Utility classes for scientific computation. More...

Classes
class	Ar1Process
	Generator for a discrete AR(1) Markov process. More...

class	Array
	Array container class template. More...

class	ArrayIterator
	Forward iterator for an Array or a C array. More...

class	ArraySet
	A container for pointers to a subset of elements of an associated array. More...

class	ArrayStack
	A stack of fixed capacity. More...

class	AutoCorr
	Auto-correlation function for one sequence of Data values. More...

class	AutoCorrArray
	Auto-correlation function for an ensemble of sequences. More...

class	AutoCorrelation
	Auto-correlation function, using hierarchical algorithm. More...

class	AutoCorrStage
	Hierarchical auto-correlation function algorithm. More...

class	Average
	Calculates the average and variance of a sampled property. More...

class	AverageStage
	Evaluate average with hierarchical blocking error analysis. More...

class	Begin
	Beginning line of a composite parameter block. More...

class	BinaryFileIArchive
	Saving archive for binary istream. More...

class	BinaryFileOArchive
	Saving / output archive for binary ostream. More...

class	Binomial
	Class for binomial coefficients (all static members) More...

class	Bit
	Represents a specific bit location within an unsigned int. More...

class	Blank
	An empty line within a parameter file. More...

class	Bool
	Wrapper for an bool value, for formatted ostream output. More...

class	CardinalBSpline
	A cardinal B-spline basis function. More...

class	CArray2DParam
	A Parameter associated with a 2D built-in C array. More...

class	CArrayParam
	A Parameter associated with a 1D C array. More...

class	Constants
	Mathematical constants. More...

class	ConstArrayIterator
	Forward const iterator for an Array or a C array. More...

class	ConstPArrayIterator
	Forward iterator for a PArray. More...

class	DArray
	Dynamically allocatable contiguous array template. More...

class	DArrayParam
	A Parameter associated with a DArray container. More...

class	Dbl
	Wrapper for a double precision number, for formatted ostream output. More...

class	Distribution
	A distribution (or histogram) of values for a real variable. More...

class	DMatrix
	Dynamically allocated Matrix. More...

class	DMatrixParam
	A Parameter associated with a 2D built-in C array. More...

class	DPArray
	A dynamic array that only holds pointers to its elements. More...

class	DRaggedMatrix
	Dynamically allocated RaggedMatrix. More...

class	DSArray
	Dynamically allocated array with variable logical size. More...

class	DSymmMatrixParam
	A Parameter associated with a symmetric DMatrix. More...

class	End
	End bracket of a ParamComposite parameter block. More...

class	Exception
	A user-defined exception. More...

class	Factory
	Factory template. More...

class	FArray
	A fixed size (static) contiguous array template. More...

class	FArrayParam
	A Parameter associated with a FArray container. More...

class	FileMaster
	A FileMaster manages input and output files for a simulation. More...

class	FlagSet
	A set of boolean variables represented by characters. More...

class	FlexPtr
	A pointer that may or may not own the object to which it points. More...

class	FMatrix
	Fixed Size Matrix. More...

class	Format
	Base class for output wrappers for formatted C++ ostream output. More...

class	FPArray
	Statically allocated pointer array. More...

class	FSArray
	A fixed capacity (static) contiguous array with a variable logical size. More...

class	GArray
	An automatically growable array, analogous to a std::vector. More...

class	GPArray
	An automatically growable PArray. More...

class	Grid
	A grid of points indexed by integer coordinates. More...

class	GridArray
	Multi-dimensional array with the dimensionality of space. More...

class	GStack
	An automatically growable Stack. More...

class	IFunctor
	Interface for functor that wraps a void function with one argument (abstract). More...

class	IFunctor< void >
	Interface for functor that wraps a void function with no arguments (abstract). More...

class	Int
	Wrapper for an int, for formatted ostream output. More...

class	IntDistribution
	A distribution (or histogram) of values for an int variable. More...

class	IntVector
	An IntVector is an integer Cartesian vector. More...

class	Label
	A label string in a file format. More...

class	List
	Linked list class template. More...

class	ListArray
	An array of objects that are accessible by one or more linked List objects. More...

class	ListIterator
	Bidirectional iterator for a List. More...

class	Lng
	Wrapper for a long int, for formatted ostream output. More...

class	Log
	A static class that holds a log output stream. More...

class	Manager
	Template container for pointers to objects with a common base class. More...

class	Matrix
	Two-dimensional array container template (abstract). More...

class	MeanSqDispArray
	Mean-squared displacement (MSD) vs. More...

class	Memory
	Provides method to allocate array. More...

class	MemoryCounter
	Archive to computed packed size of a sequence of objects, in bytes. More...

class	MemoryIArchive
	Input archive for packed heterogeneous binary data. More...

class	MemoryOArchive
	Save archive for packed heterogeneous binary data. More...

class	MethodFunctor
	Functor that wraps a one-argument class member function. More...

class	MethodFunctor< Object, void >
	Functor that wraps a class member function with no arguments. More...

class	MpiFileIo
	Identifies whether this processor may do file I/O. More...

class	MpiLoader
	Provides methods for MPI-aware loading of data from input archive. More...

class	MpiLogger
	Allows information from every processor in a communicator, to be output in rank sequence. More...

class	MpiStructBuilder
	A MpiStructBuilder objects is used to create an MPI Struct datatype. More...

class	MpiTraits
	Default MpiTraits class. More...

class	MpiTraits< bool >
	MpiTraits<bool> explicit specialization. More...

class	MpiTraits< char >
	MpiTraits<char> explicit specialization. More...

class	MpiTraits< DdMd::AtomType >
	Explicit specialization MpiTraits<AtomType>. More...

class	MpiTraits< DdMd::MaskPolicy >
	Explicit specialization MpiTraits<MaskPolicy>. More...

class	MpiTraits< double >
	MpiTraits<double> explicit specialization. More...

class	MpiTraits< float >
	MpiTraits<float> explicit specialization. More...

class	MpiTraits< int >
	MpiTraits<int> explicit specialization. More...

class	MpiTraits< IntVector >
	Explicit specialization MpiTraits<IntVector>. More...

class	MpiTraits< long >
	MpiTraits<long> explicit specialization. More...

class	MpiTraits< long double >
	MpiTraits<long double> explicit specialization. More...

class	MpiTraits< McMd::AtomType >
	Explicit specialization MpiTraits<AtomType>. More...

class	MpiTraits< McMd::MaskPolicy >
	Explicit specialization MpiTraits<MaskPolicy>. More...

class	MpiTraits< McMd::PairSelector >
	Explicit specialization MpiTraits<PairSelector>. More...

class	MpiTraits< McMd::PairSelector::PairType >
	Explicit specialization MpiTraits<PairSelector::PairType>. More...

class	MpiTraits< MonoclinicBoundary >
	Explicit specialization MpiTraits<MonoclinicBoundary>. More...

class	MpiTraits< Pair< int > >
	Explicit specialization MpiTraits< Pair<int> >. More...

class	MpiTraits< Rational >
	Explicit specialization MpiTraits<Rational>. More...

class	MpiTraits< short >
	MpiTraits<short> explicit specialization. More...

class	MpiTraits< Simp::BoundaryEnsemble >
	Explicit specialization MpiTraits<Simp::BoundaryEnsemble>. More...

class	MpiTraits< Simp::BoundaryEnsemble::Type >
	Explicit specialization MpiTraits<Simp::BoundaryEnsemble::Type>. More...

class	MpiTraits< Simp::EnergyEnsemble >
	Explicit specialization MpiTraits<Simp::EnergyEnsemble>. More...

class	MpiTraits< Simp::EnergyEnsemble::Type >
	Explicit specialization MpiTraits<Simp::EnergyEnsemble::Type>. More...

class	MpiTraits< Simp::OrthorhombicBoundary >
	Explicit specialization MpiTraits<OrthorhombicBoundary>. More...

class	MpiTraits< Simp::SpeciesEnsemble >
	Explicit specialization MpiTraits<Simp::SpeciesEnsemble>. More...

class	MpiTraits< Simp::SpeciesEnsemble::Type >
	Explicit specialization MpiTraits<Simp::SpeciesEnsemble::Type>. More...

class	MpiTraits< Simp::SpeciesGroup< 2 > >
	Explicit specialization MpiTraits< SpeciesGroup<2> >. More...

class	MpiTraits< Simp::SpeciesGroup< 3 > >
	Explicit specialization MpiTraits< SpeciesGroup<3> >. More...

class	MpiTraits< Simp::SpeciesGroup< 4 > >
	Explicit specialization MpiTraits< SpeciesGroup<4> >. More...

class	MpiTraits< Tensor >
	Explicit specialization MpiTraits<Tensor>. More...

class	MpiTraits< unsigned char >
	MpiTraits<unsigned char> explicit specialization. More...

class	MpiTraits< unsigned int >
	MpiTraits<unsigned int> explicit specialization. More...

class	MpiTraits< unsigned long >
	MpiTraits<unsigned long> explicit specialization. More...

class	MpiTraits< unsigned short >
	MpiTraits<unsigned short> explicit specialization. More...

class	MpiTraits< Util::LatticeSystem >
	Explicit specialization MpiTraits<LatticeSystem>. More...

class	MpiTraits< Vector >
	Explicit specialization MpiTraits<Vector>. More...

class	MpiTraitsNoType
	Base class for MpiTraits with no type. More...

class	MTRand
	Generates double floating point numbers in the half-open interval [0, 1) More...

class	MTRand53
	generates 53 bit resolution doubles in the half-open interval [0, 1) More...

class	MTRand_closed
	Generates double floating point numbers in the closed interval [0, 1]. More...

class	MTRand_int32
	Mersenne Twister random number generator engine. More...

class	MTRand_open
	Generates double floating point numbers in the open interval (0, 1). More...

class	Node
	Linked List Node, class template. More...

class	Notifier
	Abstract template for a notifier (or subject) in the Observer design pattern. More...

class	Observer
	Abstract class template for observer in the observer design pattern. More...

class	OptionalLabel
	An optional Label string in a file format. More...

class	Pair
	An array of exactly 2 objects. More...

class	ParamComponent
	Abstract base class for classes that input and ouput parameters to file. More...

class	ParamComposite
	An object that can read multiple parameters from file. More...

class	Parameter
	A single variable in a parameter file. More...

class	PArray
	An array that only holds pointers to its elements. More...

class	PArrayIterator
	Forward iterator for a PArray. More...

class	PointGroup
	Group of crystal symmetries with no translations. More...

class	PointSymmetry
	A PointSymmetry represents a crystallographic point group symmetry. More...

class	Polynomial
	A Polynomial (i.e,. More...

class	RadialDistribution
	Distribution (or histogram) of values for particle separations. More...

class	RaggedMatrix
	A 2D array in which different rows can have different lengths. More...

class	Random
	Random number generator. More...

class	RArray
	An Array that acts as a reference to another Array or C array. More...

class	Rational
	A Rational number (a ratio of integers). More...

class	RingBuffer
	Class for storing history of previous values in an array. More...

class	ScalarParam
	Template for a Parameter object associated with a scalar variable. More...

class	ScopedPtr
	A very simple RAII pointer. More...

class	Serializable
	Abstract class for serializable objects. More...

class	Setable
	Template for a value that can be set or declared null (i.e., unknown). More...

class	Signal
	Notifier (or subject) in the Observer design pattern. More...

class	Signal< void >
	Notifier (or subject) in the Observer design pattern (zero parameters). More...

class	SSet
	Statically allocated array of pointers to an unordered set. More...

class	Str
	Wrapper for a std::string, for formatted ostream output. More...

class	SymmetryGroup
	Class template for a group of elements of type Symmetry. More...

class	SymmTensorAverage
	Calculates averages of all components of a Tensor-valued variable. More...

class	Tensor
	A Tensor represents a Cartesian tensor. More...

class	TensorAverage
	Calculates averages of all components of a Tensor-valued variable. More...

class	TextFileIArchive
	Loading archive for text istream. More...

class	TextFileOArchive
	Saving archive for character based ostream. More...

class	Timer
	Wall clock timer. More...

class	Vector
	A Vector is a Cartesian vector. More...

class	XdrFileIArchive
	Loading / input archive for binary XDR file. More...

class	XdrFileOArchive
	Saving / output archive for binary XDR file. More...

class	XmlAttribute
	Parser for an XML attribute. More...

class	XmlBase
	Base class for classes that parse XML markup tags. More...

class	XmlEndTag
	Parser for an XML end tag. More...

class	XmlStartTag
	Parser for an XML start tag. More...

class	XmlXmlTag
	Parser for an XML file declaration tag (first line in file). More...

Typedefs
typedef unsigned char	Byte
	Define a "Byte" type. More...

Enumerations

Functions
float	product (float a, float b)
	Product for float Data. More...

double	product (double a, double b)
	Product for double Data. More...

double	product (const Vector &a, const Vector &b)
	Dot product for Vector Data. More...

double	product (const Tensor &a, const Tensor &b)
	Double contraction for Tensor Data. More...

complex< float >	product (complex< float > a, complex< float > b)
	Inner product for complex<float> Data. More...

complex< double >	product (complex< double > a, complex< double > b)
	Inner product for complex<double> Data. More...

void	setToZero (int &value)
	Set an int variable to zero. More...

void	setToZero (float &value)
	Set a float variable to zero. More...

void	setToZero (double &value)
	Set a double variable to zero. More...

void	setToZero (Vector &value)
	Set a Vector variable to zero. More...

void	setToZero (Tensor &value)
	Set a Vector variable to zero. More...

void	setToZero (complex< float > &value)
	Set a complex<float> variable to zero. More...

void	setToZero (complex< double > &value)
	Set a complex<double> variable to zero. More...

template<typename T >
int	memorySize (T &data)
	Function template to compute memory size of one object. More...

template<class Archive , typename T >
void	serialize (Archive &ar, T &data, const unsigned int version)
	Serialize one object of type T. More...

template<class Archive , typename T >
void	serializeEnum (Archive &ar, T &data, const unsigned int version=0)
	Serialize an enumeration value. More...

template<class Archive , typename T >
void	serializeCheck (Archive &ar, T &data, const char *label="")
	Save a value, or save and check correctness on loading. More...

template<typename Data >
std::istream &	operator>> (std::istream &in, Pair< Data > &pair)
	Input a Pair from an istream. More...

template<typename Data >
std::ostream &	operator<< (std::ostream &out, const Pair< Data > &pair)
	Output a Pair to an ostream, without line breaks. More...

std::istream &	operator>> (std::istream &in, LatticeSystem &lattice)
	istream extractor for a LatticeSystem. More...

std::ostream &	operator<< (std::ostream &out, LatticeSystem lattice)
	ostream inserter for an LatticeSystem. More...

template<class Archive >
void	serialize (Archive &ar, LatticeSystem &lattice, const unsigned int version)
	Serialize a LatticeSystem value. More...

std::ostream &	operator<< (std::ostream &out, const PointGroup &g)
	Output stream inserter operator writing a PointGroup to stream. More...

bool	operator== (const PointSymmetry &A, const PointSymmetry &B)
	Are two PointSymmetry objects equivalent? More...

PointSymmetry	operator* (const PointSymmetry &A, const PointSymmetry &B)
	Return the product A*B of two symmetry objects. More...

IntVector	operator* (const PointSymmetry &S, const IntVector &V)
	Return the IntVector product S*V of a rotation matrix and an IntVector. More...

IntVector	operator* (const IntVector &V, const PointSymmetry &S)
	Return the IntVector product V*S of an IntVector and a rotation matrix. More...

std::ostream &	operator<< (std::ostream &out, const PointSymmetry &A)
	Output stream inserter for a PointSymmetry. More...

bool	operator!= (const PointSymmetry &A, const PointSymmetry &B)
	Are two PointSymmetry objects not equivalent? More...

std::istream &	operator>> (std::istream &in, Bool &object)
	Input stream extractor for an Bool object. More...

std::ostream &	operator<< (std::ostream &out, const Bool &object)
	Output stream inserter for an Bool object. More...

std::istream &	operator>> (std::istream &in, Dbl &object)
	Input stream extractor for an Dbl object. More...

std::ostream &	operator<< (std::ostream &out, const Dbl &object)
	Output stream inserter for an Dbl object. More...

std::istream &	operator>> (std::istream &in, Int &object)
	Input stream extractor for an Int object. More...

std::ostream &	operator<< (std::ostream &out, const Int &object)
	Output stream inserter for an Int object. More...

std::istream &	operator>> (std::istream &in, Lng &object)
	Input stream extractor for an Lng object. More...

std::ostream &	operator<< (std::ostream &out, const Lng &object)
	Output stream inserter for an Lng object. More...

std::istream &	operator>> (std::istream &in, Str &object)
	Input stream extractor for an Str object. More...

std::ostream &	operator<< (std::ostream &out, const Str &object)
	Output stream inserter for an Str object. More...

template<>
void	write (std::ostream &out, double data)
	Explicit specialization of write for double data. More...

template<>
void	write (std::ostream &out, std::complex< double > data)
	Explicit specialization of write for double data. More...

template<>
void	write (std::ostream &out, int data)
	Explicit specialization of write for int data. More...

template<>
void	write (std::ostream &out, long data)
	Explicit specialization of write for long data. More...

template<>
void	write (std::ostream &out, bool data)
	Explicit specialization of write for bool data. More...

template<typename Type >
void	write (std::ostream &out, Type data)
	Function template for output in a standard format. More...

template<>
void	write (std::ostream &out, std::string data)
	Explicit specialization of write for std::string data. More...

bool	feq (double x, double y, double eps=1.0E-10)
	Are two floating point numbers equal to within round-off error? More...

int	gcd (int a, int b)
	Compute greatest common divisor (gcd) of two integers. More...

template<typename T >
bool	operator== (Polynomial< T > &a, Polynomial< T > &b)
	Equality operator for polynomials. More...

template<typename T >
bool	operator!= (Polynomial< T > &a, Polynomial< T > &b)
	Inequality operator for polynomials. More...

template<typename T >
Polynomial< T >	operator- (Polynomial< T > const &a)
	Unary negation of polynomial. More...

std::ostream &	operator<< (std::ostream &out, Rational const &rational)
	Output stream inserter for a Rational. More...

Rational	operator+ (Rational const &a, Rational const &b)
	Compute sum of two rationals. More...

Rational	operator+ (Rational const &a, int b)
	Compute sum of rational and integer. More...

Rational	operator+ (int b, Rational const &a)
	Compute sum of integer and integer. More...

Rational	operator- (Rational const &a, Rational const &b)
	Compute difference of rationals. More...

Rational	operator- (Rational const &a, int b)
	Compute difference of rational and integer. More...

Rational	operator- (int b, Rational const &a)
	Compute difference of integer and rational. More...

Rational	operator* (Rational const &a, Rational const &b)
	Compute product of rationals. More...

Rational	operator* (Rational const &a, int b)
	Compute product of rational and integer. More...

Rational	operator* (int b, Rational const &a)
	Compute product of integer and rational. More...

Rational	operator/ (Rational const &a, Rational const &b)
	Compute quotient of two rationals. More...

Rational	operator/ (Rational const &a, int b)
	Compute quotient Rational divided by integer. More...

Rational	operator/ (int b, Rational const &a)
	Compute quotient integer divided by Rational. More...

Rational	operator- (Rational const &a)
	Unary negation of Rational. More...

bool	operator== (Rational const &a, Rational const &b)
	Equality operators. More...

bool	operator== (Rational const &a, int b)
	Equality operator for a Rational and an integer. More...

bool	operator== (int b, Rational const &a)
	Equality operator for an integer and a Rational. More...

bool	operator!= (Rational const &a, Rational const &b)
	Inequality operators. More...

bool	operator!= (Rational const &a, int b)
	Inequality operator for a Rational and an integer. More...

bool	operator!= (int b, Rational const &a)
	Inequality operator for an integer and a Rational. More...

void	MpiThrow (Exception &e)
	Function to throw exception in MPI code. More...

void	initStatic ()
	Guarantee initialization of all static class members in Util namespace. More...

int	rStrip (std::string &string)
	Strip trailing whitespace from a string. More...

void	checkString (std::istream &in, const std::string &expected)
	Extract string from stream, and compare to expected value. More...

std::string	toString (int n)
	Return string representation of an integer. More...

bool	getLine (std::istream &in, std::stringstream &line)
	Read the next line into a stringstream. More...

bool	getNextLine (std::istream &in, std::string &line)
	Read the next non-empty line into a string, strip trailing whitespace. More...

bool	getNextLine (std::istream &in, std::stringstream &line)
	Read next non-empty line into a stringstream, strip trailing whitespace. More...

void	checkRequiredIstream (std::istream &in)
	Check status of a std::istream just before reading required variable. More...

template<typename D , typename B , typename M >
ptrdiff_t	memberOffset (D &object, M B::*memPtr)
	Template for calculating offsets of data members. More...

template<typename D , typename B >
ptrdiff_t	baseOffset (D &object)
	Template for calculating offsets of base class subobjects. More...

template<>
void	send< bool > (MPI::Comm &comm, bool &data, int dest, int tag)
	Explicit specialization of send for bool data. More...

template<>
void	recv< bool > (MPI::Comm &comm, bool &data, int source, int tag)
	Explicit specialization of recv for bool data. More...

template<>
void	bcast< bool > (MPI::Intracomm &comm, bool &data, int root)
	Explicit specialization of bcast for bool data. More...

template<>
void	send< std::string > (MPI::Comm &comm, std::string &data, int dest, int tag)
	Explicit specialization of send for std::string data. More...

template<>
void	recv< std::string > (MPI::Comm &comm, std::string &data, int source, int tag)
	Explicit specialization of recv for std::string data. More...

template<>
void	bcast< std::string > (MPI::Intracomm &comm, std::string &data, int root)
	Explicit specialization of bcast for std::string data. More...

template<typename T >
void	send (MPI::Comm &comm, T &data, int dest, int tag)
	Send a single T value. More...

template<typename T >
void	recv (MPI::Comm &comm, T &data, int source, int tag)
	Receive a single T value. More...

template<typename T >
void	bcast (MPI::Intracomm &comm, T &data, int root)
	Broadcast a single T value. More...

template<typename T >
void	send (MPI::Comm &comm, T *array, int count, int dest, int tag)
	Send a C-array of T values. More...

template<typename T >
void	recv (MPI::Comm &comm, T *array, int count, int source, int tag)
	Receive a C-array of T objects. More...

template<typename T >
void	bcast (MPI::Intracomm &comm, T *array, int count, int root)
	Broadcast a C-array of T objects. More...

template<typename T >
void	send (MPI::Comm &comm, DArray< T > &array, int count, int dest, int tag)
	Send a DArray<T> container. More...

template<typename T >
void	recv (MPI::Comm &comm, DArray< T > &array, int count, int source, int tag)
	Receive a DArray<T> container. More...

template<typename T >
void	bcast (MPI::Intracomm &comm, DArray< T > &array, int count, int root)
	Broadcast a DArray<T> container. More...

template<typename T >
void	send (MPI::Comm &comm, DMatrix< T > &matrix, int m, int n, int dest, int tag)
	Send a DMatrix<T> container. More...

template<typename T >
void	recv (MPI::Comm &comm, DMatrix< T > &matrix, int m, int n, int source, int tag)
	Receive a DMatrix<T> container. More...

template<typename T >
void	bcast (MPI::Intracomm &comm, DMatrix< T > &matrix, int m, int n, int root)
	Broadcast a DMatrix<T> container. More...

std::istream &	operator>> (std::istream &in, Label label)
	Extractor for Label. More...

std::ostream &	operator<< (std::ostream &out, Label label)
	Inserter for Label. More...

template<typename T >
bool	isNull (FlexPtr< T > p)
	Return true iff the enclosed built-in pointer is null. More...

template<typename T >
bool	isNull (T *ptr)
	Return true iff a built-in pointer is null. More...

template<typename T >
bool	isNull (ScopedPtr< T > p)
	Return true iff the enclosed built-in pointer is null. More...

bool	operator== (const IntVector &v1, const IntVector &v2)
	Equality for IntVectors. More...

bool	operator== (const IntVector &v1, const int *v2)
	Equality of IntVector and C array. More...

bool	operator== (const int *v1, const IntVector &v2)
	Equality of C array and IntVector. More...

bool	operator!= (const IntVector &v1, const IntVector &v2)
	Inequality of two IntVectors. More...

bool	operator!= (const IntVector &v1, const int *v2)
	Inequality of IntVector and C array. More...

bool	operator!= (const int *v1, const IntVector &v2)
	Inequality of C array and IntVector. More...

std::istream &	operator>> (std::istream &in, IntVector &vector)
	istream extractor for a IntVector. More...

std::ostream &	operator<< (std::ostream &out, const IntVector &vector)
	ostream inserter for a IntVector. More...

bool	operator== (const Tensor &t1, const Tensor &t2)
	Equality for Tensors. More...

bool	operator== (const Tensor &t1, const double t2[][Dimension])
	Equality of Tensor and 2D C array. More...

bool	operator== (const double t1[][Dimension], const Tensor &t2)
	Equality of C array and Tensor. More...

bool	operator!= (const Tensor &t1, const Tensor &t2)
	Negation of t1 == t2 (tensors t1 and t2) More...

bool	operator!= (const Tensor &t1, const double a2[][Dimension])
	Negation of t1 == a2 (tensor t1, 2D array a2) More...

bool	operator!= (const double a1[][Dimension], const Tensor &t2)
	Negation of t1 == a2 (tensor t2, 2D array a1) More...

std::istream &	operator>> (std::istream &in, Tensor &tensor)
	istream extractor for a Tensor. More...

std::ostream &	operator<< (std::ostream &out, const Tensor &tensor)
	ostream inserter for a Tensor. More...

bool	operator== (const Vector &v1, const Vector &v2)
	Equality for Vectors. More...

bool	operator== (const Vector &v1, const double *v2)
	Equality of Vector and C array. More...

bool	operator== (const double *v1, const Vector &v2)
	Equality of C array and Vector. More...

bool	operator!= (const Vector &v1, const Vector &v2)
	Inequality of two Vectors. More...

bool	operator!= (const Vector &v1, const double *v2)
	Inequality of Vector and C array. More...

bool	operator!= (const double *v1, const Vector &v2)
	Inequality of C array and Vector. More...

std::istream &	operator>> (std::istream &in, Vector &vector)
	istream extractor for a Vector. More...

std::ostream &	operator<< (std::ostream &out, const Vector &vector)
	ostream inserter for a Vector. More...

template<>
void	send< MonoclinicBoundary > (MPI::Comm &comm, MonoclinicBoundary &data, int dest, int tag)
	Send an MonoclinicBoundary via MPI. More...

template<>
void	recv< MonoclinicBoundary > (MPI::Comm &comm, MonoclinicBoundary &data, int source, int tag)
	Receive an MonoclinicBoundary via MPI. More...

template<>
void	bcast< MonoclinicBoundary > (MPI::Intracomm &comm, MonoclinicBoundary &data, int root)
	Broadcast an MonoclinicBoundary via MPI. More...

template<>
void	send< Simp::OrthorhombicBoundary > (MPI::Comm &comm, Simp::OrthorhombicBoundary &data, int dest, int tag)
	Send an OrthorhombicBoundary via MPI. More...

template<>
void	recv< Simp::OrthorhombicBoundary > (MPI::Comm &comm, Simp::OrthorhombicBoundary &data, int source, int tag)
	Receive an OrthorhombicBoundary via MPI. More...

template<>
void	bcast< Simp::OrthorhombicBoundary > (MPI::Intracomm &comm, Simp::OrthorhombicBoundary &data, int root)
	Broadcast an OrthorhombicBoundary via MPI. More...

template<>
void	send< McMd::AtomType > (MPI::Comm &comm, McMd::AtomType &data, int dest, int tag)
	Send an AtomType (wrapper for MPI Send). More...

template<>
void	recv< McMd::AtomType > (MPI::Comm &comm, McMd::AtomType &data, int source, int tag)
	Receive an AtomType (wrapper for MPI Recv). More...

template<>
void	bcast< McMd::AtomType > (MPI::Intracomm &comm, McMd::AtomType &data, int root)
	Broadcast an AtomType (wrapper for MPI Bcast). More...

Variables
const int	Dimension = 3
	Dimensionality of space. More...

const int	DimensionSq = Dimension*Dimension
	Square of Dimensionality of space. More...

Detailed Description

Utility classes for scientific computation.

Typedef Documentation

typedef unsigned char Util::Byte

Define a "Byte" type.

Definition at line 19 of file Byte.h.

Function Documentation

float Util::product	(	float	a,
		float	b
	)

inline

Product for float Data.

Definition at line 22 of file product.h.

Referenced by Util::AutoCorr< Data, Product >::autoCorrelation(), Util::AutoCorr< Data, Product >::corrTime(), Util::AutoCorrArray< Data, Product >::corrTime(), Simp::OrthoRegion::isValid(), Util::AutoCorr< Data, Product >::output(), McMd::CompositionProfile::sample(), Util::AutoCorrStage< Data, Product >::sample(), DdMd::OrderParamNucleation::sample(), Util::AutoCorr< Data, Product >::sample(), McMd::StructureFactor::sample(), Util::AutoCorrArray< Data, Product >::sample(), DdMd::StructureFactor::sample(), DdMd::VanHove::sample(), McMd::VanHove::sample(), McMd::StructureFactorP::sample(), and McMd::IntraStructureFactor::sample().

double Util::product	(	double	a,
		double	b
	)

inline

Product for double Data.

Definition at line 28 of file product.h.

double Util::product	(	const Vector &	a,
		const Vector &	b
	)

inline

Dot product for Vector Data.

Definition at line 34 of file product.h.

References Util::Vector::dot().

double Util::product	(	const Tensor &	a,
		const Tensor &	b
	)

inline

Double contraction for Tensor Data.

Definition at line 40 of file product.h.

References Dimension.

complex<float> Util::product	(	complex< float >	a,
		complex< float >	b
	)

inline

Inner product for complex<float> Data.

Definition at line 55 of file product.h.

complex<double> Util::product	(	complex< double >	a,
		complex< double >	b
	)

inline

Inner product for complex<double> Data.

Definition at line 61 of file product.h.

void Util::setToZero ( int & value )

inline

Set an int variable to zero.

Parameters

value value to be zeroed.

Definition at line 25 of file setToZero.h.

Referenced by McMd::BondPotentialImpl< Interaction >::addForces(), McMd::DihedralPotentialImpl< Interaction >::addForces(), McMd::AnglePotentialImpl< Interaction >::addForces(), Util::AutoCorr< Data, Product >::AutoCorr(), Util::AutoCorrArray< Data, Product >::AutoCorrArray(), Util::AutoCorrStage< Data, Product >::autoCorrelation(), Util::AutoCorrStage< Data, Product >::AutoCorrStage(), Util::AutoCorr< Data, Product >::clear(), Util::AutoCorrStage< Data, Product >::clear(), Util::MeanSqDispArray< Data >::clear(), Util::AutoCorrArray< Data, Product >::clear(), McMd::LinkPotentialImpl< Interaction >::computeEnergy(), McMd::McPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdPairPotentialImpl< Interaction >::computeEnergy(), Util::AutoCorr< Data, Product >::corrTime(), Util::AutoCorrArray< Data, Product >::corrTime(), Util::AutoCorrStage< Data, Product >::corrTime(), McMd::MdSystem::kineticEnergy(), Util::AutoCorrStage< Data, Product >::output(), Util::AutoCorrStage< Data, Product >::sample(), and McMd::McSystem::unsetPotentialEnergies().

void Util::setToZero ( float & value )

inline

Set a float variable to zero.

Parameters

value value to be zeroed.

Definition at line 33 of file setToZero.h.

void Util::setToZero ( double & value )

inline

Set a double variable to zero.

Parameters

value value to be zeroed.

Definition at line 41 of file setToZero.h.

void Util::setToZero ( Vector & value )

inline

Set a Vector variable to zero.

Parameters

value value to be zeroed.

Definition at line 49 of file setToZero.h.

References Util::Vector::zero().

void Util::setToZero ( Tensor & value )

inline

Set a Vector variable to zero.

Parameters

value value to be zeroed.

Definition at line 57 of file setToZero.h.

References Util::Tensor::zero().

void Util::setToZero ( complex< float > & value )

inline

Set a complex<float> variable to zero.

Parameters

value value to be zeroed.

Definition at line 65 of file setToZero.h.

void Util::setToZero ( complex< double > & value )

inline

Set a complex<double> variable to zero.

Parameters

value value to be zeroed.

Definition at line 73 of file setToZero.h.

template<typename T >

int Util::memorySize ( T & data )

Function template to compute memory size of one object.

Definition at line 130 of file MemoryCounter.h.

References Util::MemoryCounter::size().

Referenced by McMd::ReplicaMove::move().

template<typename Data >

std::istream& Util::operator>>	(	std::istream &	in,
		Pair< Data > &	pair
	)

Input a Pair from an istream.

Parameters

in	istream from which to read
pair	Pair to be read

Definition at line 44 of file Pair.h.

Referenced by Util::Rational::~Rational().

template<typename Data >

std::ostream& Util::operator<<	(	std::ostream &	out,
		const Pair< Data > &	pair
	)

Output a Pair to an ostream, without line breaks.

Parameters

out	ostream to which to write
pair	Pair to be written

Definition at line 57 of file Pair.h.

std::istream & Util::operator>>	(	std::istream &	in,
		LatticeSystem &	lattice
	)

istream extractor for a LatticeSystem.

Parameters

in	input stream
lattice	LatticeSystem to be read

Returns: modified input stream

Definition at line 26 of file LatticeSystem.cpp.

References checkRequiredIstream(), Util::Log::file(), and UTIL_THROW.

std::ostream & Util::operator<<	(	std::ostream &	out,
		LatticeSystem	lattice
	)

ostream inserter for an LatticeSystem.

Parameters

out	output stream
lattice	LatticeSystem to be written

Returns: modified output stream

Definition at line 78 of file LatticeSystem.cpp.

References UTIL_THROW.

template<class Archive >

void Util::serialize	(	Archive &	ar,
		LatticeSystem &	lattice,
		const unsigned int	version
	)

Serialize a LatticeSystem value.

Parameters

ar	archive object
lattice	value to be serialized
version	archive version id

Definition at line 59 of file LatticeSystem.h.

References serializeEnum().

std::ostream & Util::operator<<	(	std::ostream &	out,
		const PointGroup &	g
	)

Output stream inserter operator writing a PointGroup to stream.

Definition at line 8 of file PointGroup.cpp.

References Util::SymmetryGroup< Symmetry >::size().

bool Util::operator==	(	const PointSymmetry &	A,
		const PointSymmetry &	B
	)

Are two PointSymmetry objects equivalent?

Parameters

A	First object
B	Second object

Returns: True if A == B, false otherwise

Definition at line 96 of file PointSymmetry.cpp.

References Dimension.

PointSymmetry Util::operator*	(	const PointSymmetry &	A,
		const PointSymmetry &	B
	)

Return the product A*B of two symmetry objects.

Parameters

A	First object
B	Second object

Returns: product A*B

Definition at line 112 of file PointSymmetry.cpp.

References Dimension.

IntVector Util::operator*	(	const PointSymmetry &	S,
		const IntVector &	V
	)

Return the IntVector product S*V of a rotation matrix and an IntVector.

Parameters

S	PointSymmetry
V	Integer Vector

Returns: product S*V

Definition at line 130 of file PointSymmetry.cpp.

References Dimension.

IntVector Util::operator*	(	const IntVector &	V,
		const PointSymmetry &	S
	)

Return the IntVector product V*S of an IntVector and a rotation matrix.

Parameters

S	PointSymmetry
V	Integer Vector

Returns: product S*V

Definition at line 146 of file PointSymmetry.cpp.

References Dimension.

std::ostream & Util::operator<<	(	std::ostream &	out,
		const PointSymmetry &	A
	)

Output stream inserter for a PointSymmetry.

Parameters

out	output stream
A	PointSymmetry object to be output

Returns: modified output stream

Definition at line 162 of file PointSymmetry.cpp.

References Dimension.

bool Util::operator!=	(	const PointSymmetry &	A,
		const PointSymmetry &	B
	)

inline

Are two PointSymmetry objects not equivalent?

Parameters

A	First object
B	Second object

Returns: True if A != B, false otherwise

Definition at line 164 of file PointSymmetry.h.

std::istream & Util::operator>>	(	std::istream &	in,
		Bool &	object
	)

Input stream extractor for an Bool object.

Parameters

in	input stream
object	Bool object to be read from stream

Returns: modified input stream

Definition at line 47 of file Bool.cpp.

std::ostream & Util::operator<<	(	std::ostream &	out,
		const Bool &	object
	)

Output stream inserter for an Bool object.

Parameters

out	output stream
object	Bool to be written to stream

Returns: modified output stream

Definition at line 56 of file Bool.cpp.

std::istream & Util::operator>>	(	std::istream &	in,
		Dbl &	object
	)

Input stream extractor for an Dbl object.

Parameters

in	input stream
object	Dbl object to be read from stream

Returns: modified input stream

Definition at line 73 of file Dbl.cpp.

std::ostream & Util::operator<<	(	std::ostream &	out,
		const Dbl &	object
	)

Output stream inserter for an Dbl object.

Parameters

out	output stream
object	Dbl to be written to stream

Returns: modified output stream

Definition at line 86 of file Dbl.cpp.

std::istream & Util::operator>>	(	std::istream &	in,
		Int &	object
	)

Input stream extractor for an Int object.

Parameters

in	input stream
object	Int object to be read from stream

Returns: modified input stream

Definition at line 71 of file Int.cpp.

std::ostream & Util::operator<<	(	std::ostream &	out,
		const Int &	object
	)

Output stream inserter for an Int object.

Parameters

out	output stream
object	Int to be written to stream

Returns: modified output stream

Definition at line 84 of file Int.cpp.

std::istream & Util::operator>>	(	std::istream &	in,
		Lng &	object
	)

Input stream extractor for an Lng object.

Parameters

in	input stream
object	Lng object to be read from stream

Returns: modified input stream

Definition at line 53 of file Lng.cpp.

std::ostream & Util::operator<<	(	std::ostream &	out,
		const Lng &	object
	)

Output stream inserter for an Lng object.

Parameters

out	output stream
object	Lng to be written to stream

Returns: modified output stream

Definition at line 66 of file Lng.cpp.

std::istream & Util::operator>>	(	std::istream &	in,
		Str &	object
	)

Input stream extractor for an Str object.

Parameters

in	input stream
object	Str object to be read from stream

Returns: modified input stream

Definition at line 49 of file Str.cpp.

std::ostream & Util::operator<<	(	std::ostream &	out,
		const Str &	object
	)

Output stream inserter for an Str object.

Parameters

out	output stream
object	Str to be written to stream

Returns: modified output stream

Definition at line 58 of file Str.cpp.

template<>

void Util::write	(	std::ostream &	out,
		double	data
	)

Explicit specialization of write for double data.

Definition at line 20 of file write.cpp.

template<>

void Util::write	(	std::ostream &	out,
		std::complex< double >	data
	)

Explicit specialization of write for double data.

Definition at line 24 of file write.cpp.

template<>

void Util::write	(	std::ostream &	out,
		int	data
	)

Explicit specialization of write for int data.

Definition at line 28 of file write.cpp.

template<>

void Util::write	(	std::ostream &	out,
		long	data
	)

Explicit specialization of write for long data.

Definition at line 32 of file write.cpp.

template<>

void Util::write	(	std::ostream &	out,
		bool	data
	)

Explicit specialization of write for bool data.

Definition at line 36 of file write.cpp.

template<>

void Util::write	(	std::ostream &	out,
		std::string	data
	)

Explicit specialization of write for std::string data.

template<typename T >

bool Util::operator==	(	Polynomial< T > &	a,
		Polynomial< T > &	b
	)

Equality operator for polynomials.

Two polynomials are equal iff they have the same degree and the the same values for all coefficients.

Parameters

a	1st polynomial
b	2nd polynomial

Returns: true if a != b

Definition at line 676 of file Polynomial.h.

References Util::GArray< T >::size().

template<typename T >

bool Util::operator!=	(	Polynomial< T > &	a,
		Polynomial< T > &	b
	)

Inequality operator for polynomials.

Parameters

a	1st polynomial
b	2nd polynomial

Returns: true if a != b

Definition at line 695 of file Polynomial.h.

template<typename T >

Polynomial<T> Util::operator- ( Polynomial< T > const & a )

inline

Unary negation of polynomial.

Parameters

a	input polynomial

Returns: negated polynomial -a

Definition at line 706 of file Polynomial.h.

References Util::GArray< T >::size().

std::ostream & Util::operator<<	(	std::ostream &	out,
		Rational const &	rational
	)

Output stream inserter for a Rational.

Output elements of a rational to stream, without line breaks.

Parameters

out	output stream
rational	Rational to be written to stream

Returns: modified output stream

Definition at line 16 of file Rational.cpp.

Rational Util::operator+	(	Rational const &	a,
		Rational const &	b
	)

inline

Compute sum of two rationals.

Parameters

a	1st argument
b	2st argument

Returns: sum a + b

Definition at line 490 of file Rational.h.

References Util::Rational::den(), Util::Rational::num(), and Util::Rational::Rational().

Rational Util::operator+	(	Rational const &	a,
		int	b
	)

inline

Compute sum of rational and integer.

Parameters

a	Rational argument
b	integer argument

Returns: sum a + b

Definition at line 505 of file Rational.h.

References Util::Rational::num(), and Util::Rational::Rational().

Rational Util::operator+	(	int	b,
		Rational const &	a
	)

inline

Compute sum of integer and integer.

Parameters

b	integer argument
a	Rational argument

Returns: sum a + b

Definition at line 519 of file Rational.h.

Rational Util::operator-	(	Rational const &	a,
		Rational const &	b
	)

inline

Compute difference of rationals.

Parameters

a	1st argument
b	2st argument

Returns: difference a - b

Definition at line 530 of file Rational.h.

References Util::Rational::den(), Util::Rational::num(), and Util::Rational::Rational().

Rational Util::operator-	(	Rational const &	a,
		int	b
	)

inline

Compute difference of rational and integer.

Parameters

a	Rational argument
b	integer argument

Returns: difference a - b

Definition at line 545 of file Rational.h.

References Util::Rational::num(), and Util::Rational::Rational().

Rational Util::operator-	(	int	b,
		Rational const &	a
	)

inline

Compute difference of integer and rational.

Parameters

b	integer argument
a	Rational argument

Returns: difference b - a

Definition at line 559 of file Rational.h.

References Util::Rational::num(), and Util::Rational::Rational().

Rational Util::operator*	(	Rational const &	a,
		Rational const &	b
	)

inline

Compute product of rationals.

Parameters

a	1st Rational argument
b	2st Rational argument

Returns: product a*b

Definition at line 573 of file Rational.h.

References Util::Rational::den(), Util::Rational::num(), and Util::Rational::Rational().

Rational Util::operator*	(	Rational const &	a,
		int	b
	)

inline

Compute product of rational and integer.

Parameters

a	Rational argument
b	integer argument

Returns: product a*b

Definition at line 588 of file Rational.h.

References Util::Rational::Rational().

Rational Util::operator*	(	int	b,
		Rational const &	a
	)

inline

Compute product of integer and rational.

Parameters

b	integer argument
a	Rational argument

Returns: product a*b

Definition at line 599 of file Rational.h.

Rational Util::operator/	(	Rational const &	a,
		Rational const &	b
	)

inline

Compute quotient of two rationals.

Parameters

a	1st Rational argument (numerator)
b	2st Rational argument (denominator)

Returns: ratio a/b

Definition at line 610 of file Rational.h.

References Util::Rational::den(), Util::Rational::num(), Util::Rational::Rational(), and UTIL_THROW.

Rational Util::operator/	(	Rational const &	a,
		int	b
	)

inline

Compute quotient Rational divided by integer.

Parameters

a	Rational argument (numerator)
b	integer argument (denominator)

Returns: ratio a/b

Definition at line 628 of file Rational.h.

References Util::Rational::Rational(), and UTIL_THROW.

Rational Util::operator/	(	int	b,
		Rational const &	a
	)

inline

Compute quotient integer divided by Rational.

Parameters

b	integer argument (numerator)
a	Rational argument (denominator)

Returns: ratio b/a

Definition at line 644 of file Rational.h.

References Util::Rational::Rational(), and UTIL_THROW.

Rational Util::operator- ( Rational const & a )

inline

Unary negation of Rational.

Parameters

a	Rational number

Returns: negation -a

Definition at line 661 of file Rational.h.

References Util::Rational::Rational().

bool Util::operator==	(	Rational const &	a,
		Rational const &	b
	)

inline

Equality operators.

Equality operator for two Rational numbers.

Parameters

a	1st Rational
b	2nd Rational

Returns: true if equal, false otherwise

Definition at line 674 of file Rational.h.

bool Util::operator==	(	Rational const &	a,
		int	b
	)

inline

Equality operator for a Rational and an integer.

Parameters

a	Rational number
b	integer number

Returns: true if equal, false otherwise

Definition at line 684 of file Rational.h.

bool Util::operator==	(	int	b,
		Rational const &	a
	)

inline

Equality operator for an integer and a Rational.

Parameters

b	integer number
a	Rational number

Returns: true if equal, false otherwise

Definition at line 694 of file Rational.h.

bool Util::operator!=	(	Rational const &	a,
		Rational const &	b
	)

inline

Inequality operators.

Inequality operator for two Rational numbers.

Parameters

a	1st Rational
b	2nd Rational

Returns: true if unequal, false if equal

Definition at line 706 of file Rational.h.

bool Util::operator!=	(	Rational const &	a,
		int	b
	)

inline

Inequality operator for a Rational and an integer.

Parameters

a	Rational number
b	integer number

Returns: true if unequal, false if equal

Definition at line 716 of file Rational.h.

bool Util::operator!=	(	int	b,
		Rational const &	a
	)

inline

Inequality operator for an integer and a Rational.

Parameters

b	integer number
a	Rational number

Returns: true if unequal, false if equal

Definition at line 726 of file Rational.h.

References Util::Rational::operator<<.

void Util::MpiThrow ( Exception & e )

Function to throw exception in MPI code.

If MPI is not initialized, this function writes the message and calls MPI Abort. If MPI is not initialized, it simply throws the Exception.

Parameters

e	Exception to be thrown.

Definition at line 90 of file Exception.cpp.

References Util::Log::close(), Util::Log::file(), and Util::Exception::message().

void Util::initStatic ( )

Guarantee initialization of all static class members in Util namespace.

Definition at line 26 of file util/misc/initStatic.cpp.

References Util::Format::initStatic(), Util::Constants::initStatic(), Util::Log::initStatic(), Util::Memory::initStatic(), Util::ParamComponent::initStatic(), Util::Tensor::initStatic(), Util::Vector::initStatic(), and Util::IntVector::initStatic().

Referenced by DdMd::Simulation::Simulation(), and McMd::Simulation::Simulation().

void Util::checkRequiredIstream ( std::istream & in )

Check status of a std::istream just before reading required variable.

Throw Exception with appropriate error message if not good.

Parameters

in	input stream from which to read.

Definition at line 124 of file ioUtil.cpp.

References UTIL_THROW.

Referenced by operator>>().

template<typename D , typename B >

ptrdiff_t Util::baseOffset ( D & object )

Template for calculating offsets of base class subobjects.

Types: D - derived class B - base class

Definition at line 40 of file Offset.h.

template<>

void Util::send< bool >	(	MPI::Comm &	comm,
		bool &	data,
		int	dest,
		int	tag
	)

Explicit specialization of send for bool data.

Definition at line 19 of file MpiSendRecv.cpp.

Referenced by bcast().

template<>

void Util::recv< bool >	(	MPI::Comm &	comm,
		bool &	data,
		int	source,
		int	tag
	)

Explicit specialization of recv for bool data.

Definition at line 26 of file MpiSendRecv.cpp.

Referenced by bcast().

template<>

void Util::bcast< bool >	(	MPI::Intracomm &	comm,
		bool &	data,
		int	root
	)

Explicit specialization of bcast for bool data.

Definition at line 34 of file MpiSendRecv.cpp.

Referenced by bcast(), Util::Parameter::load(), Util::ParamComposite::loadOptional(), Util::Begin::readParam(), and Util::Parameter::readParam().

template<>

void Util::send< std::string >	(	MPI::Comm &	comm,
		std::string &	data,
		int	dest,
		int	tag
	)

Explicit specialization of send for std::string data.

Definition at line 48 of file MpiSendRecv.cpp.

template<>

void Util::recv< std::string >	(	MPI::Comm &	comm,
		std::string &	data,
		int	source,
		int	tag
	)

Explicit specialization of recv for std::string data.

Definition at line 64 of file MpiSendRecv.cpp.

template<>

void Util::bcast< std::string >	(	MPI::Intracomm &	comm,
		std::string &	data,
		int	root
	)

Explicit specialization of bcast for std::string data.

Definition at line 80 of file MpiSendRecv.cpp.

template<typename T >

void Util::send	(	MPI::Comm &	comm,
		T &	data,
		int	dest,
		int	tag
	)

Send a single T value.

Throws an Exception if no associated MPI data type is available, i.e., if MpiTraits<T>::hasType is false.

Parameters

comm	MPI communicator
data	value
dest	MPI rank of receiving processor in comm
tag	user-defined integer identifier for message

Definition at line 97 of file MpiSendRecv.h.

References UTIL_THROW.

template<typename T >

void Util::recv	(	MPI::Comm &	comm,
		T &	data,
		int	source,
		int	tag
	)

Receive a single T value.

Throws an Exception if no associated MPI data type is available, i.e., if MpiTraits<T>::hasType is false.

Parameters

comm	MPI communicator
data	value
source	MPI rank of sending processor in comm
tag	user-defined integer identifier for message

Definition at line 116 of file MpiSendRecv.h.

References UTIL_THROW.

template<typename T >

void Util::bcast	(	MPI::Intracomm &	comm,
		T &	data,
		int	root
	)

Broadcast a single T value.

Throws an Exception if no associated MPI data type is available, i.e., if MpiTraits<T>::hasType is false.

Parameters

comm	MPI communicator
data	value
root	MPI rank of root (sending) processor in comm

Definition at line 134 of file MpiSendRecv.h.

References UTIL_THROW.

Referenced by DdMd::NphIntegrator::integrateStep1(), DdMd::NptIntegrator::integrateStep1(), DdMd::NvtIntegrator::integrateStep2(), DdMd::NphIntegrator::integrateStep2(), DdMd::NptIntegrator::integrateStep2(), DdMd::Simulation::isValid(), DdMd::SerializeConfigIo::loadConfig(), DdMd::DdMdConfigIo::readConfig(), DdMd::LammpsConfigIo::readConfig(), DdMd::DdMdOrderedConfigIo::readConfig(), DdMd::NvtIntegrator::setup(), DdMd::NphIntegrator::setup(), and DdMd::NptIntegrator::setup().

template<typename T >

void Util::send	(	MPI::Comm &	comm,
		T *	array,
		int	count,
		int	dest,
		int	tag
	)

Send a C-array of T values.

Throws an exception if their exists neither an associated MPI data type nor an explicit specialization of the scalar send<T>.

Parameters

comm	MPI communicator
array	address of first element in array
count	number of elements in array
dest	MPI rank of destination (receiving) processor in comm
tag	user-defined integer identifier for this message

Definition at line 156 of file MpiSendRecv.h.

template<typename T >

void Util::recv	(	MPI::Comm &	comm,
		T *	array,
		int	count,
		int	source,
		int	tag
	)

Receive a C-array of T objects.

Throws an exception if their exists neither an associated MPI data type nor an explicit specialization of the scalar recv<T>.

Parameters

comm	MPI communicator
array	address of first element in array
count	number of elements in array
source	MPI rank of source (sending) processor in comm
tag	user-defined integer identifier for this message

Definition at line 182 of file MpiSendRecv.h.

template<typename T >

void Util::bcast	(	MPI::Intracomm &	comm,
		T *	array,
		int	count,
		int	root
	)

Broadcast a C-array of T objects.

Throws an exception if their exists neither an associated MPI data type nor an explicit specialization of the scalar bcast<T>.

Parameters

comm	MPI communicator
array	address of first element in array
count	number of elements in array
root	MPI rank of root (sending) processor in comm

Definition at line 207 of file MpiSendRecv.h.

template<typename T >

void Util::send	(	MPI::Comm &	comm,
		DArray< T > &	array,
		int	count,
		int	dest,
		int	tag
	)

Send a DArray<T> container.

Throws an exception if their exists neither an associated MPI data type nor an explicit specialization of the scalar send<T> method.

Parameters

comm	MPI communicator
array	DArray object
count	logical number of elements in array
dest	MPI rank of destination (receiving) processor in comm
tag	user-defined integer identifier for this message

Definition at line 235 of file MpiSendRecv.h.

References Util::Array< Data >::capacity(), Util::DArray< Data >::isAllocated(), and UTIL_THROW.

template<typename T >

void Util::recv	(	MPI::Comm &	comm,
		DArray< T > &	array,
		int	count,
		int	source,
		int	tag
	)

Receive a DArray<T> container.

Throws an exception if their exists neither an associated MPI data type nor an explicit specialization of the scalar recv<T> method.

Parameters

comm	MPI communicator
array	DArray object
count	logical number of elements in array
source	MPI rank of source (sending) processor in comm
tag	user-defined integer identifier for this message

Definition at line 269 of file MpiSendRecv.h.

References Util::Array< Data >::capacity(), Util::DArray< Data >::isAllocated(), and UTIL_THROW.

template<typename T >

void Util::bcast	(	MPI::Intracomm &	comm,
		DArray< T > &	array,
		int	count,
		int	root
	)

Broadcast a DArray<T> container.

Throws an exception if their exists neither an associated MPI data type nor an explicit specialization of the scalar bcast<T>.

Parameters

comm	MPI communicator
array	address of first element in array
count	number of elements in array
root	MPI rank of root (sending) processor in comm

Definition at line 302 of file MpiSendRecv.h.

References Util::Array< Data >::capacity(), Util::DArray< Data >::isAllocated(), and UTIL_THROW.

template<typename T >

void Util::send	(	MPI::Comm &	comm,
		DMatrix< T > &	matrix,
		int	m,
		int	n,
		int	dest,
		int	tag
	)

Send a DMatrix<T> container.

Throws an exception if their exists neither an associated MPI data type nor an explicit specialization of the scalar send<T>.

Parameters

comm	MPI communicator
matrix	DMatrix object to send
m	logical number of rows in matrix
n	logical number of columns in matrix
dest	MPI rank of destination (receiving) processor in comm
tag	user-defined integer identifier for this message

Definition at line 339 of file MpiSendRecv.h.

References Util::Matrix< Data >::capacity1(), Util::Matrix< Data >::capacity2(), Util::DMatrix< Data >::isAllocated(), and UTIL_THROW.

template<typename T >

void Util::recv	(	MPI::Comm &	comm,
		DMatrix< T > &	matrix,
		int	m,
		int	n,
		int	source,
		int	tag
	)

Receive a DMatrix<T> container.

Throws an exception if their exists neither an associated MPI data type nor an explicit specialization of the scalar recv<T>.

Parameters

comm	MPI communicator
matrix	DMatrix object to receive
m	logical number of rows in matrix
n	logical number of columns in matrix
source	MPI rank of source (sending) processor in comm
tag	user-defined integer identifier for this message

Definition at line 383 of file MpiSendRecv.h.

References Util::Matrix< Data >::capacity1(), Util::Matrix< Data >::capacity2(), Util::DMatrix< Data >::isAllocated(), and UTIL_THROW.

template<typename T >

void Util::bcast	(	MPI::Intracomm &	comm,
		DMatrix< T > &	matrix,
		int	m,
		int	n,
		int	root
	)

Broadcast a DMatrix<T> container.

Throws an exception if their exists neither an associated MPI data type nor an explicit specialization of the scalar bcast<T>.

Parameters

comm	MPI communicator
matrix	DMatrix object
m	logical number of rows in matrix
n	logical number of columns in matrix
root	MPI rank of root (sending) processor in comm

Definition at line 427 of file MpiSendRecv.h.

References bcast< bool >(), Util::Matrix< Data >::capacity1(), Util::Matrix< Data >::capacity2(), Util::DMatrix< Data >::isAllocated(), recv< bool >(), send< bool >(), and UTIL_THROW.

std::istream & Util::operator>>	(	std::istream &	in,
		Label	label
	)

Extractor for Label.

Parameters

in	input stream
label	Label to be read from file

Definition at line 104 of file Label.cpp.

References Util::Log::file(), Util::Label::isRequired(), UTIL_CHECK, and UTIL_THROW.

std::ostream & Util::operator<<	(	std::ostream &	out,
		Label	label
	)

Inserter for Label.

Parameters

out	output stream
label	Label to be written to file

Definition at line 158 of file Label.cpp.

References Util::Label::LabelWidth.

template<typename T >

bool Util::isNull ( FlexPtr< T > p )

inline

Return true iff the enclosed built-in pointer is null.

Definition at line 143 of file FlexPtr.h.

References Util::FlexPtr< T >::get().

template<typename T >

bool Util::isNull ( T * ptr )

inline

Return true iff a built-in pointer is null.

Definition at line 18 of file isNull.h.

template<typename T >

bool Util::isNull ( ScopedPtr< T > p )

inline

Return true iff the enclosed built-in pointer is null.

Definition at line 90 of file ScopedPtr.h.

References Util::ScopedPtr< T >::get().

bool Util::operator==	(	const IntVector &	v1,
		const IntVector &	v2
	)

Equality for IntVectors.

Definition at line 24 of file IntVector.cpp.

References Dimension.

bool Util::operator==	(	const IntVector &	v1,
		const int *	v2
	)

Equality of IntVector and C array.

Definition at line 35 of file IntVector.cpp.

References Dimension.

bool Util::operator==	(	const int *	v1,
		const IntVector &	v2
	)

Equality of C array and IntVector.

Definition at line 45 of file IntVector.cpp.

bool Util::operator!=	(	const IntVector &	v1,
		const IntVector &	v2
	)

Inequality of two IntVectors.

Definition at line 50 of file IntVector.cpp.

bool Util::operator!=	(	const IntVector &	v1,
		const int *	v2
	)

Inequality of IntVector and C array.

Definition at line 54 of file IntVector.cpp.

bool Util::operator!=	(	const int *	v1,
		const IntVector &	v2
	)

Inequality of C array and IntVector.

Definition at line 58 of file IntVector.cpp.

std::istream & Util::operator>>	(	std::istream &	in,
		IntVector &	vector
	)

istream extractor for a IntVector.

Input elements of a vector from stream, without line breaks.

Parameters

in	input stream
vector	IntVector to be read from stream

Returns: modified input stream

Definition at line 64 of file IntVector.cpp.

References Dimension.

std::ostream & Util::operator<<	(	std::ostream &	out,
		const IntVector &	vector
	)

ostream inserter for a IntVector.

Output elements of a vector to stream, without line breaks.

Parameters

out	output stream
vector	IntVector to be written to stream

Returns: modified output stream

Definition at line 75 of file IntVector.cpp.

References Dimension.

bool Util::operator==	(	const Tensor &	t1,
		const Tensor &	t2
	)

Equality for Tensors.

Definition at line 43 of file Tensor.cpp.

References DimensionSq.

bool Util::operator==	(	const Tensor &	t1,
		const double	a2[][Dimension]
	)

Equality of Tensor and 2D C array.

Definition at line 56 of file Tensor.cpp.

References Dimension.

bool Util::operator==	(	const double	a1[][Dimension],
		const Tensor &	t2
	)

Equality of C array and Tensor.

Definition at line 71 of file Tensor.cpp.

bool Util::operator!=	(	const Tensor &	t1,
		const Tensor &	t2
	)

Negation of t1 == t2 (tensors t1 and t2)

Inequality of two Tensors.

Definition at line 79 of file Tensor.cpp.

bool Util::operator!=	(	const Tensor &	t1,
		const double	a2[][Dimension]
	)

Negation of t1 == a2 (tensor t1, 2D array a2)

Inequality of Tensor and C array.

Definition at line 83 of file Tensor.cpp.

bool Util::operator!=	(	const double	a1[][Dimension],
		const Tensor &	t2
	)

Negation of t1 == a2 (tensor t2, 2D array a1)

Inequality of C array and Tensor.

Definition at line 87 of file Tensor.cpp.

std::istream & Util::operator>>	(	std::istream &	in,
		Tensor &	tensor
	)

istream extractor for a Tensor.

Input elements of a tensor from stream, without line breaks.

Parameters

in	input stream
tensor	Tensor to be read from stream

Returns: modified input stream

Definition at line 93 of file Tensor.cpp.

References DimensionSq.

std::ostream & Util::operator<<	(	std::ostream &	out,
		const Tensor &	tensor
	)

ostream inserter for a Tensor.

Output elements of a tensor to stream, without line breaks.

Parameters

out	output stream
tensor	Tensor to be written to stream

Returns: modified output stream

Definition at line 104 of file Tensor.cpp.

References DimensionSq.

bool Util::operator==	(	const Vector &	v1,
		const Vector &	v2
	)

Equality for Vectors.

Definition at line 26 of file Vector.cpp.

References Dimension.

bool Util::operator==	(	const Vector &	v1,
		const double *	v2
	)

Equality of Vector and C array.

Definition at line 36 of file Vector.cpp.

References Dimension.

bool Util::operator==	(	const double *	v1,
		const Vector &	v2
	)

Equality of C array and Vector.

Definition at line 48 of file Vector.cpp.

bool Util::operator!=	(	const Vector &	v1,
		const Vector &	v2
	)

Inequality of two Vectors.

Definition at line 53 of file Vector.cpp.

bool Util::operator!=	(	const Vector &	v1,
		const double *	v2
	)

Inequality of Vector and C array.

Definition at line 56 of file Vector.cpp.

bool Util::operator!=	(	const double *	v1,
		const Vector &	v2
	)

Inequality of C array and Vector.

Definition at line 59 of file Vector.cpp.

std::istream & Util::operator>>	(	std::istream &	in,
		Vector &	vector
	)

istream extractor for a Vector.

Input elements of a vector from stream, without line breaks.

Parameters

in	input stream
vector	Vector to be read from stream

Returns: modified input stream

Definition at line 65 of file Vector.cpp.

References Dimension.

std::ostream & Util::operator<<	(	std::ostream &	out,
		const Vector &	vector
	)

ostream inserter for a Vector.

Output elements of a vector to stream, without line breaks.

Parameters

out	output stream
vector	Vector to be written to stream

Returns: modified output stream

Definition at line 76 of file Vector.cpp.

References Dimension.

template<>

void Util::send< MonoclinicBoundary >	(	MPI::Comm &	comm,
		MonoclinicBoundary &	data,
		int	dest,
		int	tag
	)

Send an MonoclinicBoundary via MPI.

Definition at line 193 of file MonoclinicBoundary.cpp.

Referenced by Simp::MonoclinicBoundary::serialize().

template<>

void Util::recv< MonoclinicBoundary >	(	MPI::Comm &	comm,
		MonoclinicBoundary &	data,
		int	source,
		int	tag
	)

Receive an MonoclinicBoundary via MPI.

Definition at line 201 of file MonoclinicBoundary.cpp.

Referenced by Simp::MonoclinicBoundary::serialize().

template<>

void Util::bcast< MonoclinicBoundary >	(	MPI::Intracomm &	comm,
		MonoclinicBoundary &	data,
		int	root
	)

Broadcast an MonoclinicBoundary via MPI.

Definition at line 212 of file MonoclinicBoundary.cpp.

Referenced by Simp::MonoclinicBoundary::serialize().

template<>

void Util::send< Simp::OrthorhombicBoundary >	(	MPI::Comm &	comm,
		Simp::OrthorhombicBoundary &	data,
		int	dest,
		int	tag
	)

Send an OrthorhombicBoundary via MPI.

Definition at line 210 of file OrthorhombicBoundary.cpp.

References Simp::OrthorhombicBoundary::lengths().

template<>

void Util::recv< Simp::OrthorhombicBoundary >	(	MPI::Comm &	comm,
		Simp::OrthorhombicBoundary &	data,
		int	source,
		int	tag
	)

Receive an OrthorhombicBoundary via MPI.

Definition at line 218 of file OrthorhombicBoundary.cpp.

References Simp::OrthorhombicBoundary::lengths().

template<>

void Util::bcast< Simp::OrthorhombicBoundary >	(	MPI::Intracomm &	comm,
		Simp::OrthorhombicBoundary &	data,
		int	root
	)

Broadcast an OrthorhombicBoundary via MPI.

Definition at line 227 of file OrthorhombicBoundary.cpp.

References Simp::OrthorhombicBoundary::lengths().

template<>

void Util::send< McMd::AtomType >	(	MPI::Comm &	comm,
		McMd::AtomType &	data,
		int	dest,
		int	tag
	)

Send an AtomType (wrapper for MPI Send).

Parameters

comm	MPI communicator
data	AtomType data
dest	MPI rank of destination (receiving) processor
tag	integer identifier for message

Definition at line 108 of file mcMd/chemistry/AtomType.cpp.

References McMd::AtomType::charge(), McMd::AtomType::hasCharge(), McMd::AtomType::mass(), and McMd::AtomType::name().

template<>

void Util::recv< McMd::AtomType >	(	MPI::Comm &	comm,
		McMd::AtomType &	data,
		int	source,
		int	tag
	)

Receive an AtomType (wrapper for MPI Recv).

Parameters

comm	MPI communicator
data	AtomType data
source	MPI rank of source (sending) processor
tag	integer identifier for message

Definition at line 127 of file mcMd/chemistry/AtomType.cpp.

References McMd::AtomType::charge(), McMd::AtomType::hasCharge(), McMd::AtomType::mass(), and McMd::AtomType::name().

template<>

void Util::bcast< McMd::AtomType >	(	MPI::Intracomm &	comm,
		McMd::AtomType &	data,
		int	root
	)

Broadcast an AtomType (wrapper for MPI Bcast).

Parameters

comm	MPI communicator
data	AtomType data
root	MPI rank of root processor from which data is broadcast

Definition at line 150 of file mcMd/chemistry/AtomType.cpp.

References McMd::AtomType::charge(), McMd::AtomType::hasCharge(), McMd::AtomType::mass(), and McMd::AtomType::name().

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Typedefs

Enumerations

Functions

Variables

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