Open Qmin: neighborList Class Reference

take a set of positions, sort those positions according to a cellList, and create data structures of possible neighbors of each particle More...

#include <neighborList.h>

Collaboration diagram for neighborList:

[legend]

Public Member Functions
	neighborList (scalar range, BoxPtr _box, int subGridReduction=1)
	basic constructor has a box and a range More...

void	computeNeighborLists (GPUArray< dVec > &points)
	computethe neighborlist of the set of points passed in More...

virtual void	setGPU (bool _useGPU=true)
	Enforce GPU operation. More...

void	setBox (BoxPtr _bx)

Public Attributes
bool	useGPU
	whether the updater does its work on the GPU or not More...

BoxPtr	Box
	The Box used to compute periodic distances. More...

Index2D	neighborIndexer
	indexes the neighbors of each particle More...

GPUArray< unsigned int >	neighborsPerParticle
	An array containing the number of elements in each neighborhood. More...

GPUArray< int >	particleIndices
	An array containing the indices of neighbors of each particle. So, partilceIndices[neighborIndexer(nn,pp)] gives the index of the nth particle in the neighborhood of particle pp. More...

GPUArray< dVec >	neighborVectors
	An array saving the displacement data associated with each neighbor pair. distances[neighborIndexer(nn,pp)]. More...

GPUArray< scalar >	neighborDistances
	An array saving the distance data associated with each neighbor pair. distances[neighborIndexer(nn,pp)]. More...

int	computations
	An internal counter. More...

scalar	maxRange
	maximum range that neighbors need to be kept at More...

shared_ptr< hyperrectangularCellList >	cellList
	The cell list that will help out. More...

int	Nmax
	the maximum number of particles found in any neighborhood More...

shared_ptr< kernelTuner >	nlistTuner
	kernelTuner object More...

Protected Member Functions
void	computeGPU (GPUArray< dVec > &points)
	compute via GPU More...

void	computeCPU (GPUArray< dVec > &points)
	compute via CPU More...

void	resetNeighborsCPU (int size, int _nmax)
	Initialization and helper without using the GPU. More...

void	resetNeighborsGPU (int size, int _nmax)
	Initialization and helper. More...

Protected Attributes
bool	saveDistanceData
	Save the displacement and distances associated with neihgbors? More...

GPUArray< int >	assist
	first index is Nmax, second is whether to recompute More...

Detailed Description

take a set of positions, sort those positions according to a cellList, and create data structures of possible neighbors of each particle

Constructor & Destructor Documentation

◆ neighborList()

neighborList::neighborList	(	scalar	range,
		BoxPtr	_box,
		int	subGridReduction = `1`
	)

basic constructor has a box and a range

References Box, cellList, maxRange, nlistTuner, Nmax, saveDistanceData, scalar, and useGPU.

Member Function Documentation

◆ computeNeighborLists()

void neighborList::computeNeighborLists ( GPUArray< dVec > & points )

inline

computethe neighborlist of the set of points passed in

References computeCPU(), computeGPU(), and useGPU.

◆ setGPU()

virtual void neighborList::setGPU ( bool _useGPU = true )

inlinevirtual

Enforce GPU operation.

References cellList, and useGPU.

◆ setBox()

void neighborList::setBox ( BoxPtr _bx )

inline

References Box.

◆ computeGPU()

void neighborList::computeGPU ( GPUArray< dVec > & points )

protected

compute via GPU

Parameters

points the set of points to find neighbors for

call gpu function

References assist, Box, cellList, ArrayHandle< T >::data, access_location::device, GPUArray< T >::getNumElements(), gpu_compute_neighbor_list(), access_location::host, indices, maxRange, neighborIndexer, neighborsPerParticle, neighborVectors, nlistTuner, Nmax, NVTXPOP, NVTXPUSH, access_mode::overwrite, particleIndices, access_mode::read, access_mode::readwrite, and resetNeighborsGPU().

Referenced by computeNeighborLists().

◆ computeCPU()

void neighborList::computeCPU ( GPUArray< dVec > & points )

protected

compute via CPU

Parameters

points the set of points to find neighbors for

References Box, cellList, computations, ArrayHandle< T >::data, GPUArray< T >::getNumElements(), access_location::host, indices, maxRange, neighborDistances, neighborIndexer, neighborsPerParticle, neighborVectors, Nmax, norm(), particleIndices, access_mode::read, resetNeighborsCPU(), saveDistanceData, and scalar.

Referenced by computeNeighborLists().

◆ resetNeighborsCPU()

void neighborList::resetNeighborsCPU	(	int	size,
		int	_nmax
	)

protected

Initialization and helper without using the GPU.

References assist, ArrayHandle< T >::data, Index2D::getNumElements(), GPUArray< T >::getNumElements(), access_location::host, make_dVec(), neighborDistances, neighborIndexer, neighborsPerParticle, neighborVectors, Nmax, access_mode::overwrite, particleIndices, GPUArray< T >::resize(), and saveDistanceData.

Referenced by computeCPU().

◆ resetNeighborsGPU()

void neighborList::resetNeighborsGPU	(	int	size,
		int	_nmax
	)

protected

Initialization and helper.

References assist, ArrayHandle< T >::data, access_location::device, Index2D::getNumElements(), GPUArray< T >::getNumElements(), gpu_set_array(), access_location::host, neighborDistances, neighborIndexer, neighborsPerParticle, neighborVectors, Nmax, NVTXPOP, NVTXPUSH, access_mode::overwrite, particleIndices, GPUArray< T >::resize(), and saveDistanceData.

Referenced by computeGPU().

Member Data Documentation

◆ useGPU

bool neighborList::useGPU

whether the updater does its work on the GPU or not

Referenced by computeNeighborLists(), neighborList(), and setGPU().

◆ Box

BoxPtr neighborList::Box

The Box used to compute periodic distances.

Referenced by computeCPU(), computeGPU(), neighborList(), and setBox().

◆ neighborIndexer

Index2D neighborList::neighborIndexer

indexes the neighbors of each particle

Referenced by computeCPU(), computeGPU(), resetNeighborsCPU(), and resetNeighborsGPU().

◆ neighborsPerParticle

GPUArray<unsigned int> neighborList::neighborsPerParticle

An array containing the number of elements in each neighborhood.

Referenced by computeCPU(), computeGPU(), resetNeighborsCPU(), and resetNeighborsGPU().

◆ particleIndices

GPUArray<int> neighborList::particleIndices

An array containing the indices of neighbors of each particle. So, partilceIndices[neighborIndexer(nn,pp)] gives the index of the nth particle in the neighborhood of particle pp.

Referenced by computeCPU(), computeGPU(), resetNeighborsCPU(), and resetNeighborsGPU().