Simpatico: McMd::Cluster Class Reference

Simpatico v1.10

Detailed Description

Cluster of molecules.

A Cluster is implemented as a linked list of ClusterLink objects, each of which is associated with a molecule. A Cluster has a pointer to the first ClusterLink and a size member that counts the number of links (or molecules), but does not own the associated ClusterLink or Molecule objects.

Definition at line 31 of file Cluster.h.

#include <Cluster.h>

Public Member Functions
	Cluster ()
	Constructor. More...

	~Cluster ()
	Destructor. More...

void	clear ()
	Set cluster to empty. More...

void	setId (int id)
	Set cluster identifier. More...

void	addLink (ClusterLink &link)
	Add a link to the list. More...

int	id () const
	Get the cluster id. More...

int	size () const
	Get the number of molecules or links in the cluster. More...

ClusterLink *	head () const
	Get a pointer to the first link in the linked list. More...

bool	isValid () const
	Return true if valid, false otherwise. More...

Vector	clusterCOM (int atomTypeInCluster, Boundary const &boundary)
	Return the cluster COM. More...

Tensor	momentTensor (int atomTypeInCluster, Boundary const &boundary)
	Return the cluster radius of gyration tensor. More...

Constructor & Destructor Documentation

McMd::Cluster::Cluster ( )

Constructor.

Definition at line 16 of file Cluster.cpp.

McMd::Cluster::~Cluster ( )

Destructor.

Definition at line 22 of file Cluster.cpp.

Member Function Documentation

void McMd::Cluster::clear ( )

Set cluster to empty.

Definition at line 25 of file Cluster.cpp.

References McMd::ClusterLink::clear(), and McMd::ClusterLink::next().

Referenced by McMd::ClusterIdentifier::identifyClusters().

void McMd::Cluster::setId ( int id )

Set cluster identifier.

Definition at line 39 of file Cluster.cpp.

References id(), McMd::ClusterLink::next(), and UTIL_THROW.

Referenced by McMd::ClusterIdentifier::identifyClusters().

void McMd::Cluster::addLink ( ClusterLink & link )

Add a link to the list.

Parameters

link	ClusterLink associated with a Molecule.

Definition at line 52 of file Cluster.cpp.

Referenced by McMd::ClusterIdentifier::identifyClusters(), and McMd::ClusterIdentifier::initialize().

int McMd::Cluster::id ( ) const

inline

Get the cluster id.

Definition at line 66 of file Cluster.h.

Referenced by McMd::ClusterIdentifier::initialize(), and setId().

int McMd::Cluster::size ( ) const

inline

Get the number of molecules or links in the cluster.

Definition at line 72 of file Cluster.h.

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

ClusterLink* McMd::Cluster::head ( ) const

inline

Get a pointer to the first link in the linked list.

Returns 0 pointer if cluster is empty.

Definition at line 80 of file Cluster.h.

References clusterCOM(), isValid(), and momentTensor().

Referenced by clusterCOM(), momentTensor(), and McMd::ClusterHistogram::sample().

bool McMd::Cluster::isValid ( ) const

Return true if valid, false otherwise.

Definition at line 60 of file Cluster.cpp.

References McMd::ClusterLink::clusterId(), and McMd::ClusterLink::next().

Referenced by head().

Vector McMd::Cluster::clusterCOM	(	int	atomTypeInCluster,
		Boundary const &	boundary
	)

Return the cluster COM.

Definition at line 77 of file Cluster.cpp.

References McMd::Molecule::begin(), Simp::OrthorhombicBoundary::distanceSq(), head(), McMd::ClusterLink::molecule(), McMd::ClusterLink::next(), Util::ConstArrayIterator< Data >::notEnd(), Simp::OrthorhombicBoundary::shift(), and Util::Vector::zero().

Referenced by head(), momentTensor(), and McMd::ClusterHistogram::sample().

Tensor McMd::Cluster::momentTensor	(	int	atomTypeInCluster,
		Boundary const &	boundary
	)

Return the cluster radius of gyration tensor.

Definition at line 111 of file Cluster.cpp.

References McMd::Molecule::begin(), clusterCOM(), Simp::OrthorhombicBoundary::distanceSq(), Util::Tensor::dyad(), head(), McMd::ClusterLink::molecule(), McMd::ClusterLink::next(), Util::ConstArrayIterator< Data >::notEnd(), and Util::Tensor::zero().

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

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