Detailed Description

Abstract base for periodic output and/or analysis actions.

The periodic action associated with an Analyzer can involve sampling of a physical property and adding it to statistical accumulator, outputting it to file, or both. This periodic action must be implemented by the pure virtual sample() method.

The sample() method should take the desired action only when the simulation step index is an integer multiple of the associated interval parameter. The interval must be a positive integer that is a multiple of the static member Analyzer::baseInterval.

The virtual sample() method does not take any parameters. An Analyzer must thus access its parent Simulation and/or System via a pointer, which is usually initialized in its subclass constructor.

Analyzer subclasses that are associated with one System, McSystem or MdSystem (i.e., almost all of them) should be derived from the SystemAnalyzer<class SystemType> class template. This takes a reference to the parent system as parameter to its constructor. An Analyzer subclass that can be used with any System should be derived from SystemAnalyzer<System>, and one that can be used only with a MdSystem or McSystem should be derived from SystemAnalyzer<MdSystem> or SystemAnalyzer<MdSystem>, respectively.

Definition at line 52 of file mcMd/analyzers/Analyzer.h.

#include <Analyzer.h>

Inheritance diagram for McMd::Analyzer:

Public Member Functions
	Analyzer ()
	Default constructor. More...

virtual	~Analyzer ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Read parameters from archive. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load parameters from archive. More...

virtual void	save (Serializable::OArchive &ar)
	Load parameters to archive. More...

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize to/from an archive. More...

virtual void	setup ()
	Complete any required initialization. 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 the simulation. 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	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 = 0
	The interval for an Analyzer must be a multiple of baseInterval. More...

Protected Member Functions
void	setFileMaster (FileMaster &fileMaster)
	Set the FileMaster to use to open files. More...

void	readInterval (std::istream &in)
	Read interval from file, with error checking. More...

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

void	loadInterval (Serializable::IArchive &ar)
	Load interval from archive, with error checking. More...

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

FileMaster &	fileMaster ()
	Get the FileMaster 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...

Protected Attributes
std::string	outputFileName_
	Base name of output file(s). More...

long	interval_
	Number of simulation steps between subsequent actions. 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

McMd::Analyzer::Analyzer ( )

Default constructor.

Definition at line 27 of file mcMd/analyzers/Analyzer.cpp.

McMd::Analyzer::~Analyzer ( )

virtual

Destructor.

Definition at line 37 of file mcMd/analyzers/Analyzer.cpp.

Member Function Documentation

void McMd::Analyzer::readParameters ( std::istream & in )

virtual

Read parameters from archive.

Default implementation, reads interval and outputFileName.

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::IntraStructureFactor, McMd::StructureFactorP, McMd::VanHove, McMd::IntraStructureFactorGrid, McMd::StructureFactorGrid, McMd::StructureFactorPGrid, McMd::BlockRadiusGyration, McMd::EndtoEnd, McMd::RadiusGyration, McMd::IntraPairAutoCorr, McMd::EndtoEndXYZ, McMd::StructureFactor, McMd::IntraBondTensorAutoCorr< SystemType >, McMd::IntraBondTensorAutoCorr< MdSystem >, McMd::IntraBondTensorAutoCorr< McSystem >, McMd::InterIntraLink, McMd::NLinkAverage, McMd::CompositionProfile, McMd::RDF, McMd::ConfigWriter, McMd::LinkMSD, McMd::McEnergyAnalyzer, McMd::MdEnergyAnalyzer, McMd::MdPairEnergyCoefficients, McMd::IntraBondStressAutoCorr< SystemType >, McMd::LinearRouseAutoCorr, McMd::IntraBondStressAutoCorr< MdSystem >, McMd::IntraBondStressAutoCorr< McSystem >, McMd::BennettsMethod, McMd::McMuExchange, McMd::RingRouseAutoCorr, McMd::McVirialStressTensorAverage, McMd::MdVirialStressTensorAverage, McMd::VelProf, McMd::ComMSD, McMd::McNVTChemicalPotential, McMd::LinkLTPos, McMd::McPairEnergyAverage, McMd::ClusterHistogram, McMd::PressureAverage< SystemType >, McMd::StressAutoCorr< SystemType >, McMd::LinkLifeTime, McMd::PressureAverage< MdSystem >, McMd::PressureAverage< McSystem >, McMd::StressAutoCorr< MdSystem >, McMd::StressTensorAverage< SystemType >, McMd::SSChainDist, McMd::TypeDistribution, McMd::BondLengthDist, McMd::LammpsDumpWriter, McMd::TrajectoryWriter, McMd::G1MSD, McMd::SemiGrandDistribution, McMd::AtomMSD, McMd::LinkLengthDist, McMd::McEnergyOutput, McMd::AverageAnalyzer< SystemType >, McMd::AverageAnalyzer< McSystem >, McMd::MdEnergyOutput, McMd::MdKineticEnergyAverage, McMd::BoundaryAverage, McMd::MdPotentialEnergyAverage, McMd::PerturbDerivative, McMd::LogProgress, and McMd::Crosslinker.

Definition at line 43 of file mcMd/analyzers/Analyzer.cpp.

References readInterval(), and readOutputFileName().

Referenced by McMd::RDF::readParameters().

void McMd::Analyzer::loadParameters ( Serializable::IArchive & ar )

virtual

Load parameters from archive.

Default implementation, loads interval and outputFileName.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::IntraStructureFactor, McMd::StructureFactorP, McMd::VanHove, McMd::BlockRadiusGyration, McMd::IntraStructureFactorGrid, McMd::StructureFactorGrid, McMd::StructureFactorPGrid, McMd::RadiusGyration, McMd::IntraPairAutoCorr, McMd::StructureFactor, McMd::McMuExchange, McMd::CompositionProfile, McMd::ClusterHistogram, McMd::IntraBondTensorAutoCorr< SystemType >, McMd::IntraBondTensorAutoCorr< MdSystem >, McMd::IntraBondTensorAutoCorr< McSystem >, McMd::ConfigWriter, McMd::RDF, McMd::McEnergyAnalyzer, McMd::MdEnergyAnalyzer, McMd::MdPairEnergyCoefficients, McMd::IntraBondStressAutoCorr< SystemType >, McMd::LinearRouseAutoCorr, McMd::IntraBondStressAutoCorr< MdSystem >, McMd::IntraBondStressAutoCorr< McSystem >, McMd::BennettsMethod, McMd::RingRouseAutoCorr, McMd::LammpsDumpWriter, McMd::TrajectoryWriter, McMd::McVirialStressTensorAverage, McMd::MdVirialStressTensorAverage, McMd::ComMSD, McMd::McPairEnergyAverage, McMd::PressureAverage< SystemType >, McMd::StressAutoCorr< SystemType >, McMd::PressureAverage< MdSystem >, McMd::PressureAverage< McSystem >, McMd::StressAutoCorr< MdSystem >, McMd::StressTensorAverage< SystemType >, McMd::TypeDistribution, McMd::BondLengthDist, McMd::SemiGrandDistribution, McMd::AtomMSD, McMd::McEnergyOutput, McMd::AverageAnalyzer< SystemType >, McMd::AverageAnalyzer< McSystem >, McMd::MdEnergyOutput, McMd::MdKineticEnergyAverage, McMd::BoundaryAverage, McMd::MdPotentialEnergyAverage, McMd::PerturbDerivative, and McMd::LogProgress.

Definition at line 83 of file mcMd/analyzers/Analyzer.cpp.

References loadInterval(), and loadOutputFileName().

void McMd::Analyzer::save ( Serializable::OArchive & ar )

virtual

Load parameters to archive.

Default implementation saves interval and outputFileName.

Parameters

ar	loading/saving archive

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::IntraStructureFactor, McMd::StructureFactorP, McMd::VanHove, McMd::IntraStructureFactorGrid, McMd::BlockRadiusGyration, McMd::StructureFactorGrid, McMd::StructureFactorPGrid, McMd::RadiusGyration, McMd::IntraPairAutoCorr, McMd::StructureFactor, McMd::CompositionProfile, McMd::IntraBondTensorAutoCorr< SystemType >, McMd::IntraBondTensorAutoCorr< MdSystem >, McMd::IntraBondTensorAutoCorr< McSystem >, McMd::McMuExchange, McMd::ClusterHistogram, McMd::RDF, McMd::McNVTChemicalPotential, McMd::McEnergyAnalyzer, McMd::MdEnergyAnalyzer, McMd::MdPairEnergyCoefficients, McMd::IntraBondStressAutoCorr< SystemType >, McMd::LinearRouseAutoCorr, McMd::IntraBondStressAutoCorr< MdSystem >, McMd::IntraBondStressAutoCorr< McSystem >, McMd::BennettsMethod, McMd::RingRouseAutoCorr, McMd::McVirialStressTensorAverage, McMd::MdVirialStressTensorAverage, McMd::ComMSD, McMd::ConfigWriter, McMd::McPairEnergyAverage, McMd::PressureAverage< SystemType >, McMd::StressAutoCorr< SystemType >, McMd::PressureAverage< MdSystem >, McMd::PressureAverage< McSystem >, McMd::StressAutoCorr< MdSystem >, McMd::StressTensorAverage< SystemType >, McMd::TypeDistribution, McMd::BondLengthDist, McMd::SemiGrandDistribution, McMd::AtomMSD, McMd::McEnergyOutput, McMd::AverageAnalyzer< SystemType >, McMd::AverageAnalyzer< McSystem >, McMd::MdEnergyOutput, McMd::MdKineticEnergyAverage, McMd::BoundaryAverage, McMd::MdPotentialEnergyAverage, McMd::PerturbDerivative, McMd::LammpsDumpWriter, and McMd::TrajectoryWriter.

Definition at line 126 of file mcMd/analyzers/Analyzer.cpp.

References interval_, and outputFileName_.

Referenced by McMd::McEnergyAnalyzer::save(), McMd::MdEnergyAnalyzer::save(), McMd::ClusterHistogram::save(), and McMd::CompositionProfile::save().

template<class Archive >

void McMd::Analyzer::serialize	(	Archive &	ar,
		const unsigned int	version
	)

Serialize to/from an archive.

Saves interval and outputFileName.

Parameters

ar	archive
version	archive version id

Definition at line 255 of file mcMd/analyzers/Analyzer.h.

virtual void McMd::Analyzer::setup ( )

inlinevirtual

Complete any required initialization.

This method must be called just before the beginning of the main simulation loop, after an initial configuration is known. It may be used to complete any initialization that cannot be completed in the readParam method, because knowledge of the configuration is needed.

The default implementation is an empty function.

Reimplemented in McMd::IntraStructureFactor, McMd::StructureFactorP, McMd::VanHove, McMd::IntraStructureFactorGrid, McMd::StructureFactorGrid, McMd::StructureFactorPGrid, McMd::RadiusGyration, McMd::IntraPairAutoCorr, McMd::StructureFactor, McMd::IntraBondTensorAutoCorr< SystemType >, McMd::IntraBondTensorAutoCorr< MdSystem >, McMd::IntraBondTensorAutoCorr< McSystem >, McMd::BlockRadiusGyration, McMd::RDF, McMd::ConfigWriter, McMd::EndtoEnd, McMd::IntraBondStressAutoCorr< SystemType >, McMd::LinearRouseAutoCorr, McMd::IntraBondStressAutoCorr< MdSystem >, McMd::IntraBondStressAutoCorr< McSystem >, McMd::McEnergyAnalyzer, McMd::MdEnergyAnalyzer, McMd::EndtoEndXYZ, McMd::RingRouseAutoCorr, McMd::StressTensorAverage< SystemType >, McMd::BennettsMethod, McMd::ComMSD, McMd::McPairEnergyAverage, McMd::PressureAverage< SystemType >, McMd::StressAutoCorr< SystemType >, McMd::PressureAverage< MdSystem >, McMd::PressureAverage< McSystem >, McMd::StressAutoCorr< MdSystem >, McMd::BondLengthDist, McMd::LammpsDumpWriter, McMd::TrajectoryWriter, McMd::AtomMSD, McMd::AverageAnalyzer< SystemType >, McMd::InterIntraLink, McMd::AverageAnalyzer< McSystem >, McMd::MdKineticEnergyAverage, McMd::BoundaryAverage, McMd::NLinkAverage, McMd::MdPotentialEnergyAverage, McMd::PerturbDerivative, McMd::CompositionProfile, McMd::LinkMSD, McMd::McMuExchange, McMd::VelProf, McMd::McNVTChemicalPotential, McMd::LinkLTPos, McMd::ClusterHistogram, McMd::LinkLifeTime, McMd::SSChainDist, McMd::G1MSD, McMd::LinkLengthDist, and McMd::Crosslinker.

Definition at line 118 of file mcMd/analyzers/Analyzer.h.

virtual void McMd::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 McMd::IntraStructureFactor, McMd::StructureFactorP, McMd::VanHove, McMd::IntraStructureFactorGrid, McMd::StructureFactorGrid, McMd::RadiusGyration, McMd::IntraPairAutoCorr, McMd::StructureFactor, McMd::IntraBondTensorAutoCorr< SystemType >, McMd::IntraBondTensorAutoCorr< MdSystem >, McMd::IntraBondTensorAutoCorr< McSystem >, McMd::BlockRadiusGyration, McMd::RDF, McMd::ConfigWriter, McMd::EndtoEnd, McMd::IntraBondStressAutoCorr< SystemType >, McMd::LinearRouseAutoCorr, McMd::IntraBondStressAutoCorr< MdSystem >, McMd::IntraBondStressAutoCorr< McSystem >, McMd::McEnergyAnalyzer, McMd::MdEnergyAnalyzer, McMd::EndtoEndXYZ, McMd::RingRouseAutoCorr, McMd::StressTensorAverage< SystemType >, McMd::BennettsMethod, McMd::ComMSD, McMd::StressAutoCorr< SystemType >, McMd::StressAutoCorr< MdSystem >, McMd::McPairEnergyAverage, McMd::MdPairEnergyCoefficients, McMd::PressureAverage< SystemType >, McMd::PressureAverage< MdSystem >, McMd::PressureAverage< McSystem >, McMd::BondLengthDist, McMd::LammpsDumpWriter, McMd::TrajectoryWriter, McMd::AtomMSD, McMd::McVirialStressTensorAverage, McMd::MdVirialStressTensorAverage, McMd::BoundaryAverage, McMd::InterIntraLink, McMd::NLinkAverage, McMd::MdKineticEnergyAverage, McMd::TypeDistribution, McMd::CompositionProfile, McMd::MdPotentialEnergyAverage, McMd::PerturbDerivative, McMd::SemiGrandDistribution, McMd::McEnergyOutput, McMd::MdEnergyOutput, McMd::LinkMSD, McMd::VelProf, McMd::McMuExchange, McMd::LinkLTPos, McMd::ClusterHistogram, McMd::LinkLifeTime, McMd::McNVTChemicalPotential, McMd::SSChainDist, McMd::G1MSD, McMd::LinkLengthDist, McMd::LogProgress, McMd::McExternalEnergyAverage, McMd::McBondEnergyAverage, McMd::McEnergyAverage, and McMd::Crosslinker.

virtual void McMd::Analyzer::output ( )

inlinevirtual

Output any results at the end of the simulation.

The default implementation is an empty function.

Reimplemented in McMd::IntraStructureFactor, McMd::StructureFactorP, McMd::VanHove, McMd::IntraStructureFactorGrid, McMd::RadiusGyration, McMd::StructureFactorGrid, McMd::StructureFactorPGrid, McMd::IntraPairAutoCorr, McMd::StructureFactor, McMd::IntraBondTensorAutoCorr< SystemType >, McMd::IntraBondTensorAutoCorr< MdSystem >, McMd::IntraBondTensorAutoCorr< McSystem >, McMd::CompositionProfile, McMd::BlockRadiusGyration, McMd::RDF, McMd::EndtoEnd, McMd::IntraBondStressAutoCorr< SystemType >, McMd::LinearRouseAutoCorr, McMd::IntraBondStressAutoCorr< MdSystem >, McMd::IntraBondStressAutoCorr< McSystem >, McMd::McEnergyAnalyzer, McMd::MdEnergyAnalyzer, McMd::EndtoEndXYZ, McMd::RingRouseAutoCorr, McMd::StressTensorAverage< SystemType >, McMd::BennettsMethod, McMd::ComMSD, McMd::StressAutoCorr< SystemType >, McMd::StressAutoCorr< MdSystem >, McMd::McPairEnergyAverage, McMd::PressureAverage< SystemType >, McMd::PressureAverage< MdSystem >, McMd::PressureAverage< McSystem >, McMd::BondLengthDist, McMd::LammpsDumpWriter, McMd::TrajectoryWriter, McMd::MdPairEnergyCoefficients, McMd::AtomMSD, McMd::McVirialStressTensorAverage, McMd::MdVirialStressTensorAverage, McMd::BoundaryAverage, McMd::InterIntraLink, McMd::NLinkAverage, McMd::MdKineticEnergyAverage, McMd::TypeDistribution, McMd::LinkMSD, McMd::MdPotentialEnergyAverage, McMd::PerturbDerivative, McMd::SemiGrandDistribution, McMd::McEnergyOutput, McMd::AverageAnalyzer< SystemType >, McMd::AverageAnalyzer< McSystem >, McMd::MdEnergyOutput, McMd::LinkLTPos, McMd::LinkLifeTime, McMd::VelProf, McMd::McMuExchange, McMd::ClusterHistogram, McMd::McNVTChemicalPotential, McMd::SSChainDist, McMd::G1MSD, and McMd::LinkLengthDist.

Definition at line 137 of file mcMd/analyzers/Analyzer.h.

int McMd::Analyzer::interval ( ) const

inline

Get interval value.

Definition at line 234 of file mcMd/analyzers/Analyzer.h.

Referenced by McMd::LinkMSD::sample(), McMd::MdEnergyAnalyzer::sample(), and McMd::McEnergyAnalyzer::sample().

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

inline

Return true iff counter is a multiple of the interval.

Parameters

counter simulation step counter

Definition at line 240 of file mcMd/analyzers/Analyzer.h.

void McMd::Analyzer::initStatic ( )

static

Define and initialize baseInterval.

Definition at line 21 of file mcMd/analyzers/Analyzer.cpp.

Referenced by McMd::Simulation::Simulation().

void McMd::Analyzer::setFileMaster ( FileMaster & fileMaster )

protected

Set the FileMaster to use to open files.

Definition at line 135 of file mcMd/analyzers/Analyzer.cpp.

References fileMaster().

Referenced by McMd::SystemAnalyzer< SystemType >::SystemAnalyzer().

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

protected

Read interval from file, with error checking.

Parameters

in	input parameter file stream

Definition at line 52 of file mcMd/analyzers/Analyzer.cpp.

References baseInterval, interval_, and UTIL_THROW.

void McMd::Analyzer::readOutputFileName ( std::istream & in )

protected

Read outputFileName from file.

Parameters

in	input parameter file stream.

Definition at line 77 of file mcMd/analyzers/Analyzer.cpp.

References outputFileName_.

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

protected

Load interval from archive, with error checking.

Parameters

ar	input/loading archive

Definition at line 92 of file mcMd/analyzers/Analyzer.cpp.

References baseInterval, interval_, and UTIL_THROW.

Referenced by McMd::MdPotentialEnergyAverage::loadParameters(), McMd::MdEnergyOutput::loadParameters(), McMd::MdKineticEnergyAverage::loadParameters(), McMd::AtomMSD::loadParameters(), McMd::BondLengthDist::loadParameters(), McMd::MdPairEnergyCoefficients::loadParameters(), McMd::McMuExchange::loadParameters(), loadParameters(), and McMd::IntraStructureFactor::loadParameters().

void McMd::Analyzer::loadOutputFileName ( Serializable::IArchive & ar )

protected

Load output file name from archive.

Parameters

ar	input/loading archive

Definition at line 120 of file mcMd/analyzers/Analyzer.cpp.

References outputFileName_.

Referenced by McMd::MdPotentialEnergyAverage::loadParameters(), McMd::MdEnergyOutput::loadParameters(), McMd::MdKineticEnergyAverage::loadParameters(), McMd::AtomMSD::loadParameters(), McMd::BondLengthDist::loadParameters(), McMd::MdPairEnergyCoefficients::loadParameters(), McMd::McMuExchange::loadParameters(), loadParameters(), and McMd::IntraStructureFactor::loadParameters().

FileMaster & McMd::Analyzer::fileMaster ( )

protected

Get the FileMaster by reference.

This can be used to open multiple output files.

Definition at line 141 of file mcMd/analyzers/Analyzer.cpp.

const std::string & McMd::Analyzer::outputFileName ( ) const

inlineprotected

Return outputFileName string.

Definition at line 246 of file mcMd/analyzers/Analyzer.h.

std::string McMd::Analyzer::outputFileName ( const std::string & suffix ) const

protected

Return outputFileName string with added suffix.

Definition at line 150 of file mcMd/analyzers/Analyzer.cpp.

References outputFileName_.

Member Data Documentation

long McMd::Analyzer::baseInterval = 0

static

The interval for an Analyzer must be a multiple of baseInterval.

Definition at line 157 of file mcMd/analyzers/Analyzer.h.

Referenced by McMd::MdSimulation::analyzeConfigs(), McMd::McSimulation::analyzeConfigs(), McMd::MdSimulation::analyzeTrajectory(), loadInterval(), McMd::AnalyzerManager::loadParameters(), readInterval(), McMd::AnalyzerManager::readParameters(), McMd::MdSimulation::readParameters(), McMd::McSimulation::readParameters(), McMd::AnalyzerManager::sample(), McMd::AnalyzerManager::save(), McMd::MdSimulation::simulate(), and McMd::McSimulation::simulate().

std::string McMd::Analyzer::outputFileName_

protected

Base name of output file(s).

Definition at line 217 of file mcMd/analyzers/Analyzer.h.

Referenced by loadOutputFileName(), outputFileName(), readOutputFileName(), McMd::McMuExchange::save(), and save().

long McMd::Analyzer::interval_

protected

Number of simulation steps between subsequent actions.

Definition at line 220 of file mcMd/analyzers/Analyzer.h.

Referenced by loadInterval(), readInterval(), McMd::McMuExchange::save(), and save().

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

Detailed Description

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation