CriterionSimpleMolecular

java.lang.Object
- etomica.nbr.molecule.CriterionSimpleMolecular

All Implemented Interfaces:

MoleculeAgentManager.MoleculeAgentSource, NeighborCriterionMolecular
```
public class CriterionSimpleMolecular
extends java.lang.Object
implements NeighborCriterionMolecular, MoleculeAgentManager.MoleculeAgentSource
```
Simple neighbor criterion based on distance between the two molecules If the molecule moves further than r^2; the update method will kick in to update the neighborlist.

Field Summary

Fields
Modifier and Type	Field	Description
`protected MoleculeAgentManager`	`agentManager`
`protected Boundary`	`boundary`
`protected BoxAgentManager<MoleculeAgentManager>`	`boxAgentManager`
`protected double`	`displacementLimit2`
`protected Vector`	`dr`
`protected double`	`interactionRange`
`protected IMoleculePositionDefinition`	`moleculeSite`
`protected double`	`neighborRadius2`
`protected double`	`r2`
`protected double`	`r2MaxSafe`
`protected double`	`safetyFactor`
`protected Space`	`space`

Constructor Summary

Constructors
Constructor	Description
`CriterionSimpleMolecular(Simulation sim, Space _space, double interactionRange, double neighborRadius)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`accept(IMoleculeList pair)`
`double`	`getInteractionRange()`
`Dimension`	`getInteractionRangeDimension()`
`double`	`getNeighborRange()`
`Dimension`	`getNeighborRangeDimension()`
`double`	`getSafetyFactor()`
`java.lang.Object`	`makeAgent(IMolecule molecule)`	Returns an agent for the given Atom.
`boolean`	`needUpdate(IMolecule molecule)`	Indicates whether the neighbor list for the given molecule should be updated, according to this criterion.
`void`	`releaseAgent(java.lang.Object agent, IMolecule molecule)`	This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements
`void`	`reset(IMolecule molecule)`	Indicates to criterion that given molecule's neighbor list has just been updated, and that properties (e.g., record of molecule's position) used by needUpdate and unsafe() methods should be reset.
`void`	`setBox(Box box)`	Specifies the box where the criterion is being applied.
`void`	`setInteractionRange(double newInteractionRange)`
`void`	`setMoleculePosition(IMoleculePositionDefinition positionDefinition)`
`void`	`setNeighborRange(double r)`
`void`	`setSafetyFactor(double f)`
`boolean`	`unsafe()`	Indicates whether the molecule has changed (e.g.

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

- Field Detail
  - space
```
protected final Space space
```
  - interactionRange
```
protected double interactionRange
```
  - displacementLimit2
```
protected double displacementLimit2
```
  - neighborRadius2
```
protected double neighborRadius2
```
  - dr
```
protected final Vector dr
```
  - boundary
```
protected Boundary boundary
```
  - safetyFactor
```
protected double safetyFactor
```
  - r2
```
protected double r2
```
  - r2MaxSafe
```
protected double r2MaxSafe
```
  - agentManager
```
protected MoleculeAgentManager agentManager
```
  - boxAgentManager
```
protected final BoxAgentManager<MoleculeAgentManager> boxAgentManager
```
  - moleculeSite
```
protected IMoleculePositionDefinition moleculeSite
```
- Constructor Detail
  - CriterionSimpleMolecular
```
public CriterionSimpleMolecular(Simulation sim,
                                Space _space,
                                double interactionRange,
                                double neighborRadius)
```
- Method Detail
  - setMoleculePosition
```
public void setMoleculePosition(IMoleculePositionDefinition positionDefinition)
```
  - setSafetyFactor
```
public void setSafetyFactor(double f)
```
  - getSafetyFactor
```
public double getSafetyFactor()
```
  - setNeighborRange
```
public void setNeighborRange(double r)
```
  - getNeighborRange
```
public double getNeighborRange()
```
  - getNeighborRangeDimension
```
public Dimension getNeighborRangeDimension()
```
  - setInteractionRange
```
public void setInteractionRange(double newInteractionRange)
```
  - getInteractionRange
```
public double getInteractionRange()
```
  - getInteractionRangeDimension
```
public Dimension getInteractionRangeDimension()
```
  - needUpdate
```
public boolean needUpdate(IMolecule molecule)
```
    Description copied from interface: NeighborCriterionMolecular
    
    Indicates whether the neighbor list for the given molecule should be updated, according to this criterion.
    
    Specified by:
    
    needUpdate in interface NeighborCriterionMolecular
    
    Returns:
    
    true if the molecule's list should be updated.
  - setBox
```
public void setBox(Box box)
```
    Description copied from interface: NeighborCriterionMolecular
    
    Specifies the box where the criterion is being applied. Sometimes needed if the criterion depends on features of the box, such as the boundary.
    
    Specified by:
    
    setBox in interface NeighborCriterionMolecular
  - unsafe
```
public boolean unsafe()
```
    Description copied from interface: NeighborCriterionMolecular
    
    Indicates whether the molecule has changed (e.g. moved) by an amount that might have caused its neighbor list to be invalid. If this method returns true, a neighbor list failure may have introduced errors in the calculation.
    
    Specified by:
    
    unsafe in interface NeighborCriterionMolecular
  - accept
```
public boolean accept(IMoleculeList pair)
```
    Specified by:
    
    accept in interface NeighborCriterionMolecular
  - reset
```
public void reset(IMolecule molecule)
```
    Description copied from interface: NeighborCriterionMolecular
    
    Indicates to criterion that given molecule's neighbor list has just been updated, and that properties (e.g., record of molecule's position) used by needUpdate and unsafe() methods should be reset.
    
    Specified by:
    
    reset in interface NeighborCriterionMolecular
  - makeAgent
```
public java.lang.Object makeAgent(IMolecule molecule)
```
    Description copied from interface: MoleculeAgentManager.MoleculeAgentSource
    
    Returns an agent for the given Atom.
    
    Specified by:
    
    makeAgent in interface MoleculeAgentManager.MoleculeAgentSource
  - releaseAgent
```
public void releaseAgent(java.lang.Object agent,
                         IMolecule molecule)
```
    Description copied from interface: MoleculeAgentManager.MoleculeAgentSource
    
    This informs the agent source that the agent is going away and that the agent source should disconnect the agent from other elements
    
    Specified by:
    
    releaseAgent in interface MoleculeAgentManager.MoleculeAgentSource

Class CriterionSimpleMolecular

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

space

interactionRange

displacementLimit2

neighborRadius2

dr

boundary

safetyFactor

r2

r2MaxSafe

agentManager

boxAgentManager

moleculeSite

Constructor Detail

CriterionSimpleMolecular

Method Detail

setMoleculePosition

setSafetyFactor

getSafetyFactor

setNeighborRange

getNeighborRange

getNeighborRangeDimension

setInteractionRange

getInteractionRange

getInteractionRangeDimension

needUpdate

setBox

unsafe

accept

reset

makeAgent

releaseAgent