Detailed Description

Periodically write snapshots to a lammps dump (i.e., trajectory) file.

Definition at line 24 of file mcMd/analyzers/trajectory/TrajectoryWriter.h.

#include <TrajectoryWriter.h>

Inheritance diagram for McMd::TrajectoryWriter:

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

virtual	~TrajectoryWriter ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Read interval. More...

virtual void	save (Serializable::OArchive &ar)
	Save state to archive. More...

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

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

virtual void	setup ()
	Clear nSample counter. More...

virtual void	sample (long iStep)
	Write a frame/snapshot to trajectory file. More...

virtual void	output ()
	Close trajectory file after run. 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
bool	isBinary () const
	Is the file format binary (true) or text (false)? More...

virtual void	writeHeader (std::ofstream &out)
	Write data that should appear once, at beginning of the file. More...

virtual void	writeFrame (std::ofstream &out, long iStep)=0
	Write data that should appear in every frame. 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
long	nSample_
	Number of configurations dumped thus far (first dump is zero). More...

long	isInitialized_
	Has readParam been called? More...

bool	isBinary_
	Is the trajectory file a binary file? 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::TrajectoryWriter::TrajectoryWriter ( System & system )

Constructor.

Parameters

system parent System object.

virtual McMd::TrajectoryWriter::~TrajectoryWriter ( )

inlinevirtual

Destructor.

Definition at line 39 of file mcMd/analyzers/trajectory/TrajectoryWriter.h.

References McMd::serialize().

Member Function Documentation

virtual void McMd::TrajectoryWriter::readParameters ( std::istream & in )

virtual

Read interval.

Parameters

in	input parameter file

Reimplemented from McMd::Analyzer.

virtual void McMd::TrajectoryWriter::save ( Serializable::OArchive & ar )

virtual

Save state to archive.

Parameters

ar	saving (output) archive.

Reimplemented from McMd::Analyzer.

virtual void McMd::TrajectoryWriter::loadParameters ( Serializable::IArchive & ar )

virtual

Load state from an archive.

Parameters

ar	loading (input) archive.

Reimplemented from McMd::Analyzer.

template<class Archive >

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

Serialize to/from an archive.

Parameters

ar	saving or loading archive
version	archive version id

Definition at line 134 of file mcMd/analyzers/trajectory/TrajectoryWriter.h.

References McMd::Analyzer::serialize().

virtual void McMd::TrajectoryWriter::setup ( )

virtual

Clear nSample counter.

Reimplemented from McMd::Analyzer.

virtual void McMd::TrajectoryWriter::sample ( long iStep )

virtual

Write a frame/snapshot to trajectory file.

Parameters

iStep step index

Implements McMd::Analyzer.

virtual void McMd::TrajectoryWriter::output ( )

virtual

Close trajectory file after run.

Reimplemented from McMd::Analyzer.

bool McMd::TrajectoryWriter::isBinary ( ) const

protected

Is the file format binary (true) or text (false)?

virtual void McMd::TrajectoryWriter::writeHeader ( std::ofstream & out )

inlineprotectedvirtual

Write data that should appear once, at beginning of the file.

Called by sample on first invocation. Default implementation is empty.

Parameters

out	output file stream

Definition at line 114 of file mcMd/analyzers/trajectory/TrajectoryWriter.h.

virtual void McMd::TrajectoryWriter::writeFrame	(	std::ofstream &	out,
		long	iStep
	)

protectedpure virtual

Write data that should appear in every frame.

Parameters

out	output file stream
iStep	MD time step index

Member Data Documentation

long McMd::TrajectoryWriter::nSample_

protected

Number of configurations dumped thus far (first dump is zero).

Definition at line 95 of file mcMd/analyzers/trajectory/TrajectoryWriter.h.

long McMd::TrajectoryWriter::isInitialized_

protected

Has readParam been called?

Definition at line 98 of file mcMd/analyzers/trajectory/TrajectoryWriter.h.

bool McMd::TrajectoryWriter::isBinary_

protected

Is the trajectory file a binary file?

Definition at line 126 of file mcMd/analyzers/trajectory/TrajectoryWriter.h.

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

mcMd/analyzers/trajectory/TrajectoryWriter.h

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation