Detailed Description

Identifies clusters of molecules, such as micelles.

Definition at line 34 of file ClusterIdentifier.h.

#include <ClusterIdentifier.h>

Public Member Functions
	ClusterIdentifier (System &system)
	Constructor. More...

	~ClusterIdentifier ()
	Destructor. More...

virtual void	initialize (int speciesId, int atomTypeId, double cutoff)
	Clear accumulator. More...

void	identifyClusters ()
	Identify all clusters (main operation). More...

int	nCluster () const
	Get number of clusters. More...

ClusterLink &	link (int moleculeId)
	Get a specific ClusterLink, by id of the associated molecule. More...

Cluster &	cluster (int id)
	Get a specific cluster, indexed in the order identified. More...

bool	isValid () const
	Return true if valid, or throw Exception otherwise. More...

Constructor & Destructor Documentation

McMd::ClusterIdentifier::ClusterIdentifier ( System & system )

Constructor.

Parameters

system reference to parent System object

Definition at line 28 of file ClusterIdentifier.cpp.

McMd::ClusterIdentifier::~ClusterIdentifier ( )

Destructor.

Definition at line 42 of file ClusterIdentifier.cpp.

Member Function Documentation

void McMd::ClusterIdentifier::initialize	(	int	speciesId,
		int	atomTypeId,
		double	cutoff
	)

virtual

Clear accumulator.

Parameters

speciesId	index of species in clusters
atomTypeId	typeId of atoms in micelle core
cutoff	pair distance cutoff

Definition at line 49 of file ClusterIdentifier.cpp.

References McMd::Cluster::addLink(), McMd::Simulation::atomCapacity(), McMd::Molecule::begin(), McMd::System::boundary(), Simp::Species::capacity(), cluster(), McMd::ClusterLink::clusterId(), Simp::OrthorhombicBoundary::distanceSq(), McMd::CellList::getNeighbors(), McMd::Cluster::id(), McMd::Molecule::id(), McMd::ClusterLink::molecule(), McMd::Atom::molecule(), Util::ArrayIterator< Data >::notEnd(), McMd::Atom::position(), McMd::CellList::setAtomCapacity(), McMd::System::simulation(), Util::FSArray< Data, Capacity >::size(), McMd::Simulation::species(), and UTIL_THROW.

Referenced by McMd::ClusterHistogram::loadParameters(), and McMd::ClusterHistogram::readParameters().

void McMd::ClusterIdentifier::identifyClusters ( )

Identify all clusters (main operation).

Definition at line 129 of file ClusterIdentifier.cpp.

References McMd::CellList::addAtom(), McMd::Cluster::addLink(), McMd::System::begin(), McMd::System::boundary(), McMd::Cluster::clear(), McMd::ClusterLink::clusterId(), Util::PArrayIterator< Data >::get(), isValid(), McMd::ClusterLink::molecule(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Cluster::setId(), McMd::CellList::setup(), and Simp::OrthorhombicBoundary::shift().

Referenced by McMd::ClusterHistogram::sample().

int McMd::ClusterIdentifier::nCluster ( ) const

inline

Get number of clusters.

Definition at line 69 of file ClusterIdentifier.h.

Referenced by isValid(), and McMd::ClusterHistogram::sample().

ClusterLink& McMd::ClusterIdentifier::link ( int moleculeId )

inline

Get a specific ClusterLink, by id of the associated molecule.

Parameters

moleculeId molecule index.

Definition at line 77 of file ClusterIdentifier.h.

Cluster& McMd::ClusterIdentifier::cluster ( int id )

inline

Get a specific cluster, indexed in the order identified.

The id argument of this function is a consecutive array index, with 0 <= id < nCluster, which need not be equal to the cluster identifier returned by Cluster::id().

Parameters

id	cluster array index, 0 <- id < nCluster.

Definition at line 89 of file ClusterIdentifier.h.

Referenced by initialize(), and McMd::ClusterHistogram::sample().

bool McMd::ClusterIdentifier::isValid ( ) const

Return true if valid, or throw Exception otherwise.

Definition at line 197 of file ClusterIdentifier.cpp.

References McMd::System::begin(), McMd::ClusterLink::clusterId(), Util::ConstPArrayIterator< Data >::get(), McMd::ClusterLink::molecule(), nCluster(), McMd::System::nMolecule(), Util::ConstPArrayIterator< Data >::notEnd(), and UTIL_THROW.

Referenced by identifyClusters().

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

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation