MDSimulation::CellList Class Reference

This class provides the functionality of a three dimensional cell list. More...

#include <CellListFast.h>

Classes
class	NeighborCellIterator

Public Member Functions
	CellList (const int ps, const int xs, const int ys, const int zs)
	Constructor. More...
const IntVector &	ParticlePosition (const int ps) const
	Get the particle's position in the grid space.
void	ParticlePosition (const int ps, IntVector &v) const
	Return the particle position through a referenced IntVector.
void	MoveParticle (const int ps, const IntVector &mv)
	Moves a particle the set number of cells in each direction. More...
void	SetParticle (const int ps, const int x, const int y, const int z)
	Sets the position of the current particle. More...
void	SetParticle (const int particle, const IntVector &v)
	Sets the position of the current particle. More...
NeighborCellIterator	BeginNeighborCell (const int particle, const IntVector &low, const IntVector &high)
	Create an iterator into the neighboring cells of a given particle. More...
void	Resize (const int ps, const IntVector &ex)
	Resize the cell list to a new volume. More...
void	Clear ()
	Clear out the contents of the CellList. More...
unsigned long	Dims (const int i) const
	Get the number of partitions along each dimension. More...

Detailed Description

This class provides the functionality of a three dimensional cell list.

It provides the ability to quickly find neighboring particles in a three dimensional system. This is accomplished using a three dimensional array to store the contents of each voxel in the system. In that manner, neighbors can be quickly found by examining the current and adjacent voxels.

Author

Spenser Bauman

Constructor & Destructor Documentation

MDSimulation::CellList::CellList	(	const int	ps,
		const int	xs,
		const int	ys,
		const int	zs
	)

Constructor.

Fixes a 3d vector such that it "wraps" around a space with dimensions specified by x, y, and z.

Parameters

v	The vector to be fixed.
x	The size of the x dimension.
y	The size of the y dimension.
z	The size of the z dimension.

Member Function Documentation

CellList::NeighborCellIterator MDSimulation::CellList::BeginNeighborCell	(	const int	particle,
		const IntVector &	low,
		const IntVector &	high
	)

Create an iterator into the neighboring cells of a given particle.

Get an iterator into the neighboring cells of a particle, including the one the current particle is occupying.

Will include the current particle.

Parameters

particle	The particle to get the neighbors for.
low	The low bounds along each axis for traversal. This is relative to the position of the particle with the given index.
high	The high bound along each axis.
particle	The index of the particle to search around.

void MDSimulation::CellList::Clear

(

)

Clear out the contents of the CellList.

This will invalidate all of the particle placements.

unsigned long MDSimulation::CellList::Dims ( const int  i ) const

inline

Get the number of partitions along each dimension.

Parameters

i	The index of the dimension (0 = x, 1 = y, 2 = z).

Returns

The number of partitions along the given dimension.

void MDSimulation::CellList::MoveParticle	(	const int	ps,
		const IntVector &	mv
	)

Moves a particle the set number of cells in each direction.

Parameters

ps	The index of the particle to move.
mv	The displacement in each direction.

void MDSimulation::CellList::Resize	(	const int	ps,
		const IntVector &	ex
	)

Resize the cell list to a new volume.

This will invalidate and clear out the contents of the CellList. Any iterators into this object will be invalidated once this operaton is performed.

Parameters

ps	The number of particles in the new system.
xs	The number of partitions along the x-axis.
ys	The number of partitions along the y-axis.
zs	The number of partitions along the z-axis.

void MDSimulation::CellList::SetParticle	(	const int	ps,
		const int	x,
		const int	y,
		const int	z
	)

Sets the position of the current particle.

Parameters

particle	The index of the particle being set.
x	The x coordinate of the particle.
y	The y coordinate of the particle.
z	The z coordinate of the particle.

void MDSimulation::CellList::SetParticle	(	const int	particle,
		const IntVector &	v
	)

Sets the position of the current particle.

Functions as a convenient adaptor as we often wish to position the particles based on a pre computed vector.

Parameters

particle	The index of the particle being set.
v	Vector representing the coordinates of the particle.

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

• MDSimulation/CellList/CellListFast.h
• MDSimulation/CellList/CellListFast.cpp