PLMD::LinkCells Class Reference

A class for doing link cells. More...

#include <LinkCells.h>

Public Member Functions
	LinkCells (Communicator &comm)
bool	enabled () const
	Have the link cells been enabled. More...
void	setCutoff (const double &lcut)
	Set the value of the cutoff. More...
double	getCutoff () const
	Get the value of the cutoff. More...
void	buildCellLists (const std::vector< Vector > &pos, const std::vector< unsigned > &indices, const Pbc &pbc)
	Build the link cell lists. More...
void	retrieveNeighboringAtoms (const Vector &pos, unsigned &natomsper, std::vector< unsigned > &atoms) const
	Find a list of relevant atoms. More...

Private Member Functions
std::vector< unsigned >	findMyCell (const Vector &pos) const
	Find the cell in which this position is contained. More...
unsigned	findCell (const Vector &pos) const
	Find the cell in which this position is contained. More...

Private Attributes
Communicator &	comm
	Symbolic link to plumed communicator. More...
bool	cutoffwasset
	Check that the link cells were set up correctly. More...
double	link_cutoff
	The cutoff to use for the sizes of the cells. More...
Pbc	mypbc
	The pbc we are using for link cells. More...
std::vector< unsigned >	ncells
	The number of cells in each direction. More...
std::vector< unsigned >	nstride
	The number of cells to stride through to get the link cells. More...
std::vector< unsigned >	allcells
	The list of cells each atom is inside. More...
std::vector< unsigned >	lcell_starts
	The start of each block corresponding to each link cell. More...
std::vector< unsigned >	lcell_tots
	The number of atoms in each link cell. More...
std::vector< unsigned >	lcell_lists
	The atoms ordered by link cells. More...

Detailed Description

A class for doing link cells.

Constructor & Destructor Documentation

LinkCells()

PLMD::LinkCells::LinkCells ( Communicator &  comm )

explicit

Member Function Documentation

buildCellLists()

void PLMD::LinkCells::buildCellLists	(	const std::vector< Vector > &	pos,
		const std::vector< unsigned > &	indices,
		const Pbc &	pbc
	)

Build the link cell lists.

enabled()

bool PLMD::LinkCells::enabled ( ) const

inline

Have the link cells been enabled.

findCell()

unsigned PLMD::LinkCells::findCell ( const Vector &  pos ) const

private

Find the cell in which this position is contained.

findMyCell()

std::vector< unsigned > PLMD::LinkCells::findMyCell ( const Vector &  pos ) const

private

Find the cell in which this position is contained.

getCutoff()

double PLMD::LinkCells::getCutoff

(

)

const

Get the value of the cutoff.

retrieveNeighboringAtoms()

void PLMD::LinkCells::retrieveNeighboringAtoms	(	const Vector &	pos,
		unsigned &	natomsper,
		std::vector< unsigned > &	atoms
	)		const

Find a list of relevant atoms.

setCutoff()

void PLMD::LinkCells::setCutoff

(

const double &

lcut

)

Set the value of the cutoff.

Member Data Documentation

allcells

std::vector<unsigned> PLMD::LinkCells::allcells

private

The list of cells each atom is inside.

comm

Communicator& PLMD::LinkCells::comm

private

Symbolic link to plumed communicator.

cutoffwasset

bool PLMD::LinkCells::cutoffwasset

private

Check that the link cells were set up correctly.

lcell_lists

std::vector<unsigned> PLMD::LinkCells::lcell_lists

private

The atoms ordered by link cells.

lcell_starts

std::vector<unsigned> PLMD::LinkCells::lcell_starts

private

The start of each block corresponding to each link cell.

lcell_tots

std::vector<unsigned> PLMD::LinkCells::lcell_tots

private

The number of atoms in each link cell.

link_cutoff

double PLMD::LinkCells::link_cutoff

private

The cutoff to use for the sizes of the cells.

mypbc

Pbc PLMD::LinkCells::mypbc

private

The pbc we are using for link cells.

ncells

std::vector<unsigned> PLMD::LinkCells::ncells

private

The number of cells in each direction.

nstride

std::vector<unsigned> PLMD::LinkCells::nstride

private

The number of cells to stride through to get the link cells.

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

• tools/LinkCells.h
• tools/LinkCells.cpp