean gradients)
private void linearSearch()
private void saveCoordinates()
private void restoreCoordinates()
public boolean detectExplosion()
public int getCurrentStep()
public double getEnergy()
public java.lang.String getAtomList(java.lang.String title)
public double getEnergyDiff()
public java.lang.String getLogData()
double getNormalizedDE()