A class that implements neighbor lists from two lists or a single list of atoms. More...

#include <NeighborList.h>

Public Member Functions
	NeighborList (const std::vector< PLMD::AtomNumber > &list0, const std::vector< PLMD::AtomNumber > &list1, const bool &do_pair, const bool &do_pbc, const PLMD::Pbc &pbc, const double &distance=1.0e+30, const unsigned &stride=0)

	NeighborList (const std::vector< PLMD::AtomNumber > &list0, const bool &do_pbc, const PLMD::Pbc &pbc, const double &distance=1.0e+30, const unsigned &stride=0)

std::vector< PLMD::AtomNumber > &	getFullAtomList ()
	Return the list of all atoms. These are needed to rebuild the neighbor list. More...

std::vector< PLMD::AtomNumber > &	getReducedAtomList ()
	Update the indexes in the neighbor list to match the ordering in the new positions array and return the new list of atoms that must be requested to the main code. More...

void	update (const std::vector< PLMD::Vector > &positions)
	Update the neighbor list and prepare the new list of atoms that will be requested to the main code. More...

unsigned	getStride () const
	Get the update stride of the neighbor list. More...

unsigned	getLastUpdate () const
	Get the last step in which the neighbor list was updated. More...

void	setLastUpdate (unsigned step)
	Set the step of the last update. More...

unsigned	size () const
	Get the size of the neighbor list. More...

std::pair< unsigned, unsigned >	getClosePair (unsigned i) const
	Get the i-th pair of the neighbor list. More...

std::vector< unsigned >	getNeighbors (unsigned i)
	Get the list of neighbors of the i-th atom. More...

	~NeighborList ()

Private Member Functions
void	initialize ()
	Initialize the neighbor list with all possible pairs. More...

std::pair< unsigned, unsigned >	getIndexPair (unsigned i)
	Return the pair of indexes in the positions array of the two atoms forming the i-th pair among all possible pairs. More...

void	setRequestList ()
	Extract the list of atoms from the current list of close pairs. More...

Private Attributes
bool	reduced

bool	do_pair_

bool	do_pbc_

bool	twolists_

const PLMD::Pbc *	pbc_

std::vector< PLMD::AtomNumber >	fullatomlist_

std::vector< PLMD::AtomNumber >	requestlist_

std::vector< std::pair< unsigned, unsigned > >	neighbors_

double	distance_

unsigned	stride_

unsigned	nlist0_

unsigned	nlist1_

unsigned	nallpairs_

unsigned	lastupdate_

Detailed Description

A class that implements neighbor lists from two lists or a single list of atoms.

Constructor & Destructor Documentation

PLMD::NeighborList::NeighborList	(	const std::vector< PLMD::AtomNumber > &	list0,
		const std::vector< PLMD::AtomNumber > &	list1,
		const bool &	do_pair,
		const bool &	do_pbc,
		const PLMD::Pbc &	pbc,
		const double &	distance = `1.0e+30`,
		const unsigned &	stride = `0`
	)

PLMD::NeighborList::NeighborList	(	const std::vector< PLMD::AtomNumber > &	list0,
		const bool &	do_pbc,
		const PLMD::Pbc &	pbc,
		const double &	distance = `1.0e+30`,
		const unsigned &	stride = `0`
	)

PLMD::NeighborList::~NeighborList ( )

inline

Member Function Documentation

pair< unsigned, unsigned > PLMD::NeighborList::getClosePair ( unsigned i ) const

Get the i-th pair of the neighbor list.

vector< AtomNumber > & PLMD::NeighborList::getFullAtomList ( )

Return the list of all atoms. These are needed to rebuild the neighbor list.

pair< unsigned, unsigned > PLMD::NeighborList::getIndexPair ( unsigned i )

private

Return the pair of indexes in the positions array of the two atoms forming the i-th pair among all possible pairs.

unsigned PLMD::NeighborList::getLastUpdate ( ) const

Get the last step in which the neighbor list was updated.

vector< unsigned > PLMD::NeighborList::getNeighbors ( unsigned i )

Get the list of neighbors of the i-th atom.

vector< AtomNumber > & PLMD::NeighborList::getReducedAtomList ( )

Update the indexes in the neighbor list to match the ordering in the new positions array and return the new list of atoms that must be requested to the main code.

unsigned PLMD::NeighborList::getStride ( ) const

Get the update stride of the neighbor list.

void PLMD::NeighborList::initialize ( )

private

Initialize the neighbor list with all possible pairs.

void PLMD::NeighborList::setLastUpdate ( unsigned step )

Set the step of the last update.

void PLMD::NeighborList::setRequestList ( )

private

Extract the list of atoms from the current list of close pairs.

unsigned PLMD::NeighborList::size ( ) const

Get the size of the neighbor list.

void PLMD::NeighborList::update ( const std::vector< PLMD::Vector > & positions )

Update the neighbor list and prepare the new list of atoms that will be requested to the main code.

Member Data Documentation

double PLMD::NeighborList::distance_

private

bool PLMD::NeighborList::do_pair_

private

bool PLMD::NeighborList::do_pbc_

private

std::vector<PLMD::AtomNumber> PLMD::NeighborList::fullatomlist_

private

unsigned PLMD::NeighborList::lastupdate_

private

unsigned PLMD::NeighborList::nallpairs_

private

std::vector<std::pair<unsigned,unsigned> > PLMD::NeighborList::neighbors_

private

unsigned PLMD::NeighborList::nlist0_

private

unsigned PLMD::NeighborList::nlist1_

private

const PLMD::Pbc* PLMD::NeighborList::pbc_

private

bool PLMD::NeighborList::reduced

private

std::vector<PLMD::AtomNumber> PLMD::NeighborList::requestlist_

private

unsigned PLMD::NeighborList::stride_

private

bool PLMD::NeighborList::twolists_

private

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

tools/NeighborList.h
tools/NeighborList.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation