PLMD::LinkCells Class Reference

A class for doing link cells. More...

#include <LinkCells.h>

Public Member Functions
	LinkCells (Communicator &comm)
void	addRequiredCells (const std::array< unsigned, 3 > &celn, unsigned &ncells_required, std::vector< unsigned > &cells_required) const
	Get the list of cells we need to surround the a particular cell.
void	buildCellLists (const std::vector< Vector > &pos, const std::vector< unsigned > &indices, const Pbc &pbc)
	Build the link cell lists.
unsigned	convertIndicesToIndex (const unsigned &nx, const unsigned &ny, const unsigned &nz) const
	Take three indices and return the index of the corresponding cell.
bool	enabled () const
	Have the link cells been enabled.
unsigned	findCell (const Vector &pos) const
	Find the cell index in which this position is contained.
std::array< unsigned, 3 >	findMyCell (const Vector &pos) const
	Find the cell in which this position is contained.
double	getCutoff () const
	Get the value of the cutoff.
unsigned	getMaxInCell () const
	Get the nuumber of atoms in the cell that contains the most atoms.
unsigned	getNumberOfCells () const
	Get the total number of link cells.
void	retrieveAtomsInCells (const unsigned &ncells_required, const std::vector< unsigned > &cells_required, unsigned &natomsper, std::vector< unsigned > &atoms) const
	Retrieve the atoms in a list of cells.
void	retrieveNeighboringAtoms (const Vector &pos, std::vector< unsigned > &cell_list, unsigned &natomsper, std::vector< unsigned > &atoms) const
	Retrieve the atoms we need to consider.
void	setCutoff (const double &lcut)
	Set the value of the cutoff.

Private Attributes
std::vector< unsigned >	allcells
	The list of cells each atom is inside.
Communicator &	comm
	Symbolic link to plumed communicator.
bool	cutoffwasset
	Check that the link cells were set up correctly.
std::vector< unsigned >	lcell_lists
	The atoms ordered by link cells.
std::vector< unsigned >	lcell_starts
	The start of each block corresponding to each link cell.
std::vector< unsigned >	lcell_tots
	The number of atoms in each link cell.
double	link_cutoff
	The cutoff to use for the sizes of the cells.
Pbc	mypbc
	The pbc we are using for link cells.
std::vector< unsigned >	ncells
	The number of cells in each direction.
bool	nopbc
	Are there periodic boundary conditions setup.
std::vector< unsigned >	nstride
	The number of cells to stride through to get the link cells.
Vector	origin
	The location of the origin if we are not using periodic boundary conditions.

Detailed Description

A class for doing link cells.

Constructor & Destructor Documentation

LinkCells()

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

explicit

Member Function Documentation

addRequiredCells()

void PLMD::LinkCells::addRequiredCells	(	const std::array< unsigned, 3 > &	celn,
		unsigned &	ncells_required,
		std::vector< unsigned > &	cells_required ) const

Get the list of cells we need to surround the a particular cell.

buildCellLists()

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

Build the link cell lists.

convertIndicesToIndex()

unsigned PLMD::LinkCells::convertIndicesToIndex	(	const unsigned &	nx,
		const unsigned &	ny,
		const unsigned &	nz ) const

Take three indices and return the index of the corresponding cell.

enabled()

bool PLMD::LinkCells::enabled ( ) const

inline

Have the link cells been enabled.

findCell()

unsigned PLMD::LinkCells::findCell

(

const Vector &

pos

)

const

Find the cell index in which this position is contained.

findMyCell()

std::array< unsigned, 3 > PLMD::LinkCells::findMyCell

(

const Vector &

pos

)

const

Find the cell in which this position is contained.

getCutoff()

double PLMD::LinkCells::getCutoff

(

)

const

Get the value of the cutoff.

getMaxInCell()

unsigned PLMD::LinkCells::getMaxInCell

(

)

const

Get the nuumber of atoms in the cell that contains the most atoms.

getNumberOfCells()

unsigned PLMD::LinkCells::getNumberOfCells ( ) const

inline

Get the total number of link cells.

retrieveAtomsInCells()

void PLMD::LinkCells::retrieveAtomsInCells	(	const unsigned &	ncells_required,
		const std::vector< unsigned > &	cells_required,
		unsigned &	natomsper,
		std::vector< unsigned > &	atoms ) const

Retrieve the atoms in a list of cells.

retrieveNeighboringAtoms()

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

Retrieve the atoms we need to consider.

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.

nopbc

bool PLMD::LinkCells::nopbc

private

Are there periodic boundary conditions setup.

nstride

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

private

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

origin

Vector PLMD::LinkCells::origin

private

The location of the origin if we are not using periodic boundary conditions.

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

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