Detailed Description

An object that can read multiple parameters from file.

Any class that reads a block of parameters from a parameter file must be derived from ParamComposite. Each such class must implement either the readParameters() function or the readParam() function, but not both. The readParameters(), if reimplemented, should read the body of the associated parameter file block, without opening or closing lines. The readParam() function reads the the entire block, including opening line and closing lines. The default implementation of readParam() reads the opening line of the block, calls readParameters() to read the body of the block, and then reads the closing line. Most subclasses of ParamComposite re-implement the readParameters() function, and rely on the default implementation of readParam() to add the Begin and End lines.

The writeParam() function, if called after readParam(), writes the associated parameter block using the same file format as that used to read the data in the earlier call to readParam().

Implementation details:

After parameter file block is read from file, the file format is stored as a private array of ParaComponent* pointers. We will refer to this in what follows as the format_ array. Each pointer in this array may point to a Parameter, ParamComposite, Begin, End, or Blank object. Pointers to these objects are added to the format array as the associated objects are read from file, and are stored in the same order as they appear in the parameter file. The default implementation of the writeParam() function simply calls the writeParam() function of each child ParamComponent.

Subclass implementation details:

The readParameters() function of each subclass of ParamComposite should be implemented using protected member functions of ParamComposite with names that begin with "read". The read<T>() function template can be used to read an individual parameter, while readParamComposite reads the nested subblock associated with a child ParamComposite. There are also more specialized methods (e.g., readDArray<T>to read different types of arrays and matrices of parameters, and to read optional parameters. See the users manual for further details.

The setClassName() and className() functions may be used to set and get a std::string containing the subclass name. The setClassName() function should be called in the constructor of each subclass of ParamComposite. The class name set in the constructor of a subclass will replace any name set by a base class, because of the order in which constructors are called. The default implementation of ParamComposite::readParam() checks if the class name that appears in the opening line of a parameter block agrees with the class name returned by the className() function, and throws an exception if it does not.

Definition at line 89 of file ParamComposite.h.

#include <ParamComposite.h>

Inheritance diagram for Util::ParamComposite:

Public Member Functions
	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...

Read and write functions for the composite
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	readParameters (std::istream &in)
	Read the body of parameter block, without begin and end lines. More...

virtual void	writeParam (std::ostream &out)
	Write all parameters to an output stream. More...

Serialization: Load and save functions for this composite
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...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines. More...

virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive. More...

void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true. More...

read* functions for child components
Each of these functions creates a new instance of a particular subclass of ParamComponent, invokes the readParam() function of the new object to read the associated line or block of a parameter file, and adds the object to the format.
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...

load* functions for child components
Load parameters from an Archive, for restarting. Each of these functions creates a new instance of a subclass of ParamComponent, and invokes the load() function of that new object to load the associated parameter value, and adds the ParamComponent to the format list. These functions are used to load parameters when a program is restarted from a checkpoint file.
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...

add* functions for child components
These functions add a ParamComponent to the format array, but do not read data.
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...

Accessors
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	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 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...

Constructor & Destructor Documentation

Util::ParamComposite::ParamComposite ( )

Constructor.

Definition at line 23 of file ParamComposite.cpp.

Util::ParamComposite::ParamComposite ( const ParamComposite & other )

Copy constructor.

Definition at line 55 of file ParamComposite.cpp.

Util::ParamComposite::ParamComposite ( int capacity )

Constructor.

Reserve space for capacity elements in the format array.

Parameters

capacity maximum length of parameter list

Definition at line 36 of file ParamComposite.cpp.

References UTIL_THROW.

Util::ParamComposite::~ParamComposite ( )

virtual

Virtual destructor.

Definition at line 68 of file ParamComposite.cpp.

Member Function Documentation

void Util::ParamComposite::resetParam ( )

virtual

Resets ParamComposite to its empty state.

This function deletes Parameter, Begin, End, and Blank objects in the format array (i.e., all "leaf" objects in the format tree), invokes the resetParam() function of any child ParamComposite in the format array, and clears the format array.

Reimplemented from Util::ParamComponent.

Definition at line 209 of file ParamComposite.cpp.

void Util::ParamComposite::readParam ( std::istream & in )

virtual

Read the parameter file block.

Inherited from ParamComponent. This function reads the entire parameter block for this ParamComposite, including an opening line, which is of the form "ClassName{", and the closing line, which contains only a closing bracket, "}". The default implementation reads the opening line (a Begin object), calls the virtual readParameters function to read the body of the block, and reads the closing line (an End object).

Exceptions

Throws if the string in the opening line does not match the string returned by the classname() function.

Parameters

in	input stream for reading

Implements Util::ParamComponent.

Reimplemented in DdMd::Simulation, McMd::McSimulation, McMd::MdSimulation, Util::Manager< Data >, Util::Manager< Command >, Util::Manager< Modifier >, Util::Manager< McMove >, Util::Manager< Analyzer >, Util::Manager< Simp::Species >, Simp::SpeciesEnsemble, and Tools::ChainMaker.

Definition at line 88 of file ParamComposite.cpp.

References readBegin(), readEnd(), and readParameters().

Referenced by readParamComposite().

void Util::ParamComposite::readParamOptional ( std::istream & in )

virtual

Read optional parameter file block.

Read an optional ParamComposite. This function must use a Label() object to read the opening "ClassName{" line, and then continues to read the rest of the block if and only if the class name in the opening line matches the string returned by the classname() function.

If the first line matches, the default implementation calls the readParameters() member function to read the body of the block, and then reads the ending line.

Parameters

in	input stream for reading

Reimplemented in Util::Manager< Data >, Util::Manager< Command >, Util::Manager< Modifier >, Util::Manager< McMove >, Util::Manager< Analyzer >, and Util::Manager< Simp::Species >.

Definition at line 101 of file ParamComposite.cpp.

References Util::Begin::isActive(), readBegin(), readEnd(), and readParameters().

Referenced by readParamCompositeOptional().

virtual void Util::ParamComposite::readParameters ( std::istream & in )

inlinevirtual

Read the body of parameter block, without begin and end lines.

Most subclasses of ParamComposite should re-implement this function, which has an empty default implementation. Every subclass of Paramcomposite must either: (1) Re-implement this function and rely on the default implementation of readParam(), which calls this function. (2) Re-implement readParam() itself. Option (1) is far more common. Option (2) is required only for classes that require a non-standard treatment of the beginning and ending lines (e.g., the Manager class template).

Parameters

in	input stream for reading

Definition at line 180 of file ParamComposite.h.

References load(), loadOptional(), and writeParam().

Referenced by readParam(), and readParamOptional().

void Util::ParamComposite::writeParam ( std::ostream & out )

virtual

Write all parameters to an output stream.

The default implementation iterates through the format array, and calls the readParam() member function of each ParamComponent in the array. This is sufficient for most subclasses.

Parameters

out	output stream for reading

Implements Util::ParamComponent.

Reimplemented in Simp::MultiHarmonicDihedral.

Definition at line 119 of file ParamComposite.cpp.

Referenced by McMd::LinkLengthDist::output(), McMd::G1MSD::output(), McMd::SSChainDist::output(), McMd::McNVTChemicalPotential::output(), McMd::ClusterHistogram::output(), Tools::AtomMSD::output(), McMd::McMuExchange::output(), McMd::VelProf::output(), Tools::PairEnergy::output(), McMd::LinkLifeTime::output(), McMd::LinkLTPos::output(), McMd::MdEnergyOutput::output(), McMd::AverageAnalyzer< SystemType >::output(), McMd::McEnergyOutput::output(), McMd::MdPotentialEnergyAverage::output(), McMd::PerturbDerivative::output(), DdMd::PairEnergyAverage::output(), DdMd::ExternalEnergyAverage::output(), McMd::LinkMSD::output(), McMd::MdKineticEnergyAverage::output(), McMd::NLinkAverage::output(), McMd::InterIntraLink::output(), McMd::BoundaryAverage::output(), McMd::MdPairEnergyCoefficients::output(), McMd::AtomMSD::output(), DdMd::StressAutoCorr::output(), McMd::BondLengthDist::output(), McMd::McPairEnergyAverage::output(), McMd::PressureAverage< SystemType >::output(), DdMd::AutoCorrAnalyzer< Data, Product >::output(), McMd::StressAutoCorr< SystemType >::output(), McMd::ComMSD::output(), McMd::RingRouseAutoCorr::output(), McMd::EndtoEndXYZ::output(), DdMd::AverageAnalyzer::output(), McMd::MdEnergyAnalyzer::output(), McMd::McEnergyAnalyzer::output(), McMd::IntraBondStressAutoCorr< SystemType >::output(), McMd::LinearRouseAutoCorr::output(), DdMd::EnergyAnalyzer::output(), McMd::EndtoEnd::output(), DdMd::SymmTensorAverageAnalyzer::output(), DdMd::TensorAverageAnalyzer::output(), McMd::BlockRadiusGyration::output(), McMd::RDF::output(), McMd::CompositionProfile::output(), DdMd::OrderParamNucleation::output(), McMd::IntraBondTensorAutoCorr< SystemType >::output(), McMd::StructureFactor::output(), DdMd::StructureFactorGrid::output(), McMd::IntraPairAutoCorr::output(), McMd::StructureFactorPGrid::output(), McMd::StructureFactorGrid::output(), McMd::RadiusGyration::output(), McMd::IntraStructureFactorGrid::output(), DdMd::StructureFactor::output(), DdMd::VanHove::output(), McMd::VanHove::output(), McMd::StructureFactorP::output(), McMd::IntraStructureFactor::output(), and readParameters().

void Util::ParamComposite::load ( Serializable::IArchive & ar )

virtual

Load all parameters from an input archive.

This function is inherited from Serializable. The default implementation of ParamComposite::load() calls loadParameters, and adds Begin and End lines to the format array.. All subclasses of ParamComposite should overload the virtual loadParameters member function.

Parameters

ar	input/loading archive.

Reimplemented from Util::ParamComponent.

Reimplemented in McMd::McNVTChemicalPotential, Util::AutoCorrelation< Data, Product >, Util::AutoCorrelation< Tensor, double >, and Util::AutoCorrelation< Util::Tensor, double >.

Definition at line 131 of file ParamComposite.cpp.

References addBegin(), addEnd(), Util::ParamComponent::echo(), Util::Log::file(), Util::MpiFileIo::isIoProcessor(), loadParameters(), Util::End::writeParam(), and Util::Begin::writeParam().

Referenced by loadOptional(), loadParamComposite(), and readParameters().

void Util::ParamComposite::loadOptional ( Serializable::IArchive & ar )

virtual

Load an optional ParamComposite.

Loads isActive, and calls load(ar) if active.

Parameters

ar	input/loading archive.

Definition at line 152 of file ParamComposite.cpp.

References Util::bcast< bool >(), className(), Util::ParamComponent::echo(), Util::Log::file(), Util::MpiFileIo::hasIoCommunicator(), Util::ParamComponent::indent(), Util::MpiFileIo::ioCommunicator(), Util::MpiFileIo::isIoProcessor(), load(), and UTIL_THROW.

Referenced by loadParamCompositeOptional(), and readParameters().

virtual void Util::ParamComposite::loadParameters ( Serializable::IArchive & ar )

inlinevirtual

Load state from archive, without adding Begin and End lines.

This function should be re-implemented by all subclasses that have an internal state that should be saved in a restart file. The default implementation is empty. Subclass implementations should load the entire internal state from the archive, including parameters that appear in the parameter file and any persistent private member variables that do not appear in the parameter file.

Parameters

ar	input/loading archive.

Definition at line 233 of file ParamComposite.h.

References isRequired(), loadCArray(), loadDArray(), loadFArray(), loadParamComposite(), loadParamCompositeOptional(), loadParameter(), read(), readBegin(), readBlank(), readCArray(), readCArray2D(), readDArray(), readDMatrix(), readDSymmMatrix(), readEnd(), readFArray(), readOptional(), readOptionalCArray(), readOptionalCArray2D(), readOptionalDArray(), readOptionalDMatrix(), readOptionalDSymmMatrix(), readOptionalFArray(), readParamComposite(), readParamCompositeOptional(), save(), and saveOptional().

Referenced by load(), and Tools::TrajectoryWriter::readParameters().

void Util::ParamComposite::save ( Serializable::OArchive & ar )

virtual

Saves all parameters to an archive.

The default implementation simply calls the save function for all items in the parameter file format array. This is often not sufficient. Specifically, it is not sufficient for classes that contain any persistent member variables that do not appear in the parameter file format.

If a class also defines a serialize function template, which allows instances to be serialized to any type of archive, then the save function can often be implemented as follows:

void save(Serializable::OArchive& ar)

{ ar & *this; }

Parameters

ar	output/saving archive.

Reimplemented from Util::ParamComponent.

Definition at line 188 of file ParamComposite.cpp.

Referenced by loadParameters(), Tools::TrajectoryWriter::readParameters(), McMd::System::saveLinkMaster(), saveOptional(), McMd::McSystem::saveParameters(), and McMd::MdSystem::saveParameters().

void Util::ParamComposite::saveOptional ( Serializable::OArchive & ar )

Saves isActive flag, and then calls save() iff isActive is true.

Parameters

ar	output/saving archive.

Definition at line 198 of file ParamComposite.cpp.

References save().

Referenced by loadParameters().

void Util::ParamComposite::readParamComposite	(	std::istream &	in,
		ParamComposite &	child,
		bool	next = `true`
	)

Add and read a required child ParamComposite.

Parameters

in	input stream for reading
child	child ParamComposite object
next	true if the indent level is one higher than parent.

Definition at line 260 of file ParamComposite.cpp.

References addParamComposite(), and readParam().

void Util::ParamComposite::readParamCompositeOptional	(	std::istream &	in,
		ParamComposite &	child,
		bool	next = `true`
	)

Add and attempt to read an optional child ParamComposite.

Parameters

in	input stream for reading
child	child ParamComposite object
next	true if the indent level is one higher than parent.

Definition at line 271 of file ParamComposite.cpp.

References addParamComposite(), and readParamOptional().

Referenced by loadParameters(), Tools::Processor::readParameters(), McMd::MdSimulation::readParameters(), and McMd::McSimulation::readParameters().

template<typename Type >

ScalarParam< Type > & Util::ParamComposite::read	(	std::istream &	in,
		const char *	label,
		Type &	value
	)

Add and read a new required ScalarParam < Type > object.

This is equivalent to ScalarParam<Type>(in, label, value, true).

Parameters

in	input stream for reading
label	Label string
value	reference to new ScalarParam< Type >

Definition at line 1156 of file ParamComposite.h.

Referenced by loadParameters(), McMd::SpecialPotentialFacade< PotentialType, FactoryType >::readParameters(), McMd::PressureAverage< SystemType >::readParameters(), McMd::StressAutoCorr< SystemType >::readParameters(), McMd::IntraBondStressAutoCorr< SystemType >::readParameters(), and McMd::IntraBondTensorAutoCorr< SystemType >::readParameters().

template<typename Type >

ScalarParam< Type > & Util::ParamComposite::readOptional	(	std::istream &	in,
		const char *	label,
		Type &	value
	)

inline

Add and read a new optional ScalarParam < Type > object.

This is equivalent to ScalarParam<Type>(in, label, value, false).

Parameters

in	input stream for reading
label	Label string
value	reference to new ScalarParam< Type >

Definition at line 1164 of file ParamComposite.h.

Referenced by loadParameters(), Util::AutoCorrelation< Data, Product >::readParameters(), and McMd::StressAutoCorr< SystemType >::readParameters().

template<typename Type >

CArrayParam< Type > & Util::ParamComposite::readCArray	(	std::istream &	in,
		const char *	label,
		Type *	value,
		int	n
	)

inline

Add and read a required C array parameter.

Parameters

in	input stream for reading
label	Label string for new array
value	pointer to array
n	number of elements

Returns: reference to the new CArrayParam<Type> object

Definition at line 1231 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type >

CArrayParam< Type > & Util::ParamComposite::readOptionalCArray	(	std::istream &	in,
		const char *	label,
		Type *	value,
		int	n
	)

inline

Add and read an optional C array parameter.

Parameters

in	input stream for reading
label	Label string for new array
value	pointer to array
n	number of elements

Returns: reference to the new CArrayParam<Type> object

Definition at line 1240 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type >

DArrayParam< Type > & Util::ParamComposite::readDArray	(	std::istream &	in,
		const char *	label,
		DArray< Type > &	array,
		int	n
	)

inline

Add and read a required DArray < Type > parameter.

Parameters

in	input stream for reading
label	Label string for new array
array	DArray object
n	number of elements

Returns: reference to the new DArrayParam<Type> object

Definition at line 1308 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type >

DArrayParam< Type > & Util::ParamComposite::readOptionalDArray	(	std::istream &	in,
		const char *	label,
		DArray< Type > &	array,
		int	n
	)

inline

Add and read an optional DArray < Type > parameter.

Parameters

in	input stream for reading
label	Label string for new array
array	DArray object
n	number of elements

Returns: reference to the new DArrayParam<Type> object

Definition at line 1318 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type , int N>

FArrayParam< Type, N > & Util::ParamComposite::readFArray	(	std::istream &	in,
		const char *	label,
		FArray< Type, N > &	array
	)

inline

Add and read a required FArray < Type, N > array parameter.

Parameters

in	input stream for reading
label	Label string for new array
array	FArray object

Returns: reference to the new FArrayParam<Type, N> object

Definition at line 1386 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type , int N>

FArrayParam< Type, N > & Util::ParamComposite::readOptionalFArray	(	std::istream &	in,
		const char *	label,
		FArray< Type, N > &	array
	)

inline

Add and read an optional FArray < Type, N > array parameter.

Parameters

in	input stream for reading
label	Label string for new array
array	FArray object

Returns: reference to the new FArrayParam<Type, N> object

Definition at line 1396 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type >

CArray2DParam< Type > & Util::ParamComposite::readCArray2D	(	std::istream &	in,
		const char *	label,
		Type *	value,
		int	m,
		int	n,
		int	np
	)

inline

Add and read a required CArray2DParam < Type > 2D C-array.

Parameters

in	input stream for reading
label	Label string for new array
value	pointer to array
m	number of rows (1st dimension)
n	logical number of columns (2nd dimension)
np	physical number of columns (elements allocated per row)

Returns: reference to the CArray2DParam<Type> object

Definition at line 1456 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type >

CArray2DParam< Type > & Util::ParamComposite::readOptionalCArray2D	(	std::istream &	in,
		const char *	label,
		Type *	value,
		int	m,
		int	n,
		int	np
	)

inline

Add and read an optional CArray2DParam < Type > 2D C-array parameter.

Parameters

in	input stream for reading
label	Label string for new array
value	pointer to array
m	number of rows (1st dimension)
n	logical number of columns (2nd dimension)
np	physical number of columns (elements allocated per row)

Returns: reference to the CArray2DParam<Type> object

Definition at line 1465 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type >

DMatrixParam< Type > & Util::ParamComposite::readDMatrix	(	std::istream &	in,
		const char *	label,
		DMatrix< Type > &	matrix,
		int	m,
		int	n
	)

inline

Add and read a required DMatrix < Type > matrix parameter.

Parameters

in	input stream for reading
label	Label string for new array
matrix	DMatrix object
m	number of rows (1st dimension)
n	number of columns (2nd dimension)

Returns: reference to the DMatrixParam<Type> object

Definition at line 1538 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type >

DMatrixParam< Type > & Util::ParamComposite::readOptionalDMatrix	(	std::istream &	in,
		const char *	label,
		DMatrix< Type > &	matrix,
		int	m,
		int	n
	)

inline

Add and read an optional DMatrix < Type > matrix parameter.

Parameters

in	input stream for reading
label	Label string for new array
matrix	DMatrix object
m	number of rows (1st dimension)
n	number of columns (2nd dimension)

Returns: reference to the DMatrixParam<Type> object

Definition at line 1547 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type >

DSymmMatrixParam< Type > & Util::ParamComposite::readDSymmMatrix	(	std::istream &	in,
		const char *	label,
		DMatrix< Type > &	matrix,
		int	n
	)

inline

Add and read a required symmetrix DMatrix.

Parameters

in	input stream for reading
label	Label string for new array
matrix	DMatrix object
n	number of rows or columns

Returns: reference to the DMatrixParam<Type> object

Definition at line 1603 of file ParamComposite.h.

Referenced by loadParameters().

template<typename Type >

DSymmMatrixParam< Type > & Util::ParamComposite::readOptionalDSymmMatrix	(	std::istream &	in,
		const char *	label,
		DMatrix< Type > &	matrix,
		int	n
	)

inline

Add and read an optional DMatrix matrix parameter.

Parameters

in	input stream for reading
label	Label string for new array
matrix	DMatrix object
n	number of rows or columns

Returns: reference to the DMatrixParam<Type> object

Definition at line 1614 of file ParamComposite.h.

Referenced by loadParameters().

Begin & Util::ParamComposite::readBegin	(	std::istream &	in,
		const char *	label,
		bool	isRequired = `true`
	)

Add and read a class label and opening bracket.

Parameters

in	input stream for reading
label	class name string, without trailing bracket
isRequired	Is this the beginning of a required element?

Returns: reference to the new Begin object

Definition at line 316 of file ParamComposite.cpp.

References addComponent(), Util::Begin::isActive(), Util::Begin::readParam(), and setParent().

Referenced by Util::Manager< Data >::beginReadManager(), loadParameters(), Simp::SpeciesEnsemble::readParam(), McMd::MdSimulation::readParam(), McMd::McSimulation::readParam(), readParam(), McMd::LinkLTPos::readParameters(), and readParamOptional().

End & Util::ParamComposite::readEnd ( std::istream & in )

Add and read the closing bracket.

Parameters

in	input stream for reading

Returns: reference to the new End object

Definition at line 344 of file ParamComposite.cpp.

References addEnd(), and Util::End::readParam().

Referenced by loadParameters(), Simp::SpeciesEnsemble::readParam(), McMd::MdSimulation::readParam(), McMd::McSimulation::readParam(), readParam(), McMd::LinkLTPos::readParameters(), and readParamOptional().

Blank & Util::ParamComposite::readBlank ( std::istream & in )

Add and read a new Blank object, representing a blank line.

Parameters

in	input stream for reading

Returns: reference to the new Blank object

Definition at line 367 of file ParamComposite.cpp.

References addBlank(), and Util::Blank::readParam().

Referenced by loadParameters(), McMd::RigidDisplaceMove::readParameters(), and Util::Manager< Data >::readParameters().

void Util::ParamComposite::loadParamComposite	(	Serializable::IArchive &	ar,
		ParamComposite &	child,
		bool	next = `true`
	)

Add and load a required child ParamComposite.

Parameters

ar	input archive for loading
child	child ParamComposite object
next	true if the indent level is one higher than parent.

Definition at line 282 of file ParamComposite.cpp.

References addParamComposite(), and load().

void Util::ParamComposite::loadParamCompositeOptional	(	Serializable::IArchive &	ar,
		ParamComposite &	child,
		bool	next = `true`
	)

Add and load an optional child ParamComposite if isActive.

This functional loads the isActive flag, and then calls the load function of the child iff isActive is true.

Parameters

ar	input archive for loading
child	child ParamComposite object
next	true if the indent level is one higher than parent.

Definition at line 293 of file ParamComposite.cpp.

References addParamComposite(), and loadOptional().

Referenced by loadParameters().

template<typename Type >

ScalarParam< Type > & Util::ParamComposite::loadParameter	(	Serializable::IArchive &	ar,
		const char *	label,
		Type &	value,
		bool	isRequired
	)

Add and load a new ScalarParam < Type > object.

An optional parameter is indicated by setting isRequired = false. Optional parameters must be saved using the Parameter::saveOptional() static member function.

Parameters

ar	archive for loading
label	Label string
value	reference to the Type variable
isRequired	Is this a required parameter?

Returns: reference to the new ScalarParam < Type > object

Definition at line 1173 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::load(), and setParent().

Referenced by McMd::PressureAverage< SystemType >::loadParameters(), McMd::StressAutoCorr< SystemType >::loadParameters(), DdMd::StressAutoCorr::loadParameters(), DdMd::AutoCorrAnalyzer< Data, Product >::loadParameters(), McMd::IntraBondStressAutoCorr< SystemType >::loadParameters(), McMd::IntraBondTensorAutoCorr< SystemType >::loadParameters(), McMd::McMuExchange::loadParameters(), and loadParameters().

template<typename Type >

ScalarParam< Type > & Util::ParamComposite::loadParameter	(	Serializable::IArchive &	ar,
		const char *	label,
		Type &	value
	)

inline

Add and load new required ScalarParam < Type > object.

Equivalent to loadParameter < Type > (ar, label, value, true).

Parameters

ar	archive for loading
label	label string
value	reference to the Type variable

Returns: reference to the new ScalarParam < Type > object

Definition at line 1189 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::readParam(), and setParent().

template<typename Type >

CArrayParam< Type > & Util::ParamComposite::loadCArray	(	Serializable::IArchive &	ar,
		const char *	label,
		Type *	value,
		int	n,
		bool	isRequired
	)

Add a C array parameter and load its elements.

Parameters

ar	archive for loading
label	label string for new array
value	pointer to array
n	number of elements
isRequired	Is this a required parameter?

Returns: reference to the new CArrayParam<Type> object

Definition at line 1249 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::load(), and setParent().

Referenced by loadParameters().

template<typename Type >

CArrayParam< Type > & Util::ParamComposite::loadCArray	(	Serializable::IArchive &	ar,
		const char *	label,
		Type *	value,
		int	n
	)

inline

Add and load a required CArrayParam< Type > array parameter.

Equivalent to loadCArray < Type > (ar, label, value, n, true).

Parameters

ar	archive for loading
label	label string for new array
value	pointer to array
n	number of elements

Returns: reference to the new CArrayParam<Type> object

Definition at line 1265 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::readParam(), and setParent().

template<typename Type >

DArrayParam< Type > & Util::ParamComposite::loadDArray	(	Serializable::IArchive &	ar,
		const char *	label,
		DArray< Type > &	array,
		int	n,
		bool	isRequired
	)

Add an load a DArray < Type > array parameter.

Parameters

ar	archive for loading
label	Label string for new array
array	DArray object
n	number of elements (logical size)
isRequired	Is this a required parameter?

Returns: reference to the new DArrayParam<Type> object

Definition at line 1327 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::load(), and setParent().

Referenced by McMd::McMuExchange::loadParameters(), and loadParameters().

template<typename Type >

DArrayParam< Type > & Util::ParamComposite::loadDArray	(	Serializable::IArchive &	ar,
		const char *	label,
		DArray< Type > &	array,
		int	n
	)

inline

Add and load a required DArray< Type > array parameter.

Equivalent to loadDArrayParam < Type > (ar, label, array, n, true).

Parameters

ar	archive for loading
label	Label string for new array
array	DArray object
n	number of elements (logical size)

Returns: reference to the new DArrayParam<Type> object

Definition at line 1343 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::readParam(), and setParent().

template<typename Type , int N>

FArrayParam< Type, N > & Util::ParamComposite::loadFArray	(	Serializable::IArchive &	ar,
		const char *	label,
		FArray< Type, N > &	array,
		bool	isRequired
	)

Add and load an FArray < Type, N > fixed-size array parameter.

Parameters

ar	archive for loading
label	label string for new array
array	FArray object
isRequired	Is this a required parameter?

Returns: reference to the new FArrayParam<Type, N> object

Definition at line 1405 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::load(), Util::Parameter::readParam(), and setParent().

Referenced by loadParameters().

template<typename Type , int N>

FArrayParam<Type, N>& Util::ParamComposite::loadFArray	(	Serializable::IArchive &	ar,
		const char *	label,
		FArray< Type, N > &	array
	)

inline

Add and load a required FArray < Type > array parameter.

Equivalent to loadFArrayParam < Type > (ar, label, array, true).

Parameters

ar	archive for loading
label	label string for new array
array	FArray object

Returns: reference to the new FArrayParam<Type, N> object

Definition at line 675 of file ParamComposite.h.

References add(), addBegin(), addBlank(), addCArray(), addCArray2D(), addComponent(), addDArray(), addDMatrix(), addEnd(), addFArray(), addParamComposite(), className(), isActive(), isRequired(), loadCArray2D(), loadDMatrix(), loadDSymmMatrix(), setClassName(), setIsActive(), setIsRequired(), and setParent().

template<typename Type >

CArray2DParam< Type > & Util::ParamComposite::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.

Parameters

ar	archive for loading
label	Label string for new array
value	pointer to array
m	number of rows (1st dimension)
n	logical number of columns (2nd dimension)
np	physical number of columns (elements allocated per row)
isRequired	Is this a required parameter?

Returns: reference to the CArray2DParam<Type> object

Definition at line 1475 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::load(), and setParent().

Referenced by loadFArray().

template<typename Type >

CArray2DParam< Type > & Util::ParamComposite::loadCArray2D	(	Serializable::IArchive &	ar,
		const char *	label,
		Type *	value,
		int	m,
		int	n,
		int	np
	)

Add and load a required < Type > matrix parameter.

Equivalent to loadCArray2DParam < Type > (ar, label, value, m, n, np, true).

Parameters

ar	archive for loading
label	Label string for new array
value	pointer to array
m	number of rows (1st dimension)
n	logical number of columns (2nd dimension)
np	physical number of columns (elements allocated per row)

Returns: reference to the CArray2DParam<Type> object

Definition at line 1493 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::readParam(), and setParent().

template<typename Type >

DMatrixParam< Type > & Util::ParamComposite::loadDMatrix	(	Serializable::IArchive &	ar,
		const char *	label,
		DMatrix< Type > &	matrix,
		int	m,
		int	n,
		bool	isRequired
	)

Add and load a DMatrixParam < Type > matrix parameter.

Parameters

ar	archive for loading
label	Label string for new array
matrix	DMatrix object
m	number of rows (1st dimension)
n	number of columns (2nd dimension)
isRequired	Is this a required parameter?

Returns: reference to the DMatrixParam<Type> object

Definition at line 1556 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::load(), and setParent().

Referenced by loadFArray().

template<typename Type >

DMatrixParam< Type > & Util::ParamComposite::loadDMatrix	(	Serializable::IArchive &	ar,
		const char *	label,
		DMatrix< Type > &	matrix,
		int	m,
		int	n
	)

inline

Add and load a required DMatrixParam < Type > matrix parameter.

Parameters

ar	archive for loading
label	Label string for new array
matrix	DMatrix object
m	number of rows (1st dimension)
n	number of columns (2nd dimension)

Returns: reference to the DMatrixParam<Type> object

Definition at line 1573 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::readParam(), and setParent().

template<typename Type >

DSymmMatrixParam< Type > & Util::ParamComposite::loadDSymmMatrix	(	Serializable::IArchive &	ar,
		const char *	label,
		DMatrix< Type > &	matrix,
		int	n,
		bool	isRequired
	)

Add and load a symmetric DSymmMatrixParam < Type > matrix parameter.

Parameters

ar	archive for loading
label	Label string for new array
matrix	DMatrix object
n	number of rows or columns
isRequired	Is this a required parameter?

Returns: reference to the DMatrixParam<Type> object

Definition at line 1625 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::load(), and setParent().

Referenced by loadFArray().

template<typename Type >

DSymmMatrixParam< Type > & Util::ParamComposite::loadDSymmMatrix	(	Serializable::IArchive &	ar,
		const char *	label,
		DMatrix< Type > &	matrix,
		int	n
	)

inline

Add and load a required DSymmMatrixParam < Type > matrix parameter.

Parameters

ar	archive for loading
label	Label string for new array
matrix	DMatrix object
n	number of rows or columns

Returns: reference to the DMatrixParam<Type> object

Definition at line 1644 of file ParamComposite.h.

void Util::ParamComposite::addParamComposite	(	ParamComposite &	child,
		bool	next = `true`
	)

Add a child ParamComposite object to the format array.

Parameters

child	child ParamComposite object
next	true if the indent level is one higher than parent.

Definition at line 249 of file ParamComposite.cpp.

References addComponent(), and setParent().

Begin & Util::ParamComposite::addBegin ( const char * label )

Add a Begin object representing a class name and bracket.

Parameters

label class name string, without trailing bracket

Returns: reference to the new begin object.

Definition at line 305 of file ParamComposite.cpp.

References addComponent(), and setParent().

Referenced by load(), loadFArray(), Simp::CompensatedPair< BarePair, LinkPotential >::readParameters(), and Simp::CompositeBond< BareBond, BarePair >::readParameters().

End & Util::ParamComposite::addEnd ( )

Add a closing bracket.

Returns: reference to the new End object.

Definition at line 333 of file ParamComposite.cpp.

References addComponent(), and setParent().

Referenced by Util::Manager< Data >::endReadManager(), load(), loadFArray(), readEnd(), Simp::CompensatedPair< BarePair, LinkPotential >::readParameters(), and Simp::CompositeBond< BareBond, BarePair >::readParameters().

Blank & Util::ParamComposite::addBlank ( )

Create and add a new Blank object, representing a blank line.

Returns: reference to the new Blank object

Definition at line 356 of file ParamComposite.cpp.

References addComponent(), and setParent().

Referenced by loadFArray(), Util::Manager< Data >::loadParameters(), and readBlank().

std::string Util::ParamComposite::className ( ) const

inline

Get class name string.

Definition at line 1103 of file ParamComposite.h.

Referenced by Util::Manager< Data >::beginReadManager(), loadFArray(), loadOptional(), McMd::MdSystem::loadParameters(), McMd::System::loadPerturbation(), McMd::MdSimulation::readParam(), McMd::McSimulation::readParam(), McMd::MdSystem::readParameters(), McMd::System::readPerturbation(), McMd::MdSystem::saveParameters(), McMd::System::savePerturbation(), and setClassName().

bool Util::ParamComposite::isRequired ( ) const

inline

Is this ParamComposite required in the input file?

Definition at line 1109 of file ParamComposite.h.

Referenced by add(), addCArray(), addCArray2D(), addDArray(), addDMatrix(), addFArray(), Util::Manager< Data >::beginReadManager(), isActive(), loadCArray(), loadCArray2D(), loadDArray(), loadDMatrix(), loadDSymmMatrix(), loadFArray(), loadParameter(), McMd::MdEnergyAnalyzer::loadParameters(), McMd::McEnergyAnalyzer::loadParameters(), DdMd::EnergyAnalyzer::loadParameters(), DdMd::AverageAnalyzer::loadParameters(), DdMd::TensorAverageAnalyzer::loadParameters(), DdMd::SymmTensorAverageAnalyzer::loadParameters(), loadParameters(), and setIsRequired().

bool Util::ParamComposite::isActive ( ) const

inline

Is this parameter active?

Definition at line 1115 of file ParamComposite.h.

References addComponent(), isRequired(), Util::Parameter::readParam(), and setParent().

Referenced by loadFArray(), Util::Manager< Data >::readParamOptional(), McMd::LinkMaster::removeLink(), McMd::McEnergyAnalyzer::save(), McMd::MdEnergyAnalyzer::save(), DdMd::EnergyAnalyzer::save(), DdMd::AverageAnalyzer::save(), DdMd::TensorAverageAnalyzer::save(), DdMd::SymmTensorAverageAnalyzer::save(), and setIsActive().

void Util::ParamComposite::setClassName ( const char * className )

protected

Set class name string.

Should be set in subclass constructor.

Definition at line 377 of file ParamComposite.cpp.

References className().

Referenced by Tools::AnalyzerManager::AnalyzerManager(), DdMd::AnalyzerManager::AnalyzerManager(), McMd::AnalyzerManager::AnalyzerManager(), DdMd::AnglePotential::AnglePotential(), McMd::AnglePotential::AnglePotential(), DdMd::AngleStorage::AngleStorage(), DdMd::AtomCollector::AtomCollector(), McMd::AtomDisplaceMove::AtomDisplaceMove(), DdMd::AtomDistributor::AtomDistributor(), Tools::AtomMSD::AtomMSD(), McMd::AtomMSD::AtomMSD(), DdMd::AtomStorage::AtomStorage(), Util::AutoCorr< Data, Product >::AutoCorr(), DdMd::AutoCorrAnalyzer< Data, Product >::AutoCorrAnalyzer(), Util::AutoCorrArray< Data, Product >::AutoCorrArray(), Util::Average::Average(), DdMd::AverageAnalyzer::AverageAnalyzer(), McMd::BennettsMethod::BennettsMethod(), McMd::BlockRadiusGyration::BlockRadiusGyration(), McMd::BondLengthDist::BondLengthDist(), DdMd::BondPotential::BondPotential(), McMd::BondPotential::BondPotential(), DdMd::BondStorage::BondStorage(), DdMd::BondTensorAutoCorr::BondTensorAutoCorr(), McMd::BoundaryAverage::BoundaryAverage(), Simp::BoundaryEnsemble::BoundaryEnsemble(), Simp::BoxExternal::BoxExternal(), DdMd::Buffer::Buffer(), McMd::CfbDoubleRebridgeMove::CfbDoubleRebridgeMove(), McMd::CfbEndMove::CfbEndMove(), McMd::CfbLinearEndMove::CfbLinearEndMove(), McMd::CfbRebridgeMove::CfbRebridgeMove(), McMd::CfbReptateMove::CfbReptateMove(), McMd::CfbReptationMove::CfbReptationMove(), McMd::CfbRingRebridgeMove::CfbRingRebridgeMove(), McMd::ClusterHistogram::ClusterHistogram(), McMd::ColVarPotentialTmpl< ColVarType, BiasType >::ColVarPotentialTmpl(), McMd::CommandManager::CommandManager(), McMd::ComMSD::ComMSD(), Simp::CompensatedPair< BarePair, LinkPotential >::CompensatedPair(), Simp::CompositeBond< BareBond, BarePair >::CompositeBond(), McMd::CompositionProfile::CompositionProfile(), DdMd::ConfigIo::ConfigIo(), Tools::ConfigReader::ConfigReader(), Tools::Configuration::Configuration(), Tools::ConfigWriter::ConfigWriter(), McMd::ConfigWriter::ConfigWriter(), DdMd::ConfigWriter::ConfigWriter(), Simp::CosineAngle::CosineAngle(), Simp::CosineDihedral::CosineDihedral(), Simp::CosineSqAngle::CosineSqAngle(), McMd::Crosslinker::Crosslinker(), DdMd::DdMdConfigIo::DdMdConfigIo(), Tools::DdMdConfigReader::DdMdConfigReader(), Tools::DdMdConfigWriter::DdMdConfigWriter(), DdMd::DdMdOrderedConfigIo::DdMdOrderedConfigIo(), Tools::DdMdTrajectoryReader::DdMdTrajectoryReader(), DdMd::DdMdTrajectoryWriter::DdMdTrajectoryWriter(), McMd::DeformCommand::DeformCommand(), Simp::Diblock::Diblock(), DdMd::DihedralPotential::DihedralPotential(), DdMd::DihedralStorage::DihedralStorage(), Util::Distribution::Distribution(), DdMd::Domain::Domain(), McMd::DpdMove::DpdMove(), Simp::DpdPair::DpdPair(), McMd::EndSwapMove::EndSwapMove(), McMd::EndtoEnd::EndtoEnd(), McMd::EndtoEndXYZ::EndtoEndXYZ(), DdMd::EnergyAnalyzer::EnergyAnalyzer(), Simp::EnergyEnsemble::EnergyEnsemble(), Simp::EwaldInteraction::EwaldInteraction(), DdMd::ExternalEnergyAnalyzer::ExternalEnergyAnalyzer(), DdMd::ExternalEnergyAverage::ExternalEnergyAverage(), DdMd::ExternalPotential::ExternalPotential(), Simp::FeneBond::FeneBond(), Util::FileMaster::FileMaster(), McMd::G1MSD::G1MSD(), McMd::GcSliplinkMove::GcSliplinkMove(), Simp::GeneralPeriodicExternal::GeneralPeriodicExternal(), DdMd::GroupCollector< N >::GroupCollector(), DdMd::GroupDistributor< N >::GroupDistributor(), Simp::HarmonicAngle::HarmonicAngle(), Simp::HarmonicBond::HarmonicBond(), Simp::HarmonicL0Bond::HarmonicL0Bond(), McMd::HomopolymerSemiGrandMove::HomopolymerSemiGrandMove(), McMd::HomopolymerSG::HomopolymerSG(), Simp::HomoRing::HomoRing(), Tools::HoomdConfigReader::HoomdConfigReader(), Tools::HoomdConfigWriter::HoomdConfigWriter(), McMd::HybridMdMove::HybridMdMove(), McMd::HybridNphMdMove::HybridNphMdMove(), Util::IntDistribution::IntDistribution(), McMd::InterIntraLink::InterIntraLink(), McMd::IntraPairAutoCorr::IntraPairAutoCorr(), McMd::IntraStructureFactor::IntraStructureFactor(), McMd::IntraStructureFactorGrid::IntraStructureFactorGrid(), DdMd::KineticEnergyAnalyzer::KineticEnergyAnalyzer(), Simp::LamellarOrderingExternal::LamellarOrderingExternal(), Tools::LammpsDumpReader::LammpsDumpReader(), DdMd::LammpsDumpWriter::LammpsDumpWriter(), McMd::LammpsDumpWriter::LammpsDumpWriter(), McMd::LinearRouseAutoCorr::LinearRouseAutoCorr(), McMd::LinearSG::LinearSG(), McMd::LinkLengthDist::LinkLengthDist(), McMd::LinkLifeTime::LinkLifeTime(), McMd::LinkLTPos::LinkLTPos(), McMd::LinkMaster::LinkMaster(), McMd::LinkMSD::LinkMSD(), McMd::LinkPotentialImpl< Interaction >::LinkPotentialImpl(), Simp::LJPair::LJPair(), loadFArray(), Simp::LocalLamellarOrderingExternal::LocalLamellarOrderingExternal(), DdMd::LogEnergy::LogEnergy(), McMd::McBondEnergyAverage::McBondEnergyAverage(), McMd::McDeformCommand::McDeformCommand(), McMd::McEnergyAnalyzer::McEnergyAnalyzer(), McMd::McEnergyAverage::McEnergyAverage(), McMd::McEnergyOutput::McEnergyOutput(), McMd::McExternalEnergyAverage::McExternalEnergyAverage(), McMd::McIntraBondStressAutoCorr::McIntraBondStressAutoCorr(), McMd::McIntraBondTensorAutoCorr::McIntraBondTensorAutoCorr(), McMd::McMoveManager::McMoveManager(), McMd::McMuExchange::McMuExchange(), McMd::McPairEnergyAverage::McPairEnergyAverage(), McMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction >::McPairExternalPerturbation(), McMd::McPairPerturbation< Interaction >::McPairPerturbation(), McMd::McPairPotential::McPairPotential(), McMd::McPressureAverage::McPressureAverage(), McMd::McSimulation::McSimulation(), McMd::McSystem::McSystem(), McMd::McVirialStressTensorAverage::McVirialStressTensorAverage(), McMd::MdCoulombPotential::MdCoulombPotential(), McMd::MdDeformCommand::MdDeformCommand(), McMd::MdEnergyAnalyzer::MdEnergyAnalyzer(), McMd::MdIntraBondStressAutoCorr::MdIntraBondStressAutoCorr(), McMd::MdIntraBondTensorAutoCorr::MdIntraBondTensorAutoCorr(), McMd::MdKineticEnergyAverage::MdKineticEnergyAverage(), McMd::MdMove::MdMove(), McMd::MdPairEnergyCoefficients::MdPairEnergyCoefficients(), McMd::MdPairPotential::MdPairPotential(), McMd::MdPotentialEnergyAverage::MdPotentialEnergyAverage(), McMd::MdSimulation::MdSimulation(), McMd::MdStressAutoCorr::MdStressAutoCorr(), McMd::MdSystem::MdSystem(), McMd::MdVirialStressTensorAverage::MdVirialStressTensorAverage(), DdMd::ModifierManager::ModifierManager(), Simp::Multiblock::Multiblock(), Simp::MultiHarmonicDihedral::MultiHarmonicDihedral(), McMd::NLinkAverage::NLinkAverage(), DdMd::NphIntegrator::NphIntegrator(), McMd::NphIntegrator::NphIntegrator(), DdMd::NptIntegrator::NptIntegrator(), Util::MeanSqDispArray< Util::Vector >::nSample(), Simp::NucleationExternal::NucleationExternal(), DdMd::NveIntegrator::NveIntegrator(), McMd::NveVvIntegrator::NveVvIntegrator(), McMd::NvtDpdVvIntegrator::NvtDpdVvIntegrator(), DdMd::NvtIntegrator::NvtIntegrator(), DdMd::NvtLangevinIntegrator::NvtLangevinIntegrator(), McMd::NvtLangevinIntegrator::NvtLangevinIntegrator(), McMd::NvtNhIntegrator::NvtNhIntegrator(), DdMd::OrderParamNucleation::OrderParamNucleation(), Simp::OrthoBoxExternal::OrthoBoxExternal(), DdMd::OutputBoxdim::OutputBoxdim(), DdMd::OutputEnergy::OutputEnergy(), DdMd::OutputPairEnergies::OutputPairEnergies(), DdMd::OutputPressure::OutputPressure(), DdMd::OutputStressTensor::OutputStressTensor(), DdMd::OutputTemperature::OutputTemperature(), Tools::PairEnergy::PairEnergy(), DdMd::PairEnergyAnalyzer::PairEnergyAnalyzer(), DdMd::PairEnergyAverage::PairEnergyAverage(), McMd::PairList::PairList(), DdMd::PairPotential::PairPotential(), Simp::PeriodicExternal::PeriodicExternal(), McMd::Perturbation::Perturbation(), McMd::PerturbDerivative::PerturbDerivative(), DdMd::Potential::Potential(), DdMd::PressureAnalyzer::PressureAnalyzer(), Tools::Processor::Processor(), Tools::ProcessorAnalyzerManager::ProcessorAnalyzerManager(), Util::RadialDistribution::RadialDistribution(), McMd::RadiusGyration::RadiusGyration(), Util::Random::Random(), McMd::RDF::RDF(), McMd::ReplicaMove::ReplicaMove(), McMd::RigidDisplaceMove::RigidDisplaceMove(), McMd::RingOctaRebridgeMove::RingOctaRebridgeMove(), McMd::RingRouseAutoCorr::RingRouseAutoCorr(), McMd::RingTetraRebridgeMove::RingTetraRebridgeMove(), McMd::SemiGrandDistribution::SemiGrandDistribution(), DdMd::SerializeConfigIo::SerializeConfigIo(), Simp::SimplePeriodicExternal::SimplePeriodicExternal(), McMd::Simulation::Simulation(), McMd::Sliplinker::Sliplinker(), McMd::SliplinkerAll::SliplinkerAll(), McMd::SliplinkerEnd::SliplinkerEnd(), McMd::SliplinkMove::SliplinkMove(), Simp::SlitExternal::SlitExternal(), McMd::SpecialPotential::SpecialPotential(), McMd::SpecialPotentialFacade< PotentialType, FactoryType >::SpecialPotentialFacade(), Simp::Species::Species(), McMd::SpeciesManager::SpeciesManager(), Simp::SphericalTabulatedExternal::SphericalTabulatedExternal(), McMd::SSChainDist::SSChainDist(), DdMd::StressAnalyzer::StressAnalyzer(), DdMd::StressAutoCorr::StressAutoCorr(), DdMd::StressAutoCorrelation::StressAutoCorrelation(), McMd::StructureFactor::StructureFactor(), DdMd::StructureFactor::StructureFactor(), DdMd::StructureFactorGrid::StructureFactorGrid(), McMd::StructureFactorGrid::StructureFactorGrid(), McMd::StructureFactorP::StructureFactorP(), McMd::StructureFactorPGrid::StructureFactorPGrid(), Util::SymmTensorAverage::SymmTensorAverage(), DdMd::SymmTensorAverageAnalyzer::SymmTensorAverageAnalyzer(), Util::TensorAverage::TensorAverage(), DdMd::TensorAverageAnalyzer::TensorAverageAnalyzer(), Tools::TrajectoryReader::TrajectoryReader(), Tools::TrajectoryWriter::TrajectoryWriter(), DdMd::TrajectoryWriter::TrajectoryWriter(), McMd::TypeDistribution::TypeDistribution(), DdMd::VanHove::VanHove(), McMd::VanHove::VanHove(), McMd::VelProf::VelProf(), DdMd::VirialStressAnalyzer::VirialStressAnalyzer(), DdMd::VirialStressTensor::VirialStressTensor(), and DdMd::VirialStressTensorAverage::VirialStressTensorAverage().

void Util::ParamComposite::setIsRequired ( bool isRequired )

protected

Set or unset the isActive flag.

Required to re-implement readParam[Optional].

Parameters

isRequired flag to set true or false.

Definition at line 383 of file ParamComposite.cpp.

References isRequired().

Referenced by loadFArray(), Util::Manager< Data >::readParam(), and Util::Manager< Data >::readParamOptional().

void Util::ParamComposite::setIsActive ( bool isActive )

protected

Set or unset the isActive flag.

Required to re-implement readParam[Optional].

Parameters

isActive flag to set true or false.

Definition at line 394 of file ParamComposite.cpp.

References isActive(), and UTIL_THROW.

Referenced by Util::Manager< Data >::beginReadManager(), loadFArray(), Util::Manager< Data >::readParam(), and Util::Manager< Data >::readParamOptional().

void Util::ParamComposite::setParent	(	ParamComponent &	param,
		bool	next = `true`
	)

protected

Set this to the parent of a child component.

This function sets the indent and (ifdef UTIL_MPI) the ioCommunicator of the child component.

Parameters

param	child ParamComponent
next	if true, set indent level one higher than for parent.

Definition at line 224 of file ParamComposite.cpp.

References Util::MpiFileIo::hasIoCommunicator(), Util::MpiFileIo::ioCommunicator(), Util::ParamComponent::setIndent(), and Util::MpiFileIo::setIoCommunicator().

Referenced by add(), addBegin(), addBlank(), addCArray(), addCArray2D(), addDArray(), addDMatrix(), addEnd(), addFArray(), addParamComposite(), isActive(), loadCArray(), loadCArray2D(), loadDArray(), loadDMatrix(), loadDSymmMatrix(), loadFArray(), loadParameter(), and readBegin().

void Util::ParamComposite::addComponent	(	ParamComponent &	param,
		bool	isLeaf = `true`
	)

protected

Add a new ParamComponent object to the format array.

Parameters

param	Parameter object
isLeaf	Is this a leaf or a ParamComposite node?

Definition at line 237 of file ParamComposite.cpp.

Referenced by add(), addBegin(), addBlank(), addCArray(), addCArray2D(), addDArray(), addDMatrix(), addEnd(), addFArray(), addParamComposite(), isActive(), loadCArray(), loadCArray2D(), loadDArray(), loadDMatrix(), loadDSymmMatrix(), loadFArray(), loadParameter(), and readBegin().

template<typename Type >

ScalarParam< Type > & Util::ParamComposite::add	(	std::istream &	in,
		const char *	label,
		Type &	value,
		bool	isRequired = `true`
	)

protected

Add a new required ScalarParam < Type > object.

Parameters

in	input stream for reading
label	Label string
value	reference to new ScalarParam< Type >
isRequired	Is this a required parameter?

Returns: reference to the new ScalarParam<Type> object

Definition at line 1141 of file ParamComposite.h.

References addComponent(), isRequired(), and setParent().

Referenced by loadFArray().

template<typename Type >

CArrayParam< Type > & Util::ParamComposite::addCArray	(	std::istream &	in,
		const char *	label,
		Type *	value,
		int	n,
		bool	isRequired = `true`
	)

protected

Add (but do not read) a required C array parameter.

Parameters

in	input stream for reading
label	Label string for new array
value	pointer to array
n	number of elements
isRequired	Is this a required parameter?

Returns: reference to the new CArrayParam<Type> object

Definition at line 1216 of file ParamComposite.h.

References addComponent(), isRequired(), and setParent().

Referenced by loadFArray().

template<typename Type >

DArrayParam< Type > & Util::ParamComposite::addDArray	(	std::istream &	in,
		const char *	label,
		DArray< Type > &	array,
		int	n,
		bool	isRequired = `true`
	)

protected

Add (but do not read) a DArray < Type > parameter.

Parameters

in	input stream for reading
label	Label string for new array
array	DArray object
n	number of elements
isRequired	Is this a required parameter?

Returns: reference to the new DArrayParam<Type> object

Definition at line 1292 of file ParamComposite.h.

References addComponent(), isRequired(), and setParent().

Referenced by loadFArray().

template<typename Type , int N>

FArrayParam< Type, N > & Util::ParamComposite::addFArray	(	std::istream &	in,
		const char *	label,
		FArray< Type, N > &	array,
		bool	isRequired = `true`
	)

protected

Add (but do not read) a FArray < Type, N > array parameter.

Parameters

in	input stream for reading
label	Label string for new array
array	FArray object
isRequired	Is this a required parameter?

Returns: reference to the new FArrayParam<Type, N> object

Definition at line 1370 of file ParamComposite.h.

References addComponent(), isRequired(), and setParent().

Referenced by loadFArray().

template<typename Type >

CArray2DParam< Type > & Util::ParamComposite::addCArray2D	(	std::istream &	in,
		const char *	label,
		Type *	value,
		int	m,
		int	n,
		int	np,
		bool	isRequired = `true`
	)

protected

Add (but do not read) a CArray2DParam < Type > 2D C-array.

Parameters

in	input stream for reading
label	Label string for new array
value	pointer to array
m	number of rows (1st dimension)
n	logical number of columns (2nd dimension)
np	physical number of columns (elements allocated per row)
isRequired	Is this a required parameter?

Returns: reference to the CArray2DParam<Type> object

Definition at line 1440 of file ParamComposite.h.

References addComponent(), isRequired(), and setParent().

Referenced by loadFArray().

template<typename Type >

DMatrixParam< Type > & Util::ParamComposite::addDMatrix	(	std::istream &	in,
		const char *	label,
		DMatrix< Type > &	matrix,
		int	m,
		int	n,
		bool	isRequired = `true`
	)

protected

Add and read a required DMatrix < Type > matrix parameter.

Parameters

in	input stream for reading
label	Label string for new array
matrix	DMatrix object
m	number of rows (1st dimension)
n	number of columns (2nd dimension)
isRequired	Is this a required parameter?

Returns: reference to the DMatrixParam<Type> object

Definition at line 1522 of file ParamComposite.h.

References addComponent(), isRequired(), and setParent().

Referenced by loadFArray().

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

Detailed Description

Implementation details:

Subclass implementation details:

Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation