A class for full (non-sparse) matrices with Fortran-compatible data storage, which adds matrix operations to class Array2D. More...

#include <DenseMatrix.h>

Inheritance diagram for DenseMatrix:

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Public Types
typedef vector_fp::iterator	iterator
	Type definition for the iterator class that is can be used by Array2D types.

typedef vector_fp::const_iterator	const_iterator
	Type definition for the const_iterator class that is can be used by Array2D types.

Public Member Functions
	DenseMatrix ()
	Default Constructor.

	DenseMatrix (size_t n, size_t m, doublereal v=0.0)
	Constructor.

	DenseMatrix (const DenseMatrix &y)
	Copy constructor.

DenseMatrix &	operator= (const DenseMatrix &y)
	Assignment operator.

virtual	~DenseMatrix ()
	Destructor. Does nothing.

void	resize (size_t n, size_t m, doublereal v=0.0)
	Resize the matrix.

virtual doublereal const	colPts ()
	Return a vector of const pointers to the columns.

const doublereal const	const_colPts () const
	Return a const vector of const pointers to the columns.

virtual void	mult (const double b, double prod) const
	Multiply A*b and write result to `prod`.

virtual void	leftMult (const double const b, double const prod) const
	Left-multiply the matrix by transpose(b), and write the result to prod.

vector_int &	ipiv ()
	Return a changeable value of the pivot vector.

const vector_int &	ipiv () const
	Return a changeable value of the pivot vector.

void	copyData (const Array2D &y)
	Copy the data from one array into another without doing any checking.

void	appendColumn (const vector_fp &c)
	Append a column to the existing matrix using a std vector.

void	appendColumn (const doublereal *const c)
	Append a column to the existing matrix.

void	setRow (size_t n, const doublereal *const rw)
	Set the nth row to array rw.

void	getRow (size_t n, doublereal *const rw)
	Get the nth row and return it in a vector.

void	setColumn (size_t m, doublereal *const col)
	Set the values in column m to those in array col.

void	getColumn (size_t m, doublereal *const col)
	Get the values in column m.

void	axpy (doublereal a, const Array2D &x, const Array2D &y)
	Evaluate z = a*x + y.

void	zero ()
	Set all of the entries to zero.

doublereal &	operator() (size_t i, size_t j)
	Allows setting elements using the syntax A(i,j) = x.

doublereal	operator() (size_t i, size_t j) const
	Allows retrieving elements using the syntax x = A(i,j).

doublereal &	value (size_t i, size_t j)
	Returns a changeable reference to position in the matrix.

doublereal	value (size_t i, size_t j) const
	Returns the value of a single matrix entry.

size_t	nRows () const
	Number of rows.

size_t	nColumns () const
	Number of columns.

iterator	begin ()
	Return an iterator pointing to the first element.

const_iterator	begin () const
	Return a const iterator pointing to the first element.

iterator	end ()
	Return an iterator pointing past the last element.

const_iterator	end () const
	Return a const iterator pointing to past the last element.

vector_fp &	data ()
	Return a reference to the data vector.

const vector_fp &	data () const
	Return a const reference to the data vector.

doublereal *	ptrColumn (size_t j)
	Return a pointer to the top of column j, columns are contiguous in memory.

const doublereal *	ptrColumn (size_t j) const
	Return a const pointer to the top of column j, columns are contiguous in memory.

Public Attributes
int	m_useReturnErrorCode
	Error Handling Flag.

int	m_printLevel
	Print Level.

Protected Attributes
vector_int	m_ipiv
	Vector of pivots. Length is equal to the max of m and n.

std::vector< doublereal * >	m_colPts
	Vector of column pointers.

vector_fp	m_data
	Data stored in a single array.

size_t	m_nrows
	Number of rows.

size_t	m_ncols
	Number of columns.

Friends
int	solve (DenseMatrix &A, double *b)
	Solve Ax = b. Array b is overwritten on exit with x.

int	solve (DenseMatrix &A, DenseMatrix &b)
	Solve Ax = b for multiple right-hand-side vectors.

int	invert (DenseMatrix &A, int nn)

Detailed Description

A class for full (non-sparse) matrices with Fortran-compatible data storage, which adds matrix operations to class Array2D.

The dense matrix class adds matrix operations onto the Array2D class. These matrix operations are carried out by the appropriate BLAS and LAPACK routines

Error handling from BLAS and LAPACK are handled via the following formulation. Depending on a variable, a singular matrix or other terminal error condition from LAPACK is handled by either throwing an exception of type, CELapackError, or by returning the error code condition to the calling routine.

The int variable, m_useReturnErrorCode, determines which method is used. The default value of zero means that an exception is thrown. A value of 1 means that a return code is used.

Reporting of these LAPACK error conditions is handled by the class variable m_printLevel. The default is for no reporting. If m_printLevel is nonzero, the error condition is reported to Cantera's log file.

Definition at line 70 of file DenseMatrix.h.

Member Typedef Documentation

typedef vector_fp::iterator iterator

inherited

Type definition for the iterator class that is can be used by Array2D types.

this is just equal to vector_fp iterator.

Definition at line 43 of file Array.h.

typedef vector_fp::const_iterator const_iterator

inherited

Type definition for the const_iterator class that is can be used by Array2D types.

this is just equal to vector_fp const_iterator.

Definition at line 51 of file Array.h.

Constructor & Destructor Documentation

DenseMatrix ( )

Default Constructor.

Definition at line 18 of file DenseMatrix.cpp.

DenseMatrix	(	size_t	n,
		size_t	m,
		doublereal	v = `0.0`
	)

Constructor.

Create an n by m matrix, and initialize all elements to v.

Parameters

n	New number of rows
m	New number of columns
v	Default fill value. defaults to zero.

Definition at line 30 of file DenseMatrix.cpp.

References DenseMatrix::m_colPts, Array2D::m_data, DenseMatrix::m_ipiv, Array2D::m_nrows, and ckr::max().

DenseMatrix ( const DenseMatrix & y )

Copy constructor.

Parameters

y	Object to be copied

Definition at line 49 of file DenseMatrix.cpp.

References DenseMatrix::ipiv(), DenseMatrix::m_colPts, Array2D::m_data, DenseMatrix::m_ipiv, Array2D::m_ncols, and Array2D::m_nrows.

~DenseMatrix ( )

virtual

Destructor. Does nothing.

Definition at line 82 of file DenseMatrix.cpp.

Member Function Documentation

DenseMatrix & operator= ( const DenseMatrix & y )

Assignment operator.

Parameters

y	Object to be copied

Definition at line 65 of file DenseMatrix.cpp.

References DenseMatrix::ipiv(), DenseMatrix::m_colPts, Array2D::m_data, DenseMatrix::m_ipiv, Array2D::m_ncols, Array2D::m_nrows, DenseMatrix::m_printLevel, DenseMatrix::m_useReturnErrorCode, and Array2D::operator=().

Referenced by SquareMatrix::operator=().

void resize	(	size_t	n,
		size_t	m,
		doublereal	v = `0.0`
	)

Resize the matrix.

Resize the matrix to n rows by m cols.

Parameters

n	New number of rows
m	New number of columns
v	Default fill value. defaults to zero.

Definition at line 86 of file DenseMatrix.cpp.

References DenseMatrix::m_colPts, Array2D::m_data, DenseMatrix::m_ipiv, Array2D::m_ncols, Array2D::m_nrows, ckr::max(), and Array2D::resize().

Referenced by LTI_Pairwise_Interaction::getMatrixTransProp(), LTI_StefanMaxwell_PPN::getMatrixTransProp(), LiquidTranInteraction::init(), MultiPhase::init(), GasTransport::initGas(), MultiTransport::initGas(), DustyGasTransport::initialize(), LiquidTransport::initLiquid(), AqueousTransport::initLiquid(), MultiPhaseEquil::MultiPhaseEquil(), SquareMatrix::resize(), TransportFactory::setupLiquidTransport(), TransportFactory::setupMM(), MultiTransport::solveLMatrixEquation(), and LiquidTransport::stefan_maxwell_solve().

doublereal *const * colPts ( )

virtual

Return a vector of const pointers to the columns.

Note the value of the pointers are protected by their being const. However, the value of the matrix is open to being changed.

Returns: returns a vector of pointers to the top of the columns of the matrices.

Reimplemented in SquareMatrix.

Definition at line 98 of file DenseMatrix.cpp.

References DenseMatrix::m_colPts.

Referenced by SquareMatrix::colPts().

const doublereal *const * const_colPts ( ) const

Return a const vector of const pointers to the columns.

Note, the jacobian can not be altered by this routine, and therefore the member function is const.

Returns: returns a vector of pointers to the top of the columns of the matrices.

Definition at line 103 of file DenseMatrix.cpp.

References DenseMatrix::m_colPts.

void mult	(	const double *	b,
		double *	prod
	)		const

virtual

Multiply A*b and write result to prod.

Parameters

b	input vector b with length N
prod	output output vector prod length = M

Reimplemented in SquareMatrix, and L_Matrix.

Definition at line 108 of file DenseMatrix.cpp.

References Array2D::nRows(), and Array2D::ptrColumn().

Referenced by SquareMatrix::mult().

void leftMult	(	const double *const	b,
		double *const	prod
	)		const

virtual

Left-multiply the matrix by transpose(b), and write the result to prod.

Parameters

b	left multiply by this vector. The length must be equal to n the number of rows in the matrix.
prod	Resulting vector. This is of length m, the number of columns in the matrix

Reimplemented in SquareMatrix.

Definition at line 116 of file DenseMatrix.cpp.

References Array2D::nColumns(), Array2D::nRows(), and Array2D::value().

Referenced by ChemEquil::equilibrate(), and SquareMatrix::leftMult().

vector_int & ipiv ( )

Return a changeable value of the pivot vector.

Returns: Returns a reference to the pivot vector as a vector_int

Definition at line 130 of file DenseMatrix.cpp.

References DenseMatrix::m_ipiv.

Referenced by DenseMatrix::DenseMatrix(), SquareMatrix::factor(), MultiTransport::getMassFluxes(), MultiTransport::getSpeciesFluxes(), Cantera::invert(), DenseMatrix::operator=(), SquareMatrix::solve(), and Cantera::solve().

const vector_int& ipiv ( ) const

inline

Return a changeable value of the pivot vector.

Returns: Returns a reference to the pivot vector as a vector_int

Definition at line 161 of file DenseMatrix.h.

References DenseMatrix::m_ipiv.

void copyData ( const Array2D & y )

inlineinherited

Copy the data from one array into another without doing any checking.

This differs from the assignment operator as no resizing is done and memcpy() is used.

Parameters

y	Array to be copied

Definition at line 139 of file Array.h.

References DATA_PTR, Array2D::m_data, Array2D::m_ncols, Array2D::m_nrows, and Array2D::ptrColumn().

Referenced by SquareMatrix::copyData().

void appendColumn ( const vector_fp & c )

inlineinherited

Append a column to the existing matrix using a std vector.

This operation will add a column onto the existing matrix.

Parameters

c	This vector<doublereal> is the entries in the column to be added. It must have a length equal to m_nrows or greater.

Definition at line 152 of file Array.h.

References Array2D::m_data, Array2D::m_ncols, Array2D::m_nrows, and Array2D::value().

void appendColumn ( const doublereal *const c )

inlineinherited

Append a column to the existing matrix.

This operation will add a column onto the existing matrix.

Parameters

c	This vector of doubles is the entries in the column to be added. It must have a length equal to m_nrows or greater.

Definition at line 169 of file Array.h.

References Array2D::m_data, Array2D::m_ncols, Array2D::m_nrows, and Array2D::value().

void setRow	(	size_t	n,
		const doublereal *const	rw
	)

inlineinherited

Set the nth row to array rw.

Parameters

n	Index of the row to be changed
rw	Vector for the row. Must have a length of m_ncols.

Definition at line 183 of file Array.h.

References Array2D::m_data, Array2D::m_ncols, and Array2D::m_nrows.

void getRow	(	size_t	n,
		doublereal *const	rw
	)

inlineinherited

Get the nth row and return it in a vector.

Parameters

n	Index of the row to be returned.
rw	Return Vector for the operation. Must have a length of m_ncols.

Definition at line 195 of file Array.h.

References Array2D::m_data, Array2D::m_ncols, and Array2D::m_nrows.

Referenced by StFlow::save().

void setColumn	(	size_t	m,
		doublereal *const	col
	)

inlineinherited

Set the values in column m to those in array col.

A(i,m) = col(i)

Parameters

m	Column to set
col	pointer to a col vector. Vector must have a length of m_nrows.

Definition at line 209 of file Array.h.

References Array2D::m_data, and Array2D::m_nrows.

void getColumn	(	size_t	m,
		doublereal *const	col
	)

inlineinherited

Get the values in column m.

col(i) = A(i,m)

Parameters

m	Column to set
col	pointer to a col vector that will be returned

Definition at line 222 of file Array.h.

References Array2D::m_data, and Array2D::m_nrows.

void axpy	(	doublereal	a,
		const Array2D &	x,
		const Array2D &	y
	)

inlineinherited

Evaluate z = a*x + y.

This function evaluates the AXPY operation, and stores the result in the object's Array2D object. It's assumed that all 3 objects have the same dimensions, but no error checking is done.

Parameters

a	scalar to multiply x with
x	First Array2D object to be used
y	Second Array2D object to be used

Definition at line 246 of file Array.h.

References Array2D::begin(), and Array2D::end().

void zero ( )

inlineinherited

Set all of the entries to zero.

Definition at line 256 of file Array.h.

References Array2D::m_data, Array2D::m_ncols, and Array2D::m_nrows.

Referenced by IonsFromNeutralVPSSTP::s_update_dlnActCoeff_dlnN(), PhaseCombo_Interaction::s_update_dlnActCoeff_dlnN(), MargulesVPSSTP::s_update_dlnActCoeff_dlnN(), MixedSolventElectrolyte::s_update_dlnActCoeff_dlnN(), and RedlichKisterVPSSTP::s_update_dlnActCoeff_dX_().

doublereal& operator()	(	size_t	i,
		size_t	j
	)

inlineinherited

Allows setting elements using the syntax A(i,j) = x.

Parameters

i	row index
j	column index.

Returns: Returns a reference to A(i,j) which may be assigned.

Definition at line 274 of file Array.h.

References Array2D::value().

Referenced by SquareMatrix::operator()().

doublereal operator()	(	size_t	i,
		size_t	j
	)		const

inlineinherited

Allows retrieving elements using the syntax x = A(i,j).

Parameters

i	Index for the row to be retrieved
j	Index for the column to be retrieved.

Returns: Returns the value of the matrix entry

Definition at line 286 of file Array.h.

References Array2D::value().

doublereal& value	(	size_t	i,
		size_t	j
	)

inlineinherited

Returns a changeable reference to position in the matrix.

This is a key entry. Returns a reference to the matrixes (i,j) element. This may be used as an L value.

Parameters

i	The row index
j	The column index

Returns: Returns a changeable reference to the matrix entry

Definition at line 300 of file Array.h.

References Array2D::m_data, and Array2D::m_nrows.

Referenced by Array2D::appendColumn(), SquareMatrix::checkColumns(), SquareMatrix::checkRows(), DenseMatrix::leftMult(), Array2D::operator()(), and DebyeHuckel::s_update_lnMolalityActCoeff().

doublereal value	(	size_t	i,
		size_t	j
	)		const

inlineinherited

Returns the value of a single matrix entry.

This is a key entry. Returns the value of the matrix position (i,j) element.

Parameters

i	The row index
j	The column index

Definition at line 312 of file Array.h.

References Array2D::m_data, and Array2D::m_nrows.

size_t nRows ( ) const

inlineinherited

Number of rows.

Definition at line 317 of file Array.h.

References Array2D::m_nrows.

Referenced by MultiTransport::getMassFluxes(), ctml::getMatrixValues(), MultiTransport::getSpeciesFluxes(), Cantera::increment(), Cantera::invert(), DenseMatrix::leftMult(), DenseMatrix::mult(), Cantera::multiply(), Cantera::operator<<(), Cantera::outputExcel(), Cantera::outputTEC(), and Cantera::solve().

size_t nColumns ( ) const

inlineinherited

Number of columns.

Definition at line 322 of file Array.h.

References Array2D::m_ncols.

Referenced by MultiTransport::getMassFluxes(), ctml::getMatrixValues(), MultiTransport::getSpeciesFluxes(), DenseMatrix::leftMult(), Cantera::multiply(), Cantera::operator<<(), Cantera::outputExcel(), Cantera::outputTEC(), StFlow::save(), SquareMatrix::solve(), and Cantera::solve().

iterator begin ( )

inlineinherited

Return an iterator pointing to the first element.

Definition at line 327 of file Array.h.

References Array2D::m_data.

Referenced by Array2D::axpy(), Cantera::operator*=(), and Cantera::operator+=().

const_iterator begin ( ) const

inlineinherited

Return a const iterator pointing to the first element.

Definition at line 337 of file Array.h.

References Array2D::m_data.

iterator end ( )

inlineinherited

Return an iterator pointing past the last element.

Definition at line 332 of file Array.h.

References Array2D::m_data.

Referenced by Array2D::axpy(), Cantera::operator*=(), and Cantera::operator+=().

const_iterator end ( ) const

inlineinherited

Return a const iterator pointing to past the last element.

Definition at line 342 of file Array.h.

References Array2D::m_data.

vector_fp& data ( )

inlineinherited

Return a reference to the data vector.

Definition at line 347 of file Array.h.

References Array2D::m_data.

const vector_fp& data ( ) const

inlineinherited

Return a const reference to the data vector.

Definition at line 352 of file Array.h.

References Array2D::m_data.

doublereal* ptrColumn ( size_t j )

inlineinherited

Return a pointer to the top of column j, columns are contiguous in memory.

Parameters

j	Value of the column

Returns: Returns a pointer to the top of the column

Definition at line 363 of file Array.h.

References Array2D::m_data, and Array2D::m_nrows.

Referenced by Array2D::copyData(), MultiTransport::getMassFluxes(), MultiTransport::getSpeciesFluxes(), Cantera::increment(), Cantera::invert(), DenseMatrix::mult(), Cantera::multiply(), SquareMatrix::ptrColumn(), HMWSoln::s_updatePitzer_CoeffWRTemp(), Cantera::solve(), solveProb::solveProb(), solveSP::solveSP(), AqueousTransport::stefan_maxwell_solve(), DustyGasTransport::updateBinaryDiffCoeffs(), and StFlow::updateTransport().

const doublereal* ptrColumn ( size_t j ) const

inlineinherited

Return a const pointer to the top of column j, columns are contiguous in memory.

Parameters

j	Value of the column

Returns: Returns a const pointer to the top of the column

Definition at line 374 of file Array.h.

References Array2D::m_data, and Array2D::m_nrows.

Friends And Related Function Documentation

int solve	(	DenseMatrix &	A,
		double *	b
	)

friend

Solve Ax = b. Array b is overwritten on exit with x.

The solve class uses the LAPACK routine dgetrf to invert the m xy n matrix.

The factorization has the form A = P * L * U where P is a permutation matrix, L is lower triangular with unit diagonal elements (lower trapezoidal if m > n), and U is upper triangular (upper trapezoidal if m < n).

The system is then solved using the LAPACK routine dgetrs

Parameters

A	Dense matrix to be factored
b	rhs to be solved.

Definition at line 135 of file DenseMatrix.cpp.

int solve	(	DenseMatrix &	A,
		DenseMatrix &	b
	)

friend

Solve Ax = b for multiple right-hand-side vectors.

Parameters

A	Dense matrix to be factored
b	Dense matrix of rhs's. Each column is a rhs

Definition at line 181 of file DenseMatrix.cpp.

Member Data Documentation

vector_int m_ipiv

protected

Vector of pivots. Length is equal to the max of m and n.

Definition at line 168 of file DenseMatrix.h.

Referenced by DenseMatrix::DenseMatrix(), DenseMatrix::ipiv(), DenseMatrix::operator=(), and DenseMatrix::resize().

std::vector<doublereal*> m_colPts

protected

Vector of column pointers.

Definition at line 171 of file DenseMatrix.h.

Referenced by DenseMatrix::colPts(), DenseMatrix::const_colPts(), DenseMatrix::DenseMatrix(), DenseMatrix::operator=(), and DenseMatrix::resize().

int m_useReturnErrorCode

Error Handling Flag.

The default is to set this to 0. In this case, if a factorization is requested and can't be achieved, a CESingularMatrix exception is triggered. No return code is used, because an exception is thrown. If this is set to 1, then an exception is not thrown. Routines return with an error code, that is up to the calling routine to handle correctly. Negative return codes always throw an exception.

Definition at line 182 of file DenseMatrix.h.

Referenced by SquareMatrix::factor(), SquareMatrix::factorQR(), Cantera::invert(), DenseMatrix::operator=(), SquareMatrix::rcond(), SquareMatrix::rcondQR(), SquareMatrix::solve(), Cantera::solve(), and SquareMatrix::solveQR().