Detailed Description

Base class to write a trajectory to a single file.

Definition at line 40 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

#include <TrajectoryWriter.h>

Inheritance diagram for DdMd::TrajectoryWriter:

Public Member Functions
	TrajectoryWriter (Simulation &simulation, bool isBinary=false)
	Constructor. More...

virtual	~TrajectoryWriter ()
	Destructor. More...

virtual void	readParameters (std::istream &in)
	Read parameters and initialize. 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...

virtual void	setup ()
	Open the trajectory file. More...

virtual void	sample (long iStep)
	Dump configuration to file. More...

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

virtual void	output ()
	Close ouput 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
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...

Domain &	domain ()
	Get the Domain by reference. More...

Boundary &	boundary ()
	Get Boundary by reference. More...

AtomStorage &	atomStorage ()
	Get AtomStorage by reference. More...

AtomCollector &	atomCollector ()
	Get the AtomCollector by reference. More...

BondStorage &	bondStorage ()
	Get BondStorage by reference. More...

GroupCollector< 2 > &	bondCollector ()
	Get the bond collector by reference. More...

AngleStorage &	angleStorage ()
	Get AngleStorage by reference. More...

GroupCollector< 3 > &	angleCollector ()
	Get the angle collector by reference. More...

DihedralStorage &	dihedralStorage ()
	Get DihedralStorage by reference. More...

GroupCollector< 4 > &	dihedralCollector ()
	Get the dihedral collector by reference. 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::TrajectoryWriter::TrajectoryWriter	(	Simulation &	simulation,
		bool	isBinary = `false`
	)

Constructor.

Parameters

simulation	parent Simulation object
isBinary	Is the trajectory file a binary file?

Definition at line 23 of file ddMd/analyzers/trajectory/TrajectoryWriter.cpp.

References DdMd::Simulation::angleStorage(), DdMd::Simulation::atomStorage(), DdMd::Simulation::bondStorage(), DdMd::Simulation::boundary(), DdMd::Simulation::dihedralStorage(), DdMd::Simulation::domain(), and Util::ParamComposite::setClassName().

virtual DdMd::TrajectoryWriter::~TrajectoryWriter ( )

inlinevirtual

Destructor.

Definition at line 56 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

Member Function Documentation

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

virtual

Read parameters and initialize.

Parameters

in	input parameter file

Reimplemented from Util::ParamComposite.

Reimplemented in DdMd::DdMdGroupTrajectoryWriter.

Definition at line 59 of file ddMd/analyzers/trajectory/TrajectoryWriter.cpp.

References DdMd::Analyzer::readInterval(), and DdMd::Analyzer::readOutputFileName().

Referenced by DdMd::DdMdGroupTrajectoryWriter::readParameters().

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

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from DdMd::Analyzer.

Reimplemented in DdMd::DdMdGroupTrajectoryWriter.

Definition at line 69 of file ddMd/analyzers/trajectory/TrajectoryWriter.cpp.

References DdMd::Analyzer::loadInterval(), and DdMd::Analyzer::loadOutputFileName().

Referenced by DdMd::DdMdGroupTrajectoryWriter::loadParameters().

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

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from DdMd::Analyzer.

Reimplemented in DdMd::DdMdGroupTrajectoryWriter.

Definition at line 79 of file ddMd/analyzers/trajectory/TrajectoryWriter.cpp.

References DdMd::Analyzer::saveInterval(), and DdMd::Analyzer::saveOutputFileName().

Referenced by DdMd::DdMdGroupTrajectoryWriter::save().

void DdMd::TrajectoryWriter::setup ( )

virtual

Open the trajectory file.

Reimplemented from DdMd::Analyzer.

Definition at line 88 of file ddMd/analyzers/trajectory/TrajectoryWriter.cpp.

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

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

virtual

Dump configuration to file.

Parameters

iStep MC step index

Implements DdMd::Analyzer.

Definition at line 105 of file ddMd/analyzers/trajectory/TrajectoryWriter.cpp.

References DdMd::Analyzer::isAtInterval(), and writeFrame().

void DdMd::TrajectoryWriter::clear ( )

virtual

Clear nSample counter.

Reimplemented from DdMd::Analyzer.

Definition at line 115 of file ddMd/analyzers/trajectory/TrajectoryWriter.cpp.

Referenced by output().

void DdMd::TrajectoryWriter::output ( )

virtual

Close ouput file.

Reimplemented from DdMd::Analyzer.

Definition at line 125 of file ddMd/analyzers/trajectory/TrajectoryWriter.cpp.

References clear().

bool DdMd::TrajectoryWriter::isBinary ( ) const

inlineprotected

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

Definition at line 219 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

Referenced by setup().

virtual void DdMd::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

Reimplemented in DdMd::DdMdGroupTrajectoryWriter, and DdMd::DdMdTrajectoryWriter.

Definition at line 116 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

Referenced by setup().

virtual void DdMd::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

Implemented in DdMd::DdMdGroupTrajectoryWriter, DdMd::DdMdTrajectoryWriter, and DdMd::LammpsDumpWriter.

Referenced by sample().

Domain & DdMd::TrajectoryWriter::domain ( )

inlineprotected

Get the Domain by reference.

Definition at line 222 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

Referenced by DdMd::LammpsDumpWriter::writeFrame(), DdMd::DdMdTrajectoryWriter::writeFrame(), DdMd::DdMdGroupTrajectoryWriter::writeFrame(), DdMd::DdMdTrajectoryWriter::writeHeader(), and DdMd::DdMdGroupTrajectoryWriter::writeHeader().

Boundary & DdMd::TrajectoryWriter::boundary ( )

inlineprotected

Get Boundary by reference.

Definition at line 225 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

Referenced by DdMd::LammpsDumpWriter::writeFrame(), DdMd::DdMdTrajectoryWriter::writeFrame(), and DdMd::DdMdGroupTrajectoryWriter::writeFrame().

AtomStorage & DdMd::TrajectoryWriter::atomStorage ( )

inlineprotected

Get AtomStorage by reference.

Definition at line 228 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

Referenced by DdMd::LammpsDumpWriter::writeFrame(), DdMd::DdMdTrajectoryWriter::writeFrame(), DdMd::DdMdGroupTrajectoryWriter::writeFrame(), and DdMd::DdMdTrajectoryWriter::writeHeader().

AtomCollector & DdMd::TrajectoryWriter::atomCollector ( )

inlineprotected

Get the AtomCollector by reference.

Definition at line 231 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

Referenced by DdMd::LammpsDumpWriter::writeFrame(), DdMd::DdMdTrajectoryWriter::writeFrame(), DdMd::DdMdGroupTrajectoryWriter::writeFrame(), and DdMd::DdMdGroupTrajectoryWriter::writeHeader().

BondStorage & DdMd::TrajectoryWriter::bondStorage ( )

inlineprotected

Get BondStorage by reference.

Definition at line 235 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

GroupCollector< 2 > & DdMd::TrajectoryWriter::bondCollector ( )

inlineprotected

Get the bond collector by reference.

Definition at line 238 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

AngleStorage & DdMd::TrajectoryWriter::angleStorage ( )

inlineprotected

Get AngleStorage by reference.

Definition at line 243 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

GroupCollector< 3 > & DdMd::TrajectoryWriter::angleCollector ( )

inlineprotected

Get the angle collector by reference.

Definition at line 246 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

DihedralStorage & DdMd::TrajectoryWriter::dihedralStorage ( )

inlineprotected

Get DihedralStorage by reference.

Definition at line 251 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

GroupCollector< 4 > & DdMd::TrajectoryWriter::dihedralCollector ( )

inlineprotected

Get the dihedral collector by reference.

Definition at line 254 of file ddMd/analyzers/trajectory/TrajectoryWriter.h.

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

Detailed Description

Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation