Detailed Description

Class for exchanging Atoms, Ghosts and Groups between processors.

Definition at line 35 of file Exchanger.h.

#include <Exchanger.h>

Public Types

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

	~Exchanger ()
	Destructor. More...

void	associate (const Domain &domain, const Boundary &boundary, AtomStorage &atomStorage, Buffer &buffer)
	Set pointers to associated objects. More...

void	addGroupExchanger (GroupExchanger &groupExchanger)
	Add a GroupExchanger to an internal list. More...

void	allocate ()
	Allocate all required memory. More...

void	setPairCutoff (double pairCutoff)
	Set width of slab for ghosts. More...

void	exchange ()
	Exchange local atoms and ghosts. More...

void	update ()
	Update ghost atom coordinates. More...

void	reverseUpdate ()
	Update ghost atom forces. More...

void	outputStatistics (std::ostream &out, double time, int nStep)
	Output statistics. More...

DdTimer &	timer ()
	Return internal timer by reference. More...

Member Enumeration Documentation

enum DdMd::Exchanger::timeId

Enumeration of time stamp identifiers.

Definition at line 128 of file Exchanger.h.

Constructor & Destructor Documentation

DdMd::Exchanger::Exchanger ( )

Constructor.

Definition at line 34 of file Exchanger.cpp.

DdMd::Exchanger::~Exchanger ( )

Destructor.

Definition at line 53 of file Exchanger.cpp.

Member Function Documentation

void DdMd::Exchanger::associate	(	const Domain &	domain,
		const Boundary &	boundary,
		AtomStorage &	atomStorage,
		Buffer &	buffer
	)

Set pointers to associated objects.

Parameters

domain	associated Domain object
boundary	associated Boundary object
atomStorage	associated AtomStorage object
buffer	associated Buffer object

Definition at line 59 of file Exchanger.cpp.

void DdMd::Exchanger::addGroupExchanger ( GroupExchanger & groupExchanger )

Add a GroupExchanger to an internal list.

Parameters

groupExchanger GroupExchanger object to add to list.

Definition at line 71 of file Exchanger.cpp.

void DdMd::Exchanger::allocate ( )

Allocate all required memory.

Must be called after Buffer is initialized.

Definition at line 77 of file Exchanger.cpp.

References Util::Dimension, DdMd::Buffer::ghostCapacity(), DdMd::Buffer::isInitialized(), and UTIL_THROW.

void DdMd::Exchanger::setPairCutoff ( double pairCutoff )

Set width of slab for ghosts.

Parameters

pairCutoff cutoff radius for pair list (potential + skin).

Definition at line 99 of file Exchanger.cpp.

void DdMd::Exchanger::exchange ( )

Exchange local atoms and ghosts.

This method should be called just before rebuilding the neighbor list on each processor, to exchange ownership of local atoms and to exchange ghost atoms. The lists of which atoms were sent and received as ghosts by this method are used in subsequent calls to update.

Definition at line 106 of file Exchanger.cpp.

Referenced by DdMd::TwoStepIntegrator::run(), and DdMd::Integrator::setupAtoms().

void DdMd::Exchanger::update ( )

Update ghost atom coordinates.

This method should be called every time step for which there is no exhange of atom ownership. It communicates ghost coordinates for the same ghosts as those sent by the most recent call to the exchangeGhosts() methods.

Definition at line 821 of file Exchanger.cpp.

References Simp::OrthorhombicBoundary::applyShift(), DdMd::Buffer::beginRecvBlock(), DdMd::Buffer::beginSendBlock(), DdMd::Buffer::clearSendBuffer(), DdMd::Domain::communicator(), DdMd::Atom::copyLocalUpdate(), DdMd::Domain::destRank(), Util::Dimension, DdMd::Buffer::endRecvBlock(), DdMd::Buffer::endSendBlock(), DdMd::AtomStorage::isCartesian(), DdMd::Atom::packUpdate(), DdMd::Atom::position(), DdMd::Buffer::sendRecv(), DdMd::Domain::shift(), DdMd::Domain::sourceRank(), DdMd::Atom::unpackUpdate(), and UTIL_THROW.

Referenced by DdMd::TwoStepIntegrator::run().

void DdMd::Exchanger::reverseUpdate ( )

Update ghost atom forces.

This method reverse the communication pattern used to communicate ghost atom positions in update() to reverse communicate forces acting on ghost atoms. It should be called only if reverse force communication is enabled, in which case it should be called after all force calculation on every time step for which update() is called.

Definition at line 902 of file Exchanger.cpp.

References DdMd::Buffer::beginRecvBlock(), DdMd::Buffer::beginSendBlock(), DdMd::Buffer::clearSendBuffer(), DdMd::Domain::communicator(), DdMd::Domain::destRank(), Util::Dimension, DdMd::Buffer::endRecvBlock(), DdMd::Buffer::endSendBlock(), DdMd::Atom::force(), DdMd::Atom::packForce(), DdMd::Buffer::sendRecv(), DdMd::Domain::sourceRank(), and DdMd::Atom::unpackForce().