Detailed Description

Abstract base for periodic output and/or analysis actions.

The periodic action associated with an Analyzer is implemented by the pure virtual sample() method. This action often involves computation of a physical property, which may be either added it to statistical accumulator or output to a file, or both. The sample() method is called periodically during a simulation, with a period determined by the interval member variable. The interval for each analyzer must be a multiple of the static member variable Analyzer::baseInterval.

An AnalyzerManager object acts as a container for Analyzers that are associated with a simulation. The AnalyzerManager::sample() function is called every time step, and calls the sample() function of each Analyzer only on time steps when the simulation step index is an integer multiple of the interval for that Analyzer.

An Analyzer has access to its parent Simulation via the protected Analyzer::simulation() method, which returns the parent Simulation by reference.

Definition at line 49 of file ddMd/analyzers/Analyzer.h.

#include <Analyzer.h>

Inheritance diagram for DdMd::Analyzer:

Public Member Functions
	Analyzer (Simulation &simulation)
	Constructor. More...

virtual	~Analyzer ()
	Destructor. More...

virtual void	setup ()
	Setup before simulation. More...

virtual void	clear ()
	Clear statistical accumulators. More...

virtual void	sample (long iStep)=0
	Calculate, analyze and/or output a physical quantity. More...

virtual void	output ()
	Output any results at the end of a simulation. 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...

int	interval () const
	Get interval value. More...

bool	isAtInterval (long counter) const
	Return true iff counter is a multiple of the interval. 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	readParameters (std::istream &in)
	Read the body of parameter block, without begin and end lines. 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...

Static Public Member Functions
static void	initStatic ()
	Define and initialize baseInterval. 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...

Static Public Attributes
static long	baseInterval = 1
	The interval for an Analyzer must be a multiple of baseInterval. More...

Protected Member Functions
void	readInterval (std::istream &in)
	Read parameter interval from file. More...

void	loadInterval (Serializable::IArchive &ar)
	Load parameter interval from input archive. More...

void	saveInterval (Serializable::OArchive &ar)
	Save interval parameter to an archive. More...

void	readOutputFileName (std::istream &in)
	Read outputFileName from file. More...

void	loadOutputFileName (Serializable::IArchive &ar)
	Load output file name to an archive. More...

void	saveOutputFileName (Serializable::OArchive &ar)
	Save output file name to an archive. More...

Simulation &	simulation ()
	Get the parent Simulation by reference. More...

const std::string &	outputFileName () const
	Return outputFileName string. More...

std::string	outputFileName (const std::string &suffix) const
	Return outputFileName string with added suffix. 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...

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...

Constructor & Destructor Documentation

DdMd::Analyzer::Analyzer ( Simulation & simulation )

Constructor.

Definition at line 26 of file ddMd/analyzers/Analyzer.cpp.

DdMd::Analyzer::~Analyzer ( )

virtual

Destructor.

Definition at line 36 of file ddMd/analyzers/Analyzer.cpp.

Member Function Documentation

virtual void DdMd::Analyzer::setup ( )

inlinevirtual

Setup before simulation.

This method is called just before the beginning of the main simulation loop within the Integrator::run() method. It may be used to complete any initialization or checks that require knowledge of the configuration. It will be called every time run is invoked, not just the first.

The default implementation is empty.

Reimplemented in DdMd::SymmTensorAverageAnalyzer, DdMd::EnergyAnalyzer, DdMd::TensorAverageAnalyzer, DdMd::AverageAnalyzer, DdMd::TrajectoryWriter, DdMd::AutoCorrAnalyzer< Data, Product >, DdMd::AutoCorrAnalyzer< Tensor, double >, DdMd::OutputPressure, DdMd::StressAutoCorr, DdMd::OutputEnergy, DdMd::OutputTemperature, DdMd::OutputBoxdim, and DdMd::OutputStressTensor.

Definition at line 77 of file ddMd/analyzers/Analyzer.h.

virtual void DdMd::Analyzer::clear ( )

inlinevirtual

Clear statistical accumulators.

This method is called by the Integrator::clear() method, which is called before the main simulation loop only the first time that the integrator is run, and when invoked explicitly thereafter.

The default implementation is empty.

Reimplemented in DdMd::VanHove, DdMd::StructureFactor, DdMd::StructureFactorGrid, DdMd::TrajectoryWriter, DdMd::OrderParamNucleation, DdMd::SymmTensorAverageAnalyzer, DdMd::TensorAverageAnalyzer, DdMd::AverageAnalyzer, DdMd::EnergyAnalyzer, DdMd::ConfigWriter, DdMd::AutoCorrAnalyzer< Data, Product >, DdMd::AutoCorrAnalyzer< Tensor, double >, DdMd::LogEnergy, DdMd::VirialStressTensorAverage, DdMd::OutputPairEnergies, DdMd::OutputPressure, DdMd::StressAutoCorr, DdMd::VirialStressTensor, DdMd::ExternalEnergyAverage, DdMd::OutputEnergy, DdMd::OutputTemperature, DdMd::PairEnergyAverage, DdMd::OutputBoxdim, and DdMd::OutputStressTensor.

Definition at line 90 of file ddMd/analyzers/Analyzer.h.

virtual void DdMd::Analyzer::sample ( long iStep )

pure virtual

Calculate, analyze and/or output a physical quantity.

Take an action if iStep is a multiple of interval. If iStep is not a multiple of interval, this method should do nothing and return immediately.

Parameters

iStep current simulation step index.

Implemented in DdMd::VanHove, DdMd::StructureFactor, DdMd::StructureFactorGrid, DdMd::OrderParamNucleation, DdMd::TensorAverageAnalyzer, DdMd::SymmTensorAverageAnalyzer, DdMd::EnergyAnalyzer, DdMd::AverageAnalyzer, DdMd::TrajectoryWriter, DdMd::ConfigWriter, DdMd::AutoCorrAnalyzer< Data, Product >, DdMd::AutoCorrAnalyzer< Tensor, double >, DdMd::OutputPressure, DdMd::StressAutoCorr, DdMd::OutputEnergy, DdMd::OutputTemperature, DdMd::OutputBoxdim, DdMd::OutputStressTensor, DdMd::LogEnergy, DdMd::VirialStressTensorAverage, DdMd::OutputPairEnergies, DdMd::VirialStressTensor, DdMd::ExternalEnergyAverage, and DdMd::PairEnergyAverage.

virtual void DdMd::Analyzer::output ( )

inlinevirtual

Output any results at the end of a simulation.

The default implementation is empty.

Reimplemented in DdMd::VanHove, DdMd::StructureFactor, DdMd::StructureFactorGrid, DdMd::OrderParamNucleation, DdMd::TensorAverageAnalyzer, DdMd::TrajectoryWriter, DdMd::SymmTensorAverageAnalyzer, DdMd::EnergyAnalyzer, DdMd::AverageAnalyzer, DdMd::AutoCorrAnalyzer< Data, Product >, DdMd::AutoCorrAnalyzer< Tensor, double >, DdMd::StressAutoCorr, DdMd::VirialStressTensorAverage, DdMd::ExternalEnergyAverage, and DdMd::PairEnergyAverage.

Definition at line 109 of file ddMd/analyzers/Analyzer.h.

virtual void DdMd::Analyzer::loadParameters ( Serializable::IArchive & ar )

inlinevirtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Reimplemented in DdMd::VanHove, DdMd::StructureFactor, DdMd::StructureFactorGrid, DdMd::OrderParamNucleation, DdMd::TrajectoryWriter, DdMd::SymmTensorAverageAnalyzer, DdMd::TensorAverageAnalyzer, DdMd::AverageAnalyzer, DdMd::EnergyAnalyzer, DdMd::ConfigWriter, DdMd::AutoCorrAnalyzer< Data, Product >, DdMd::AutoCorrAnalyzer< Tensor, double >, DdMd::LogEnergy, DdMd::VirialStressTensorAverage, DdMd::OutputPairEnergies, DdMd::OutputPressure, DdMd::StressAutoCorr, DdMd::VirialStressTensor, DdMd::ExternalEnergyAverage, DdMd::OutputEnergy, DdMd::OutputTemperature, DdMd::PairEnergyAverage, DdMd::OutputBoxdim, DdMd::OutputStressTensor, DdMd::PairEnergyAnalyzer, and DdMd::DdMdGroupTrajectoryWriter.

Definition at line 117 of file ddMd/analyzers/Analyzer.h.

virtual void DdMd::Analyzer::save ( Serializable::OArchive & ar )

inlinevirtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Reimplemented in DdMd::VanHove, DdMd::StructureFactor, DdMd::StructureFactorGrid, DdMd::OrderParamNucleation, DdMd::TrajectoryWriter, DdMd::SymmTensorAverageAnalyzer, DdMd::TensorAverageAnalyzer, DdMd::AverageAnalyzer, DdMd::EnergyAnalyzer, DdMd::ConfigWriter, DdMd::AutoCorrAnalyzer< Data, Product >, DdMd::AutoCorrAnalyzer< Tensor, double >, DdMd::LogEnergy, DdMd::VirialStressTensorAverage, DdMd::OutputPairEnergies, DdMd::OutputPressure, DdMd::StressAutoCorr, DdMd::VirialStressTensor, DdMd::ExternalEnergyAverage, DdMd::OutputEnergy, DdMd::OutputTemperature, DdMd::PairEnergyAverage, DdMd::OutputBoxdim, DdMd::OutputStressTensor, DdMd::PairEnergyAnalyzer, and DdMd::DdMdGroupTrajectoryWriter.

Definition at line 125 of file ddMd/analyzers/Analyzer.h.

int DdMd::Analyzer::interval ( ) const

inline

Get interval value.

Definition at line 237 of file ddMd/analyzers/Analyzer.h.

Referenced by DdMd::AverageAnalyzer::sample(), DdMd::EnergyAnalyzer::sample(), DdMd::SymmTensorAverageAnalyzer::sample(), and DdMd::TensorAverageAnalyzer::sample().

bool DdMd::Analyzer::isAtInterval ( long counter ) const

inline

Return true iff counter is a multiple of the interval.

Parameters

counter simulation step counter

Definition at line 243 of file ddMd/analyzers/Analyzer.h.

Referenced by DdMd::ExternalEnergyAverage::sample(), DdMd::PairEnergyAverage::sample(), DdMd::OutputPairEnergies::sample(), DdMd::VirialStressTensor::sample(), DdMd::VirialStressTensorAverage::sample(), DdMd::LogEnergy::sample(), DdMd::OutputStressTensor::sample(), DdMd::OutputEnergy::sample(), DdMd::OutputTemperature::sample(), DdMd::OutputBoxdim::sample(), DdMd::OutputPressure::sample(), DdMd::StressAutoCorr::sample(), DdMd::AutoCorrAnalyzer< Data, Product >::sample(), DdMd::ConfigWriter::sample(), DdMd::TrajectoryWriter::sample(), DdMd::AverageAnalyzer::sample(), DdMd::EnergyAnalyzer::sample(), DdMd::SymmTensorAverageAnalyzer::sample(), DdMd::TensorAverageAnalyzer::sample(), DdMd::OrderParamNucleation::sample(), DdMd::StructureFactorGrid::sample(), DdMd::StructureFactor::sample(), and DdMd::VanHove::sample().

void DdMd::Analyzer::initStatic ( )

static

Define and initialize baseInterval.

Definition at line 20 of file ddMd/analyzers/Analyzer.cpp.

void DdMd::Analyzer::readInterval ( std::istream & in )

protected

Read parameter interval from file.

This function throws an exception if the value of interval is not a multiple of Analyzer::baseInterval, or if baseInterval has not been set to a nonzero positive value.

Parameters

in	input parameter file stream.

Definition at line 42 of file ddMd/analyzers/Analyzer.cpp.

References baseInterval, and UTIL_THROW.

void DdMd::Analyzer::loadInterval ( Serializable::IArchive & ar )

protected

Load parameter interval from input archive.

This function throws an exception if the value of interval is not a multiple of Analyzer::baseInterval, or if baseInterval has not been set to a nonzero positive value.

Parameters