Tools::Species Class Reference

Detailed Description

A set of identical molecules.

Definition at line 27 of file tools/chemistry/Species.h.

#include <Species.h>

Public Member Functions
	Species ()
	Constructor. More...
	~Species ()
	Destructor. More...
void	setId (int id)
	Set the index for this species. More...
void	initialize (int nAtom, int capacity)
	Initialize memory for this species and set sizes. More...
void	addAtom (Atom &atom)
	Add an atom to the species. More...
void	clear ()
	Clear all molecules, reset to empty. More...
void	begin (Iterator &iterator)
	Initialize an iterator over molecules. More...
Molecule &	molecule (int i)
	Return a specific molecule by reference. More...
int	id () const
	Return integer id for this species. More...
int	nAtom () const
	Return number of atoms per molecule. More...
int	size () const
	Return number of molecules in this species (=maximum id + 1) More...
int	capacity () const
	Return maximum number of molecules in this species. More...
bool	isValid () const
	Return true if valid, or throw Exception. More...
template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize to/from an archive. More...

Friends
std::istream &	operator>> (std::istream &in, Species &species)
	istream extractor (>>) for a Species. More...
std::ostream &	operator<< (std::ostream &out, const Species &species)
	ostream inserter (<<) for a Species. More...

Constructor & Destructor Documentation

Tools::Species::Species

(

)

Constructor.

Tools::Species::~Species

(

)

Destructor.

Member Function Documentation

void Tools::Species::setId

(

int

id

)

Set the index for this species.

Parameters

id	species index

void Tools::Species::initialize	(	int	nAtom,
		int	capacity
	)

Initialize memory for this species and set sizes.

Parameters

nAtom	number of atoms per molecule (exact)
capacity	maximum number of molecules in species

Definition at line 36 of file tools/chemistry/Species.cpp.

References Simp::Species::capacity(), Simp::Species::nAtom(), Simp::Species::nAtom_, and UTIL_THROW.

void Tools::Species::addAtom

(

Atom &

atom

)

Add an atom to the species.

Parameters

atom	Atom object to be added, must have AtomContext info.

Definition at line 105 of file tools/chemistry/Species.cpp.

References Tools::Atom::atomId, Simp::Species::id_, Tools::Atom::moleculeId, Simp::Species::nAtom_, Tools::Atom::speciesId, and UTIL_THROW.

void Tools::Species::clear

(

)

Clear all molecules, reset to empty.

Definition at line 91 of file tools/chemistry/Species.cpp.

void Tools::Species::begin

(

Iterator &

iterator

)

Initialize an iterator over molecules.

Definition at line 138 of file tools/chemistry/Species.cpp.

References Tools::Atom::atomId, Tools::Molecule::id(), Simp::Species::id_, Simp::Species::isValid(), Tools::Atom::moleculeId, Simp::Species::nAtom_, Tools::Atom::speciesId, and UTIL_THROW.

Molecule & Tools::Species::molecule ( int  i )

inline

Return a specific molecule by reference.

Parameters

i	molecule index

Definition at line 185 of file tools/chemistry/Species.h.

References Simp::Species::id(), Simp::Species::id_, Simp::Species::nAtom(), and Simp::Species::nAtom_.

int Tools::Species::id

(

)

const

Return integer id for this species.

int Tools::Species::nAtom

(

)

const

Return number of atoms per molecule.

int Tools::Species::size ( ) const

inline

Return number of molecules in this species (=maximum id + 1)

Definition at line 203 of file tools/chemistry/Species.h.

References Simp::Species::capacity(), Simp::Species::nAtom_, and Util::ParamComponent::serialize().

int Tools::Species::capacity

(

)

const

Return maximum number of molecules in this species.

bool Tools::Species::isValid

(

)

const

Return true if valid, or throw Exception.

template<class Archive >

void Tools::Species::serialize	(	Archive &	ar,
		const unsigned int	version
	)

Serialize to/from an archive.

Friends And Related Function Documentation

std::istream& operator>> ( std::istream &  in, Species &  species  )

friend

istream extractor (>>) for a Species.

Parameters

in	input stream
species	Species to be read from stream

Returns

modified input stream

Definition at line 206 of file tools/chemistry/Species.cpp.

std::ostream& operator<< ( std::ostream &  out, const Species &  species  )

friend

ostream inserter (<<) for a Species.

Format on one line with no line break:

Parameters

out	output stream
species	Species to be written to stream

Returns

modified output stream

Definition at line 217 of file tools/chemistry/Species.cpp.

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

• tools/chemistry/Species.h
• tools/chemistry/Species.cpp