Detailed Description

Associative container for finding atoms identified by integer id.

Definition at line 36 of file AtomMap.h.

#include <AtomMap.h>

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

	~AtomMap ()
	Destructor. More...

void	allocate (int totalAtomCapacity)
	Set parameters, allocate memory and initialize. More...

void	addLocal (Atom *ptr)
	Add local atom. More...

void	removeLocal (Atom *ptr)
	Remove a specific Atom. More...

void	addGhost (Atom *ptr)
	Add ghost atom. More...

void	removeGhost (Atom *ptr)
	Remove a ghost Atom. More...

void	clearGhosts (const ArraySet< Atom > &ghostSet)
	Clear all ghosts from this map. More...

Accessors
Atom *	find (int atomId) const
	Return pointer to Atom with specified id. More...

int	nLocal () const
	Return the number of local atoms. More...

int	nGhostDistinct () const
	Return the number of ghosts with distinct ids. More...

int	nGhost () const
	Return the number of ghosts, including images. More...

template<int N>
int	findGroupLocalAtoms (Group< N > &group) const
	Set handles to local atoms in a Group<N> object. More...

template<int N>
int	findGroupGhostAtoms (Group< N > &group) const
	Set handles to ghost atoms in a Group<N> object. More...

bool	isValid () const
	Check validity of this AtomMap. More...

Constructor & Destructor Documentation

DdMd::AtomMap::AtomMap ( )

Constructor.

Definition at line 23 of file AtomMap.cpp.

DdMd::AtomMap::~AtomMap ( )

Destructor.

Definition at line 34 of file AtomMap.cpp.

Member Function Documentation

void DdMd::AtomMap::allocate ( int totalAtomCapacity )

Set parameters, allocate memory and initialize.

Call this or (read|load)Parameters to initialize, but not both.

Parameters

totalAtomCapacity max number of atoms on all processors.

Definition at line 40 of file AtomMap.cpp.

References UTIL_THROW.

Referenced by DdMd::AtomStorage::save().

void DdMd::AtomMap::addLocal ( Atom * ptr )

Add local atom.

Parameters

ptr	Pointer to new Atom.

Definition at line 57 of file AtomMap.cpp.

References Util::Log::file(), DdMd::Atom::id(), DdMd::Atom::position(), and UTIL_THROW.

Referenced by DdMd::AtomStorage::addNewAtom().

void DdMd::AtomMap::removeLocal ( Atom * ptr )

Remove a specific Atom.

Exceptions

Exception if atom is not present.

Parameters

ptr	Pointer to Atom to be removed.

Definition at line 83 of file AtomMap.cpp.

References Util::Log::file(), DdMd::Atom::id(), and UTIL_THROW.

Referenced by DdMd::AtomStorage::clearAtoms(), and DdMd::AtomStorage::removeAtom().

void DdMd::AtomMap::addGhost ( Atom * ptr )

Add ghost atom.

Parameters

ptr	Pointer to new Atom.

Definition at line 120 of file AtomMap.cpp.

References DdMd::Atom::id(), and UTIL_THROW.

Referenced by DdMd::AtomStorage::addNewGhost().

void DdMd::AtomMap::removeGhost ( Atom * ptr )

Remove a ghost Atom.

This function throws an exception if no atom with this id is present, but not if it does not match this pointer.

Parameters

ptr	Pointer to Atom to be removed.

Definition at line 139 of file AtomMap.cpp.

References DdMd::Atom::id(), and UTIL_THROW.

Referenced by DdMd::AtomStorage::removeGhost().

void DdMd::AtomMap::clearGhosts ( const ArraySet< Atom > & ghostSet )

Clear all ghosts from this map.

Parameters

ghostSet Set containing all ghosts on this processor.

Definition at line 185 of file AtomMap.cpp.

References Util::PArray< Data >::begin(), Util::ConstPArrayIterator< Data >::get(), nGhost(), Util::ConstPArrayIterator< Data >::notEnd(), Util::PArray< Data >::size(), and UTIL_THROW.

Referenced by DdMd::AtomStorage::clearGhosts().

Atom * DdMd::AtomMap::find ( int atomId ) const

inline

Return pointer to Atom with specified id.

This function returns a pointer to an Atom with the specified id if it is present, or returns a null pointer otherwise.

Parameters

atomId integer index of atom

Definition at line 230 of file AtomMap.h.

Referenced by DdMd::GroupStorage< N >::isValid(), DdMd::AtomStorage::isValid(), DdMd::GroupStorage< N >::markGhosts(), and DdMd::ConfigIo::setAtomMasks().

int DdMd::AtomMap::nLocal ( ) const

inline

Return the number of local atoms.

Definition at line 236 of file AtomMap.h.

Referenced by DdMd::AtomStorage::clearAtoms().

int DdMd::AtomMap::nGhostDistinct ( ) const

inline

Return the number of ghosts with distinct ids.

Definition at line 242 of file AtomMap.h.

Referenced by DdMd::AtomStorage::clearGhosts().

int DdMd::AtomMap::nGhost ( ) const

inline

Return the number of ghosts, including images.

Definition at line 248 of file AtomMap.h.

Referenced by clearGhosts(), DdMd::AtomStorage::clearGhosts(), and DdMd::AtomStorage::isValid().

template<int N>

int DdMd::AtomMap::findGroupLocalAtoms ( Group< N > & group ) const

Set handles to local atoms in a Group<N> object.

On entry, group is a Group<N> object for which the atom ids for all N atoms in the Group have been set to valid values, in the range 0 <= atomId < totalAtomCapacity, but in which some or all pointers have not been set. The AtomMap may not contain any ghosts.

On exit, pointers are set correctly for all local atoms that exist in this AtomMap, or set to null for absent atoms. All old pointer values are overwritten.

Parameters

group Group<N> object with known atom ids.

Returns: number of atoms found on this processor.

Definition at line 257 of file AtomMap.h.

References DdMd::Group< N >::atomId(), DdMd::Group< N >::clearAtomPtr(), DdMd::Atom::id(), DdMd::Atom::isGhost(), and DdMd::Group< N >::setAtomPtr().

Referenced by DdMd::GroupDistributor< N >::add(), DdMd::GroupDistributor< N >::receive(), and DdMd::GroupStorage< N >::unpack().

template<int N>

int DdMd::AtomMap::findGroupGhostAtoms ( Group< N > & group ) const

Set handles to ghost atoms in a Group<N> object.

On entry, group is a Group<N> object for which the atom ids for all N atoms in the Group have been set to valid values, in the range 0 <= atomId < totalAtomCapacity, and in which all pointers to local atoms have been set, but in which no pointers to ghosts have been set. This function may only be called after all pointers have been set for all local atoms and after this AtomMap contains all ghost atoms.

On exit, pointers are set for all ghost atoms present in this AtomMap.

Parameters

group Group<N> object with known atom ids.

Returns: number of atoms found on this processor.

Definition at line 279 of file AtomMap.h.

References DdMd::Group< N >::atomId(), DdMd::Group< N >::atomPtr(), DdMd::Group< N >::clearAtomPtr(), DdMd::Atom::id(), DdMd::Atom::isGhost(), and DdMd::Group< N >::setAtomPtr().

Referenced by DdMd::GroupStorage< N >::findGhosts().

bool DdMd::AtomMap::isValid ( ) const

Check validity of this AtomMap.

Returns true if all is ok, or throws an Exception.

Definition at line 215 of file AtomMap.cpp.

References Util::Log::file(), DdMd::Atom::id(), and UTIL_THROW.

Referenced by DdMd::AtomStorage::isValid().

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

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation