MpiIntraspecies1A

java.lang.Object
- etomica.molecule.iterator.MpiIntraspecies1A

All Implemented Interfaces:

AtomsetIterator, AtomsetIteratorDirectable, MoleculesetIterator, MoleculesetIteratorBoxDependent, MoleculesetIteratorPDT, MoleculesetIteratorTargetable, java.io.Serializable
```
public class MpiIntraspecies1A
extends java.lang.Object
implements MoleculesetIteratorPDT, java.io.Serializable
```
Gives pairs formed from the molecules of a species in a box, taking one molecule the species with all of its other molecules. Species is specified at construction and cannot be changed afterwards.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`protected MoleculeIteratorSinglet`	`aiOuter`
`protected MpiInnerVariable`	`apiDown`
`protected MpiInnerVariable`	`apiUp`
`protected MoleculeToMoleculeListSpecies`	`atomToAtomSet`
`protected Box`	`box`
`protected IteratorDirective.Direction`	`direction`
`protected boolean`	`doGoDown`
`protected boolean`	`upListNow`

Constructor Summary

Constructors
Modifier	Constructor	Description
	`MpiIntraspecies1A(ISpecies species)`
`protected`	`MpiIntraspecies1A(ISpecies species, MoleculeToMoleculeListSpecies atomToAtomSet)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`nBody()`	Returns the number of atoms given in each iterate, i.e., the size of the atom array returned with each call to next().
`IMoleculeList`	`next()`	Returns the next AtomSet iterate, or null if hasNext() is false.
`void`	`reset()`	Resets the iterator to loop through its iterates again.
`void`	`setBox(Box newBox)`	Configures iterator to return molecules from the set species in the given box.
`void`	`setDirection(IteratorDirective.Direction direction)`	Specifies the direction, which applies only if iterating pairs with a target atom; otherwise, if all pairs from group are indicated, direction is ignored.
`void`	`setTarget(IMolecule newTargetAtom)`	Sets the target molecule with which all pairs are formed.
`int`	`size()`	Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
`void`	`unset()`	Puts iterator in a state in which hasNext() returns false.

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

- Field Detail
  - aiOuter
```
protected final MoleculeIteratorSinglet aiOuter
```
  - direction
```
protected IteratorDirective.Direction direction
```
  - apiUp
```
protected final MpiInnerVariable apiUp
```
  - apiDown
```
protected final MpiInnerVariable apiDown
```
  - doGoDown
```
protected boolean doGoDown
```
  - upListNow
```
protected boolean upListNow
```
  - box
```
protected Box box
```
  - atomToAtomSet
```
protected MoleculeToMoleculeListSpecies atomToAtomSet
```
- Constructor Detail
  - MpiIntraspecies1A
```
public MpiIntraspecies1A(ISpecies species)
```
    Parameters:
    
    species - species whose molecules will form the pair iterates
  - MpiIntraspecies1A
```
protected MpiIntraspecies1A(ISpecies species,
                            MoleculeToMoleculeListSpecies atomToAtomSet)
```
- Method Detail
  - nBody
```
public int nBody()
```
    Description copied from interface: AtomsetIterator
    
    Returns the number of atoms given in each iterate, i.e., the size of the atom array returned with each call to next().
    
    Specified by:
    
    nBody in interface AtomsetIterator
    
    Returns:
  - setBox
```
public void setBox(Box newBox)
```
    Configures iterator to return molecules from the set species in the given box.
    
    Specified by:
    
    setBox in interface MoleculesetIteratorBoxDependent
    
    Throws:
    
    java.lang.NullPointerException - if the Box is null
  - setTarget
```
public void setTarget(IMolecule newTargetAtom)
```
    Sets the target molecule with which all pairs are formed. Molecule is determined from the atom specified by the atomSet (which must have count() == 1), which may be the molecule itself or an atom that is part of it. If the atom is not in the species given at construction, no iterates will be returned.
    
    Specified by:
    
    setTarget in interface MoleculesetIteratorTargetable
    
    Throws:
    
    java.lang.NullPointerException - if targetAtom is null
  - reset
```
public void reset()
```
    Description copied from interface: AtomsetIterator
    
    Resets the iterator to loop through its iterates again.
    
    Specified by:
    
    reset in interface AtomsetIterator
  - unset
```
public void unset()
```
    Description copied from interface: AtomsetIterator
    
    Puts iterator in a state in which hasNext() returns false.
    
    Specified by:
    
    unset in interface AtomsetIterator
  - setDirection
```
public void setDirection(IteratorDirective.Direction direction)
```
    Specifies the direction, which applies only if iterating pairs with a target atom; otherwise, if all pairs from group are indicated, direction is ignored.
    
    Specified by:
    
    setDirection in interface AtomsetIteratorDirectable
  - size
```
public int size()
```
    Returns the number of atom pairs the iterator will return if reset and iterated in its present state.
    
    Specified by:
    
    size in interface AtomsetIterator
  - next
```
public IMoleculeList next()
```
    Description copied from interface: MoleculesetIterator
    
    Returns the next AtomSet iterate, or null if hasNext() is false.
    
    Specified by:
    
    next in interface MoleculesetIterator

Class MpiIntraspecies1A

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

aiOuter

direction

apiUp

apiDown

doGoDown

upListNow

box

atomToAtomSet

Constructor Detail

MpiIntraspecies1A

MpiIntraspecies1A

Method Detail

nBody

setBox

setTarget

reset

unset

setDirection

size

next