Simpatico: DdMd::PairList Class Reference

Simpatico v1.10

Detailed Description

A Verlet nonbonded pair list.

A PairList (or Verlet list) is a list of neighboring pairs of Atoms that are separated by a distance less than a specified cutoff.

The allocate() method must be called once before use.

To build or rebuild a PairList, after it has been allocated, one must first build the associated CellList, and then call PairList::build() to build the actual PairList.

A PairIterator object must be used to iterate over all of the pairs in in completed PairList (see documentation of PairIterator for usage).

Definition at line 41 of file ddMd/neighbor/PairList.h.

#include <PairList.h>

Public Member Functions
	PairList ()
	Default constructor. More...

virtual	~PairList ()
	Destructor. More...

Mutators
void	allocate (int atomCapacity, int pairCapacity, double cutoff)
	Allocate memory and set cutoff. More...

void	clear ()
	Reset this to empty state. More...

void	build (CellList &cellList, bool reverseUpdateFlag=false)
	Use a CellList to build a new PairList. More...

Accessors (miscellaneous)
void	begin (PairIterator &iterator) const
	Initialize a PairIterator. More...

int	nAtom () const
	Get the number of primary atoms in the PairList. More...

int	nPair () const
	Get the number of pairs in the PairList. More...

int	pairCapacity () const
	Get the maximum number of pairs. More...

int	atomCapacity () const
	Get the maximum number of primary atoms. More...

bool	isAllocated () const
	Has memory been allocated for this PairList? More...

Statistics
virtual void	computeStatistics (MPI::Intracomm &communicator)
	Compute statistics (reduce from all processors). More...

void	clearStatistics ()
	Clear statistical accumulators (call on all processors). More...

void	outputStatistics (std::ostream &out)
	Output statistics. More...

int	maxNAtom () const
	Get the maximum number of primary atoms encountered thus far. More...

int	maxNPair () const
	Get the maximum number of pairs encountered thus far. More...

int	buildCounter () const
	Return number of times the PairList has been built thus far. More...

Constructor & Destructor Documentation

DdMd::PairList::PairList ( )

Default constructor.

Definition at line 23 of file ddMd/neighbor/PairList.cpp.

DdMd::PairList::~PairList ( )

virtual

Destructor.

Definition at line 41 of file ddMd/neighbor/PairList.cpp.

Member Function Documentation

void DdMd::PairList::allocate	(	int	atomCapacity,
		int	pairCapacity,
		double	cutoff
	)

Allocate memory and set cutoff.

Parameters

atomCapacity	maximum number of primary atoms
pairCapacity	maximum number of pairs
cutoff	pair list cutoff = potential cutoff + skin

Definition at line 47 of file ddMd/neighbor/PairList.cpp.

References atomCapacity(), pairCapacity(), and Util::GArray< Data >::reserve().

Referenced by DdMd::PairPotential::save().

void DdMd::PairList::clear ( )

Reset this to empty state.

Definition at line 63 of file ddMd/neighbor/PairList.cpp.

References Util::GArray< Data >::clear().

void DdMd::PairList::build	(	CellList &	cellList,
		bool	reverseUpdateFlag = `false`
	)

Use a CellList to build a new PairList.

Parameters

cellList	a CellList object that was just built.
reverseUpdateFlag	is reverse communication enabled?

Definition at line 73 of file ddMd/neighbor/PairList.cpp.

References Util::GArray< Data >::append(), DdMd::CellList::begin(), Util::GArray< Data >::clear(), DdMd::Cell::getNeighbors(), isAllocated(), DdMd::Mask::isMasked(), DdMd::Cell::nAtom(), DdMd::Cell::nextCellPtr(), Util::FSArray< Data, Capacity >::size(), Util::GArray< Data >::size(), Util::Vector::square(), Util::Vector::subtract(), DdMd::CellList::update(), and UTIL_THROW.

Referenced by DdMd::PairPotential::buildPairList().

void DdMd::PairList::begin ( PairIterator & iterator ) const

Initialize a PairIterator.

Parameters

iterator a PairList, initialized on output

Definition at line 168 of file ddMd/neighbor/PairList.cpp.

Referenced by DdMd::PairPotentialImpl< Interaction >::computeEnergy(), DdMd::PairPotentialImpl< Interaction >::computeForcesAndStress(), DdMd::PairPotentialImpl< Interaction >::computePairEnergies(), DdMd::PairPotentialImpl< Interaction >::computeStress(), DdMd::PairPotential::nPair(), and DdMd::PairIterator::PairIterator().

int DdMd::PairList::nAtom ( ) const

inline

Get the number of primary atoms in the PairList.

Definition at line 255 of file ddMd/neighbor/PairList.h.

int DdMd::PairList::nPair ( ) const

inline

Get the number of pairs in the PairList.

Definition at line 261 of file ddMd/neighbor/PairList.h.

Referenced by DdMd::PairPotentialImpl< Interaction >::computeEnergy().

int DdMd::PairList::pairCapacity ( ) const

inline

Get the maximum number of pairs.

Definition at line 267 of file ddMd/neighbor/PairList.h.

Referenced by allocate().

int DdMd::PairList::atomCapacity ( ) const

inline

Get the maximum number of primary atoms.

Definition at line 273 of file ddMd/neighbor/PairList.h.

Referenced by allocate().

bool DdMd::PairList::isAllocated ( ) const

inline

Has memory been allocated for this PairList?

Definition at line 297 of file ddMd/neighbor/PairList.h.

Referenced by build().

void DdMd::PairList::computeStatistics ( MPI::Intracomm & communicator )

virtual

Compute statistics (reduce from all processors).

Call on all processors.

Definition at line 185 of file ddMd/neighbor/PairList.cpp.

References Util::Setable< T >::set().

void DdMd::PairList::clearStatistics ( )

Clear statistical accumulators (call on all processors).

Definition at line 210 of file ddMd/neighbor/PairList.cpp.

References Util::Setable< T >::unset().

Referenced by DdMd::Integrator::clear().

void DdMd::PairList::outputStatistics ( std::ostream & out )

Output statistics.

Call on master, after calling computeStatistics on all procs.

Parameters

out	output stream

Definition at line 222 of file ddMd/neighbor/PairList.cpp.

References Util::Setable< T >::value().

int DdMd::PairList::maxNAtom ( ) const

inline

Get the maximum number of primary atoms encountered thus far.

Call only on master.

Definition at line 279 of file ddMd/neighbor/PairList.h.

int DdMd::PairList::maxNPair ( ) const

inline

Get the maximum number of pairs encountered thus far.

Call only on master.

Definition at line 285 of file ddMd/neighbor/PairList.h.

int DdMd::PairList::buildCounter ( ) const

inline

Return number of times the PairList has been built thus far.

Definition at line 291 of file ddMd/neighbor/PairList.h.

Referenced by DdMd::Integrator::outputStatistics().

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