McMd::StressTensorAverage< SystemType > Class Template Reference

Detailed Description

template<class SystemType>
class McMd::StressTensorAverage< SystemType >

Periodically write (tensor) StressTensor to file.

Definition at line 26 of file StressTensorAverage.h.

#include <StressTensorAverage.h>

Inheritance diagram for McMd::StressTensorAverage< SystemType >:

Public Member Functions
	StressTensorAverage (SystemType &system)
	Constructor. More...
virtual	~StressTensorAverage ()
	Destructor. More...
virtual void	readParameters (std::istream &in)
	Read dumpPrefix and interval. 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...
template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize to/from an archive. More...
virtual void	clear ()
	Clear nSample counter. More...
virtual void	setup ()
	Setup accumulator! More...
virtual void	sample (long iStep)
	Sample virial stress components to accumulators. More...
virtual void	output ()
	Output final results to file. More...
Public Member Functions inherited from McMd::SystemAnalyzer< SystemType >
	SystemAnalyzer (SystemType &system)
	Constructor. More...
virtual	~SystemAnalyzer ()
	Destructor. More...
Public Member Functions inherited from McMd::Analyzer
	Analyzer ()
	Default constructor. More...
virtual	~Analyzer ()
	Destructor. More...
template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize to/from 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	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 McMd::Analyzer
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 inherited from McMd::Analyzer
static long	baseInterval = 0
	The interval for an Analyzer must be a multiple of baseInterval. More...
Protected Member Functions inherited from McMd::SystemAnalyzer< SystemType >
SystemType &	system ()
	Return reference to parent system. More...
Protected Member Functions inherited from McMd::Analyzer
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 inherited from McMd::Analyzer
std::string	outputFileName_
	Base name of output file(s). More...
long	interval_
	Number of simulation steps between subsequent actions. More...

Constructor & Destructor Documentation

template<class SystemType >

McMd::StressTensorAverage< SystemType >::StressTensorAverage

(

SystemType &

system

)

Constructor.

Parameters

system

parent SystemType object.

Definition at line 150 of file StressTensorAverage.h.

template<class SystemType >

virtual McMd::StressTensorAverage< SystemType >::~StressTensorAverage ( )

inlinevirtual

Destructor.

Definition at line 41 of file StressTensorAverage.h.

References McMd::serialize().

Member Function Documentation

template<class SystemType >

void McMd::StressTensorAverage< SystemType >::readParameters ( std::istream &  in )

virtual

Read dumpPrefix and interval.

Parameters

in	input parameter file

Reimplemented from McMd::Analyzer.

Definition at line 170 of file StressTensorAverage.h.

References McMd::Analyzer::outputFileName(), McMd::Analyzer::readInterval(), McMd::Analyzer::readOutputFileName(), Util::Average::setNSamplePerBlock(), and McMd::SystemAnalyzer< SystemType >::system().

template<class SystemType >

void McMd::StressTensorAverage< SystemType >::loadParameters ( Serializable::IArchive &  ar )

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from McMd::Analyzer.

Definition at line 197 of file StressTensorAverage.h.

References McMd::Analyzer::fileMaster(), McMd::Analyzer::loadParameters(), Util::Average::loadParameters(), Util::FileMaster::openOutputFile(), and McMd::Analyzer::outputFileName().

template<class SystemType >

void McMd::StressTensorAverage< SystemType >::save ( Serializable::OArchive &  ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from McMd::Analyzer.

Definition at line 222 of file StressTensorAverage.h.

template<class SystemType >

template<class Archive >

void McMd::StressTensorAverage< SystemType >::serialize	(	Archive &	ar,
		const unsigned int	version
	)

Serialize to/from an archive.

Parameters

ar	saving or loading archive
version	archive version id

template<class SystemType >

void McMd::StressTensorAverage< SystemType >::clear ( )

virtual

Clear nSample counter.

Definition at line 230 of file StressTensorAverage.h.

References Util::Average::clear(), and UTIL_THROW.

template<class SystemType >

virtual void McMd::StressTensorAverage< SystemType >::setup ( )

virtual

Setup accumulator!

Reimplemented from McMd::Analyzer.

template<class SystemType >

void McMd::StressTensorAverage< SystemType >::sample ( long  iStep )

virtual

Sample virial stress components to accumulators.

Parameters

iStep

MD or MC step index

Implements McMd::Analyzer.

Definition at line 251 of file StressTensorAverage.h.

References Util::Tensor::add(), McMd::Analyzer::isAtInterval(), Util::Average::sample(), and McMd::SystemAnalyzer< SystemType >::system().

template<class SystemType >

void McMd::StressTensorAverage< SystemType >::output ( )

virtual

Output final results to file.

Reimplemented from McMd::Analyzer.

Definition at line 281 of file StressTensorAverage.h.

References Util::AverageStage::average(), and Util::AverageStage::error().

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

• StressTensorAverage.h