PLMD::NeighborList Class Reference

#include <NeighborList.h>

Public Types
using	pairAtomNumbers = std::pair< PLMD::AtomNumber, PLMD::AtomNumber >
using	pairIDs = std::pair< unsigned, unsigned >

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 ()
double	distance () const
	Get the distance used to create the neighbor list. More...
pairIDs	getClosePair (unsigned i) const
	Get the i-th pair of the neighbor list. More...
pairAtomNumbers	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
pairIDs	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_ =0
size_t	nallpairs_
std::vector< pairIDs >	neighbors_ {}
size_t	nlist0_ =0
size_t	nlist1_ =0
const PLMD::Pbc *	pbc_
bool	reduced =false
std::vector< PLMD::AtomNumber >	requestlist_ {}
bool	serial_
unsigned	stride_ =0
bool	twolists_

Detailed Description

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

Member Typedef Documentation

pairAtomNumbers

using PLMD::NeighborList::pairAtomNumbers = std::pair<PLMD::AtomNumber,PLMD::AtomNumber>

pairIDs

using PLMD::NeighborList::pairIDs = std::pair<unsigned,unsigned>

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 ( )

default

Member Function Documentation

distance()

double PLMD::NeighborList::distance

(

)

const

Get the distance used to create the neighbor list.

getClosePair()

NeighborList::pairIDs PLMD::NeighborList::getClosePair

(

unsigned

i

)

const

Get the i-th pair of the neighbor list.

getClosePairAtomNumber()

NeighborList::pairAtomNumbers 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()

NeighborList::pairIDs 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_ =0

private

nallpairs_

size_t PLMD::NeighborList::nallpairs_

private

neighbors_

std::vector<pairIDs > PLMD::NeighborList::neighbors_ {}

private

nlist0_

size_t PLMD::NeighborList::nlist0_ =0

private

nlist1_

size_t PLMD::NeighborList::nlist1_ =0

private

pbc_

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

private

reduced

bool PLMD::NeighborList::reduced =false

private

requestlist_

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

private

serial_

bool PLMD::NeighborList::serial_

private

stride_

unsigned PLMD::NeighborList::stride_ =0

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