public abstract class ForceField
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
ABI_IJ |
static int |
ABI_JK |
(package private) BS |
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) MinAngle[] |
minAngles |
(package private) int |
minAtomCount |
(package private) MinAtom[] |
minAtoms |
(package private) int |
minBondCount |
(package private) MinBond[] |
minBonds |
(package private) Minimizer |
minimizer |
(package private) MinPosition[] |
minPositions |
(package private) MinTorsion[] |
minTorsions |
java.lang.String |
name |
static int |
R3 |
static int |
R4 |
static int |
R5 |
static int |
R56 |
private int |
stepMax |
static int |
TBI_AB |
static int |
TBI_BC |
static int |
TBI_CD |
Constructor and Description |
---|
ForceField() |
Modifier and Type | Method and Description |
---|---|
abstract void |
clear() |
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 |
energyStretchBend(boolean gradients) |
(package private) double |
energyTorsion(boolean gradients) |
(package private) double |
energyVDW(boolean gradients) |
java.lang.String |
getAtomList(java.lang.String title) |
protected java.io.BufferedReader |
getBufferedReader(java.lang.String resourceName) |
int |
getCurrentStep() |
private double |
getDE(MinAtom atom,
int terms,
int i,
double delta) |
private double |
getEnergies(int terms,
boolean gradients) |
double |
getEnergy() |
double |
getEnergyDiff() |
java.lang.String |
getLogData() |
(package private) double |
getNormalizedDE() |
private void |
linearSearch() |
void |
log(java.lang.String s) |
private void |
restoreCoordinates() |
private void |
saveCoordinates() |
void |
setConstraints(Minimizer m) |
private void |
setForcesUsingNumericalDerivative(MinAtom atom,
int terms) |
abstract boolean |
setModel(BS bsElements,
int elemnoMax) |
protected void |
setModelFields() |
void |
steepestDescentInitialize(int stepMax,
double criterion) |
boolean |
steepestDescentTakeNSteps(int n) |
private float |
toUnits(double energy,
java.lang.String units) |
float |
toUserUnits(double energy) |
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
public static final int ABI_IJ
public static final int ABI_JK
public static final int TBI_AB
public static final int TBI_BC
public static final int TBI_CD
public static final int R3
public static final int R4
public static final int R5
public static final int R56
public java.lang.String name
Calculations calc
private double criterion
private double e0
private double dE
int currentStep
private int stepMax
private double[][] coordSaved
int minAtomCount
int minBondCount
MinAtom[] minAtoms
MinBond[] minBonds
MinAngle[] minAngles
MinTorsion[] minTorsions
MinPosition[] minPositions
BS bsFixed
Minimizer minimizer
public abstract void clear()
public abstract boolean setModel(BS bsElements, int elemnoMax) throws JmolAsyncException
JmolAsyncException
protected void setModelFields()
public void setConstraints(Minimizer m)
public void steepestDescentInitialize(int stepMax, double criterion)
private void clearForces()
public boolean steepestDescentTakeNSteps(int n)
private double getEnergies(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 energyStretchBend(boolean gradients)
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()
public float toUserUnits(double energy)
private float toUnits(double energy, java.lang.String units)
public void log(java.lang.String s)
protected java.io.BufferedReader getBufferedReader(java.lang.String resourceName) throws java.io.IOException
java.io.IOException