Detailed Description

template<int N>
class DdMd::Group< N >

A group of covalently interacting atoms.

A group of atoms that interact via a permanent (covalent) N Atom potential. Specializations of Group with N=2, 3, 4 are used to represent groups that interact via covalent bond, angle and torsion interaction potentials, respectively.

A Group<N> contains both: (1) an array of integer ids for atoms in the group, and (2) an array of pointers to these atoms. Each Group<N> also has an integer type id and a unique global id for the group.

Definition at line 22 of file ddMd/chemistry/Group.h.

#include <Group.h>

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

void	clear ()
	Set group to empty initial state. More...

void	setId (int id)
	Set the global id for this group. More...

void	setTypeId (int typeId)
	Set the group type id for this group. More...

void	setAtomId (int i, int atomId)
	Set the id for a specific atom. More...

void	setAtomPtr (int i, Atom *atomPtr)
	Set the pointer to a specific atom. More...

void	clearAtomPtr (int i)
	Clear the pointer to a specific atom. More...

Plan &	plan ()
	Get communication plan by reference. More...

int	id () const
	Get the global id for this group. More...

int	typeId () const
	Get the typeId for this group. More...

int	atomId (int i) const
	Get the id for a specific atom in the Group. More...

Atom *	atomPtr (int i) const
	Get a pointer to a specific Atom. More...

int	nPtr () const
	Return the number of non-null atom pointers in this group. More...

const Plan &	plan () const
	Get communication plan (const reference). More...

void	pack (Buffer &buffer)
	Pack a Group into a send buffer. More...

void	unpack (Buffer &buffer)
	Unpack a Group from the recv buffer. More...

Static Public Member Functions
static int	packedSize ()
	Return packed size of a Group<N> object in a send buffer, in bytes. More...

Friends
std::istream &	operator>> (std::istream &in, Group< N > &group)
	istream extractor (>>) for a Group. More...

std::ostream &	operator<< (std::ostream &out, const Group< N > &group)
	ostream inserter (<<) for a Group. More...

template<class Archive >
void	serialize (Archive &ar, Group< N > &group, const unsigned int version)
	Serialize one Group<N>. More...

Constructor & Destructor Documentation

template<int N>

DdMd::Group< N >::Group ( )

Constructor.

Definition at line 245 of file ddMd/chemistry/Group.h.

References DdMd::Plan::clearFlags().

Member Function Documentation

template<int N>

int DdMd::Group< N >::packedSize ( )

static

Return packed size of a Group<N> object in a send buffer, in bytes.

Definition at line 441 of file ddMd/chemistry/Group.h.

template<int N>

void DdMd::Group< N >::clear ( )

Set group to empty initial state.

Definition at line 261 of file ddMd/chemistry/Group.h.

References DdMd::Plan::clearFlags().

template<int N>

void DdMd::Group< N >::setId ( int id )

inline

Set the global id for this group.

Parameters

id	value of global id (tag) for this group.

Definition at line 277 of file ddMd/chemistry/Group.h.

References DdMd::Group< N >::id().

Referenced by DdMd::GroupStorage< N >::add(), DdMd::GroupStorage< N >::clearGroups(), DdMd::LammpsConfigIo::LammpsConfigIo(), DdMd::GroupStorage< N >::remove(), and DdMd::Group< N >::unpack().

template<int N>

void DdMd::Group< N >::setTypeId ( int typeId )

inline

Set the group type id for this group.

Parameters

typeId value of covalent group typeId

Definition at line 284 of file ddMd/chemistry/Group.h.

References DdMd::Group< N >::typeId().

Referenced by DdMd::LammpsConfigIo::LammpsConfigIo(), and DdMd::Group< N >::unpack().

template<int N>

void DdMd::Group< N >::setAtomId	(	int	i,
		int	atomId
	)

inline

Set the id for a specific atom.

Parameters

i	index within group (0,..., N-1)
atomId	global atom identifier (atom tag)

Definition at line 291 of file ddMd/chemistry/Group.h.

References DdMd::Group< N >::atomId().

Referenced by DdMd::LammpsConfigIo::LammpsConfigIo(), and DdMd::Group< N >::unpack().

template<int N>

void DdMd::Group< N >::setAtomPtr	(	int	i,
		Atom *	atomPtr
	)

Set the pointer to a specific atom.

Parameters

i	index of atom within group
atomPtr	pointer to Atom to be added

Definition at line 298 of file ddMd/chemistry/Group.h.

References DdMd::Group< N >::atomPtr(), and UTIL_THROW.

Referenced by DdMd::AtomMap::findGroupGhostAtoms(), and DdMd::AtomMap::findGroupLocalAtoms().

template<int N>

void DdMd::Group< N >::clearAtomPtr ( int i )

inline

Clear the pointer to a specific atom.

Parameters

i	index of atom within group.

Definition at line 313 of file ddMd/chemistry/Group.h.

Referenced by DdMd::AtomMap::findGroupGhostAtoms(), DdMd::AtomMap::findGroupLocalAtoms(), and DdMd::Group< N >::unpack().

template<int N>

Plan & DdMd::Group< N >::plan ( )

inline

Get communication plan by reference.

Definition at line 325 of file ddMd/chemistry/Group.h.

Referenced by DdMd::Group< N >::pack(), and DdMd::Group< N >::unpack().

template<int N>

int DdMd::Group< N >::id ( ) const

inline

Get the global id for this group.

Definition at line 334 of file ddMd/chemistry/Group.h.

Referenced by DdMd::GroupStorage< N >::clearGroups(), DdMd::GroupStorage< N >::isValid(), DdMd::Group< N >::pack(), DdMd::LammpsConfigIo::readConfig(), DdMd::DdMdOrderedConfigIo::readConfig(), DdMd::GroupStorage< N >::remove(), DdMd::Group< N >::setId(), and DdMd::GroupStorage< N >::unpack().

template<int N>

int DdMd::Group< N >::typeId ( ) const

inline

Get the typeId for this group.

Definition at line 341 of file ddMd/chemistry/Group.h.

Referenced by DdMd::Group< N >::pack(), and DdMd::Group< N >::setTypeId().

template<int N>

int DdMd::Group< N >::atomId ( int i ) const

inline

Get the id for a specific atom in the Group.

Parameters

i	index of atom within group (0,..., N-1)

Definition at line 348 of file ddMd/chemistry/Group.h.

Referenced by DdMd::ConfigIo::associate(), DdMd::AtomMap::findGroupGhostAtoms(), DdMd::AtomMap::findGroupLocalAtoms(), DdMd::Group< N >::pack(), and DdMd::Group< N >::setAtomId().

template<int N>

Atom * DdMd::Group< N >::atomPtr ( int i ) const

inline

Get a pointer to a specific Atom.

Parameters

i	index of atom within group (0,...,N-1)

Definition at line 355 of file ddMd/chemistry/Group.h.

Referenced by DdMd::AtomMap::findGroupGhostAtoms(), DdMd::GroupCollector< N >::nextPtr(), and DdMd::Group< N >::setAtomPtr().

template<int N>

int DdMd::Group< N >::nPtr ( ) const

inline

Return the number of non-null atom pointers in this group.

Definition at line 362 of file ddMd/chemistry/Group.h.

template<int N>

const Plan & DdMd::Group< N >::plan ( ) const

inline

Get communication plan (const reference).

Definition at line 369 of file ddMd/chemistry/Group.h.

template<int N>

void DdMd::Group< N >::pack ( Buffer & buffer )

Pack a Group into a send buffer.

Parameters

buffer Buffer object into which data should be packed.

Definition at line 448 of file ddMd/chemistry/Group.h.

References DdMd::Group< N >::atomId(), DdMd::Plan::flags(), DdMd::Group< N >::id(), DdMd::Buffer::incrementSendSize(), DdMd::Buffer::pack(), DdMd::Group< N >::plan(), and DdMd::Group< N >::typeId().

template<int N>

void DdMd::Group< N >::unpack ( Buffer & buffer )

Unpack a Group from the recv buffer.

Upon return:

all atom ids are set
group type id and global id are set
all atom pointers are null.

Parameters

buffer Buffer object from which data should be unpacked.

Definition at line 463 of file ddMd/chemistry/Group.h.

References DdMd::Group< N >::clearAtomPtr(), DdMd::Buffer::decrementRecvSize(), DdMd::Group< N >::plan(), DdMd::Group< N >::setAtomId(), DdMd::Plan::setFlags(), DdMd::Group< N >::setId(), DdMd::Group< N >::setTypeId(), and DdMd::Buffer::unpack().

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

Friends And Related Function Documentation

template<int N>

std::istream& operator>>	(	std::istream &	in,
		Group< N > &	group
	)

friend

istream extractor (>>) for a Group.

Parameters

in	input stream
group	Group to be read from stream

Returns: modified input stream

Definition at line 378 of file ddMd/chemistry/Group.h.

template<int N>

std::ostream& operator<<	(	std::ostream &	out,
		const Group< N > &	group
	)

friend

ostream inserter (<<) for a Group.

Format on one line with no line break:

Parameters

out	output stream
group	Group to be written to stream

Returns: modified output stream

Definition at line 392 of file ddMd/chemistry/Group.h.

template<int N>

template<class Archive >

void serialize	(	Archive &	ar,
		Group< N > &	group,
		const unsigned int	version
	)

friend

Serialize one Group<N>.

Default implementation calls serialize method of data object. Can be overridden by any explicit specialization.

Parameters

ar	archive object
group	object to be serialized
version	archive version id

Referenced by DdMd::operator<<().

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

ddMd/chemistry/Group.h

Detailed Description

template<int N> class DdMd::Group< N >

Public Member Functions

Static Public Member Functions

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

template<int N>
class DdMd::Group< N >