java.lang.Object

org.jmol.minimize.forcefield.ForceField

Direct Known Subclasses:: ForceFieldMMFF, ForceFieldUFF

public abstract class ForceField extends Object

Field Summary

Fields

Modifier and Type

Field

Description

static final int

ABI_IJ

static final int

ABI_JK

(package private) javajs.util.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 final int

EANGLE

(package private) static final int

EBOND

(package private) static final int

EELECTROSTATIC

(package private) static final int

ENERGY

(package private) static final int

EOOP

(package private) static final int

ESTRBND

(package private) static final int

ETORSION

(package private) static final 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

String

name

static final int

R3

static final int

R4

static final int

R5

static final int

Raromatic

private int

stepMax

static final int

TBI_AB

static final int

TBI_BC

static final int

TBI_CD

(package private) double

trustRadius
Constructor Summary

Constructors

Constructor

Description

ForceField()
Method Summary

Modifier and Type

Method

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)

String

getAtomList(String title)

protected BufferedReader

getBufferedReader(String resourceName)

int

getCurrentStep()

private double

getDE(MinAtom atom, int terms, int i, double delta)

private double

getEnergies(int terms, boolean gradients)

Get the energy of a given type or types.

double

getEnergy()

double

getEnergyDiff()

String

getLogData()

(package private) double

getNormalizedDE()

private void

linearSearch()

void

log(String s)

private void

restoreCoordinates()

private void

saveCoordinates()

void

setConstraints(Minimizer m)

private void

setForcesUsingNumericalDerivative(MinAtom atom, int terms)

abstract boolean

setModel(javajs.util.BS bsElements, int elemnoMax)

protected void

setModelFields()

void

steepestDescentInitialize(int stepMax, double criterion, double trustRadius)

boolean

steepestDescentTakeNSteps(int n)

private float

toUnits(double energy, String units)

float

toUserUnits(double energy)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- ENERGY
  
  static final int ENERGY
  See Also:
  
  Constant Field Values
- EBOND
  
  static final int EBOND
  See Also:
  
  Constant Field Values
- EANGLE
  
  static final int EANGLE
  See Also:
  
  Constant Field Values
- ESTRBND
  
  static final int ESTRBND
  See Also:
  
  Constant Field Values
- ETORSION
  
  static final int ETORSION
  See Also:
  
  Constant Field Values
- EOOP
  
  static final int EOOP
  See Also:
  
  Constant Field Values
- EVDW
  
  static final int EVDW
  See Also:
  
  Constant Field Values
- EELECTROSTATIC
  
  static final int EELECTROSTATIC
  See Also:
  
  Constant Field Values
- ABI_IJ
  
  public static final int ABI_IJ
  See Also:
  
  Constant Field Values
- ABI_JK
  
  public static final int ABI_JK
  See Also:
  
  Constant Field Values
- TBI_AB
  
  public static final int TBI_AB
  See Also:
  
  Constant Field Values
- TBI_BC
  
  public static final int TBI_BC
  See Also:
  
  Constant Field Values
- TBI_CD
  
  public static final int TBI_CD
  See Also:
  
  Constant Field Values
- R3
  
  public static final int R3
  See Also:
  
  Constant Field Values
- R4
  
  public static final int R4
  See Also:
  
  Constant Field Values
- R5
  
  public static final int R5
  See Also:
  
  Constant Field Values
- Raromatic
  
  public static final int Raromatic
  See Also:
  
  Constant Field Values
- name
  
  public String name
- calc
  
  Calculations calc
- criterion
  
  private double criterion
- e0
  
  private double e0
- dE
  
  private double dE
- currentStep
  
  int currentStep
- stepMax
  
  private int stepMax
- coordSaved
  
  private double[][] coordSaved
- minAtomCount
  
  int minAtomCount
- minBondCount
  
  int minBondCount
- minAtoms
  
  MinAtom[] minAtoms
- minBonds
  
  MinBond[] minBonds
- minAngles
  
  MinAngle[] minAngles
- minTorsions
  
  MinTorsion[] minTorsions
- minPositions
  
  MinPosition[] minPositions
- bsFixed
  
  javajs.util.BS bsFixed
- trustRadius
  
  double trustRadius
- minimizer
  
  Minimizer minimizer
Constructor Details
- ForceField
  
  public ForceField()
Method Details
- clear
  
  public abstract void clear()
- setModel
  
  public abstract boolean setModel(javajs.util.BS bsElements, int elemnoMax) throws JmolAsyncException
  
  Throws:
  
  JmolAsyncException
- setModelFields
  
  protected void setModelFields()
- setConstraints
  
  public void setConstraints(Minimizer m)
- steepestDescentInitialize
  
  public void steepestDescentInitialize(int stepMax, double criterion, double trustRadius)
- clearForces
  
  private void clearForces()
- steepestDescentTakeNSteps
  
  public boolean steepestDescentTakeNSteps(int n)
- getEnergies
  
  private double getEnergies(int terms, boolean gradients)
  
  Get the energy of a given type or types. Note: gradients is always false
  
  Parameters:
  
  terms -
  
  gradients - ignored (false)
  
  Returns:
  
  energy
- setForcesUsingNumericalDerivative
  
  private void setForcesUsingNumericalDerivative(MinAtom atom, int terms)
- getDE
  
  private double getDE(MinAtom atom, int terms, int i, double delta)
- energyFull
  
  public double energyFull(boolean gradients, boolean isSilent)
- energyStretchBend
  
  double energyStretchBend(boolean gradients)
  
  Parameters:
  
  gradients -
  
  Returns:
  
  energy
- energyBond
  
  double energyBond(boolean gradients)
- energyAngle
  
  double energyAngle(boolean gradients)
- energyTorsion
  
  double energyTorsion(boolean gradients)
- energyOOP
  
  double energyOOP(boolean gradients)
- energyVDW
  
  double energyVDW(boolean gradients)
- energyES
  
  double energyES(boolean gradients)
- linearSearch
  
  private void linearSearch()
- saveCoordinates
  
  private void saveCoordinates()
- restoreCoordinates
  
  private void restoreCoordinates()
- detectExplosion
  
  public boolean detectExplosion()
- getCurrentStep
  
  public int getCurrentStep()
- getEnergy
  
  public double getEnergy()
- getAtomList
  
  public String getAtomList(String title)
- getEnergyDiff
  
  public double getEnergyDiff()
- getLogData
  
  public String getLogData()
- getNormalizedDE
  
  double getNormalizedDE()
- toUserUnits
  
  public float toUserUnits(double energy)
- toUnits
  
  private float toUnits(double energy, String units)
- log
  
  public void log(String s)
- getBufferedReader
  
  protected BufferedReader getBufferedReader(String resourceName) throws IOException
  
  Throws:
  
  IOException

Class ForceField

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

ENERGY

EBOND

EANGLE

ESTRBND

ETORSION

EOOP

EVDW

EELECTROSTATIC

ABI_IJ

ABI_JK

TBI_AB

TBI_BC

TBI_CD

R3

R4

R5

Raromatic

name

calc

criterion

e0

dE

currentStep

stepMax

coordSaved

minAtomCount

minBondCount

minAtoms

minBonds

minAngles

minTorsions

minPositions

bsFixed

trustRadius

minimizer

Constructor Details

ForceField

Method Details

clear

setModel

setModelFields

setConstraints

steepestDescentInitialize

clearForces

steepestDescentTakeNSteps

getEnergies

setForcesUsingNumericalDerivative

getDE

energyFull

energyStretchBend

energyBond

energyAngle

energyTorsion

energyOOP

energyVDW

energyES

linearSearch

saveCoordinates

restoreCoordinates

detectExplosion

getCurrentStep

getEnergy

getAtomList

getEnergyDiff

getLogData

getNormalizedDE

toUserUnits

toUnits

log

getBufferedReader