Grid Class Reference

A fast algorithm for finding all pairs of neighboring atoms. More...

#include <trackers.hpp>

Public Types
typedef GridIterator	iterator
typedef GridPairedIterator	pair_iter

Public Member Functions
vector< uint >	neighbors (uint i)
uint	get_loc (Vec v, Vec bsize)
	Grid (sptr< OriginBox > box, sptr< AtomGroup > atoms, const uint width=1)
	/param width Number of divisions along all axes More...
	Grid (sptr< OriginBox > box, sptr< AtomGroup > atoms, vector< uint > width)
	/param widths Number of divisions along each axis More...
	Grid (sptr< OriginBox > box, sptr< AtomGroup > atoms, const flt minwidth, const flt goalwidth)
	/param minwidth The minimum size of a box, e.g. the widest diameter of a particle. More...
void	optimize_widths ()
	Reshape the grid to optimize number of Atom pairs. More...
void	make_grid ()
	Reshape the grid to optimize number of Atom pairs. More...
iterator	begin ()
	Iterator over pairs. More...
iterator	end ()
pair_iter	pairs (AtomID a)
	Get all pairs of a specific Atom. More...
flt	time_to_edge (Atom &a)
	Find the amount of time until an Atom leaves its current cell. More...
flt	time_to_edge (uint i)
vector< IDPair >	all_pairs ()
	Return a list of all pairs. SLOW function, but useful for debugging. More...
vector< AtomID >	all_pairs (AtomID a)
	Return a list of all neighbors of a given Atom. SLOW function, but useful for debugging. More...
uint	numcells (uint i)
uint	numcells ()

Public Attributes
sptr< OriginBox >	box
sptr< AtomGroup >	atoms
flt	minwidth
	minwidth is minimum size of a box, in real units. More...
flt	goalwidth
	goalwidth is how many atoms per box (goal). More...
uint	widths [NDIM]
	Number of box divisions per dimension. More...
vector< set< AtomID > >	gridlocs
	Atoms in each grid location. More...

Friends
class	GridIterator
class	GridPairedIterator

Detailed Description

A fast algorithm for finding all pairs of neighboring atoms.

A Grid splits the OriginBox into "cells", where no cell is narrower than any Atom. For any given Atom, all atoms within the same cell or any neighboring cell are considered "neighbors".

Member Typedef Documentation

typedef GridIterator Grid::iterator

typedef GridPairedIterator Grid::pair_iter

Constructor & Destructor Documentation

Grid::Grid	(	sptr< OriginBox >	box,
		sptr< AtomGroup >	atoms,
		const uint	width = 1
	)

/param width Number of divisions along all axes

Grid::Grid	(	sptr< OriginBox >	box,
		sptr< AtomGroup >	atoms,
		vector< uint >	width
	)

/param widths Number of divisions along each axis

Grid::Grid	(	sptr< OriginBox >	box,
		sptr< AtomGroup >	atoms,
		const flt	minwidth,
		const flt	goalwidth
	)

/param minwidth The minimum size of a box, e.g. the widest diameter of a particle.

/param goalwidth Number of atoms to try and fit per box.

Member Function Documentation

vector< IDPair > Grid::all_pairs

(

)

Return a list of all pairs. SLOW function, but useful for debugging.

vector< AtomID > Grid::all_pairs

(

AtomID

a

)

Return a list of all neighbors of a given Atom. SLOW function, but useful for debugging.

Grid::iterator Grid::begin

(

)

Iterator over pairs.

Grid::iterator Grid::end

(

)

uint Grid::get_loc	(	Vec	v,
		Vec	bsize
	)

void Grid::make_grid

(

)

Reshape the grid to optimize number of Atom pairs.

vector< uint > Grid::neighbors

(

uint

i

)

uint Grid::numcells ( uint  i )

inline

uint Grid::numcells ( )

inline

void Grid::optimize_widths

(

)

Reshape the grid to optimize number of Atom pairs.

No-op if minwidth <= 1 or goalwidth <= 0.

Grid::pair_iter Grid::pairs

(

AtomID

a

)

Get all pairs of a specific Atom.

flt Grid::time_to_edge

(

Atom &

a

)

Find the amount of time until an Atom leaves its current cell.

flt Grid::time_to_edge ( uint  i )

inline

Friends And Related Function Documentation

friend class GridIterator

friend

friend class GridPairedIterator

friend

Member Data Documentation

sptr<AtomGroup> Grid::atoms

sptr<OriginBox> Grid::box

flt Grid::goalwidth

goalwidth is how many atoms per box (goal).

See minwidth.

vector<set<AtomID> > Grid::gridlocs

Atoms in each grid location.

flt Grid::minwidth

minwidth is minimum size of a box, in real units.

This is used to calculate the widths of new boxes in optimize_widths().

May be 0 or negative, to indicate that optimize_widths() should never change the box sizes.

uint Grid::widths[NDIM]

Number of box divisions per dimension.

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

• src/trackers.hpp
• src/trackers.cpp