Detailed Description

A point particle in an MD simulation.

An Atom has:

a position Util::Vector
a force Util::Vector
a velocity Util::Vector
an integer atom type Id
a boolean isGhost flag
a global integer id
a Mask (list of other atoms with masked pair interactions)
a communication Plan

An Atom may only be constructed as an element of an AtomArray. The Atom constructor is private, to prevent instantiation of an indivual Atom, but is accessible by the AtomArray class via a a friend declaration.

The interface of the Atom class provides access to each Atom data field through an accessor function, as if all were true C++ class data members. In fact, some of the above are "pseudo-members" that are stored in separate arrays. All arrays that store atom data are private members of the associated AtomArray, all of which use the same indexing scheme to identify atoms. Each Atom object has a pointer to its parent AtomArray and its array index, in private members. The public accessor method for each pseudo-member simply retrieves the required array element for this atom.

In the current implementation, the position, force, atom type id, and isGhost flag are stored in true member variables of an Atom object, while the velocity, mask, plan, id (the global atom index), and AtomContext (if any) are all pseudo-members stored in separate arrays. See documentation of the private member localId_ and other comments in the Atom.h file for further implementation details.

Definition at line 64 of file ddMd/chemistry/Atom.h.

#include <Atom.h>

Public Member Functions
Mutators
Atom &	operator= (Atom const &other)
	Assignment. More...

void	clear ()
	Reset integer members to initial null values. More...

void	setId (int Id)
	Set unique global id for this Atom. More...

void	setTypeId (int Id)
	Set the atom type index. More...

void	setIsGhost (bool isGhost)
	Mark as ghost or local atom for this processor. More...

Accessors (return non-const references)
Vector &	position ()
	Get position Vector by reference. More...

Vector &	velocity ()
	Get velocity Vector by reference. More...

Vector &	force ()
	Get force Vector by reference. More...

Mask &	mask ()
	Get the associated Mask by reference. More...

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

AtomContext &	context ()
	Get the AtomContext struct by non-const reference. More...

unsigned int &	groups ()
	Get groups bit field by non-const reference. More...

Accessors (return by value or const references).
int	id () const
	Get unique global index for this atom. More...

int	typeId () const
	Get atom type index. More...

bool	isGhost () const
	Is this atom a ghost? More...

const Vector &	position () const
	Get the position Vector (const reference). More...

const Vector &	velocity () const
	Get the velocity Vector (const reference). More...

const Vector &	force () const
	Get the force Vector (const reference). More...

const Mask &	mask () const
	Get the associated Mask by const reference. More...

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

const AtomContext &	context () const
	Get the AtomContext struct by const reference. More...

unsigned int	groups () const
	Get bit field of groups to which this atom belongs. More...

Pack and Unpack Methods (Interprocessor Communication)
void	packAtom (Buffer &buffer)
	Pack an Atom into a send buffer, for exchange of ownership. More...

void	unpackAtom (Buffer &buffer)
	Unpack an atom from a recv buffer and receive ownership. More...

void	packGhost (Buffer &buffer)
	Pack a ghost Atom into a send buffer. More...

void	unpackGhost (Buffer &buffer)
	Unpack a ghost Atom from a recv buffer. More...

void	packUpdate (Buffer &buffer)
	Pack updated ghost position into send buffer. More...

void	unpackUpdate (Buffer &buffer)
	Unpack updated ghost position from recv buffer. More...

void	packForce (Buffer &buffer)
	Pack update of ghost Atom force into send buffer. More...

void	unpackForce (Buffer &buffer)
	Unpack updated position of ghost Atom from recv buffer. More...

void	copyLocalGhost (Atom const &sendAtom)
	Copies data from local atom to update this ghost atom. More...

void	copyLocalUpdate (Atom const &sendAtom)
	Copies position of local atom to update this ghost atom. More...

Static Public Member Functions
static void	setHasAtomContext (bool hasAtomContext)
	Enable (true) or disable (false) use of AtomContext data. More...

static bool	hasAtomContext ()
	Is AtomContext data enabled? More...

static int	packedAtomSize ()
	Return max size of an atom packed for exchange, in bytes. More...

static int	packedGhostSize ()
	Return size of ghost atom packed for communication, in bytes. More...

Friends
class	Util::Memory

Member Function Documentation

void DdMd::Atom::setHasAtomContext ( bool hasAtomContext )

static

Enable (true) or disable (false) use of AtomContext data.

Parameters

hasAtomContext new value for hasAtomContext static bool flag.

Definition at line 29 of file ddMd/chemistry/Atom.cpp.

Referenced by DdMd::Simulation::loadParameters(), and DdMd::Simulation::readParameters().

bool DdMd::Atom::hasAtomContext ( )

inlinestatic

Is AtomContext data enabled?

Definition at line 591 of file ddMd/chemistry/Atom.h.

Referenced by DdMd::AtomArray::allocate(), DdMd::ConfigIoFactory::factory(), DdMd::SerializeConfigIo::loadConfig(), DdMd::DdMdConfigIo::readConfig(), DdMd::DdMdOrderedConfigIo::readConfig(), DdMd::SerializeConfigIo::saveConfig(), DdMd::Simulation::setConfigIo(), DdMd::Simulation::unsetVirialStress(), DdMd::DdMdConfigIo::writeConfig(), and DdMd::DdMdOrderedConfigIo::writeConfig().

int DdMd::Atom::packedAtomSize ( )

static

Return max size of an atom packed for exchange, in bytes.

Definition at line 149 of file ddMd/chemistry/Atom.cpp.

Referenced by DdMd::Buffer::isInitialized().

int DdMd::Atom::packedGhostSize ( )

static

Return size of ghost atom packed for communication, in bytes.

Definition at line 204 of file ddMd/chemistry/Atom.cpp.

Referenced by DdMd::Buffer::isInitialized().

Atom & DdMd::Atom::operator= ( Atom const & other )

Assignment.

Definition at line 49 of file ddMd/chemistry/Atom.cpp.

References context(), groups(), id(), isGhost(), mask(), plan(), and velocity().

void DdMd::Atom::clear ( )

Reset integer members to initial null values.

Definition at line 69 of file ddMd/chemistry/Atom.cpp.

Referenced by DdMd::AtomDistributor::newAtomPtr(), DdMd::AtomStorage::newAtomPtr(), and DdMd::AtomStorage::newGhostPtr().

void DdMd::Atom::setId ( int Id )

inline

Set unique global id for this Atom.

This id must be unique among all atoms on all processors, and must be less than totalAtomCapacity of the AtomStorage.

Parameters

Id	unique atom id.

Definition at line 551 of file ddMd/chemistry/Atom.h.

Referenced by DdMd::AtomStorage::addAtom(), DdMd::AtomStorage::addGhost(), DdMd::Exchanger::exchange(), DdMd::SerializeConfigIo::loadConfig(), DdMd::DdMdConfigIo::readConfig(), DdMd::LammpsConfigIo::readConfig(), and DdMd::DdMdOrderedConfigIo::readConfig().

void DdMd::Atom::setTypeId ( int Id )

inline

Set the atom type index.

Parameters

Id	integer index that identifies atom type

Definition at line 433 of file ddMd/chemistry/Atom.h.

Referenced by DdMd::Exchanger::exchange(), DdMd::SerializeConfigIo::loadConfig(), DdMd::DdMdConfigIo::readConfig(), DdMd::LammpsConfigIo::readConfig(), and DdMd::DdMdOrderedConfigIo::readConfig().

void DdMd::Atom::setIsGhost ( bool isGhost )

inline

Mark as ghost or local atom for this processor.

Parameters

isGhost true if this is a ghost, or false if local.

Definition at line 439 of file ddMd/chemistry/Atom.h.

Referenced by DdMd::AtomStorage::addNewAtom(), DdMd::AtomStorage::addNewGhost(), and DdMd::AtomStorage::newGhostPtr().

Vector & DdMd::Atom::position ( )

inline

Get position Vector by reference.

Definition at line 468 of file ddMd/chemistry/Atom.h.

Vector & DdMd::Atom::velocity ( )

inline

Get velocity Vector by reference.

Definition at line 509 of file ddMd/chemistry/Atom.h.

Referenced by DdMd::SerializeConfigIo::loadConfig(), operator=(), DdMd::DdMdConfigIo::readConfig(), DdMd::DdMdOrderedConfigIo::readConfig(), DdMd::SerializeConfigIo::saveConfig(), DdMd::DdMdConfigIo::writeConfig(), and DdMd::DdMdOrderedConfigIo::writeConfig().

Vector & DdMd::Atom::force ( )

inline

Get force Vector by reference.

Definition at line 480 of file ddMd/chemistry/Atom.h.

Referenced by DdMd::PairPotentialImpl< Interaction >::computeEnergy(), DdMd::AnglePotentialImpl< Interaction >::computeForces(), DdMd::BondPotentialImpl< Interaction >::computeForces(), DdMd::DihedralPotentialImpl< Interaction >::computeForces(), DdMd::BondPotentialImpl< Interaction >::computeForcesAndStress(), DdMd::PairPotentialImpl< Interaction >::computeForcesAndStress(), and DdMd::Exchanger::reverseUpdate().

Mask & DdMd::Atom::mask ( )

inline

Get the associated Mask by reference.

Definition at line 521 of file ddMd/chemistry/Atom.h.

Referenced by operator=(), and DdMd::ConfigIo::setAtomMasks().

Plan & DdMd::Atom::plan ( )

inline

Get communication plan by reference.

Definition at line 533 of file ddMd/chemistry/Atom.h.

Referenced by copyLocalGhost(), DdMd::Exchanger::exchange(), DdMd::GroupStorage< N >::markGhosts(), DdMd::GroupStorage< N >::markSpanningGroups(), operator=(), and DdMd::GroupStorage< N >::pack().

AtomContext & DdMd::Atom::context ( )

inline

Get the AtomContext struct by non-const reference.

Throws and Exception if atom context data is disabled.

A DdMd::AtomContext struct contains public members speciesId, moleculeId and atomId that identify the species of molecule to which this atom belongs, the index of the molecule within it species, and the index of the atom with the molecule.

Definition at line 557 of file ddMd/chemistry/Atom.h.

References UTIL_THROW.

Referenced by copyLocalGhost(), DdMd::SerializeConfigIo::loadConfig(), operator=(), DdMd::DdMdConfigIo::readConfig(), DdMd::DdMdOrderedConfigIo::readConfig(), DdMd::SerializeConfigIo::saveConfig(), DdMd::DdMdConfigIo::writeConfig(), and DdMd::DdMdOrderedConfigIo::writeConfig().

unsigned int & DdMd::Atom::groups ( )

inline

Get groups bit field by non-const reference.

The unsigned int groups is used as a bit field in which bit number i (with i=0 the least signficant bit), is set true/1 if this atom belongs to group i, and is false/0 if this atom of not belong to group i. By default, all bits are clear.

Individual bits may be set, unset and queried using an instance of class Util::Bit.

Definition at line 579 of file ddMd/chemistry/Atom.h.

Referenced by DdMd::SerializeConfigIo::loadConfig(), operator=(), DdMd::SerializeConfigIo::saveConfig(), DdMd::DdMdGroupTrajectoryWriter::writeFrame(), and DdMd::DdMdGroupTrajectoryWriter::writeHeader().

int DdMd::Atom::id ( ) const

inline

Get unique global index for this atom.

Definition at line 545 of file ddMd/chemistry/Atom.h.

Referenced by DdMd::AtomMap::addGhost(), DdMd::AtomMap::addLocal(), copyLocalGhost(), DdMd::Exchanger::exchange(), DdMd::AtomMap::findGroupGhostAtoms(), DdMd::AtomMap::findGroupLocalAtoms(), DdMd::AtomMap::isValid(), operator=(), DdMd::AtomMap::removeGhost(), DdMd::AtomMap::removeLocal(), DdMd::SerializeConfigIo::saveConfig(), DdMd::DdMdConfigIo::writeConfig(), DdMd::LammpsConfigIo::writeConfig(), DdMd::DdMdOrderedConfigIo::writeConfig(), DdMd::LammpsDumpWriter::writeFrame(), DdMd::DdMdTrajectoryWriter::writeFrame(), and DdMd::DdMdGroupTrajectoryWriter::writeFrame().

int DdMd::Atom::typeId ( ) const

inline

Get atom type index.

Definition at line 453 of file ddMd/chemistry/Atom.h.

Referenced by DdMd::PairPotentialImpl< Interaction >::computeEnergy(), DdMd::PairPotentialImpl< Interaction >::computeForcesAndStress(), DdMd::PairPotentialImpl< Interaction >::computePairEnergies(), DdMd::PairPotentialImpl< Interaction >::computeStress(), copyLocalGhost(), DdMd::Exchanger::exchange(), DdMd::SerializeConfigIo::saveConfig(), DdMd::DdMdConfigIo::writeConfig(), DdMd::LammpsConfigIo::writeConfig(), DdMd::DdMdOrderedConfigIo::writeConfig(), and DdMd::LammpsDumpWriter::writeFrame().

bool DdMd::Atom::isGhost ( ) const

inline

Is this atom a ghost?

Definition at line 459 of file ddMd/chemistry/Atom.h.

Vector const & DdMd::Atom::position ( ) const

inline

Get the position Vector (const reference).

Definition at line 474 of file ddMd/chemistry/Atom.h.

Vector const & DdMd::Atom::velocity ( ) const

inline

Get the velocity Vector (const reference).

Definition at line 515 of file ddMd/chemistry/Atom.h.

Vector const & DdMd::Atom::force ( ) const

inline

Get the force Vector (const reference).

Definition at line 486 of file ddMd/chemistry/Atom.h.

Mask const & DdMd::Atom::mask ( ) const

inline

Get the associated Mask by const reference.

Definition at line 527 of file ddMd/chemistry/Atom.h.

Plan const & DdMd::Atom::plan ( ) const

inline

Get communication plan by const reference.

Definition at line 539 of file ddMd/chemistry/Atom.h.

AtomContext const & DdMd::Atom::context ( ) const

inline

Get the AtomContext struct by const reference.

Throws an Exception if atom context data is disabled.

See also: AtomContext& context() non-const accessor for

Definition at line 568 of file ddMd/chemistry/Atom.h.

References UTIL_THROW.

unsigned int DdMd::Atom::groups ( ) const

inline

Get bit field of groups to which this atom belongs.

See also: Atom::groups() non-const accessor.

Definition at line 585 of file ddMd/chemistry/Atom.h.

void DdMd::Atom::packAtom ( Buffer & buffer )

Pack an Atom into a send buffer, for exchange of ownership.

Packs required data, increments buffer sendSize counter.

Parameters

buffer communication buffer

Definition at line 88 of file ddMd/chemistry/Atom.cpp.

References DdMd::Buffer::incrementSendSize(), and DdMd::Buffer::pack().

Referenced by DdMd::AtomDistributor::addAtom(), DdMd::AtomDistributor::newAtomPtr(), and DdMd::AtomDistributor::send().

void DdMd::Atom::unpackAtom ( Buffer & buffer )

Unpack an atom from a recv buffer and receive ownership.

Parameters

buffer communication buffer

Definition at line 114 of file ddMd/chemistry/Atom.cpp.

References DdMd::Buffer::decrementRecvSize(), and DdMd::Buffer::unpack().

Referenced by DdMd::Exchanger::exchange(), and DdMd::AtomDistributor::receive().

void DdMd::Atom::packGhost ( Buffer & buffer )

Pack a ghost Atom into a send buffer.

Packs required data, increments buffer sendSize counter.

Parameters

buffer communication buffer

Definition at line 168 of file ddMd/chemistry/Atom.cpp.

References DdMd::Buffer::incrementSendSize(), and DdMd::Buffer::pack().

Referenced by DdMd::Exchanger::exchange().

void DdMd::Atom::unpackGhost ( Buffer & buffer )

Unpack a ghost Atom from a recv buffer.

Unpacks required data, decrements buffer recvSize counter.

Parameters

buffer communication buffer

Definition at line 184 of file ddMd/chemistry/Atom.cpp.

References DdMd::Buffer::decrementRecvSize(), and DdMd::Buffer::unpack().

Referenced by DdMd::Exchanger::exchange().

void DdMd::Atom::packUpdate ( Buffer & buffer )

Pack updated ghost position into send buffer.

Packs position Vector, increments buffer sendSize counter.

Parameters

buffer communication buffer

Definition at line 221 of file ddMd/chemistry/Atom.cpp.

References DdMd::Buffer::incrementSendSize(), and DdMd::Buffer::pack().

Referenced by DdMd::Exchanger::update().

void DdMd::Atom::unpackUpdate ( Buffer & buffer )

Unpack updated ghost position from recv buffer.

Unpacks position Vector, decrements buffer recvSize counter.

Parameters

buffer communication buffer

Definition at line 230 of file ddMd/chemistry/Atom.cpp.

References DdMd::Buffer::decrementRecvSize(), and DdMd::Buffer::unpack().

Referenced by DdMd::Exchanger::update().

void DdMd::Atom::packForce ( Buffer & buffer )

Pack update of ghost Atom force into send buffer.

Packs force Vector, increments buffer sendSize counter.

Parameters

buffer communication buffer

Definition at line 241 of file ddMd/chemistry/Atom.cpp.

References DdMd::Buffer::incrementSendSize(), and DdMd::Buffer::pack().

Referenced by DdMd::Exchanger::reverseUpdate().

void DdMd::Atom::unpackForce ( Buffer & buffer )

Unpack updated position of ghost Atom from recv buffer.

Reads force from buffer and increments the atomic force (rather than overwriting), then decrements recvSize counter.

Parameters

buffer communication buffer

Definition at line 250 of file ddMd/chemistry/Atom.cpp.

References DdMd::Buffer::decrementRecvSize(), and DdMd::Buffer::unpack().

Referenced by DdMd::Exchanger::reverseUpdate().

void DdMd::Atom::copyLocalGhost ( Atom const & sendAtom )

Copies data from local atom to update this ghost atom.

Parameters

sendAtom Local atom to be copied to this atom.

Definition at line 262 of file ddMd/chemistry/Atom.cpp.

References context(), DdMd::Plan::flags(), id(), plan(), position(), and typeId().

Referenced by DdMd::Exchanger::exchange().

void DdMd::Atom::copyLocalUpdate ( Atom const & sendAtom )

Copies position of local atom to update this ghost atom.

Parameters

sendAtom Local atom to be copied to update this atom.

Definition at line 276 of file ddMd/chemistry/Atom.cpp.

References position().

Referenced by DdMd::Exchanger::update().

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

Detailed Description

Public Member Functions

Static Public Member Functions

Friends

Member Function Documentation