A class for doing link cells. More...

#include <LinkCells.h>

Classes
struct	CellCollection
	This struct contains the configuration of cells. More...

Public Member Functions
	LinkCells (Communicator &comm)

void	addRequiredCells (const std::array< unsigned, 3 > &celn, unsigned &ncells_required, std::vector< unsigned > &cells_required, bool usePbc=true) const
	Get the list of cells we need to surround the a particular cell.

template<typename T, typename Y>
void	buildCellLists (const T &pos, const Y &indices, const Pbc &pbc)

void	buildCellLists (View< const Vector > pos, View< const unsigned > indices, const Pbc &pbc)
	Build the link cell lists.

unsigned	convertIndicesToIndex (std::array< unsigned, 3 > cellCoord) const
	Take three indices and return the index of the corresponding cell.

void	createNeighborList (unsigned nat, View< const Vector > pos, View< const unsigned > ind, View< const unsigned > tind, View< const Vector > neigh_pos, View< const unsigned > neigh_ind, const Pbc &pbc, unsigned &natoms_per_list, std::vector< std::size_t > &nlist)
	Create a neighbour list for the specified input atoms.

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 (unsigned cellIndex) const
	Returns the "coordinate" of the cell index, assumes that cellIndex < getNumberOfCells()

std::array< unsigned, 3 >	findMyCell (Vector pos) const
	Find the cell in which this position is contained.

const std::array< unsigned, 3 > &	getCellLimits () const
	Get the number of cells per dimension.

template<typename T, typename Y>
CellCollection	getCollection (const T &pos, const Y &indices)

CellCollection	getCollection (View< const Vector > pos, View< const unsigned > indices)

double	getCutoff () const
	Get the value of the cutoff.

unsigned	getMaxInCell () const
	Get the number of atoms in the cell that contains the most atoms.

unsigned	getNumberOfCells () const
	Get the total number of link cells.

void	resetCollection (CellCollection &collection, View< const Vector > pos, View< const unsigned > indices)

void	retrieveAtomsInCells (unsigned ncells_required, View< const unsigned > cells_required, unsigned &natomsper, std::vector< unsigned > &atoms, unsigned avoidIndex=std::numeric_limits< unsigned >::max()) 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 (double lcut)
	Set the value of the cutoff.

void	setupCells (const Pbc &pbc)
	Sets up the cells using the box stored in the Pbc object.

template<typename T>
void	setupCells (const T &pos)

template<typename T>
void	setupCells (const T &pos, const Pbc &pbc)

void	setupCells (View< const Vector > pos)
	Sets up the cells ignoring the pbcs.

void	setupCells (View< const Vector > pos, const Pbc &pbc)
	setups the cells

Private Member Functions
void	createCells (const PLMD::Tensor &)

Private Attributes
std::vector< unsigned >	allcells
	Work vector with the list of cells each atom is inside.

Communicator &	comm
	Symbolic link to plumed communicator.

bool	cutoffwasset =false
	Check that the link cells were set up correctly.

CellCollection	innerCollection
	The collection of indexes per cell created by buildCellLists.

double	link_cutoff =0.0
	The cutoff to use for the sizes of the cells.

Pbc	mypbc
	The pbc we are using for link cells.

std::array< unsigned, 3 >	ncells {0,0,0}
	The number of cells in each direction.

bool	nopbc =false
	Are there periodic boundary conditions setup.

std::array< unsigned, 3 >	nstride {1,0,0}
	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,
		bool	usePbc = true ) const

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

usePbc toggles the use of pbcs for the input cell (celln)

◆ buildCellLists() [1/2]

template<typename T, typename Y>

void PLMD::LinkCells::buildCellLists	(	const T &	pos,
		const Y &	indices,
		const Pbc &	pbc )

inline

◆ buildCellLists() [2/2]

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

Build the link cell lists.

◆ convertIndicesToIndex()

unsigned PLMD::LinkCells::convertIndicesToIndex ( std::array< unsigned, 3 > cellCoord ) const

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

◆ createCells()

void PLMD::LinkCells::createCells ( const PLMD::Tensor & box )

private

◆ createNeighborList()

void PLMD::LinkCells::createNeighborList	(	unsigned	nat,
		View< const Vector >	pos,
		View< const unsigned >	ind,
		View< const unsigned >	tind,
		View< const Vector >	neigh_pos,
		View< const unsigned >	neigh_ind,
		const Pbc &	pbc,
		unsigned &	natoms_per_list,
		std::vector< std::size_t > &	nlist )

Create a neighbour list for the specified input atoms.

Parameters

nat	number of atoms
pos	position of the "central atoms"
ind	indexes of the central atoms
tind	temporary indexes
neigh_pos	position of the candidate neighbors
neigh_ind	indexes of the candidate neighbors
pbc
natoms_per_list	output number of atom per list (mapped on tind) `nlist[tind[i]]=natoms[i]`
nlist	output list of the central atoms plus their neigbors

◆ 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() [1/2]

std::array< unsigned, 3 > PLMD::LinkCells::findMyCell ( unsigned cellIndex ) const

Returns the "coordinate" of the cell index, assumes that cellIndex < getNumberOfCells()

◆ findMyCell() [2/2]

std::array< unsigned, 3 > PLMD::LinkCells::findMyCell ( Vector pos ) const

Find the cell in which this position is contained.

◆ getCellLimits()

const std::array< unsigned, 3 > & PLMD::LinkCells::getCellLimits ( ) const

inline

Get the number of cells per dimension.

◆ getCollection() [1/2]

template<typename T, typename Y>

CellCollection PLMD::LinkCells::getCollection	(	const T &	pos,
		const Y &	indices )

inline

◆ getCollection() [2/2]

LinkCells::CellCollection PLMD::LinkCells::getCollection	(	View< const Vector >	pos,
		View< const unsigned >	indices )

◆ getCutoff()

double PLMD::LinkCells::getCutoff ( ) const

Get the value of the cutoff.

◆ getMaxInCell()

unsigned PLMD::LinkCells::getMaxInCell ( ) const

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

◆ getNumberOfCells()

unsigned PLMD::LinkCells::getNumberOfCells ( ) const

inline

Get the total number of link cells.

◆ resetCollection()

void PLMD::LinkCells::resetCollection	(	LinkCells::CellCollection &	collection,
		View< const Vector >	pos,
		View< const unsigned >	indices )

◆ retrieveAtomsInCells()

void PLMD::LinkCells::retrieveAtomsInCells	(	unsigned	ncells_required,
		View< const unsigned >	cells_required,
		unsigned &	natomsper,
		std::vector< unsigned > &	atoms,
		unsigned	avoidIndex = std::numeric_limits<unsigned>::max() ) 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 ( double lcut )

Set the value of the cutoff.

◆ setupCells() [1/5]

void PLMD::LinkCells::setupCells ( const Pbc & pbc )

Sets up the cells using the box stored in the Pbc object.

◆ setupCells() [2/5]

template<typename T>

void PLMD::LinkCells::setupCells ( const T & pos )

inline

◆ setupCells() [3/5]

template<typename T>

void PLMD::LinkCells::setupCells	(	const T &	pos,
		const Pbc &	pbc )

inline

◆ setupCells() [4/5]

void PLMD::LinkCells::setupCells ( View< const Vector > pos )

Sets up the cells ignoring the pbcs.

This creates an orthogonal box that encloses all the atoms

◆ setupCells() [5/5]

void PLMD::LinkCells::setupCells	(	View< const Vector >	pos,
		const Pbc &	pbc )

setups the cells

Usually it only uses the pbcs if the pbc box is null (three zero vectors) it builds an orthorombic box from the given positions

Member Data Documentation

◆ allcells

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

private

Work vector with the list of cells each atom is inside.

◆ comm

Communicator& PLMD::LinkCells::comm

private

Symbolic link to plumed communicator.

◆ cutoffwasset

bool PLMD::LinkCells::cutoffwasset =false

private

Check that the link cells were set up correctly.

◆ innerCollection

CellCollection PLMD::LinkCells::innerCollection

private

The collection of indexes per cell created by buildCellLists.

◆ link_cutoff

double PLMD::LinkCells::link_cutoff =0.0

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::array<unsigned,3> PLMD::LinkCells::ncells {0,0,0}

private

The number of cells in each direction.

◆ nopbc

bool PLMD::LinkCells::nopbc =false

private

Are there periodic boundary conditions setup.

◆ nstride

std::array<unsigned,3> PLMD::LinkCells::nstride {1,0,0}

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.

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

tools/LinkCells.h
tools/LinkCells.cpp

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ LinkCells()

Member Function Documentation

◆ addRequiredCells()

◆ buildCellLists() [1/2]

◆ buildCellLists() [2/2]

◆ convertIndicesToIndex()

◆ createCells()

◆ createNeighborList()

◆ enabled()

◆ findCell()

◆ findMyCell() [1/2]

◆ findMyCell() [2/2]

◆ getCellLimits()

◆ getCollection() [1/2]

◆ getCollection() [2/2]

◆ getCutoff()

◆ getMaxInCell()

◆ getNumberOfCells()

◆ resetCollection()

◆ retrieveAtomsInCells()

◆ retrieveNeighboringAtoms()

◆ setCutoff()

◆ setupCells() [1/5]

◆ setupCells() [2/5]

◆ setupCells() [3/5]

◆ setupCells() [4/5]

◆ setupCells() [5/5]

Member Data Documentation

◆ allcells

◆ comm

◆ cutoffwasset

◆ innerCollection

◆ link_cutoff

◆ mypbc

◆ ncells

◆ nopbc

◆ nstride

◆ origin