NeighborList Class Reference

Maintains a Verlet list of "neighbors": molecules within a 'skin radius' of each other. More...

#include <trackers.hpp>

Inheritance diagram for NeighborList:

Public Member Functions
	NeighborList (sptr< Box > box, sptr< AtomVec > atoms, const flt skin)
void	update (Box &newbox)
	Calls update_list(false); exists as a requirement of StateTracker. More...
bool	update_list (bool force=true)
	Update the neighbor list based on current positions. More...
AtomVec &	vec ()
uint	which ()
uint	numpairs ()
void	ignore (AtomID a, AtomID b)
void	add (AtomID a, flt diameter)
uint	ignore_size () const
	Number of pairs currently being ignored. More...
uint	size () const
	Number of atoms in list. More...
vector< IDPair >::iterator	begin ()
vector< IDPair >::iterator	end ()
IDPair	get (uint i)
	~NeighborList ()
Public Member Functions inherited from StateTracker
virtual	~StateTracker ()

Protected Attributes
sptr< Box >	box
flt	skin
SubGroup	atoms
vector< flt >	diameters
vector< IDPair >	curpairs
PairList	ignorepairs
vector< Vec >	lastlocs
uint	updatenum
bool	ignorechanged

Detailed Description

Maintains a Verlet list of "neighbors": molecules within a 'skin radius' of each other.

When the list is updated (update_list(true)), molecules are counted as neighbors if the distance between them is \(d_{ij} < r_i + r_j + R\), where \(r_i\) and \(r_j\) are the radii, and \(R\) is the "skin radius". On "normal" updates (update(box) or update_list(false), All atoms fulfilling the condition \(d_{ij} < r_i + r_j\) are guaranteed to be in the list, but there may be some false positives.

update_list(false) should be called frequently (i.e. every timestep); it checks ( \(O(N)\)) if any two molecules might conceivably overlap by more than a critical distance, and if so, it updates all the neighbor lists.

The NeighborList has an inherent tradeoff, set by the skin radius: If the skin is large, then full updates (which are slow) will be needed less often, but more particles will be considered "neighbors" even when they are not within \(d_{ij} < r_i + r_j\), i.e. there will be more false positives.

Constructor & Destructor Documentation

NeighborList::NeighborList	(	sptr< Box >	box,
		sptr< AtomVec >	atoms,
		const flt	skin
	)

NeighborList::~NeighborList ( )

inline

Member Function Documentation

void NeighborList::add ( AtomID  a, flt  diameter  )

inline

vector<IDPair>::iterator NeighborList::begin ( )

inline

vector<IDPair>::iterator NeighborList::end ( )

inline

IDPair NeighborList::get ( uint  i )

inline

void NeighborList::ignore ( AtomID  a, AtomID  b  )

inline

uint NeighborList::ignore_size ( ) const

inline

Number of pairs currently being ignored.

uint NeighborList::numpairs ( )

inline

uint NeighborList::size ( ) const

inline

Number of atoms in list.

void NeighborList::update ( Box &  newbox )

inlinevirtual

Calls update_list(false); exists as a requirement of StateTracker.

Implements StateTracker.

bool NeighborList::update_list

(

bool

force = true

)

Update the neighbor list based on current positions.

If force, the list is updated immediately \(O(N^2)\); otherwise, NeighborList checks if an update is necessary \(O(N)\), and updates the list if so.

AtomVec& NeighborList::vec ( )

inline

uint NeighborList::which ( )

inline

Member Data Documentation

SubGroup NeighborList::atoms

protected

sptr<Box> NeighborList::box

protected

vector<IDPair> NeighborList::curpairs

protected

vector<flt> NeighborList::diameters

protected

bool NeighborList::ignorechanged

protected

PairList NeighborList::ignorepairs

protected

vector<Vec> NeighborList::lastlocs

protected

flt NeighborList::skin

protected

uint NeighborList::updatenum

protected

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The documentation for this class was generated from the following files:

• src/trackers.hpp
• src/trackers.cpp