Simpatico: Tools::AtomStorage Class Reference

Simpatico v1.10

Detailed Description

Container for a set of atoms.

Definition at line 29 of file tools/storage/AtomStorage.h.

#include <AtomStorage.h>

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

	~AtomStorage ()
	Destructor. More...

void	allocate (int capacity)
	Allocate and initialize memory. More...

Atom *	newPtr ()
	Return pointer to location for new atom. More...

void	add ()
	Finalize addition of atom (allows lookup by id). More...

void	clear ()
	Clear all atoms and groups. More...

Atom *	ptr (int id)
	Get a pointer to an atom by global id. More...

void	begin (Iterator &iter)
	Initialize an iterator for atoms. More...

int	capacity () const
	Get atom capacity (maximum id + 1). More...

int	size () const
	Get number of atoms. More...

Constructor & Destructor Documentation

Tools::AtomStorage::AtomStorage ( )

Constructor.

Definition at line 16 of file tools/storage/AtomStorage.cpp.

Tools::AtomStorage::~AtomStorage ( )

Destructor.

Definition at line 23 of file tools/storage/AtomStorage.cpp.

Member Function Documentation

void Tools::AtomStorage::allocate ( int capacity )

Allocate and initialize memory.

Parameters

capacity Maximum number of atoms

Definition at line 29 of file tools/storage/AtomStorage.cpp.

References clear().

Referenced by Tools::Configuration::readParameters().

Atom * Tools::AtomStorage::newPtr ( )

Return pointer to location for new atom.

Returns: pointer to location of new atom

Definition at line 39 of file tools/storage/AtomStorage.cpp.

References size(), and UTIL_THROW.

Referenced by Tools::DdMdConfigReader::readConfig(), and Tools::HoomdConfigReader::readConfig().

void Tools::AtomStorage::add ( )

Finalize addition of atom (allows lookup by id).

Definition at line 53 of file tools/storage/AtomStorage.cpp.

References Tools::Atom::id, and UTIL_THROW.

Referenced by Tools::DdMdConfigReader::readConfig(), and Tools::HoomdConfigReader::readConfig().

void Tools::AtomStorage::clear ( )

Clear all atoms and groups.

Definition at line 66 of file tools/storage/AtomStorage.cpp.

References capacity().

Referenced by allocate(), and Tools::Configuration::clear().

Atom * Tools::AtomStorage::ptr ( int id )

inline

Get a pointer to an atom by global id.

Returns a null pointer if no such atom is present.

Parameters

id	global index / tag of desired atom.

Definition at line 125 of file tools/storage/AtomStorage.h.

Referenced by Tools::HoomdConfigReader::readConfig(), Tools::LammpsDumpReader::readFrame(), Tools::DdMdTrajectoryReader::readFrame(), and Tools::ConfigReader::setAtomContexts().

void Tools::AtomStorage::begin ( AtomStorage::Iterator & iter )

inline

Initialize an iterator for atoms.

Definition at line 132 of file tools/storage/AtomStorage.h.

Referenced by Tools::ConfigReader::addAtomsToSpecies(), Tools::PairEnergy::sample(), Tools::DdMdConfigWriter::writeConfig(), Tools::HoomdConfigWriter::writeConfig(), and Tools::LammpsDumpWriter::~LammpsDumpWriter().

int Tools::AtomStorage::capacity ( ) const

inline

Get atom capacity (maximum id + 1).

Definition at line 119 of file tools/storage/AtomStorage.h.

Referenced by clear(), and Tools::DdMdConfigReader::readConfig().

int Tools::AtomStorage::size ( ) const

inline

Get number of atoms.

Definition at line 112 of file tools/storage/AtomStorage.h.

Referenced by newPtr(), Tools::HoomdConfigReader::readConfig(), Tools::ConfigReader::setAtomContexts(), Tools::DdMdConfigWriter::writeConfig(), Tools::HoomdConfigWriter::writeConfig(), and Tools::LammpsDumpWriter::~LammpsDumpWriter().

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