DdMd::SymmTensorAverageAnalyzer Class Reference

Detailed Description

Analyzer that computes average of a sequence of symmetric Tensor values.

This class evaluates the average of a sequences of symmetric Tensor values, and optionally writes block averages to a data file during the run. It is intended for use as a base class for classes that compute and average specific symmetric-tensor-valued physical variables.

Definition at line 35 of file SymmTensorAverageAnalyzer.h.

#include <SymmTensorAverageAnalyzer.h>

Inheritance diagram for DdMd::SymmTensorAverageAnalyzer:

Public Member Functions
	SymmTensorAverageAnalyzer (Simulation &simulation)
	Constructor. More...
virtual	~SymmTensorAverageAnalyzer ()
	Destructor. More...
virtual void	readParameters (std::istream &in)
	Read interval, outputFileName and (optionally) nSamplePerBlock. More...
virtual void	loadParameters (Serializable::IArchive &ar)
	Load internal state from an input archive. More...
virtual void	save (Serializable::OArchive &ar)
	Save internal state to an output archive. More...
virtual void	clear ()
	Clear accumulator on master, do nothing on other processors. More...
virtual void	setup ()
	Setup before loop. More...
virtual void	sample (long iStep)
	Compute a sampled value and add it to the accumulator. More...
virtual void	output ()
	Write final results to a file. More...
Public Member Functions inherited from DdMd::Analyzer
	Analyzer (Simulation &simulation)
	Constructor. More...
virtual	~Analyzer ()
	Destructor. 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...

Protected Member Functions
virtual void	compute ()=0
	Compute value of sampled quantity. More...
virtual Tensor	value ()=0
	Get current value, set by compute function. More...
Protected Member Functions inherited from DdMd::Analyzer
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...
Static Public Member Functions inherited from DdMd::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 DdMd::Analyzer
static long	baseInterval = 1
	The interval for an Analyzer must be a multiple of baseInterval. More...

Constructor & Destructor Documentation

DdMd::SymmTensorAverageAnalyzer::SymmTensorAverageAnalyzer

(

Simulation &

simulation

)

Constructor.

Parameters

simulation

parent Simulation object.

Definition at line 27 of file SymmTensorAverageAnalyzer.cpp.

References Util::ParamComposite::setClassName().

DdMd::SymmTensorAverageAnalyzer::~SymmTensorAverageAnalyzer ( )

virtual

Destructor.

Definition at line 38 of file SymmTensorAverageAnalyzer.cpp.

Member Function Documentation

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

virtual

Read interval, outputFileName and (optionally) nSamplePerBlock.

The optional variable nSamplePerBlock defaults to 0, which disables computation and output of block averages. Setting nSamplePerBlock = 1 outputs every sampled value.

Parameters

in	input parameter file

Reimplemented from Util::ParamComposite.

Definition at line 48 of file SymmTensorAverageAnalyzer.cpp.

References DdMd::Simulation::domain(), DdMd::Domain::isMaster(), DdMd::Analyzer::readInterval(), DdMd::Analyzer::readOutputFileName(), Util::SymmTensorAverage::setNSamplePerBlock(), and DdMd::Analyzer::simulation().

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

virtual

Load internal state from an input archive.

Parameters

ar	input/loading archive

Reimplemented from DdMd::Analyzer.

Definition at line 64 of file SymmTensorAverageAnalyzer.cpp.

References DdMd::Simulation::domain(), DdMd::Domain::isMaster(), Util::ParamComposite::isRequired(), DdMd::Analyzer::loadInterval(), DdMd::Analyzer::loadOutputFileName(), DdMd::Analyzer::simulation(), and UTIL_THROW.

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

virtual

Save internal state to an output archive.

Parameters

ar	output/saving archive

Reimplemented from DdMd::Analyzer.

Definition at line 86 of file SymmTensorAverageAnalyzer.cpp.

References Util::ParamComposite::isActive(), DdMd::Analyzer::saveInterval(), Util::Parameter::saveOptional(), DdMd::Analyzer::saveOutputFileName(), and DdMd::Analyzer::simulation().

void DdMd::SymmTensorAverageAnalyzer::clear ( )

virtual

Clear accumulator on master, do nothing on other processors.

Reimplemented from DdMd::Analyzer.

Definition at line 101 of file SymmTensorAverageAnalyzer.cpp.

References Util::SymmTensorAverage::clear(), and DdMd::Analyzer::simulation().

void DdMd::SymmTensorAverageAnalyzer::setup ( )

virtual

Setup before loop.

Opens output file, if any required.

Reimplemented from DdMd::Analyzer.

Definition at line 111 of file SymmTensorAverageAnalyzer.cpp.

References DdMd::Simulation::fileMaster(), Util::FileMaster::openOutputFile(), DdMd::Analyzer::outputFileName(), and DdMd::Analyzer::simulation().

void DdMd::SymmTensorAverageAnalyzer::sample ( long  iStep )

virtual

Compute a sampled value and add it to the accumulator.

Parameters

iStep

MD step index

Implements DdMd::Analyzer.

Definition at line 124 of file SymmTensorAverageAnalyzer.cpp.

References compute(), Util::Dimension, DdMd::Analyzer::interval(), DdMd::Analyzer::isAtInterval(), Util::SymmTensorAverage::isBlockComplete(), Util::SymmTensorAverage::sample(), DdMd::Analyzer::simulation(), UTIL_THROW, and value().

void DdMd::SymmTensorAverageAnalyzer::output ( )

virtual

Write final results to a file.

Reimplemented from DdMd::Analyzer.

Definition at line 152 of file SymmTensorAverageAnalyzer.cpp.

References Util::Dimension, DdMd::Simulation::fileMaster(), Util::FileMaster::openOutputFile(), DdMd::Analyzer::outputFileName(), DdMd::Analyzer::simulation(), and Util::ParamComposite::writeParam().

virtual void DdMd::SymmTensorAverageAnalyzer::compute ( )

protectedpure virtual

Compute value of sampled quantity.

Call on all processors.

Implemented in DdMd::StressAnalyzer, and DdMd::VirialStressAnalyzer.

Referenced by sample().

virtual Tensor DdMd::SymmTensorAverageAnalyzer::value ( )

protectedpure virtual

Get current value, set by compute function.

Call only on master.

Implemented in DdMd::StressAnalyzer, and DdMd::VirialStressAnalyzer.

Referenced by sample().

---

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

• SymmTensorAverageAnalyzer.h
• SymmTensorAverageAnalyzer.cpp