PLMD::NeighborList Class Reference

#include <NeighborList.h>

Public Member Functions
	NeighborList (const std::vector< PLMD::AtomNumber > &list0, const bool &serial, const bool &do_pbc, const PLMD::Pbc &pbc, Communicator &cm, const double &distance=1.0e+30, const unsigned &stride=0)
	NeighborList (const std::vector< PLMD::AtomNumber > &list0, const std::vector< PLMD::AtomNumber > &list1, const bool &serial, const bool &do_pair, const bool &do_pbc, const PLMD::Pbc &pbc, Communicator &cm, const double &distance=1.0e+30, const unsigned &stride=0)
	~NeighborList ()
std::pair< unsigned, unsigned >	getClosePair (unsigned i) const
	Get the i-th pair of the neighbor list. More...
std::pair< AtomNumber, AtomNumber >	getClosePairAtomNumber (unsigned i) const
	Get the i-th pair of AtomNumbers from the neighbor list. More...
std::vector< PLMD::AtomNumber > &	getFullAtomList ()
	Return the list of all atoms. These are needed to rebuild the neighbor list. More...
unsigned	getLastUpdate () const
	Get the last step in which the neighbor list was updated. More...
std::vector< unsigned >	getNeighbors (unsigned i)
	Get the list of neighbors of the i-th atom. 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...
unsigned	getStride () const
	Get the update stride of the neighbor list. More...
void	setLastUpdate (unsigned step)
	Set the step of the last update. More...
unsigned	size () const
	Get the size of the neighbor list. 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...

Private Member Functions
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	initialize ()
	Initialize the neighbor list with all possible pairs. More...
void	setRequestList ()
	Extract the list of atoms from the current list of close pairs. More...

Private Attributes
Communicator &	comm
double	distance_
bool	do_pair_
bool	do_pbc_
std::vector< PLMD::AtomNumber >	fullatomlist_
unsigned	lastupdate_
unsigned	nallpairs_
std::vector< std::pair< unsigned, unsigned > >	neighbors_
unsigned	nlist0_
unsigned	nlist1_
const PLMD::Pbc *	pbc_
bool	reduced
std::vector< PLMD::AtomNumber >	requestlist_
bool	serial_
unsigned	stride_
bool	twolists_

Detailed Description

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

Constructor & Destructor Documentation

NeighborList() [1/2]

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

NeighborList() [2/2]

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

~NeighborList()

PLMD::NeighborList::~NeighborList ( )

inline

Member Function Documentation

getClosePair()

std::pair< unsigned, unsigned > PLMD::NeighborList::getClosePair

(

unsigned

i

)

const

Get the i-th pair of the neighbor list.

getClosePairAtomNumber()

std::pair< AtomNumber, AtomNumber > PLMD::NeighborList::getClosePairAtomNumber

(

unsigned

i

)

const

Get the i-th pair of AtomNumbers from the neighbor list.

getFullAtomList()

std::vector< AtomNumber > & PLMD::NeighborList::getFullAtomList

(

)

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

getIndexPair()

std::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.

getLastUpdate()

unsigned PLMD::NeighborList::getLastUpdate

(

)

const

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

getNeighbors()

std::vector< unsigned > PLMD::NeighborList::getNeighbors

(

unsigned

i

)

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

getReducedAtomList()

std::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.

getStride()

unsigned PLMD::NeighborList::getStride

(

)

const

Get the update stride of the neighbor list.

initialize()

void PLMD::NeighborList::initialize ( )

private

Initialize the neighbor list with all possible pairs.

setLastUpdate()

void PLMD::NeighborList::setLastUpdate

(

unsigned

step

)

Set the step of the last update.

setRequestList()

void PLMD::NeighborList::setRequestList ( )

private

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

size()

unsigned PLMD::NeighborList::size

(

)

const

Get the size of the neighbor list.

update()

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

comm

Communicator& PLMD::NeighborList::comm

private

distance_

double PLMD::NeighborList::distance_

private

do_pair_

bool PLMD::NeighborList::do_pair_

private

do_pbc_

bool PLMD::NeighborList::do_pbc_

private

fullatomlist_

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

private

lastupdate_

unsigned PLMD::NeighborList::lastupdate_

private

nallpairs_

unsigned PLMD::NeighborList::nallpairs_

private

neighbors_

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

private

nlist0_

unsigned PLMD::NeighborList::nlist0_

private

nlist1_

unsigned PLMD::NeighborList::nlist1_

private

pbc_

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

private

reduced

bool PLMD::NeighborList::reduced

private

requestlist_

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

private

serial_

bool PLMD::NeighborList::serial_

private

stride_

unsigned PLMD::NeighborList::stride_

private

twolists_

bool PLMD::NeighborList::twolists_

private

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

• tools/NeighborList.h
• tools/NeighborList.cpp