Detailed Description

Manages all Link objects in a System.

A LinkMaster allows links between Atoms, or Link objects, to be added to or removed from a system, and provides access to existing links.

Definition at line 39 of file LinkMaster.h.

#include <LinkMaster.h>

Inheritance diagram for McMd::LinkMaster:

Public Types
typedef PArrayIterator< Link >	LinkIterator
	Iterator for set of active links. More...

typedef ConstPArrayIterator< Link >	ConstLinkIterator
	Const iterator for set of active links. More...

typedef SSet< Link, 400 >	AtomLinkSet
	A set of links involving a particular atom. More...

Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method. More...

typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method. More...

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

void	readParameters (std::istream &in)
	Read linkCapacity and allocate. More...

void	addLink (Atom &atom0, Atom &atom1, int typeId)
	Add a link betwen two specific Atoms. More...

void	removeLink (int id)
	Remove a Link. More...

const AtomLinkSet &	atomLinkSet (const Atom &atom) const
	Return a set of links associated with an Atom by const reference. More...

AtomLinkSet &	atomLinkSet (const Atom &atom)
	Return a set of links associated with an Atom. More...

Link &	link (int id) const
	Return an active link by an internal set index. More...

void	reSetAtoms (Link &link, Atom &atom0, Atom &atom1)
	Modify the atoms attached to a link. More...

void	reSetAtom (Link &link, Atom &atom, int endId)
	Modify one atom attached to a link. More...

int	nLink () const
	Get the total number of active Links. More...

void	begin (LinkIterator &iterator)
	Initialize iterator to beginning of list of active links. More...

void	begin (ConstLinkIterator &iterator) const
	Initialize iterator to beginning of list of active links. More...

Link &	randomLink (Random &random)
	Get a randomly chosen link by reference. More...

bool	isValid () const
	Return true if this LinkMaster is valid, or throw an Exception. More...

void	clear ()
	Clear LinkMaster. More...

Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor. More...

	ParamComposite (const ParamComposite &other)
	Copy constructor. More...

	ParamComposite (int capacity)
	Constructor. More...

virtual	~ParamComposite ()
	Virtual destructor. More...

void	resetParam ()
	Resets ParamComposite to its empty state. More...

virtual void	readParam (std::istream &in)
	Read the parameter file block. More...

virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block. More...

virtual void	writeParam (std::ostream &out)
	Write all parameters to an output stream. More...

virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive. More...

virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines. More...

virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive. More...

void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true. More...

void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite. More...

void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite. More...

template<typename Type >
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter. More...

template<typename Type >
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter. More...

template<typename Type >
DArrayParam< Type > &	readDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read a required DArray < Type > parameter. More...

template<typename Type >
DArrayParam< Type > &	readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read an optional DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read a required FArray < Type, N > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read an optional FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	readCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read a required CArray2DParam < Type > 2D C-array. More...

template<typename Type >
CArray2DParam< Type > &	readOptionalCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read an optional CArray2DParam < Type > 2D C-array parameter. More...

template<typename Type >
DMatrixParam< Type > &	readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read a required DMatrix < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read an optional DMatrix < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix. More...

template<typename Type >
DSymmMatrixParam< Type > &	readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read an optional DMatrix matrix parameter. More...

Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket. More...

End &	readEnd (std::istream &in)
	Add and read the closing bracket. More...

Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line. More...

void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite. More...

void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n, bool isRequired)
	Add a C array parameter and load its elements. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n)
	Add and load a required CArrayParam< Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)
	Add an load a DArray < Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)
	Add and load a required DArray< Type > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)
	Add and load an FArray < Type, N > fixed-size array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)
	Add and load a required FArray < Type > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np, bool isRequired)
	Add and load a CArray2DParam < Type > C 2D array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np)
	Add and load a required < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)
	Add and load a DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and load a required DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)
	Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)
	Add and load a required DSymmMatrixParam < Type > matrix parameter. More...

void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array. More...

Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket. More...

End &	addEnd ()
	Add a closing bracket. More...

Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line. More...

std::string	className () const
	Get class name string. More...

bool	isRequired () const
	Is this ParamComposite required in the input file? More...

bool	isActive () const
	Is this parameter active? More...

Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor. More...

void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level. More...

std::string	indent () const
	Return indent string for this object (string of spaces). More...

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string. More...

Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor. More...

Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor. More...

	MpiFileIo (const MpiFileIo &other)
	Copy constructor. More...

bool	isIoProcessor () const
	Can this processor do file I/O ? More...

void	setIoCommunicator (MPI::Intracomm &communicator)
	Set the communicator. More...

void	clearCommunicator ()
	Clear (nullify) the communicator. More...

bool	hasIoCommunicator () const
	Does this object have an associated MPI communicator? More...

MPI::Intracomm &	ioCommunicator () const
	Get the MPI communicator by reference. More...

Public Member Functions inherited from Util::Notifier< LinkAddEvent >
void	registerObserver (Observer< LinkAddEvent > &observer)
	Register an observer. More...

void	removeObserver (Observer< LinkAddEvent > &observer)
	Remove an analyzer observer from the container list. More...

void	notifyObservers (const LinkAddEvent &event)
	Notify the list of observers about an Event. More...

Public Member Functions inherited from Util::Notifier< LinkResetEvent >
void	registerObserver (Observer< LinkResetEvent > &observer)
	Register an observer. More...

void	removeObserver (Observer< LinkResetEvent > &observer)
	Remove an analyzer observer from the container list. More...

void	notifyObservers (const LinkResetEvent &event)
	Notify the list of observers about an Event. More...

Public Member Functions inherited from Util::Notifier< LinkRemoveEvent >
void	registerObserver (Observer< LinkRemoveEvent > &observer)
	Register an observer. More...

void	removeObserver (Observer< LinkRemoveEvent > &observer)
	Remove an analyzer observer from the container list. More...

void	notifyObservers (const LinkRemoveEvent &event)
	Notify the list of observers about an Event. More...

Public Member Functions inherited from Util::Notifier< ReSetAtomEvent >
void	registerObserver (Observer< ReSetAtomEvent > &observer)
	Register an observer. More...

void	removeObserver (Observer< ReSetAtomEvent > &observer)
	Remove an analyzer observer from the container list. More...

void	notifyObservers (const ReSetAtomEvent &event)
	Notify the list of observers about an Event. More...

Additional Inherited Members
Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false. More...

static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent. More...

static bool	echo ()
	Get echo parameter. More...

Protected Member Functions inherited from Util::ParamComposite
void	setClassName (const char *className)
	Set class name string. More...

void	setIsRequired (bool isRequired)
	Set or unset the isActive flag. More...

void	setIsActive (bool isActive)
	Set or unset the isActive flag. More...

void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component. More...

void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array. More...

template<typename Type >
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	addCArray (std::istream &in, const char label, Type value, int n, bool isRequired=true)
	Add (but do not read) a required C array parameter. More...

template<typename Type >
DArrayParam< Type > &	addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true)
	Add (but do not read) a DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true)
	Add (but do not read) a FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	addCArray2D (std::istream &in, const char label, Type value, int m, int n, int np, bool isRequired=true)
	Add (but do not read) a CArray2DParam < Type > 2D C-array. More...

template<typename Type >
DMatrixParam< Type > &	addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true)
	Add and read a required DMatrix < Type > matrix parameter. More...

Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor. More...

	ParamComponent (const ParamComponent &other)
	Copy constructor. More...

Member Typedef Documentation

typedef PArrayIterator<Link> McMd::LinkMaster::LinkIterator

Iterator for set of active links.

Definition at line 49 of file LinkMaster.h.

typedef ConstPArrayIterator<Link> McMd::LinkMaster::ConstLinkIterator

Const iterator for set of active links.

Definition at line 52 of file LinkMaster.h.

typedef SSet<Link,400> McMd::LinkMaster::AtomLinkSet

A set of links involving a particular atom.

Definition at line 57 of file LinkMaster.h.

Constructor & Destructor Documentation

McMd::LinkMaster::LinkMaster ( )

Constructor.

Definition at line 21 of file LinkMaster.cpp.

References Util::ParamComposite::setClassName().

Member Function Documentation

void McMd::LinkMaster::readParameters ( std::istream & in )

virtual

Read linkCapacity and allocate.

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 29 of file LinkMaster.cpp.

void McMd::LinkMaster::addLink	(	Atom &	atom0,
		Atom &	atom1,
		int	typeId
	)

Add a link betwen two specific Atoms.

Add a new link.

The associated Link object is taken from a reservoir of unused links.

Parameters

atom0	first Atom object to which a Link should be attached
atom1	second Atom object to which a Link should be attached
typeId	id for the type of Link

Definition at line 39 of file LinkMaster.cpp.

References Util::Log::file(), McMd::Atom::id(), Util::Notifier< Event >::notifyObservers(), McMd::Link::setIsActive(), and UTIL_THROW.

Referenced by McMd::GcSliplinkMove::move(), McMd::SliplinkMove::move(), McMd::Sliplinker::move(), McMd::SliplinkerAll::move(), McMd::SliplinkerEnd::move(), McMd::McMdConfigIo::read(), and McMd::Crosslinker::sample().

void McMd::LinkMaster::removeLink ( int id )

Remove a Link.

Precondition: The Link must be active.

Parameters

id	Link index in linkSet_, the ArraySet < Link > container.

Definition at line 77 of file LinkMaster.cpp.

References McMd::Link::atom0(), McMd::Link::atom1(), McMd::Atom::id(), Util::ParamComposite::isActive(), link(), Util::Notifier< Event >::notifyObservers(), and UTIL_THROW.

Referenced by clear(), McMd::SliplinkMove::move(), McMd::SliplinkerEnd::move(), McMd::SliplinkerAll::move(), McMd::Sliplinker::move(), and McMd::GcSliplinkMove::move().

const LinkMaster::AtomLinkSet & McMd::LinkMaster::atomLinkSet ( const Atom & atom ) const

inline

Return a set of links associated with an Atom by const reference.

Parameters

atom	Atom object of interest.

Definition at line 226 of file LinkMaster.h.

References McMd::Atom::id().

Referenced by McMd::LinkPotentialImpl< Interaction >::atomEnergy().

LinkMaster::AtomLinkSet & McMd::LinkMaster::atomLinkSet ( const Atom & atom )

inline

Return a set of links associated with an Atom.

Parameters

atom	Atom object of interest.

Definition at line 235 of file LinkMaster.h.

References McMd::Atom::id().

Link & McMd::LinkMaster::link ( int id ) const

inline

Return an active link by an internal set index.

An "active" Link object is one that is attached to two atoms. Pointers to all of the active Link objects are maintained by an ArraySet < Link > container. At any instant, this container assigns every active link an index in the range 0 <= id < nLink, where nLink is the total number of active links. The index associated with any Link in the set can change, however, whenever another Link is removed from the set by calling removeLink() (not yet implemented).

Parameters