Detailed Description

Decomposition of the system into domains associated with processors.

Definition at line 31 of file Domain.h.

#include <Domain.h>

Inheritance diagram for DdMd::Domain:

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

virtual	~Domain ()
	Destructor. More...

void	setGridCommunicator (MPI::Intracomm &communicator)
	Set the grid communicator. More...

void	setBoundary (Boundary &boundary)
	Set the associated Boundary object. More...

virtual void	readParameters (std::istream &in)
	Read parameters and initialize. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load internal state from an archive. More...

virtual void	save (Serializable::OArchive &ar)
	Save internal state to an archive. More...

const Grid &	grid () const
	Return processor Grid by const reference. More...

int	gridCoordinate (int i) const
	Get coordinate of processor within grid in specified direction. More...

int	gridDimension (int i) const
	Get dimension of processor grid in specified direction. More...

bool	gridIsPeriodic (int i) const
	Is the grid periodic in the specified direction? More...

int	gridRank () const
	Get rank of this processor in the processor grid. More...

bool	isMaster () const
	Is this the master processor (gridRank == 0) ? More...

int	sourceRank (int i, int j) const
	Rank of the processor from which to receive for transfer (i, j). More...

int	destRank (int i, int j) const
	Rank of the processor to which to send for transfer (i, j). More...

int	shift (int i, int j) const
	Shift to be applied to sent coordinates in transfer (i, j). More...

MPI::Intracomm &	communicator () const
	Return Cartesian communicator by reference. More...

double	domainBound (int i, int j) const
	Get one boundary of the domain owned by this processor. More...

int	ownerRank (const Vector &position) const
	Return rank of the processor whose domain contains a position. More...

bool	isInDomain (const Vector &position) const
	Is a position in the domain owned by this processor? More...

bool	isInitialized () const
	Has this Domain been initialized by calling readParam? More...

bool	hasBoundary () const
	Has an associated Boundary been set? More...

Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor. More...

	ParamComposite (const ParamComposite &other)
	Copy constructor. More...

	ParamComposite (int capacity)
	Constructor. More...

virtual	~ParamComposite ()
	Virtual destructor. More...

void	resetParam ()
	Resets ParamComposite to its empty state. More...

virtual void	readParam (std::istream &in)
	Read the parameter file block. More...

virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block. More...

virtual void	writeParam (std::ostream &out)
	Write all parameters to an output stream. More...

virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive. More...

virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite. More...

void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true. More...

void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite. More...

void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite. More...

template<typename Type >
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter. More...

template<typename Type >
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter. More...

template<typename Type >
DArrayParam< Type > &	readDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read a required DArray < Type > parameter. More...

template<typename Type >
DArrayParam< Type > &	readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read an optional DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read a required FArray < Type, N > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read an optional FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	readCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read a required CArray2DParam < Type > 2D C-array. More...

template<typename Type >
CArray2DParam< Type > &	readOptionalCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read an optional CArray2DParam < Type > 2D C-array parameter. More...

template<typename Type >
DMatrixParam< Type > &	readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read a required DMatrix < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read an optional DMatrix < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix. More...

template<typename Type >
DSymmMatrixParam< Type > &	readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read an optional DMatrix matrix parameter. More...

Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket. More...

End &	readEnd (std::istream &in)
	Add and read the closing bracket. More...

Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line. More...

void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite. More...

void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n, bool isRequired)
	Add a C array parameter and load its elements. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n)
	Add and load a required CArrayParam< Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)
	Add an load a DArray < Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)
	Add and load a required DArray< Type > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)
	Add and load an FArray < Type, N > fixed-size array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)
	Add and load a required FArray < Type > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np, bool isRequired)
	Add and load a CArray2DParam < Type > C 2D array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np)
	Add and load a required < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)
	Add and load a DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and load a required DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)
	Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)
	Add and load a required DSymmMatrixParam < Type > matrix parameter. More...

void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array. More...

Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket. More...

End &	addEnd ()
	Add a closing bracket. More...

Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line. More...

std::string	className () const
	Get class name string. More...

bool	isRequired () const
	Is this ParamComposite required in the input file? More...

bool	isActive () const
	Is this parameter active? More...

Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor. More...

void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level. More...

std::string	indent () const
	Return indent string for this object (string of spaces). More...

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string. More...

Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor. More...

Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor. More...

	MpiFileIo (const MpiFileIo &other)
	Copy constructor. More...

bool	isIoProcessor () const
	Can this processor do file I/O ? More...

void	setIoCommunicator (MPI::Intracomm &communicator)
	Set the communicator. More...

void	clearCommunicator ()
	Clear (nullify) the communicator. More...

bool	hasIoCommunicator () const
	Does this object have an associated MPI communicator? More...

MPI::Intracomm &	ioCommunicator () const
	Get the MPI communicator by reference. More...

Additional Inherited Members
Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method. More...

typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method. More...

Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false. More...

static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent. More...

static bool	echo ()
	Get echo parameter. More...

Protected Member Functions inherited from Util::ParamComposite
void	setClassName (const char *className)
	Set class name string. More...

void	setIsRequired (bool isRequired)
	Set or unset the isActive flag. More...

void	setIsActive (bool isActive)
	Set or unset the isActive flag. More...

void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component. More...

void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array. More...

template<typename Type >
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	addCArray (std::istream &in, const char label, Type value, int n, bool isRequired=true)
	Add (but do not read) a required C array parameter. More...

template<typename Type >
DArrayParam< Type > &	addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true)
	Add (but do not read) a DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true)
	Add (but do not read) a FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	addCArray2D (std::istream &in, const char label, Type value, int m, int n, int np, bool isRequired=true)
	Add (but do not read) a CArray2DParam < Type > 2D C-array. More...

template<typename Type >
DMatrixParam< Type > &	addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true)
	Add and read a required DMatrix < Type > matrix parameter. More...

Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor. More...

	ParamComponent (const ParamComponent &other)
	Copy constructor. More...

Constructor & Destructor Documentation

DdMd::Domain::Domain ( )

Constructor.

Definition at line 19 of file Domain.cpp.

References Util::ParamComposite::setClassName().

DdMd::Domain::~Domain ( )

virtual

Destructor.

Definition at line 38 of file Domain.cpp.

Member Function Documentation

void DdMd::Domain::setGridCommunicator ( MPI::Intracomm & communicator )

Set the grid communicator.

Parameters

communicator Intramcommunicator to be used.

Definition at line 45 of file Domain.cpp.

void DdMd::Domain::setBoundary ( Boundary & boundary )

Set the associated Boundary object.

Parameters

boundary Boundary object.

Definition at line 58 of file Domain.cpp.

void DdMd::Domain::readParameters ( std::istream & in )

virtual

Read parameters and initialize.

Parameters

in	parameter input stream

Reimplemented from Util::ParamComposite.

Definition at line 64 of file Domain.cpp.

References hasBoundary(), and UTIL_THROW.

void DdMd::Domain::loadParameters ( Serializable::IArchive & ar )

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 90 of file Domain.cpp.

References hasBoundary(), and UTIL_THROW.

void DdMd::Domain::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 115 of file Domain.cpp.

References Util::Dimension, Util::Grid::isInGrid(), Util::Grid::position(), Util::Grid::rank(), Util::Grid::setDimensions(), Util::Grid::shift(), and UTIL_THROW.

const Grid & DdMd::Domain::grid ( ) const

inline

Return processor Grid by const reference.

Definition at line 268 of file Domain.h.

Referenced by DdMd::AtomDistributor::addAtom(), DdMd::Exchanger::exchange(), DdMd::AtomCollector::nextPtr(), DdMd::GroupCollector< N >::nextPtr(), DdMd::AtomDistributor::readParameters(), DdMd::AtomDistributor::send(), and DdMd::AtomDistributor::setup().

int DdMd::Domain::gridCoordinate ( int i ) const

inline

Get coordinate of processor within grid in specified direction.

Parameters

i	index of Cartesian direction 0 <= i < Dimension

Definition at line 277 of file Domain.h.

int DdMd::Domain::gridDimension ( int i ) const

inline

Get dimension of processor grid in specified direction.

Dimension of processor grid in specified direction.

Parameters

i	index of Cartesian direction 0 <= i < Dimension

Definition at line 286 of file Domain.h.

bool DdMd::Domain::gridIsPeriodic ( int i ) const

inline

Is the grid periodic in the specified direction?

Is the grid periodic in a specified direction?

Parameters

i	index of Cartesian direction 0 <= i < Dimension

Definition at line 295 of file Domain.h.

int DdMd::Domain::gridRank ( ) const

inline

Get rank of this processor in the processor grid.

Definition at line 304 of file Domain.h.

Referenced by DdMd::GroupDistributor< N >::add(), DdMd::AtomDistributor::addAtom(), DdMd::Exchanger::exchange(), DdMd::AtomDistributor::newAtomPtr(), DdMd::GroupDistributor< N >::newPtr(), DdMd::GroupDistributor< N >::receive(), DdMd::AtomDistributor::receive(), DdMd::GroupDistributor< N >::send(), DdMd::AtomDistributor::send(), and DdMd::AtomDistributor::setup().

bool DdMd::Domain::isMaster ( ) const

inline

Is this the master processor (gridRank == 0) ?

Definition at line 313 of file Domain.h.

Referenced by DdMd::EnergyAnalyzer::clear(), DdMd::NphIntegrator::integrateStep1(), DdMd::NptIntegrator::integrateStep1(), DdMd::NphIntegrator::integrateStep2(), DdMd::NptIntegrator::integrateStep2(), DdMd::ExternalEnergyAverage::loadParameters(), DdMd::PairEnergyAverage::loadParameters(), DdMd::VirialStressTensorAverage::loadParameters(), DdMd::AverageAnalyzer::loadParameters(), DdMd::SymmTensorAverageAnalyzer::loadParameters(), DdMd::TensorAverageAnalyzer::loadParameters(), DdMd::AtomCollector::nextPtr(), DdMd::GroupCollector< N >::nextPtr(), DdMd::EnergyAnalyzer::output(), DdMd::Exchanger::outputStatistics(), DdMd::ExternalEnergyAverage::readParameters(), DdMd::PairEnergyAverage::readParameters(), DdMd::StressAutoCorr::readParameters(), DdMd::AutoCorrAnalyzer< Data, Product >::readParameters(), DdMd::AverageAnalyzer::readParameters(), DdMd::SymmTensorAverageAnalyzer::readParameters(), DdMd::TensorAverageAnalyzer::readParameters(), DdMd::OutputPairEnergies::sample(), DdMd::LogEnergy::sample(), DdMd::VirialStressTensorAverage::sample(), DdMd::OutputStressTensor::sample(), DdMd::OutputEnergy::sample(), DdMd::OutputBoxdim::sample(), DdMd::OutputTemperature::sample(), DdMd::StressAutoCorr::sample(), DdMd::OutputPressure::sample(), DdMd::EnergyAnalyzer::sample(), DdMd::AtomCollector::send(), DdMd::GroupCollector< N >::send(), DdMd::AtomCollector::setup(), DdMd::GroupCollector< N >::setup(), and DdMd::AtomDistributor::validate().

int DdMd::Domain::sourceRank	(	int	i,
		int	j
	)		const

inline

Rank of the processor from which to receive for transfer (i, j).

Parameters

i	index of Cartesian direction 0 <= i < Dimension
j	index for positive (j = 0) or negative transfer (j = 1)

Definition at line 322 of file Domain.h.

Referenced by DdMd::Exchanger::exchange(), DdMd::Exchanger::reverseUpdate(), and DdMd::Exchanger::update().

int DdMd::Domain::destRank	(	int	i,
		int	j
	)		const

inline

Rank of the processor to which to send for transfer (i, j).

Parameters

i	index of Cartesian direction 0 <= i < Dimension
j	index for positive (j = 0) or negative transfer (j = 1)

Definition at line 331 of file Domain.h.

Referenced by DdMd::Exchanger::exchange(), DdMd::Exchanger::reverseUpdate(), and DdMd::Exchanger::update().

int DdMd::Domain::shift	(	int	i,
		int	j
	)		const

inline

Shift to be applied to sent coordinates in transfer (i, j).

When communicating an atomic position that is stored on the sending processsor as x = {x[0], x[1], x[2]}, the value of coordinate x[i] should be sent as x[i] - shift(i, j)*length[i] during transfer (i, j), where length[i] is the length of the unit cell in direction i.

Parameters