MCMoveClusterAtomHSRing

java.lang.Object
- etomica.integrator.mcmove.MCMove
- - etomica.integrator.mcmove.MCMoveBox
  - - etomica.integrator.mcmove.MCMoveBoxStep
    - - etomica.integrator.mcmove.MCMoveAtom
      - etomica.virial.MCMoveClusterAtomHSRing

All Implemented Interfaces:: MCMoveStepDependent

public class MCMoveClusterAtomHSRing
extends MCMoveAtom

Field Summary

Fields
Modifier and Type	Field	Description
`protected Vector`	`axis0`
`protected static double`	`fac10`
`protected static double`	`fac3`
`protected static double`	`fac4`
`protected static double`	`fac5`
`protected static double`	`fac6`
`protected static double`	`fac7`
`protected static double`	`fac8`
`protected static double`	`fac9`
`protected boolean[]`	`inserted`
`protected double[]`	`maxBias`
`protected double[]`	`maxBiasR`
`protected Vector3D`	`normalVector`
`protected double[]`	`normalWidth`
`protected long[]`	`numInserts`
`protected long[]`	`numTrials`
`protected double[]`	`p0`
`int[]`	`seq`
`protected double`	`sigma`
`protected Vector3D`	`standardLensPoint`
`protected long`	`totalCount`

Fields inherited from class etomica.integrator.mcmove.MCMove
moveTracker, nominalFrequency, potential

Fields inherited from class etomica.integrator.mcmove.MCMoveAtom
affectedAtomIterator, atom, atomSource, energyMeter, fixOverlap, random, space, translationVector, uNew, uOld

Fields inherited from class etomica.integrator.mcmove.MCMoveBox
box, perParticleFrequency

Fields inherited from class etomica.integrator.mcmove.MCMoveBoxStep
stepSize, stepSizeMax, stepSizeMin

Constructor Summary

Constructors
Constructor Description

MCMoveClusterAtomHSRing(IRandom random, Space _space, double sigma)

Constructors
Constructor	Description
`MCMoveClusterAtomHSRing(IRandom random, Space _space, double sigma)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`acceptNotify()`	Method called by IntegratorMC in the event that the most recent trial is accepted.
`boolean`	`doTrial()`	Method to perform trial move.
`double`	`getChi(double temperature)`	Chi is the parameter within standard Metropolis Monte Carlo.
`static void`	`main(java.lang.String[] args)`
`protected void`	`randomLensPoint(double d, Vector3D point)`	Returns a randomly selected point from within the lens-shaped region of overlap of two spheres of unit radius separated by a distance d.
`protected void`	`randomLensPoint(Vector r1, Vector r2, Vector3D point, Vector r12, double rSquared)`	Sets a given vector to a point chosen uniformly at random in the lens-shaped region formed by the overlap of two spheres of unit radius located at the given positions r1 and r2.
`protected void`	`randomLensPointInBox(Vector r0, Vector r1, Vector point)`
`void`	`rejectNotify()`	Method called by IntegratorMC in the event that the most recent trial move is rejected.
`static double`	`separationProbability(int n, double r)`	Normalized probability for the separation of the centers of two spheres located at the end of a chain of (n+1) overlapping spheres.
`void`	`setBox(Box box)`	Sets the box on which this move acts.

Methods inherited from class etomica.integrator.mcmove.MCMove
getNominalFrequency, getTracker, setTracker

Methods inherited from class etomica.integrator.mcmove.MCMoveAtom
affectedAtoms, energyChange, getAtomSource, setAtomSource

Methods inherited from class etomica.integrator.mcmove.MCMoveBox
affectedAtoms, energyChange, getBox, isNominallyPerParticleFrequency, toString

Methods inherited from class etomica.integrator.mcmove.MCMoveBoxStep
getStepSize, getStepSizeDimension, getStepSizeMax, getStepSizeMaxDimension, getStepSizeMin, getStepSizeMinDimension, setStepSize, setStepSizeMax, setStepSizeMin

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

- Field Detail
  - standardLensPoint
```
protected final Vector3D standardLensPoint
```
  - normalVector
```
protected final Vector3D normalVector
```
  - maxBias
```
protected double[] maxBias
```
  - maxBiasR
```
protected double[] maxBiasR
```
  - p0
```
protected double[] p0
```
  - seq
```
public int[] seq
```
  - sigma
```
protected final double sigma
```
  - axis0
```
protected final Vector axis0
```
  - normalWidth
```
protected final double[] normalWidth
```
  - inserted
```
protected boolean[] inserted
```
  - numInserts
```
protected long[] numInserts
```
  - numTrials
```
protected long[] numTrials
```
  - totalCount
```
protected long totalCount
```
  - fac3
```
protected static final double fac3
```
  - fac4
```
protected static final double fac4
```
  - fac5
```
protected static final double fac5
```
  - fac6
```
protected static final double fac6
```
  - fac7
```
protected static final double fac7
```
  - fac8
```
protected static final double fac8
```
  - fac9
```
protected static final double fac9
```
    See Also:
    
    Constant Field Values
  - fac10
```
protected static final double fac10
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - MCMoveClusterAtomHSRing
```
public MCMoveClusterAtomHSRing(IRandom random,
                               Space _space,
                               double sigma)
```
- Method Detail
  - setBox
```
public void setBox(Box box)
```
    Description copied from class: MCMoveBox
    
    Sets the box on which this move acts. The box itself can be changed via this method, if desired.
    
    Overrides:
    
    setBox in class MCMoveAtom
  - doTrial
```
public boolean doTrial()
```
    Description copied from class: MCMove
    
    Method to perform trial move. Returns false if the trial could not be attempted, for example if there were no molecules in the box and the trial is designed to displace an atom; returns true otherwise.
    
    Overrides:
    
    doTrial in class MCMoveAtom
  - randomLensPoint
```
protected void randomLensPoint(Vector r1,
                               Vector r2,
                               Vector3D point,
                               Vector r12,
                               double rSquared)
```
    Sets a given vector to a point chosen uniformly at random in the lens-shaped region formed by the overlap of two spheres of unit radius located at the given positions r1 and r2.
    
    Parameters:
    
    r1 - (input) position of one sphere
    
    r2 - (input) position of other sphere
    
    point - (output) random position selected in overlap of the given spheres
    
    Throws:
    
    java.lang.IllegalArgumentException - if given spheres do not overlap
  - randomLensPointInBox
```
protected void randomLensPointInBox(Vector r0,
                                    Vector r1,
                                    Vector point)
```
  - randomLensPoint
```
protected void randomLensPoint(double d,
                               Vector3D point)
```
    Returns a randomly selected point from within the lens-shaped region of overlap of two spheres of unit radius separated by a distance d. The positions of the spheres are on the x-axis, with the midpoint between them at the origin. This is used to select a point where a third sphere could be positioned such that it would overlap the two others, with all having unit diameter.
    
    Parameters:
    
    d - the distance between the spheres
    
    point - (output) the randomly selected point
    
    Throws:
    
    java.lang.IllegalArgumentException - if d > 2, corresponding to non-overlapping spheres
  - separationProbability
```
public static double separationProbability(int n,
                                           double r)
```
    Normalized probability for the separation of the centers of two spheres located at the end of a chain of (n+1) overlapping spheres. All spheres of unit diameter.
    
    Parameters:
    
    n - number of bonds in the chain, such that number of spheres is n+1
    
    r - end-to-end separation
    
    Returns:
    
    value of normalized probability density
  - getChi
```
public double getChi(double temperature)
```
    Description copied from class: MCMove
    
    Chi is the parameter within standard Metropolis Monte Carlo. The probability of accepting the move is given by min(1,chi).
    
    Overrides:
    
    getChi in class MCMoveAtom
    
    Parameters:
    
    temperature - used to compute chi
    
    Returns:
    
    chi
  - rejectNotify
```
public void rejectNotify()
```
    Description copied from class: MCMove
    
    Method called by IntegratorMC in the event that the most recent trial move is rejected. This method should cause the system to be restored to the condition before the most recent call to doTrial.
    
    Overrides:
    
    rejectNotify in class MCMoveAtom
  - acceptNotify
```
public void acceptNotify()
```
    Description copied from class: MCMove
    
    Method called by IntegratorMC in the event that the most recent trial is accepted.
    
    Overrides:
    
    acceptNotify in class MCMoveAtom
  - main
```
public static void main(java.lang.String[] args)
```

Class MCMoveClusterAtomHSRing

Field Summary

Fields inherited from class etomica.integrator.mcmove.MCMove

Fields inherited from class etomica.integrator.mcmove.MCMoveAtom

Fields inherited from class etomica.integrator.mcmove.MCMoveBox

Fields inherited from class etomica.integrator.mcmove.MCMoveBoxStep

Constructor Summary

Method Summary

Methods inherited from class etomica.integrator.mcmove.MCMove

Methods inherited from class etomica.integrator.mcmove.MCMoveAtom

Methods inherited from class etomica.integrator.mcmove.MCMoveBox

Methods inherited from class etomica.integrator.mcmove.MCMoveBoxStep

Methods inherited from class java.lang.Object

Field Detail

standardLensPoint

normalVector

maxBias

maxBiasR

p0

seq

sigma

axis0

normalWidth

inserted

numInserts

numTrials

totalCount

fac3

fac4

fac5

fac6

fac7

fac8

fac9

fac10

Constructor Detail

MCMoveClusterAtomHSRing

Method Detail

setBox

doTrial

randomLensPoint

randomLensPointInBox

randomLensPoint

separationProbability

getChi

rejectNotify

acceptNotify

main