Detailed Description

CompositionProfile evaluates the distribution of monomer positions along several user-specified directions.

A direction vector is specified as an IntVector containing integer Miller indices.

The dot product of monomer position vector and unit direction vector is added to distribution function of particular monomer type and direction vector.

Definition at line 34 of file CompositionProfile.h.

#include <CompositionProfile.h>

Inheritance diagram for McMd::CompositionProfile:

Public Member Functions
	CompositionProfile (System &system)
	Constructor. More...

	~CompositionProfile ()
	Destructor. More...

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

virtual void	setup ()
	Clear accumulators. More...

void	sample (long iStep)
	Add particle positions to histogram. 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 internal state to/from archive. More...

virtual void	output ()
	Output results to predefined output file. More...

Public Member Functions inherited from McMd::SystemAnalyzer< System >
	SystemAnalyzer (System &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...

Protected Member Functions
void	makeWaveVectors ()
	Update wavevectors. More...

Protected Member Functions inherited from McMd::SystemAnalyzer< System >
System &	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
std::ofstream	outputFile_
	Output file stream. More...

DArray< Distribution >	accumulators_
	Distribution statistical accumulators. More...

DArray< IntVector >	intVectors_
	Array of Miller index vectors for directions. More...

DArray< Vector >	waveVectors_
	Array of direction vectors. More...

int	nDirection_
	Number of directions. More...

int	nSample_
	Number of samples thus far. More...

int	nAtomType_
	Number of atom types, copied from Simulation::nAtomType(). More...

int	nBins_
	Number of bins for density profile. More...

bool	isFirstStep_
	True if this is the first step. More...

bool	isInitialized_
	Has readParam been called? More...

DArray< Distribution >	currentAccumulators_
	Distribution statistical accumulators. 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...

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...

Constructor & Destructor Documentation

McMd::CompositionProfile::CompositionProfile ( System & system )

Constructor.

Parameters

system reference to parent System object

Definition at line 26 of file CompositionProfile.cpp.

References Util::ParamComposite::setClassName().

McMd::CompositionProfile::~CompositionProfile ( )

Destructor.

Definition at line 32 of file CompositionProfile.cpp.

Member Function Documentation

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

virtual

Read parameters from file.

Read parameters from file, and allocate direction vectors.

Input format:

int interval sampling interval
string outputFileName output file base name
int nDirection number of directions
DArray<IntVector> intVectors IntVector directions

Parameters

in	input parameter stream

Reimplemented from McMd::Analyzer.

Definition at line 36 of file CompositionProfile.cpp.

References accumulators_, Util::DArray< Data >::allocate(), currentAccumulators_, intVectors_, isInitialized_, McMd::Simulation::nAtomType(), nAtomType_, nBins_, nDirection_, McMd::Analyzer::readInterval(), McMd::Analyzer::readOutputFileName(), McMd::System::simulation(), McMd::SystemAnalyzer< System >::system(), and waveVectors_.

void McMd::CompositionProfile::setup ( )

virtual

Clear accumulators.

Reimplemented from McMd::Analyzer.

Definition at line 105 of file CompositionProfile.cpp.

References accumulators_, currentAccumulators_, makeWaveVectors(), nAtomType_, nBins_, nDirection_, and nSample_.

void McMd::CompositionProfile::sample ( long iStep )

virtual

Add particle positions to histogram.

Parameters

iStep step counter

Implements McMd::Analyzer.

Definition at line 131 of file CompositionProfile.cpp.

References accumulators_, McMd::System::begin(), McMd::System::boundary(), currentAccumulators_, Util::Dimension, Util::Vector::dot(), McMd::Analyzer::fileMaster(), intVectors_, McMd::Analyzer::isAtInterval(), isFirstStep_, Simp::OrthorhombicBoundary::lengths(), nAtomType_, nDirection_, Util::ConstArrayIterator< Data >::notEnd(), Util::ConstPArrayIterator< Data >::notEnd(), nSample_, McMd::Simulation::nSpecies(), Util::FileMaster::openOutputFile(), McMd::Analyzer::outputFileName(), Util::product(), McMd::System::simulation(), McMd::SystemAnalyzer< System >::system(), and waveVectors_.

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

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from McMd::Analyzer.

Definition at line 60 of file CompositionProfile.cpp.

References accumulators_, intVectors_, isInitialized_, McMd::Analyzer::loadParameters(), McMd::Simulation::nAtomType(), nAtomType_, nDirection_, nSample_, McMd::System::simulation(), McMd::SystemAnalyzer< System >::system(), UTIL_THROW, and waveVectors_.

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

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from McMd::Analyzer.

Definition at line 89 of file CompositionProfile.cpp.

References accumulators_, intVectors_, isFirstStep_, nAtomType_, nBins_, nDirection_, nSample_, McMd::Analyzer::save(), and waveVectors_.

template<class Archive >

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

Serialize internal state to/from archive.

Parameters

ar	archive
version	index for archive version

Definition at line 156 of file CompositionProfile.h.

References McMd::Analyzer::serialize().

void McMd::CompositionProfile::output ( )

virtual

Output results to predefined output file.

Reimplemented from McMd::Analyzer.

Definition at line 245 of file CompositionProfile.cpp.

References accumulators_, Util::Dimension, McMd::Analyzer::fileMaster(), nAtomType_, nDirection_, Util::FileMaster::openOutputFile(), outputFile_, McMd::Analyzer::outputFileName(), waveVectors_, and Util::ParamComposite::writeParam().

void McMd::CompositionProfile::makeWaveVectors ( )

protected

Update wavevectors.

Calculate floating point wavevectors.

Definition at line 227 of file CompositionProfile.cpp.

References McMd::System::boundary(), Util::Dimension, intVectors_, nDirection_, Simp::OrthorhombicBoundary::reciprocalBasisVector(), McMd::SystemAnalyzer< System >::system(), waveVectors_, and Util::Vector::Zero.

Referenced by setup().

Member Data Documentation

std::ofstream McMd::CompositionProfile::outputFile_

protected

Output file stream.

Definition at line 109 of file CompositionProfile.h.

Referenced by output().

DArray<Distribution> McMd::CompositionProfile::accumulators_

protected

Distribution statistical accumulators.

Definition at line 112 of file CompositionProfile.h.

Referenced by loadParameters(), output(), readParameters(), sample(), save(), and setup().

DArray<IntVector> McMd::CompositionProfile::intVectors_

protected

Array of Miller index vectors for directions.

Definition at line 115 of file CompositionProfile.h.

Referenced by loadParameters(), makeWaveVectors(), readParameters(), sample(), and save().

DArray<Vector> McMd::CompositionProfile::waveVectors_

protected

Array of direction vectors.

Definition at line 118 of file CompositionProfile.h.

Referenced by loadParameters(), makeWaveVectors(), output(), readParameters(), sample(), and save().

int McMd::CompositionProfile::nDirection_

protected

Number of directions.

Definition at line 124 of file CompositionProfile.h.

Referenced by loadParameters(), makeWaveVectors(), output(), readParameters(), sample(), save(), and setup().

int McMd::CompositionProfile::nSample_

protected

Number of samples thus far.

Definition at line 127 of file CompositionProfile.h.

Referenced by loadParameters(), sample(), save(), and setup().

int McMd::CompositionProfile::nAtomType_

protected

Number of atom types, copied from Simulation::nAtomType().

Definition at line 130 of file CompositionProfile.h.

Referenced by loadParameters(), output(), readParameters(), sample(), save(), and setup().

int McMd::CompositionProfile::nBins_

protected

Number of bins for density profile.

Definition at line 133 of file CompositionProfile.h.

Referenced by readParameters(), save(), and setup().

bool McMd::CompositionProfile::isFirstStep_

protected

True if this is the first step.

Definition at line 136 of file CompositionProfile.h.

Referenced by sample(), and save().

bool McMd::CompositionProfile::isInitialized_

protected

Has readParam been called?

Definition at line 139 of file CompositionProfile.h.

Referenced by loadParameters(), and readParameters().

DArray<Distribution> McMd::CompositionProfile::currentAccumulators_

protected

Distribution statistical accumulators.

Definition at line 142 of file CompositionProfile.h.

Referenced by readParameters(), sample(), and setup().

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

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation