Cantera
2.2.1
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A class for banded matrices, involving matrix inversion processes. More...
#include <BandMatrix.h>
Public Member Functions | |
BandMatrix () | |
Base Constructor. More... | |
BandMatrix (size_t n, size_t kl, size_t ku, doublereal v=0.0) | |
Creates a banded matrix and sets all elements to zero. More... | |
BandMatrix (const BandMatrix &y) | |
Copy constructor. More... | |
BandMatrix & | operator= (const BandMatrix &y) |
assignment operator More... | |
void | resize (size_t n, size_t kl, size_t ku, doublereal v=0.0) |
Resize the matrix problem. More... | |
void | bfill (doublereal v=0.0) |
Fill or zero the matrix. More... | |
doublereal & | operator() (size_t i, size_t j) |
Index into the (i,j) element. More... | |
doublereal | operator() (size_t i, size_t j) const |
Constant Index into the (i,j) element. More... | |
doublereal & | value (size_t i, size_t j) |
Return a changeable reference to element (i,j). More... | |
doublereal | value (size_t i, size_t j) const |
Return the value of element (i,j). More... | |
size_t | index (size_t i, size_t j) const |
Returns the location in the internal 1D array corresponding to the (i,j) element in the banded array. More... | |
doublereal | _value (size_t i, size_t j) const |
Return the value of the (i,j) element for (i,j) within the bandwidth. More... | |
virtual size_t | nRows () const |
Return the number of rows in the matrix. More... | |
virtual size_t | nRowsAndStruct (size_t *const iStruct=0) const |
Return the size and structure of the matrix. More... | |
size_t | nColumns () const |
Number of columns. More... | |
size_t | nSubDiagonals () const |
Number of subdiagonals. More... | |
size_t | nSuperDiagonals () const |
Number of superdiagonals. More... | |
size_t | ldim () const |
Return the number of rows of storage needed for the band storage. More... | |
vector_int & | ipiv () |
Return a reference to the pivot vector. More... | |
virtual void | mult (const doublereal *b, doublereal *prod) const |
Multiply A*b and write result to prod . More... | |
virtual void | leftMult (const doublereal *const b, doublereal *const prod) const |
Multiply b*A and write result to prod. More... | |
int | factor () |
Perform an LU decomposition, the LAPACK routine DGBTRF is used. More... | |
int | solve (const doublereal *const b, doublereal *const x) |
Solve the matrix problem Ax = b. More... | |
int | solve (doublereal *b, size_t nrhs=1, size_t ldb=0) |
Solve the matrix problem Ax = b. More... | |
virtual vector_fp::iterator | begin () |
Returns an iterator for the start of the band storage data. More... | |
vector_fp::iterator | end () |
Returns an iterator for the end of the band storage data. More... | |
vector_fp::const_iterator | begin () const |
Returns a const iterator for the start of the band storage data. More... | |
vector_fp::const_iterator | end () const |
Returns a const iterator for the end of the band storage data. More... | |
virtual void | zero () |
Zero the matrix elements. More... | |
virtual doublereal | rcond (doublereal a1norm) |
Returns an estimate of the inverse of the condition number for the matrix. More... | |
virtual int | factorAlgorithm () const |
Returns the factor algorithm used. More... | |
virtual doublereal | oneNorm () const |
Returns the one norm of the matrix. More... | |
virtual GeneralMatrix * | duplMyselfAsGeneralMatrix () const |
Duplicator member function. More... | |
virtual doublereal * | ptrColumn (size_t j) |
Return a pointer to the top of column j, column values are assumed to be contiguous in memory. More... | |
virtual doublereal *const * | colPts () |
Return a vector of const pointers to the columns. More... | |
virtual void | copyData (const GeneralMatrix &y) |
Copy the data from one array into another without doing any checking. More... | |
virtual size_t | checkRows (doublereal &valueSmall) const |
Check to see if we have any zero rows in the Jacobian. More... | |
virtual size_t | checkColumns (doublereal &valueSmall) const |
Check to see if we have any zero columns in the Jacobian. More... | |
virtual void | useFactorAlgorithm (int fAlgorithm) |
Change the way the matrix is factored. More... | |
Public Member Functions inherited from GeneralMatrix | |
GeneralMatrix (int matType) | |
Base Constructor. More... | |
GeneralMatrix (const GeneralMatrix &right) | |
Copy Constructor. More... | |
GeneralMatrix & | operator= (const GeneralMatrix &right) |
Assignment operator. More... | |
virtual | ~GeneralMatrix () |
Destructor. Does nothing. More... | |
virtual int | factorQR () |
Factors the A matrix using the QR algorithm, overwriting A. More... | |
virtual doublereal | rcondQR () |
Returns an estimate of the inverse of the condition number for the matrix. More... | |
virtual void | clearFactorFlag () |
clear the factored flag More... | |
virtual bool | factored () const |
true if the current factorization is up to date with the matrix More... | |
Protected Attributes | |
vector_fp | data |
Matrix data. More... | |
vector_fp | ludata |
Factorized data. More... | |
size_t | m_n |
Number of rows and columns of the matrix. More... | |
size_t | m_kl |
Number of subdiagonals of the matrix. More... | |
size_t | m_ku |
Number of super diagonals of the matrix. More... | |
doublereal | m_zero |
value of zero More... | |
vector_int | m_ipiv |
Pivot vector. More... | |
std::vector< doublereal * > | m_colPtrs |
Vector of column pointers. More... | |
vector_int | iwork_ |
Extra work array needed - size = n. More... | |
vector_fp | work_ |
Extra dp work array needed - size = 3n. More... | |
Protected Attributes inherited from GeneralMatrix | |
int | m_factored |
Indicates whether the matrix is factored. More... | |
Additional Inherited Members | |
Public Attributes inherited from GeneralMatrix | |
int | matrixType_ |
Matrix type. More... | |
A class for banded matrices, involving matrix inversion processes.
The class is based upon the LAPACK banded storage matrix format.
An important issue with this class is that it stores both the original data and the LU factorization of the data. This means that the banded matrix typically will take up twice the room that it is expected to take.
QR factorizations of banded matrices are not included in the original LAPACK work. Add-ons are available. However, they are not included here. Instead we just use the stock LU decompositions.
This class is a derived class of the base class GeneralMatrix. However, within the oneD directory, the class is used as is, without reference to the GeneralMatrix base type.
Definition at line 33 of file BandMatrix.h.
BandMatrix | ( | ) |
Base Constructor.
0
by 0
matrix, and initialize all elements to 0
. Definition at line 22 of file BandMatrix.cpp.
Referenced by BandMatrix::duplMyselfAsGeneralMatrix().
BandMatrix | ( | size_t | n, |
size_t | kl, | ||
size_t | ku, | ||
doublereal | v = 0.0 |
||
) |
Creates a banded matrix and sets all elements to zero.
Create an n
by n
banded matrix, and initialize all elements to v
.
n | size of the square matrix |
kl | band size on the lower portion of the matrix |
ku | band size on the upper portion of the matrix |
v | initial value of all matrix components. |
Definition at line 31 of file BandMatrix.cpp.
References BandMatrix::data, BandMatrix::ludata, BandMatrix::m_colPtrs, BandMatrix::m_ipiv, and BandMatrix::m_n.
BandMatrix | ( | const BandMatrix & | y | ) |
Copy constructor.
y | Matrix to be copied |
Definition at line 50 of file BandMatrix.cpp.
References BandMatrix::data, BandMatrix::ludata, BandMatrix::m_colPtrs, BandMatrix::m_ipiv, BandMatrix::m_kl, BandMatrix::m_ku, and BandMatrix::m_n.
BandMatrix & operator= | ( | const BandMatrix & | y | ) |
assignment operator
y | reference to the matrix to be copied |
Definition at line 70 of file BandMatrix.cpp.
References BandMatrix::data, BandMatrix::ludata, BandMatrix::m_colPtrs, BandMatrix::m_ipiv, BandMatrix::m_kl, BandMatrix::m_ku, BandMatrix::m_n, and GeneralMatrix::operator=().
void resize | ( | size_t | n, |
size_t | kl, | ||
size_t | ku, | ||
doublereal | v = 0.0 |
||
) |
Resize the matrix problem.
All data is lost
n | size of the square matrix |
kl | band size on the lower portion of the matrix |
ku | band size on the upper portion of the matrix |
v | initial value of all matrix components. |
Definition at line 90 of file BandMatrix.cpp.
References BandMatrix::data, BandMatrix::ludata, BandMatrix::m_colPtrs, GeneralMatrix::m_factored, BandMatrix::m_ipiv, BandMatrix::m_kl, BandMatrix::m_ku, and BandMatrix::m_n.
void bfill | ( | doublereal | v = 0.0 | ) |
Fill or zero the matrix.
v | Fill value, defaults to zero. |
Definition at line 107 of file BandMatrix.cpp.
References BandMatrix::data, and GeneralMatrix::m_factored.
Referenced by MultiJac::eval().
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Index into the (i,j) element.
i | row |
j | column |
Returns a changeable reference to the matrix entry
Implements GeneralMatrix.
Definition at line 119 of file BandMatrix.cpp.
References BandMatrix::value().
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Constant Index into the (i,j) element.
i | row |
j | column |
Returns an unchangeable reference to the matrix entry
Implements GeneralMatrix.
Definition at line 124 of file BandMatrix.cpp.
References BandMatrix::value().
doublereal & value | ( | size_t | i, |
size_t | j | ||
) |
Return a changeable reference to element (i,j).
Since this method may alter the element value, it may need to be refactored, so the flag m_factored is set to false.
i | row |
j | column |
Definition at line 129 of file BandMatrix.cpp.
References BandMatrix::data, BandMatrix::index(), GeneralMatrix::m_factored, BandMatrix::m_kl, and BandMatrix::m_zero.
Referenced by BandMatrix::checkColumns(), BandMatrix::checkRows(), MultiJac::eval(), BandMatrix::oneNorm(), and BandMatrix::operator()().
doublereal value | ( | size_t | i, |
size_t | j | ||
) | const |
Return the value of element (i,j).
This method does not alter the array.
i | row |
j | column |
Definition at line 138 of file BandMatrix.cpp.
References BandMatrix::data, BandMatrix::index(), and BandMatrix::m_kl.
size_t index | ( | size_t | i, |
size_t | j | ||
) | const |
Returns the location in the internal 1D array corresponding to the (i,j) element in the banded array.
i | row |
j | column |
Definition at line 146 of file BandMatrix.cpp.
References BandMatrix::m_kl, and BandMatrix::m_ku.
Referenced by BandMatrix::_value(), and BandMatrix::value().
doublereal _value | ( | size_t | i, |
size_t | j | ||
) | const |
Return the value of the (i,j) element for (i,j) within the bandwidth.
For efficiency, this method does not check that (i,j) are within the bandwidth; it is up to the calling program to insure that this is true.
i | row |
j | column |
Definition at line 154 of file BandMatrix.cpp.
References BandMatrix::data, and BandMatrix::index().
Referenced by BandMatrix::leftMult(), and BandMatrix::mult().
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Return the number of rows in the matrix.
Implements GeneralMatrix.
Definition at line 159 of file BandMatrix.cpp.
References BandMatrix::m_n.
Referenced by BandMatrix::factor(), BandMatrix::mult(), and Cantera::operator<<().
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Return the size and structure of the matrix.
iStruct | OUTPUT Pointer to a vector of ints that describe the structure of the matrix. istruct[0] = kl istruct[1] = ku |
Implements GeneralMatrix.
Definition at line 164 of file BandMatrix.cpp.
References BandMatrix::m_kl, BandMatrix::m_ku, and BandMatrix::m_n.
size_t nColumns | ( | ) | const |
Number of columns.
Definition at line 173 of file BandMatrix.cpp.
References BandMatrix::m_n.
Referenced by BandMatrix::factor(), BandMatrix::leftMult(), Cantera::operator<<(), and BandMatrix::solve().
size_t nSubDiagonals | ( | ) | const |
Number of subdiagonals.
Definition at line 178 of file BandMatrix.cpp.
References BandMatrix::m_kl.
Referenced by BandMatrix::factor(), and BandMatrix::solve().
size_t nSuperDiagonals | ( | ) | const |
Number of superdiagonals.
Definition at line 183 of file BandMatrix.cpp.
References BandMatrix::m_ku.
Referenced by BandMatrix::factor(), and BandMatrix::solve().
size_t ldim | ( | ) | const |
Return the number of rows of storage needed for the band storage.
Definition at line 188 of file BandMatrix.cpp.
References BandMatrix::m_kl, and BandMatrix::m_ku.
Referenced by BandMatrix::factor(), and BandMatrix::solve().
vector_int & ipiv | ( | ) |
Return a reference to the pivot vector.
Definition at line 193 of file BandMatrix.cpp.
References BandMatrix::m_ipiv.
Referenced by BandMatrix::factor(), and BandMatrix::solve().
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Multiply A*b and write result to prod
.
Implements GeneralMatrix.
Definition at line 198 of file BandMatrix.cpp.
References BandMatrix::_value(), BandMatrix::m_kl, BandMatrix::m_ku, BandMatrix::m_n, and BandMatrix::nRows().
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Multiply b*A and write result to prod.
b | Vector to do the lh multiplication |
prod | OUTPUT vector to receive the result |
Implements GeneralMatrix.
Definition at line 215 of file BandMatrix.cpp.
References BandMatrix::_value(), BandMatrix::m_kl, BandMatrix::m_ku, BandMatrix::m_n, and BandMatrix::nColumns().
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Perform an LU decomposition, the LAPACK routine DGBTRF is used.
The factorization is saved in ludata.
Implements GeneralMatrix.
Definition at line 233 of file BandMatrix.cpp.
References BandMatrix::data, DATA_PTR, BandMatrix::ipiv(), BandMatrix::ldim(), BandMatrix::ludata, GeneralMatrix::m_factored, BandMatrix::nColumns(), BandMatrix::nRows(), BandMatrix::nSubDiagonals(), and BandMatrix::nSuperDiagonals().
Referenced by BandMatrix::solve().
int solve | ( | const doublereal *const | b, |
doublereal *const | x | ||
) |
Solve the matrix problem Ax = b.
b | INPUT RHS of the problem |
x | OUTPUT solution to the problem |
Definition at line 252 of file BandMatrix.cpp.
References BandMatrix::m_n.
Referenced by MultiNewton::step().
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Solve the matrix problem Ax = b.
b | INPUT RHS of the problem OUTPUT solution to the problem |
nrhs | Number of right hand sides to solve |
ldb | Leading dimension of b . Default is nColumns() |
Implements GeneralMatrix.
Definition at line 258 of file BandMatrix.cpp.
References DATA_PTR, BandMatrix::factor(), BandMatrix::ipiv(), BandMatrix::ldim(), BandMatrix::ludata, GeneralMatrix::m_factored, BandMatrix::nColumns(), BandMatrix::nSubDiagonals(), and BandMatrix::nSuperDiagonals().
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Returns an iterator for the start of the band storage data.
Iterator points to the beginning of the data, and it is changeable.
Implements GeneralMatrix.
Definition at line 281 of file BandMatrix.cpp.
References BandMatrix::data, and GeneralMatrix::m_factored.
vector_fp::iterator end | ( | ) |
Returns an iterator for the end of the band storage data.
Iterator points to the end of the data, and it is changeable.
Definition at line 287 of file BandMatrix.cpp.
References BandMatrix::data, and GeneralMatrix::m_factored.
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Returns a const iterator for the start of the band storage data.
Iterator points to the beginning of the data, and it is not changeable.
Implements GeneralMatrix.
Definition at line 293 of file BandMatrix.cpp.
References BandMatrix::data.
vector_fp::const_iterator end | ( | ) | const |
Returns a const iterator for the end of the band storage data.
Iterator points to the end of the data, and it is not changeable.
Definition at line 298 of file BandMatrix.cpp.
References BandMatrix::data.
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Zero the matrix elements.
Implements GeneralMatrix.
Definition at line 113 of file BandMatrix.cpp.
References BandMatrix::data, and GeneralMatrix::m_factored.
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Returns an estimate of the inverse of the condition number for the matrix.
The matrix must have been previously factored using the LU algorithm
a1norm | Norm of the matrix |
Implements GeneralMatrix.
Definition at line 316 of file BandMatrix.cpp.
References DATA_PTR, Cantera::int2str(), BandMatrix::iwork_, BandMatrix::ludata, GeneralMatrix::m_factored, BandMatrix::m_ipiv, BandMatrix::m_kl, BandMatrix::m_ku, BandMatrix::m_n, BandMatrix::work_, and Cantera::writelogf().
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Returns the factor algorithm used.
This method will always return 0 (LU) for band matrices.
Implements GeneralMatrix.
Definition at line 346 of file BandMatrix.cpp.
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Returns the one norm of the matrix.
Implements GeneralMatrix.
Definition at line 351 of file BandMatrix.cpp.
References BandMatrix::m_colPtrs, BandMatrix::m_kl, BandMatrix::m_ku, BandMatrix::m_n, and BandMatrix::value().
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Duplicator member function.
This function will duplicate the matrix given a generic GeneralMatrix
Implements GeneralMatrix.
Definition at line 411 of file BandMatrix.cpp.
References BandMatrix::BandMatrix().
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Return a pointer to the top of column j, column values are assumed to be contiguous in memory.
The LAPACK bandstructure has column values which are contiguous in memory:
On entry, the matrix A in band storage, in rows KL+1 to 2*KL+KU+1; rows 1 to KL of the array need not be set. The j-th column of A is stored in the j-th column of the array AB as follows: AB(KL + KU + 1 + i - j,j) = A(i,j) for max(1, j - KU) <= i <= min(m, j + KL)
This routine returns the position of AB(1,j) (fortran-1 indexing) in the above format
So to address the (i,j) position, you use the following indexing:
double *colP_j = matrix.ptrColumn(j); double a_i_j = colP_j[kl + ku + i - j];
j | Value of the column |
Implements GeneralMatrix.
Definition at line 416 of file BandMatrix.cpp.
References BandMatrix::m_colPtrs.
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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.
Implements GeneralMatrix.
Definition at line 421 of file BandMatrix.cpp.
References BandMatrix::m_colPtrs.
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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.
y | Array to be copied |
Implements GeneralMatrix.
Definition at line 426 of file BandMatrix.cpp.
References BandMatrix::data, DATA_PTR, GeneralMatrix::m_factored, BandMatrix::m_kl, BandMatrix::m_ku, BandMatrix::m_n, GeneralMatrix::ptrColumn(), and Cantera::warn_deprecated().
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Check to see if we have any zero rows in the Jacobian.
This utility routine checks to see if any rows are zero. The smallest row is returned along with the largest coefficient in that row
valueSmall | OUTPUT value of the largest coefficient in the smallest row |
Implements GeneralMatrix.
Definition at line 367 of file BandMatrix.cpp.
References BandMatrix::m_kl, BandMatrix::m_ku, BandMatrix::m_n, Cantera::npos, and BandMatrix::value().
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Check to see if we have any zero columns in the Jacobian.
This utility routine checks to see if any columns are zero. The smallest column is returned along with the largest coefficient in that column
valueSmall | OUTPUT value of the largest coefficient in the smallest column |
Implements GeneralMatrix.
Definition at line 389 of file BandMatrix.cpp.
References BandMatrix::m_kl, BandMatrix::m_ku, BandMatrix::m_n, Cantera::npos, and BandMatrix::value().
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Change the way the matrix is factored.
fAlgorithm | integer 0 LU factorization 1 QR factorization |
Reimplemented from GeneralMatrix.
Definition at line 435 of file BandMatrix.cpp.
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Matrix data.
Definition at line 315 of file BandMatrix.h.
Referenced by BandMatrix::_value(), BandMatrix::BandMatrix(), BandMatrix::begin(), BandMatrix::bfill(), BandMatrix::copyData(), BandMatrix::end(), BandMatrix::factor(), BandMatrix::operator=(), BandMatrix::resize(), BandMatrix::value(), and BandMatrix::zero().
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Factorized data.
Definition at line 318 of file BandMatrix.h.
Referenced by BandMatrix::BandMatrix(), BandMatrix::factor(), BandMatrix::operator=(), BandMatrix::rcond(), BandMatrix::resize(), and BandMatrix::solve().
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Number of rows and columns of the matrix.
Definition at line 321 of file BandMatrix.h.
Referenced by BandMatrix::BandMatrix(), BandMatrix::checkColumns(), BandMatrix::checkRows(), BandMatrix::copyData(), BandMatrix::leftMult(), BandMatrix::mult(), BandMatrix::nColumns(), BandMatrix::nRows(), BandMatrix::nRowsAndStruct(), BandMatrix::oneNorm(), BandMatrix::operator=(), BandMatrix::rcond(), BandMatrix::resize(), and BandMatrix::solve().
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Number of subdiagonals of the matrix.
Definition at line 324 of file BandMatrix.h.
Referenced by BandMatrix::BandMatrix(), BandMatrix::checkColumns(), BandMatrix::checkRows(), BandMatrix::copyData(), BandMatrix::index(), BandMatrix::ldim(), BandMatrix::leftMult(), BandMatrix::mult(), BandMatrix::nRowsAndStruct(), BandMatrix::nSubDiagonals(), BandMatrix::oneNorm(), BandMatrix::operator=(), BandMatrix::rcond(), BandMatrix::resize(), and BandMatrix::value().
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Number of super diagonals of the matrix.
Definition at line 327 of file BandMatrix.h.
Referenced by BandMatrix::BandMatrix(), BandMatrix::checkColumns(), BandMatrix::checkRows(), BandMatrix::copyData(), BandMatrix::index(), BandMatrix::ldim(), BandMatrix::leftMult(), BandMatrix::mult(), BandMatrix::nRowsAndStruct(), BandMatrix::nSuperDiagonals(), BandMatrix::oneNorm(), BandMatrix::operator=(), BandMatrix::rcond(), and BandMatrix::resize().
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Pivot vector.
Definition at line 333 of file BandMatrix.h.
Referenced by BandMatrix::BandMatrix(), BandMatrix::ipiv(), BandMatrix::operator=(), BandMatrix::rcond(), and BandMatrix::resize().
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Vector of column pointers.
Definition at line 336 of file BandMatrix.h.
Referenced by BandMatrix::BandMatrix(), BandMatrix::colPts(), BandMatrix::oneNorm(), BandMatrix::operator=(), BandMatrix::ptrColumn(), and BandMatrix::resize().
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Extra work array needed - size = n.
Definition at line 339 of file BandMatrix.h.
Referenced by BandMatrix::rcond().
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Extra dp work array needed - size = 3n.
Definition at line 342 of file BandMatrix.h.
Referenced by BandMatrix::rcond().