Auto-correlation function for an ensemble of sequences. More...

#include <AutoCorrArray.h>

Inheritance diagram for Util::AutoCorrArray< Data, Product >:

Public Member Functions
	AutoCorrArray ()
	Default constructor.
	~AutoCorrArray ()
	Default destructor.
virtual void	readParameters (std::istream &in)
	Read parameters, allocate memory and clear history.
void	setParam (int ensembleCapacity, int bufferCapacity)
	Allocate memory, and clear history.
virtual void	loadParameters (Serializable::IArchive &ar)
	Load internal state from an archive.
virtual void	save (Serializable::OArchive &ar)
	Save internal state to an archive.
void	setNEnsemble (int nEnsemble)
	Set actual number of sequences in ensemble.
void	clear ()
	Reset to empty state.
void	sample (const Array< Data > &values)
	Sample an array of current values.
void	output (std::ostream &out)
	Output the autocorrelation function.
template<class Archive>
void	serialize (Archive &ar, const unsigned int version)
	Serialize this AutoCorrArray to/from an archive.
int	bufferCapacity () const
	Return maximum number of samples in history for each sequence.
int	nEnsemble () const
	Return nEnsemble.
int	nSample () const
	Return the total number of samples per sequence thus far.
Data	average () const
	Return average of sampled values.
double	corrTime () const
	Numerical integral of autocorrelation function.
Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor.
	ParamComposite (const ParamComposite &other)
	Copy constructor.
	ParamComposite (int capacity)
	Constructor.
virtual	~ParamComposite ()
	Virtual destructor.
void	resetParam ()
	Resets ParamComposite to its empty state.
virtual void	readParam (std::istream &in)
	Read the parameter file block.
virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block.
virtual void	writeParam (std::ostream &out) const
	Write all parameters to an output stream.
virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive.
virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite.
void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true.
void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite.
void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite.
template<typename Type>
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object.
template<typename Type>
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object.
template<typename Type>
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter.
template<typename Type>
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter.
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.
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.
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.
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.
template<typename Type, int N>
FSArrayParam< Type, N > &	readFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read a required FSArray < Type, N > array parameter.
template<typename Type, int N>
FSArrayParam< Type, N > &	readOptionalFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read an optional FSArray < Type, N > array parameter.
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.
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.
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.
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.
template<typename Type>
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix.
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.
Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket.
End &	readEnd (std::istream &in)
	Add and read the closing bracket.
Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line.
void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite.
void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive.
template<typename Type>
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object.
template<typename Type>
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object.
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.
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.
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.
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.
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.
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.
template<typename Type, int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size, bool isRequired)
	Add and load an FSArray < Type, N > array parameter.
template<typename Type, int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size)
	Add and load a required FSArray < Type > array parameter.
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.
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.
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.
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.
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.
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.
void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array.
Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket.
End &	addEnd ()
	Add a closing bracket.
Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line.
std::string	className () const
	Get class name string.
bool	isRequired () const
	Is this ParamComposite required in the input file?
bool	isActive () const
	Is this parameter active?
Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor.
void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level.
std::string	indent () const
	Return indent string for this object (string of spaces).
template<class Archive>
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string.
Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor.
Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor.
	MpiFileIo (const MpiFileIo &other)
	Copy constructor.
bool	isIoProcessor () const
	Can this processor do file I/O ?

Additional Inherited Members
Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method.
typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method.
Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false.
static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent.
static bool	echo ()
	Get echo parameter.
void	setClassName (const char *className)
	Set class name string.
void	setIsRequired (bool isRequired)
	Set or unset the isActive flag.
void	setIsActive (bool isActive)
	Set or unset the isActive flag.
void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component.
void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array.
template<typename Type>
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object.
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.
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.
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.
template<typename Type, int N>
FSArrayParam< Type, N > &	addFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size, bool isRequired=true)
	Add (but do not read) a FSArray < Type, N > array parameter.
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.
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.
Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor.
	ParamComponent (const ParamComponent &other)
	Copy constructor.

Detailed Description

template<typename Data, typename Product>
class Util::AutoCorrArray< Data, Product >

Auto-correlation function for an ensemble of sequences.

This class calculates an autocorrelation function for a ensemble of statistically equivalent sequences x(i) of values of a variable of type Data. The resulting autocorrelation function is an array of values of type Product, where C(j) = <x(i-j), x(i)>. Here <A,B> denotes an inner product of type Product for objects A and B of type Data.

The meaning of <A,B> for two Data values is defined for various data types by the overloaded functions product(Data, Data) defined in file "product.h" . These functions define a product as an arithmetic product for floating point numbers, and use the following definitions for complex numbers and Vector objects:

double  product(double, double)   = A*B
complex product(complex, complex) = conjug(A)*B
double  product(Vector,  Vector)  = A.dot(B)

The meaning of setting a variable to zero is defined for various types of data by the overloaded functions setToZero(Data&) that are defined in file setToZero.h.

Definition at line 57 of file AutoCorrArray.h.

Constructor & Destructor Documentation

◆ AutoCorrArray()

template<typename Data, typename Product>

Util::AutoCorrArray< Data, Product >::AutoCorrArray ( )

Default constructor.

Definition at line 205 of file AutoCorrArray.h.

References Util::ParamComposite::setClassName(), and Util::setToZero().

◆ ~AutoCorrArray()

template<typename Data, typename Product>

Util::AutoCorrArray< Data, Product >::~AutoCorrArray ( )

Default destructor.

Definition at line 222 of file AutoCorrArray.h.

Member Function Documentation

◆ readParameters()

template<typename Data, typename Product>

void Util::AutoCorrArray< Data, Product >::readParameters ( std::istream & in )

virtual

Read parameters, allocate memory and clear history.

Reads parameters ensembleCapacity and bufferCapacity, allocates memory, sets nEnsemble=ensembleCapacity, and calls clear().

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 229 of file AutoCorrArray.h.

References Util::ParamComposite::read().

◆ setParam()

template<typename Data, typename Product>

void Util::AutoCorrArray< Data, Product >::setParam	(	int	ensembleCapacity,
		int	bufferCapacity )

Allocate memory, and clear history.

Sets parameters ensembleCapacity and bufferCapacity, allocates memory, sets nEnsemble=ensembleCapacity, and calls clear().

Parameters

ensembleCapacity	maximum number of sequences in ensemble
bufferCapacity	maximum number of values in each history

Definition at line 241 of file AutoCorrArray.h.

References bufferCapacity().

◆ loadParameters()

template<typename Data, typename Product>

void Util::AutoCorrArray< Data, Product >::loadParameters ( Serializable::IArchive & ar )

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 253 of file AutoCorrArray.h.

References Util::ParamComposite::loadParameter().

◆ save()

template<typename Data, typename Product>

void Util::AutoCorrArray< Data, Product >::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 269 of file AutoCorrArray.h.

◆ setNEnsemble()

template<typename Data, typename Product>

void Util::AutoCorrArray< Data, Product >::setNEnsemble ( int nEnsemble )

Set actual number of sequences in ensemble.

Precondition: readParam() or setParam() must have been called previously; nEnsemble <= ensembleCapacity

Parameters

nEnsemble actual number of sequences in ensemble

Definition at line 276 of file AutoCorrArray.h.

References nEnsemble(), and UTIL_THROW.

◆ clear()

template<typename Data, typename Product>

void Util::AutoCorrArray< Data, Product >::clear ( )

Reset to empty state.

Definition at line 291 of file AutoCorrArray.h.

References Util::setToZero().

◆ sample()

template<typename Data, typename Product>

void Util::AutoCorrArray< Data, Product >::sample ( const Array< Data > & values )

Sample an array of current values.

Parameters

values Array of current values

Definition at line 331 of file AutoCorrArray.h.

References Util::product().

◆ output()

template<typename Data, typename Product>

void Util::AutoCorrArray< Data, Product >::output ( std::ostream & out )

Output the autocorrelation function.

Definition at line 386 of file AutoCorrArray.h.

◆ serialize()

template<typename Data, typename Product>

template<class Archive>

void Util::AutoCorrArray< Data, Product >::serialize	(	Archive &	ar,
		const unsigned int	version )

Serialize this AutoCorrArray to/from an archive.

Parameters

ar	input or output archive
version	file version id

Definition at line 436 of file AutoCorrArray.h.

◆ bufferCapacity()

template<typename Data, typename Product>

int Util::AutoCorrArray< Data, Product >::bufferCapacity ( ) const

Return maximum number of samples in history for each sequence.

Definition at line 354 of file AutoCorrArray.h.

Referenced by setParam().

◆ nEnsemble()

template<typename Data, typename Product>

int Util::AutoCorrArray< Data, Product >::nEnsemble ( ) const

Return nEnsemble.

Definition at line 361 of file AutoCorrArray.h.

Referenced by setNEnsemble().

◆ nSample()

template<typename Data, typename Product>

int Util::AutoCorrArray< Data, Product >::nSample ( ) const

Return the total number of samples per sequence thus far.

Definition at line 368 of file AutoCorrArray.h.

◆ average()

template<typename Data, typename Product>

Data Util::AutoCorrArray< Data, Product >::average ( ) const

Return average of sampled values.

Definition at line 375 of file AutoCorrArray.h.

◆ corrTime()

template<typename Data, typename Product>

double Util::AutoCorrArray< Data, Product >::corrTime ( ) const

Numerical integral of autocorrelation function.

Definition at line 407 of file AutoCorrArray.h.

References Util::product(), and Util::setToZero().

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

AutoCorrArray.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AutoCorrArray()

◆ ~AutoCorrArray()

Member Function Documentation

◆ readParameters()

◆ setParam()

◆ loadParameters()

◆ save()

◆ setNEnsemble()

◆ clear()

◆ sample()

◆ output()

◆ serialize()

◆ bufferCapacity()

◆ nEnsemble()

◆ nSample()

◆ average()

◆ corrTime()