Reference documentation for deal.II version 8.1.0
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TrilinosWrappers::SparseMatrix Class Reference

#include <trilinos_sparse_matrix.h>

Inheritance diagram for TrilinosWrappers::SparseMatrix:
[legend]

Classes

struct  Traits
 

Public Types

typedef ::types::global_dof_index size_type
 
typedef
SparseMatrixIterators::Iterator
< false > 
iterator
 
typedef
SparseMatrixIterators::Iterator
< true > 
const_iterator
 
typedef TrilinosScalar value_type
 

Public Member Functions

 DeclException1 (ExcTrilinosError, int,<< "An error with error number "<< arg1<< " occurred while calling a Trilinos function")
 
 DeclException2 (ExcInvalidIndex, size_type, size_type,<< "The entry with index <"<< arg1<< ','<< arg2<< "> does not exist.")
 
 DeclException0 (ExcSourceEqualsDestination)
 
 DeclException0 (ExcMatrixNotCompressed)
 
 DeclException4 (ExcAccessToNonLocalElement, size_type, size_type, size_type, size_type,<< "You tried to access element ("<< arg1<< "/"<< arg2<< ")"<< " of a distributed matrix, but only rows "<< arg3<< " through "<< arg4<< " are stored locally and can be accessed.")
 
 DeclException2 (ExcAccessToNonPresentElement, size_type, size_type,<< "You tried to access element ("<< arg1<< "/"<< arg2<< ")"<< " of a sparse matrix, but it appears to not"<< " exist in the Trilinos sparsity pattern.")
 
Constructors and initialization.
 SparseMatrix ()
 
 SparseMatrix (const size_type m, const size_type n, const unsigned int n_max_entries_per_row)
 
 SparseMatrix (const size_type m, const size_type n, const std::vector< unsigned int > &n_entries_per_row)
 
 SparseMatrix (const SparsityPattern &InputSparsityPattern)
 
 SparseMatrix (const SparseMatrix &InputMatrix)
 
virtual ~SparseMatrix ()
 
template<typename SparsityType >
void reinit (const SparsityType &sparsity_pattern)
 
void reinit (const SparsityPattern &sparsity_pattern)
 
void reinit (const SparseMatrix &sparse_matrix)
 
template<typename number >
void reinit (const ::SparseMatrix< number > &dealii_sparse_matrix, const double drop_tolerance=1e-13, const bool copy_values=true, const ::SparsityPattern *use_this_sparsity=0)
 
void reinit (const Epetra_CrsMatrix &input_matrix, const bool copy_values=true)
 
Constructors and initialization using an Epetra_Map description
 SparseMatrix (const Epetra_Map &parallel_partitioning, const size_type n_max_entries_per_row=0)
 
 SparseMatrix (const Epetra_Map &parallel_partitioning, const std::vector< unsigned int > &n_entries_per_row)
 
 SparseMatrix (const Epetra_Map &row_parallel_partitioning, const Epetra_Map &col_parallel_partitioning, const size_type n_max_entries_per_row=0)
 
 SparseMatrix (const Epetra_Map &row_parallel_partitioning, const Epetra_Map &col_parallel_partitioning, const std::vector< unsigned int > &n_entries_per_row)
 
template<typename SparsityType >
void reinit (const Epetra_Map &parallel_partitioning, const SparsityType &sparsity_pattern, const bool exchange_data=false)
 
template<typename SparsityType >
void reinit (const Epetra_Map &row_parallel_partitioning, const Epetra_Map &col_parallel_partitioning, const SparsityType &sparsity_pattern, const bool exchange_data=false)
 
template<typename number >
void reinit (const Epetra_Map &parallel_partitioning, const ::SparseMatrix< number > &dealii_sparse_matrix, const double drop_tolerance=1e-13, const bool copy_values=true, const ::SparsityPattern *use_this_sparsity=0)
 
template<typename number >
void reinit (const Epetra_Map &row_parallel_partitioning, const Epetra_Map &col_parallel_partitioning, const ::SparseMatrix< number > &dealii_sparse_matrix, const double drop_tolerance=1e-13, const bool copy_values=true, const ::SparsityPattern *use_this_sparsity=0)
 
Constructors and initialization using an IndexSet description
 SparseMatrix (const IndexSet &parallel_partitioning, const MPI_Comm &communicator=MPI_COMM_WORLD, const unsigned int n_max_entries_per_row=0)
 
 SparseMatrix (const IndexSet &parallel_partitioning, const MPI_Comm &communicator, const std::vector< unsigned int > &n_entries_per_row)
 
 SparseMatrix (const IndexSet &row_parallel_partitioning, const IndexSet &col_parallel_partitioning, const MPI_Comm &communicator=MPI_COMM_WORLD, const size_type n_max_entries_per_row=0)
 
 SparseMatrix (const IndexSet &row_parallel_partitioning, const IndexSet &col_parallel_partitioning, const MPI_Comm &communicator, const std::vector< unsigned int > &n_entries_per_row)
 
template<typename SparsityType >
void reinit (const IndexSet &parallel_partitioning, const SparsityType &sparsity_pattern, const MPI_Comm &communicator=MPI_COMM_WORLD, const bool exchange_data=false)
 
template<typename SparsityType >
void reinit (const IndexSet &row_parallel_partitioning, const IndexSet &col_parallel_partitioning, const SparsityType &sparsity_pattern, const MPI_Comm &communicator=MPI_COMM_WORLD, const bool exchange_data=false)
 
template<typename number >
void reinit (const IndexSet &parallel_partitioning, const ::SparseMatrix< number > &dealii_sparse_matrix, const MPI_Comm &communicator=MPI_COMM_WORLD, const double drop_tolerance=1e-13, const bool copy_values=true, const ::SparsityPattern *use_this_sparsity=0)
 
template<typename number >
void reinit (const IndexSet &row_parallel_partitioning, const IndexSet &col_parallel_partitioning, const ::SparseMatrix< number > &dealii_sparse_matrix, const MPI_Comm &communicator=MPI_COMM_WORLD, const double drop_tolerance=1e-13, const bool copy_values=true, const ::SparsityPattern *use_this_sparsity=0)
 
Information on the matrix
size_type m () const
 
size_type n () const
 
unsigned int local_size () const
 
std::pair< size_type, size_typelocal_range () const
 
bool in_local_range (const size_type index) const
 
size_type n_nonzero_elements () const
 
unsigned int row_length (const size_type row) const
 
bool is_compressed () const
 
size_type memory_consumption () const
 
Modifying entries
SparseMatrixoperator= (const double d)
 
void clear ()
 
void compress (::VectorOperation::values operation)
 
void compress () DEAL_II_DEPRECATED
 
void set (const size_type i, const size_type j, const TrilinosScalar value)
 
void set (const std::vector< size_type > &indices, const FullMatrix< TrilinosScalar > &full_matrix, const bool elide_zero_values=false)
 
void set (const std::vector< size_type > &row_indices, const std::vector< size_type > &col_indices, const FullMatrix< TrilinosScalar > &full_matrix, const bool elide_zero_values=false)
 
void set (const size_type row, const std::vector< size_type > &col_indices, const std::vector< TrilinosScalar > &values, const bool elide_zero_values=false)
 
void set (const size_type row, const size_type n_cols, const size_type *col_indices, const TrilinosScalar *values, const bool elide_zero_values=false)
 
void add (const size_type i, const size_type j, const TrilinosScalar value)
 
void add (const std::vector< size_type > &indices, const FullMatrix< TrilinosScalar > &full_matrix, const bool elide_zero_values=true)
 
void add (const std::vector< size_type > &row_indices, const std::vector< size_type > &col_indices, const FullMatrix< TrilinosScalar > &full_matrix, const bool elide_zero_values=true)
 
void add (const size_type row, const std::vector< size_type > &col_indices, const std::vector< TrilinosScalar > &values, const bool elide_zero_values=true)
 
void add (const size_type row, const size_type n_cols, const size_type *col_indices, const TrilinosScalar *values, const bool elide_zero_values=true, const bool col_indices_are_sorted=false)
 
SparseMatrixoperator*= (const TrilinosScalar factor)
 
SparseMatrixoperator/= (const TrilinosScalar factor)
 
void copy_from (const SparseMatrix &source)
 
void add (const TrilinosScalar factor, const SparseMatrix &matrix)
 
void clear_row (const size_type row, const TrilinosScalar new_diag_value=0)
 
void clear_rows (const std::vector< size_type > &rows, const TrilinosScalar new_diag_value=0)
 
void transpose ()
 
Entry Access
TrilinosScalar operator() (const size_type i, const size_type j) const
 
TrilinosScalar el (const size_type i, const size_type j) const
 
TrilinosScalar diag_element (const size_type i) const
 
Multiplications
template<typename VectorType >
void vmult (VectorType &dst, const VectorType &src) const
 
template<typename VectorType >
void Tvmult (VectorType &dst, const VectorType &src) const
 
template<typename VectorType >
void vmult_add (VectorType &dst, const VectorType &src) const
 
template<typename VectorType >
void Tvmult_add (VectorType &dst, const VectorType &src) const
 
TrilinosScalar matrix_norm_square (const VectorBase &v) const
 
TrilinosScalar matrix_scalar_product (const VectorBase &u, const VectorBase &v) const
 
TrilinosScalar residual (VectorBase &dst, const VectorBase &x, const VectorBase &b) const
 
void mmult (SparseMatrix &C, const SparseMatrix &B, const VectorBase &V=VectorBase()) const
 
void Tmmult (SparseMatrix &C, const SparseMatrix &B, const VectorBase &V=VectorBase()) const
 
Matrix norms
TrilinosScalar l1_norm () const
 
TrilinosScalar linfty_norm () const
 
TrilinosScalar frobenius_norm () const
 
Access to underlying Trilinos data
const Epetra_CrsMatrix & trilinos_matrix () const
 
const Epetra_CrsGraph & trilinos_sparsity_pattern () const
 
const Epetra_Map & domain_partitioner () const
 
const Epetra_Map & range_partitioner () const
 
const Epetra_Map & row_partitioner () const
 
const Epetra_Map & col_partitioner () const
 
Iterators
const_iterator begin () const
 
const_iterator end () const
 
const_iterator begin (const size_type r) const
 
const_iterator end (const size_type r) const
 
iterator begin ()
 
iterator end ()
 
iterator begin (const size_type r)
 
iterator end (const size_type r)
 
Input/Output
void write_ascii ()
 
void print (std::ostream &out, const bool write_extended_trilinos_info=false) const
 
- Public Member Functions inherited from Subscriptor
 Subscriptor ()
 
 Subscriptor (const Subscriptor &)
 
virtual ~Subscriptor ()
 
Subscriptoroperator= (const Subscriptor &)
 
void subscribe (const char *identifier=0) const
 
void unsubscribe (const char *identifier=0) const
 
unsigned int n_subscriptions () const
 
void list_subscribers () const
 
 DeclException3 (ExcInUse, int, char *, std::string &,<< "Object of class "<< arg2<< " is still used by "<< arg1<< " other objects.\n"<< "(Additional information: "<< arg3<< ")\n"<< "Note the entry in the Frequently Asked Questions of "<< "deal.II (linked to from http://www.dealii.org/) for "<< "more information on what this error means.")
 
 DeclException2 (ExcNoSubscriber, char *, char *,<< "No subscriber with identifier \""<< arg2<< "\" did subscribe to this object of class "<< arg1)
 
template<class Archive >
void serialize (Archive &ar, const unsigned int version)
 

Protected Member Functions

void prepare_add ()
 
void prepare_set ()
 

Private Attributes

std_cxx1x::shared_ptr< Epetra_Map > column_space_map
 
std_cxx1x::shared_ptr
< Epetra_FECrsMatrix > 
matrix
 
Epetra_CombineMode last_action
 
bool compressed
 

Friends

class BlockMatrixBase< SparseMatrix >
 

Detailed Description

This class implements a wrapper to use the Trilinos distributed sparse matrix class Epetra_FECrsMatrix. This is precisely the kind of matrix we deal with all the time - we most likely get it from some assembly process, where also entries not locally owned might need to be written and hence need to be forwarded to the owner process. This class is designed to be used in a distributed memory architecture with an MPI compiler on the bottom, but works equally well also for serial processes. The only requirement for this class to work is that Trilinos has been installed with the same compiler as is used for generating deal.II.

The interface of this class is modeled after the existing SparseMatrix class in deal.II. It has almost the same member functions, and is often exchangable. However, since Trilinos only supports a single scalar type (double), it is not templated, and only works with doubles.

Note that Trilinos only guarantees that operations do what you expect if the functions GlobalAssemble has been called after matrix assembly. Therefore, you need to call SparseMatrix::compress() before you actually use the matrix. This also calls FillComplete that compresses the storage format for sparse matrices by discarding unused elements. Trilinos allows to continue with assembling the matrix after calls to these functions, though.

Author
Martin Kronbichler, Wolfgang Bangerth, 2008, 2009

Definition at line 515 of file trilinos_sparse_matrix.h.

Member Typedef Documentation

Declare the type for container size.

Definition at line 521 of file trilinos_sparse_matrix.h.

Declare a typedef for the iterator class.

Definition at line 549 of file trilinos_sparse_matrix.h.

Declare a typedef for the const iterator class.

Definition at line 555 of file trilinos_sparse_matrix.h.

Declare a typedef in analogy to all the other container classes.

Definition at line 562 of file trilinos_sparse_matrix.h.

Constructor & Destructor Documentation

TrilinosWrappers::SparseMatrix::SparseMatrix ( )

Default constructor. Generates an empty (zero-size) matrix.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const size_type  m,
const size_type  n,
const unsigned int  n_max_entries_per_row 
)

Generate a matrix that is completely stored locally, having m rows and n columns.

The number of columns entries per row is specified as the maximum number of entries argument.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const size_type  m,
const size_type  n,
const std::vector< unsigned int > &  n_entries_per_row 
)

Generate a matrix that is completely stored locally, having m rows and n columns.

The vector n_entries_per_row specifies the number of entries in each row.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const SparsityPattern InputSparsityPattern)

Generate a matrix from a Trilinos sparsity pattern object.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const SparseMatrix InputMatrix)

Copy constructor. Sets the calling matrix to be the same as the input matrix, i.e., using the same sparsity pattern and entries.

virtual TrilinosWrappers::SparseMatrix::~SparseMatrix ( )
virtual

Destructor. Made virtual so that one can use pointers to this class.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const Epetra_Map &  parallel_partitioning,
const size_type  n_max_entries_per_row = 0 
)

Constructor using an Epetra_Map to describe the parallel partitioning. The parameter n_max_entries_per_row sets the number of nonzero entries in each row that will be allocated. Note that this number does not need to be exact, and it is even allowed that the actual matrix structure has more nonzero entries than specified in the constructor. However it is still advantageous to provide good estimates here since this will considerably increase the performance of the matrix setup. However, there is no effect in the performance of matrix-vector products, since Trilinos reorganizes the matrix memory prior to use (in the compress() step).

TrilinosWrappers::SparseMatrix::SparseMatrix ( const Epetra_Map &  parallel_partitioning,
const std::vector< unsigned int > &  n_entries_per_row 
)

Same as before, but now set a value of nonzeros for each matrix row. Since we know the number of elements in the matrix exactly in this case, we can already allocate the right amount of memory, which makes the creation process including the insertion of nonzero elements by the respective SparseMatrix::reinit call considerably faster.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const Epetra_Map &  row_parallel_partitioning,
const Epetra_Map &  col_parallel_partitioning,
const size_type  n_max_entries_per_row = 0 
)

This constructor is similar to the one above, but it now takes two different Epetra maps for rows and columns. This interface is meant to be used for generating rectangular matrices, where one map describes the parallel partitioning of the dofs associated with the matrix rows and the other one the partitioning of dofs in the matrix columns. Note that there is no real parallelism along the columns – the processor that owns a certain row always owns all the column elements, no matter how far they might be spread out. The second Epetra_Map is only used to specify the number of columns and for internal arrangements when doing matrix-vector products with vectors based on that column map.

The integer input n_max_entries_per_row defines the number of columns entries per row that will be allocated.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const Epetra_Map &  row_parallel_partitioning,
const Epetra_Map &  col_parallel_partitioning,
const std::vector< unsigned int > &  n_entries_per_row 
)

This constructor is similar to the one above, but it now takes two different Epetra maps for rows and columns. This interface is meant to be used for generating rectangular matrices, where one map specifies the parallel distribution of degrees of freedom associated with matrix rows and the second one specifies the parallel distribution the dofs associated with columns in the matrix. The second map also provides information for the internal arrangement in matrix vector products (i.e., the distribution of vector this matrix is to be multiplied with), but is not used for the distribution of the columns – rather, all column elements of a row are stored on the same processor in any case. The vector n_entries_per_row specifies the number of entries in each row of the newly generated matrix.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const IndexSet parallel_partitioning,
const MPI_Comm &  communicator = MPI_COMM_WORLD,
const unsigned int  n_max_entries_per_row = 0 
)

Constructor using an IndexSet and an MPI communicator to describe the parallel partitioning. The parameter n_max_entries_per_row sets the number of nonzero entries in each row that will be allocated. Note that this number does not need to be exact, and it is even allowed that the actual matrix structure has more nonzero entries than specified in the constructor. However it is still advantageous to provide good estimates here since this will considerably increase the performance of the matrix setup. However, there is no effect in the performance of matrix-vector products, since Trilinos reorganizes the matrix memory prior to use (in the compress() step).

TrilinosWrappers::SparseMatrix::SparseMatrix ( const IndexSet parallel_partitioning,
const MPI_Comm &  communicator,
const std::vector< unsigned int > &  n_entries_per_row 
)

Same as before, but now set the number of nonzeros in each matrix row separately. Since we know the number of elements in the matrix exactly in this case, we can already allocate the right amount of memory, which makes the creation process including the insertion of nonzero elements by the respective SparseMatrix::reinit call considerably faster.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const IndexSet row_parallel_partitioning,
const IndexSet col_parallel_partitioning,
const MPI_Comm &  communicator = MPI_COMM_WORLD,
const size_type  n_max_entries_per_row = 0 
)

This constructor is similar to the one above, but it now takes two different IndexSet partitions for row and columns. This interface is meant to be used for generating rectangular matrices, where the first index set describes the parallel partitioning of the degrees of freedom associated with the matrix rows and the second one the partitioning of the matrix columns. The second index set specifies the partitioning of the vectors this matrix is to be multiplied with, not the distribution of the elements that actually appear in the matrix.

The parameter n_max_entries_per_row defines how much memory will be allocated for each row. This number does not need to be accurate, as the structure is reorganized in the compress() call.

TrilinosWrappers::SparseMatrix::SparseMatrix ( const IndexSet row_parallel_partitioning,
const IndexSet col_parallel_partitioning,
const MPI_Comm &  communicator,
const std::vector< unsigned int > &  n_entries_per_row 
)

This constructor is similar to the one above, but it now takes two different Epetra maps for rows and columns. This interface is meant to be used for generating rectangular matrices, where one map specifies the parallel distribution of degrees of freedom associated with matrix rows and the second one specifies the parallel distribution the dofs associated with columns in the matrix. The second map also provides information for the internal arrangement in matrix vector products (i.e., the distribution of vector this matrix is to be multiplied with), but is not used for the distribution of the columns – rather, all column elements of a row are stored on the same processor in any case. The vector n_entries_per_row specifies the number of entries in each row of the newly generated matrix.

Member Function Documentation

template<typename SparsityType >
void TrilinosWrappers::SparseMatrix::reinit ( const SparsityType &  sparsity_pattern)

This function initializes the Trilinos matrix with a deal.II sparsity pattern, i.e. it makes the Trilinos Epetra matrix know the position of nonzero entries according to the sparsity pattern. This function is meant for use in serial programs, where there is no need to specify how the matrix is going to be distributed among different processors. This function works in parallel, too, but it is recommended to manually specify the parallel partioning of the matrix using an Epetra_Map. When run in parallel, it is currently necessary that each processor holds the sparsity_pattern structure because each processor sets its rows.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

void TrilinosWrappers::SparseMatrix::reinit ( const SparsityPattern sparsity_pattern)

This function reinitializes the Trilinos sparse matrix from a (possibly distributed) Trilinos sparsity pattern.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

void TrilinosWrappers::SparseMatrix::reinit ( const SparseMatrix sparse_matrix)

This function copies the content in sparse_matrix to the calling matrix.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

template<typename number >
void TrilinosWrappers::SparseMatrix::reinit ( const ::SparseMatrix< number > &  dealii_sparse_matrix,
const double  drop_tolerance = 1e-13,
const bool  copy_values = true,
const ::SparsityPattern use_this_sparsity = 0 
)

This function initializes the Trilinos matrix using the deal.II sparse matrix and the entries stored therein. It uses a threshold to copy only elements with modulus larger than the threshold (so zeros in the deal.II matrix can be filtered away).

The optional parameter copy_values decides whether only the sparsity structure of the input matrix should be used or the matrix entries should be copied, too.

This is a collective operation that needs to be called on all processors in order to avoid a deadlock.

Note
If a different sparsity pattern is given in the last argument (i.e., one that differs from the one used in the sparse matrix given in the first argument), then the resulting Trilinos matrix will have the sparsity pattern so given. This of course also means that all entries in the given matrix that are not part of this separate sparsity pattern will in fact be dropped.
void TrilinosWrappers::SparseMatrix::reinit ( const Epetra_CrsMatrix &  input_matrix,
const bool  copy_values = true 
)

This reinit function takes as input a Trilinos Epetra_CrsMatrix and copies its sparsity pattern. If so requested, even the content (values) will be copied.

template<typename SparsityType >
void TrilinosWrappers::SparseMatrix::reinit ( const Epetra_Map &  parallel_partitioning,
const SparsityType &  sparsity_pattern,
const bool  exchange_data = false 
)

This function is initializes the Trilinos Epetra matrix according to the specified sparsity_pattern, and also reassigns the matrix rows to different processes according to a user-supplied Epetra map. In programs following the style of the tutorial programs, this function (and the respective call for a rectangular matrix) are the natural way to initialize the matrix size, its distribution among the MPI processes (if run in parallel) as well as the locatoin of non-zero elements. Trilinos stores the sparsity pattern internally, so it won't be needed any more after this call, in contrast to the deal.II own object. The optional argument exchange_data can be used for reinitialization with a sparsity pattern that is not fully constructed. This feature is only implemented for input sparsity patterns of type CompressedSimpleSparsityPattern. If the flag is not set, each processor just sets the elements in the sparsity pattern that belong to its rows.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

template<typename SparsityType >
void TrilinosWrappers::SparseMatrix::reinit ( const Epetra_Map &  row_parallel_partitioning,
const Epetra_Map &  col_parallel_partitioning,
const SparsityType &  sparsity_pattern,
const bool  exchange_data = false 
)

This function is similar to the other initialization function above, but now also reassigns the matrix rows and columns according to two user-supplied Epetra maps. To be used for rectangular matrices. The optional argument exchange_data can be used for reinitialization with a sparsity pattern that is not fully constructed. This feature is only implemented for input sparsity patterns of type CompressedSimpleSparsityPattern.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

template<typename number >
void TrilinosWrappers::SparseMatrix::reinit ( const Epetra_Map &  parallel_partitioning,
const ::SparseMatrix< number > &  dealii_sparse_matrix,
const double  drop_tolerance = 1e-13,
const bool  copy_values = true,
const ::SparsityPattern use_this_sparsity = 0 
)

This function initializes the Trilinos matrix using the deal.II sparse matrix and the entries stored therein. It uses a threshold to copy only elements with modulus larger than the threshold (so zeros in the deal.II matrix can be filtered away). In contrast to the other reinit function with deal.II sparse matrix argument, this function takes a parallel partitioning specified by the user instead of internally generating it.

The optional parameter copy_values decides whether only the sparsity structure of the input matrix should be used or the matrix entries should be copied, too.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

template<typename number >
void TrilinosWrappers::SparseMatrix::reinit ( const Epetra_Map &  row_parallel_partitioning,
const Epetra_Map &  col_parallel_partitioning,
const ::SparseMatrix< number > &  dealii_sparse_matrix,
const double  drop_tolerance = 1e-13,
const bool  copy_values = true,
const ::SparsityPattern use_this_sparsity = 0 
)

This function is similar to the other initialization function with deal.II sparse matrix input above, but now takes Epetra maps for both the rows and the columns of the matrix. Chosen for rectangular matrices.

The optional parameter copy_values decides whether only the sparsity structure of the input matrix should be used or the matrix entries should be copied, too.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

template<typename SparsityType >
void TrilinosWrappers::SparseMatrix::reinit ( const IndexSet parallel_partitioning,
const SparsityType &  sparsity_pattern,
const MPI_Comm &  communicator = MPI_COMM_WORLD,
const bool  exchange_data = false 
)

This function is initializes the Trilinos Epetra matrix according to the specified sparsity_pattern, and also reassigns the matrix rows to different processes according to a user-supplied index set and parallel communicator. In programs following the style of the tutorial programs, this function (and the respective call for a rectangular matrix) are the natural way to initialize the matrix size, its distribution among the MPI processes (if run in parallel) as well as the locatoin of non-zero elements. Trilinos stores the sparsity pattern internally, so it won't be needed any more after this call, in contrast to the deal.II own object. The optional argument exchange_data can be used for reinitialization with a sparsity pattern that is not fully constructed. This feature is only implemented for input sparsity patterns of type CompressedSimpleSparsityPattern. If the flag is not set, each processor just sets the elements in the sparsity pattern that belong to its rows.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

template<typename SparsityType >
void TrilinosWrappers::SparseMatrix::reinit ( const IndexSet row_parallel_partitioning,
const IndexSet col_parallel_partitioning,
const SparsityType &  sparsity_pattern,
const MPI_Comm &  communicator = MPI_COMM_WORLD,
const bool  exchange_data = false 
)

This function is similar to the other initialization function above, but now also reassigns the matrix rows and columns according to two user-supplied index sets. To be used for rectangular matrices. The optional argument exchange_data can be used for reinitialization with a sparsity pattern that is not fully constructed. This feature is only implemented for input sparsity patterns of type CompressedSimpleSparsityPattern.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

template<typename number >
void TrilinosWrappers::SparseMatrix::reinit ( const IndexSet parallel_partitioning,
const ::SparseMatrix< number > &  dealii_sparse_matrix,
const MPI_Comm &  communicator = MPI_COMM_WORLD,
const double  drop_tolerance = 1e-13,
const bool  copy_values = true,
const ::SparsityPattern use_this_sparsity = 0 
)

This function initializes the Trilinos matrix using the deal.II sparse matrix and the entries stored therein. It uses a threshold to copy only elements with modulus larger than the threshold (so zeros in the deal.II matrix can be filtered away). In contrast to the other reinit function with deal.II sparse matrix argument, this function takes a parallel partitioning specified by the user instead of internally generating it.

The optional parameter copy_values decides whether only the sparsity structure of the input matrix should be used or the matrix entries should be copied, too.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

template<typename number >
void TrilinosWrappers::SparseMatrix::reinit ( const IndexSet row_parallel_partitioning,
const IndexSet col_parallel_partitioning,
const ::SparseMatrix< number > &  dealii_sparse_matrix,
const MPI_Comm &  communicator = MPI_COMM_WORLD,
const double  drop_tolerance = 1e-13,
const bool  copy_values = true,
const ::SparsityPattern use_this_sparsity = 0 
)

This function is similar to the other initialization function with deal.II sparse matrix input above, but now takes index sets for both the rows and the columns of the matrix. Chosen for rectangular matrices.

The optional parameter copy_values decides whether only the sparsity structure of the input matrix should be used or the matrix entries should be copied, too.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

size_type TrilinosWrappers::SparseMatrix::m ( ) const

Return the number of rows in this matrix.

size_type TrilinosWrappers::SparseMatrix::n ( ) const

Return the number of columns in this matrix.

unsigned int TrilinosWrappers::SparseMatrix::local_size ( ) const

Return the local dimension of the matrix, i.e. the number of rows stored on the present MPI process. For sequential matrices, this number is the same as m(), but for parallel matrices it may be smaller.

To figure out which elements exactly are stored locally, use local_range().

std::pair<size_type, size_type> TrilinosWrappers::SparseMatrix::local_range ( ) const

Return a pair of indices indicating which rows of this matrix are stored locally. The first number is the index of the first row stored, the second the index of the one past the last one that is stored locally. If this is a sequential matrix, then the result will be the pair (0,m()), otherwise it will be a pair (i,i+n), where n=local_size().

bool TrilinosWrappers::SparseMatrix::in_local_range ( const size_type  index) const

Return whether index is in the local range or not, see also local_range().

size_type TrilinosWrappers::SparseMatrix::n_nonzero_elements ( ) const

Return the number of nonzero elements of this matrix.

unsigned int TrilinosWrappers::SparseMatrix::row_length ( const size_type  row) const

Number of entries in a specific row.

bool TrilinosWrappers::SparseMatrix::is_compressed ( ) const

Returns the state of the matrix, i.e., whether compress() needs to be called after an operation requiring data exchange. A call to compress() is also needed when the method set() has been called (even when working in serial).

size_type TrilinosWrappers::SparseMatrix::memory_consumption ( ) const

Determine an estimate for the memory consumption (in bytes) of this object. Note that only the memory reserved on the current processor is returned in case this is called in an MPI-based program.

SparseMatrix& TrilinosWrappers::SparseMatrix::operator= ( const double  d)

This operator assigns a scalar to a matrix. Since this does usually not make much sense (should we set all matrix entries to this value? Only the nonzero entries of the sparsity pattern?), this operation is only allowed if the actual value to be assigned is zero. This operator only exists to allow for the obvious notation matrix=0, which sets all elements of the matrix to zero, but keeps the sparsity pattern previously used.

void TrilinosWrappers::SparseMatrix::clear ( )

Release all memory and return to a state just like after having called the default constructor.

This is a collective operation that needs to be called on all processors in order to avoid a dead lock.

void TrilinosWrappers::SparseMatrix::compress ( ::VectorOperation::values  operation)

This command does two things:

  • If the matrix was initialized without a sparsity pattern, elements have been added manually using the set() command. When this process is completed, a call to compress() reorganizes the internal data structures (aparsity pattern) so that a fast access to data is possible in matrix-vector products.
  • If the matrix structure has already been fixed (either by initialization with a sparsity pattern or by calling compress() during the setup phase), this command does the parallel exchange of data. This is necessary when we perform assembly on more than one (MPI) process, because then some non-local row data will accumulate on nodes that belong to the current's processor element, but are actually held by another. This command is usually called after all elements have been traversed.

In both cases, this function compresses the data structures and allows the resulting matrix to be used in all other operations like matrix-vector products. This is a collective operation, i.e., it needs to be run on all processors when used in parallel.

See Compressing distributed objects for more information.

void TrilinosWrappers::SparseMatrix::compress ( )
void TrilinosWrappers::SparseMatrix::set ( const size_type  i,
const size_type  j,
const TrilinosScalar  value 
)

Set the element (i,j) to value.

This function is able to insert new elements into the matrix as long as compress() has not been called, so the sparsity pattern will be extended. When compress() is called for the first time, then this is no longer possible and an insertion of elements at positions which have not been initialized will throw an exception. Note that in case elements need to be inserted, it is mandatory that elements are inserted only once. Otherwise, the elements will actually be added in the end (since it is not possible to efficiently find values to the same entry before compress() has been called). In the case that an element is set more than once, initialize the matrix with a sparsity pattern first.

void TrilinosWrappers::SparseMatrix::set ( const std::vector< size_type > &  indices,
const FullMatrix< TrilinosScalar > &  full_matrix,
const bool  elide_zero_values = false 
)

Set all elements given in a FullMatrix<double> into the sparse matrix locations given by indices. In other words, this function writes the elements in full_matrix into the calling matrix, using the local-to-global indexing specified by indices for both the rows and the columns of the matrix. This function assumes a quadratic sparse matrix and a quadratic full_matrix, the usual situation in FE calculations.

This function is able to insert new elements into the matrix as long as compress() has not been called, so the sparsity pattern will be extended. When compress() is called for the first time, then this is no longer possible and an insertion of elements at positions which have not been initialized will throw an exception.

The optional parameter elide_zero_values can be used to specify whether zero values should be inserted anyway or they should be filtered away. The default value is false, i.e., even zero values are inserted/replaced.

void TrilinosWrappers::SparseMatrix::set ( const std::vector< size_type > &  row_indices,
const std::vector< size_type > &  col_indices,
const FullMatrix< TrilinosScalar > &  full_matrix,
const bool  elide_zero_values = false 
)

Same function as before, but now including the possibility to use rectangular full_matrices and different local-to-global indexing on rows and columns, respectively.

void TrilinosWrappers::SparseMatrix::set ( const size_type  row,
const std::vector< size_type > &  col_indices,
const std::vector< TrilinosScalar > &  values,
const bool  elide_zero_values = false 
)

Set several elements in the specified row of the matrix with column indices as given by col_indices to the respective value.

This function is able to insert new elements into the matrix as long as compress() has not been called, so the sparsity pattern will be extended. When compress() is called for the first time, then this is no longer possible and an insertion of elements at positions which have not been initialized will throw an exception.

The optional parameter elide_zero_values can be used to specify whether zero values should be inserted anyway or they should be filtered away. The default value is false, i.e., even zero values are inserted/replaced.

void TrilinosWrappers::SparseMatrix::set ( const size_type  row,
const size_type  n_cols,
const size_type col_indices,
const TrilinosScalar *  values,
const bool  elide_zero_values = false 
)

Set several elements to values given by values in a given row in columns given by col_indices into the sparse matrix.

This function is able to insert new elements into the matrix as long as compress() has not been called, so the sparsity pattern will be extended. When compress() is called for the first time, then this is no longer possible and an insertion of elements at positions which have not been initialized will throw an exception.

The optional parameter elide_zero_values can be used to specify whether zero values should be inserted anyway or they should be filtered away. The default value is false, i.e., even zero values are inserted/replaced.

void TrilinosWrappers::SparseMatrix::add ( const size_type  i,
const size_type  j,
const TrilinosScalar  value 
)

Add value to the element (i,j).

Just as the respective call in deal.II SparseMatrix<Number> class (but in contrast to the situation for PETSc based matrices), this function throws an exception if an entry does not exist in the sparsity pattern. Moreover, if value is not a finite number an exception is thrown.

void TrilinosWrappers::SparseMatrix::add ( const std::vector< size_type > &  indices,
const FullMatrix< TrilinosScalar > &  full_matrix,
const bool  elide_zero_values = true 
)

Add all elements given in a FullMatrix<double> into sparse matrix locations given by indices. In other words, this function adds the elements in full_matrix to the respective entries in calling matrix, using the local-to-global indexing specified by indices for both the rows and the columns of the matrix. This function assumes a quadratic sparse matrix and a quadratic full_matrix, the usual situation in FE calculations.

Just as the respective call in deal.II SparseMatrix<Number> class (but in contrast to the situation for PETSc based matrices), this function throws an exception if an entry does not exist in the sparsity pattern.

The optional parameter elide_zero_values can be used to specify whether zero values should be added anyway or these should be filtered away and only non-zero data is added. The default value is true, i.e., zero values won't be added into the matrix.

void TrilinosWrappers::SparseMatrix::add ( const std::vector< size_type > &  row_indices,
const std::vector< size_type > &  col_indices,
const FullMatrix< TrilinosScalar > &  full_matrix,
const bool  elide_zero_values = true 
)

Same function as before, but now including the possibility to use rectangular full_matrices and different local-to-global indexing on rows and columns, respectively.

void TrilinosWrappers::SparseMatrix::add ( const size_type  row,
const std::vector< size_type > &  col_indices,
const std::vector< TrilinosScalar > &  values,
const bool  elide_zero_values = true 
)

Set several elements in the specified row of the matrix with column indices as given by col_indices to the respective value.

Just as the respective call in deal.II SparseMatrix<Number> class (but in contrast to the situation for PETSc based matrices), this function throws an exception if an entry does not exist in the sparsity pattern.

The optional parameter elide_zero_values can be used to specify whether zero values should be added anyway or these should be filtered away and only non-zero data is added. The default value is true, i.e., zero values won't be added into the matrix.

void TrilinosWrappers::SparseMatrix::add ( const size_type  row,
const size_type  n_cols,
const size_type col_indices,
const TrilinosScalar *  values,
const bool  elide_zero_values = true,
const bool  col_indices_are_sorted = false 
)

Add an array of values given by values in the given global matrix row at columns specified by col_indices in the sparse matrix.

Just as the respective call in deal.II SparseMatrix<Number> class (but in contrast to the situation for PETSc based matrices), this function throws an exception if an entry does not exist in the sparsity pattern.

The optional parameter elide_zero_values can be used to specify whether zero values should be added anyway or these should be filtered away and only non-zero data is added. The default value is true, i.e., zero values won't be added into the matrix.

SparseMatrix& TrilinosWrappers::SparseMatrix::operator*= ( const TrilinosScalar  factor)

Multiply the entire matrix by a fixed factor.

SparseMatrix& TrilinosWrappers::SparseMatrix::operator/= ( const TrilinosScalar  factor)

Divide the entire matrix by a fixed factor.

void TrilinosWrappers::SparseMatrix::copy_from ( const SparseMatrix source)

Copy the given (Trilinos) matrix (sparsity pattern and entries).

void TrilinosWrappers::SparseMatrix::add ( const TrilinosScalar  factor,
const SparseMatrix matrix 
)

Add matrix scaled by factor to this matrix, i.e. the matrix factor*matrix is added to this. If the sparsity pattern of the calling matrix does not contain all the elements in the sparsity pattern of the input matrix, this function will throw an exception.

void TrilinosWrappers::SparseMatrix::clear_row ( const size_type  row,
const TrilinosScalar  new_diag_value = 0 
)

Remove all elements from this row by setting them to zero. The function does not modify the number of allocated nonzero entries, it only sets some entries to zero. It may drop them from the sparsity pattern, though (but retains the allocated memory in case new entries are again added later). Note that this is a global operation, so this needs to be done on all MPI processes.

This operation is used in eliminating constraints (e.g. due to hanging nodes) and makes sure that we can write this modification to the matrix without having to read entries (such as the locations of non-zero elements) from it — without this operation, removing constraints on parallel matrices is a rather complicated procedure.

The second parameter can be used to set the diagonal entry of this row to a value different from zero. The default is to set it to zero.

void TrilinosWrappers::SparseMatrix::clear_rows ( const std::vector< size_type > &  rows,
const TrilinosScalar  new_diag_value = 0 
)

Same as clear_row(), except that it works on a number of rows at once.

The second parameter can be used to set the diagonal entries of all cleared rows to something different from zero. Note that all of these diagonal entries get the same value – if you want different values for the diagonal entries, you have to set them by hand.

void TrilinosWrappers::SparseMatrix::transpose ( )

Make an in-place transpose of a matrix.

TrilinosScalar TrilinosWrappers::SparseMatrix::operator() ( const size_type  i,
const size_type  j 
) const

Return the value of the entry (i,j). This may be an expensive operation and you should always take care where to call this function. As in the deal.II sparse matrix class, we throw an exception if the respective entry doesn't exist in the sparsity pattern of this class, which is requested from Trilinos. Moreover, an exception will be thrown when the requested element is not saved on the calling process.

TrilinosScalar TrilinosWrappers::SparseMatrix::el ( const size_type  i,
const size_type  j 
) const

Return the value of the matrix entry (i,j). If this entry does not exist in the sparsity pattern, then zero is returned. While this may be convenient in some cases, note that it is simple to write algorithms that are slow compared to an optimal solution, since the sparsity of the matrix is not used. On the other hand, if you want to be sure the entry exists, you should use operator() instead.

The lack of error checking in this function can also yield surprising results if you have a parallel matrix. In that case, just because you get a zero result from this function does not mean that either the entry does not exist in the sparsity pattern or that it does but has a value of zero. Rather, it could also be that it simply isn't stored on the current processor; in that case, it may be stored on a different processor, and possibly so with a nonzero value.

TrilinosScalar TrilinosWrappers::SparseMatrix::diag_element ( const size_type  i) const

Return the main diagonal element in the ith row. This function throws an error if the matrix is not quadratic and it also throws an error if (i,i) is not element of the local matrix. See also the comment in trilinos_sparse_matrix.cc.

template<typename VectorType >
void TrilinosWrappers::SparseMatrix::vmult ( VectorType &  dst,
const VectorType &  src 
) const

Matrix-vector multiplication: let dst = M*src with M being this matrix.

Source and destination must not be the same vector.

This function can be called with several different vector objects, namely TrilinosWrappers::Vector, TrilinosWrappers::MPI::Vector as well as deal.II's own vector classes Vector<double> and parallel::distributed::Vector<double>.

Note that both vectors have to be distributed vectors generated using the same Map as was used for the matrix in case you work on a distributed memory architecture, using the interface in the TrilinosWrappers::VectorBase class (or one of the two derived classes Vector and MPI::Vector).

In case of a localized Vector, this function will only work when running on one processor, since the matrix object is inherently distributed. Otherwise, and exception will be thrown.

template<typename VectorType >
void TrilinosWrappers::SparseMatrix::Tvmult ( VectorType &  dst,
const VectorType &  src 
) const

Matrix-vector multiplication: let dst = MT*src with M being this matrix. This function does the same as vmult() but takes the transposed matrix.

Source and destination must not be the same vector.

This function can be called with several different vector objects, namely TrilinosWrappers::Vector, TrilinosWrappers::MPI::Vector as well as deal.II's own vector classes Vector<double> and parallel::distributed::Vector<double>.

Note that both vectors have to be distributed vectors generated using the same Map as was used for the matrix in case you work on a distributed memory architecture, using the interface in the TrilinosWrappers::VectorBase class (or one of the two derived classes Vector and MPI::Vector).

In case of a localized Vector, this function will only work when running on one processor, since the matrix object is inherently distributed. Otherwise, and exception will be thrown.

template<typename VectorType >
void TrilinosWrappers::SparseMatrix::vmult_add ( VectorType &  dst,
const VectorType &  src 
) const

Adding matrix-vector multiplication. Add M*src on dst with M being this matrix.

Source and destination must not be the same vector.

This function can be called with several different vector objects, namely TrilinosWrappers::Vector, TrilinosWrappers::MPI::Vector as well as deal.II's own vector classes Vector<double> and parallel::distributed::Vector<double>.

When using a vector of type TrilinosWrappers::MPI::Vector, both vectors have to be distributed vectors generated using the same Map as was used for the matrix rows and columns in case you work on a distributed memory architecture, using the interface in the TrilinosWrappers::VectorBase class.

In case of a localized Vector (i.e., TrilinosWrappers::Vector or Vector<double>), this function will only work when running on one processor, since the matrix object is inherently distributed. Otherwise, and exception will be thrown.

template<typename VectorType >
void TrilinosWrappers::SparseMatrix::Tvmult_add ( VectorType &  dst,
const VectorType &  src 
) const

Adding matrix-vector multiplication. Add MT*src to dst with M being this matrix. This function does the same as vmult_add() but takes the transposed matrix.

Source and destination must not be the same vector.

This function can be called with several different vector objects, namely TrilinosWrappers::Vector, TrilinosWrappers::MPI::Vector as well as deal.II's own vector classes Vector<double> and parallel::distributed::Vector<double>.

When using a vector of type TrilinosWrappers::MPI::Vector, both vectors have to be distributed vectors generated using the same Map as was used for the matrix rows and columns in case you work on a distributed memory architecture, using the interface in the TrilinosWrappers::VectorBase class.

In case of a localized Vector (i.e., TrilinosWrappers::Vector or Vector<double>), this function will only work when running on one processor, since the matrix object is inherently distributed. Otherwise, and exception will be thrown.

TrilinosScalar TrilinosWrappers::SparseMatrix::matrix_norm_square ( const VectorBase v) const

Return the square of the norm of the vector $v$ with respect to the norm induced by this matrix, i.e., $\left(v,Mv\right)$. This is useful, e.g. in the finite element context, where the $L_2$ norm of a function equals the matrix norm with respect to the mass matrix of the vector representing the nodal values of the finite element function.

Obviously, the matrix needs to be quadratic for this operation.

The implementation of this function is not as efficient as the one in the SparseMatrix class used in deal.II (i.e. the original one, not the Trilinos wrapper class) since Trilinos doesn't support this operation and needs a temporary vector.

Note that both vectors have to be distributed vectors generated using the same Map as was used for the matrix in case you work on a distributed memory architecture, using the interface in the TrilinosWrappers::VectorBase class (or one of the two derived classes Vector and MPI::Vector).

In case of a localized Vector, this function will only work when running on one processor, since the matrix object is inherently distributed. Otherwise, and exception will be thrown.

TrilinosScalar TrilinosWrappers::SparseMatrix::matrix_scalar_product ( const VectorBase u,
const VectorBase v 
) const

Compute the matrix scalar product $\left(u,Mv\right)$.

The implementation of this function is not as efficient as the one in the SparseMatrix class used in deal.II (i.e. the original one, not the Trilinos wrapper class) since Trilinos doesn't support this operation and needs a temporary vector.

Note that both vectors have to be distributed vectors generated using the same Map as was used for the matrix in case you work on a distributed memory architecture, using the interface in the TrilinosWrappers::VectorBase class (or one of the two derived classes Vector and MPI::Vector).

In case of a localized Vector, this function will only work when running on one processor, since the matrix object is inherently distributed. Otherwise, and exception will be thrown.

TrilinosScalar TrilinosWrappers::SparseMatrix::residual ( VectorBase dst,
const VectorBase x,
const VectorBase b 
) const

Compute the residual of an equation Mx=b, where the residual is defined to be r=b-Mx. Write the residual into dst. The l2 norm of the residual vector is returned.

Source x and destination dst must not be the same vector.

Note that both vectors have to be distributed vectors generated using the same Map as was used for the matrix in case you work on a distributed memory architecture, using the interface in the TrilinosWrappers::VectorBase class (or one of the two derived classes Vector and MPI::Vector).

In case of a localized Vector, this function will only work when running on one processor, since the matrix object is inherently distributed. Otherwise, and exception will be thrown.

void TrilinosWrappers::SparseMatrix::mmult ( SparseMatrix C,
const SparseMatrix B,
const VectorBase V = VectorBase() 
) const

Perform the matrix-matrix multiplication C = A * B, or, if an optional vector argument is given, C = A * diag(V) * B, where diag(V) defines a diagonal matrix with the vector entries.

This function assumes that the calling matrix A and B have compatible sizes. The size of C will be set within this function.

The content as well as the sparsity pattern of the matrix C will be changed by this function, so make sure that the sparsity pattern is not used somewhere else in your program. This is an expensive operation, so think twice before you use this function.

void TrilinosWrappers::SparseMatrix::Tmmult ( SparseMatrix C,
const SparseMatrix B,
const VectorBase V = VectorBase() 
) const

Perform the matrix-matrix multiplication with the transpose of this, i.e., C = AT * B, or, if an optional vector argument is given, C = AT * diag(V) * B, where diag(V) defines a diagonal matrix with the vector entries.

This function assumes that the calling matrix A and B have compatible sizes. The size of C will be set within this function.

The content as well as the sparsity pattern of the matrix C will be changed by this function, so make sure that the sparsity pattern is not used somewhere else in your program. This is an expensive operation, so think twice before you use this function.

TrilinosScalar TrilinosWrappers::SparseMatrix::l1_norm ( ) const

Return the l1-norm of the matrix, that is $|M|_1= \max_{\mathrm{all\ columns\ } j} \sum_{\mathrm{all\ rows\ } i} |M_{ij}|$, (max. sum of columns). This is the natural matrix norm that is compatible to the l1-norm for vectors, i.e. $|Mv|_1 \leq |M|_1 |v|_1$. (cf. Haemmerlin-Hoffmann: Numerische Mathematik)

TrilinosScalar TrilinosWrappers::SparseMatrix::linfty_norm ( ) const

Return the linfty-norm of the matrix, that is $|M|_\infty=\max_{\mathrm{all\ rows\ } i}\sum_{\mathrm{all\ columns\ } j} |M_{ij}|$, (max. sum of rows). This is the natural matrix norm that is compatible to the linfty-norm of vectors, i.e. $|Mv|_\infty \leq |M|_\infty |v|_\infty$. (cf. Haemmerlin-Hoffmann: Numerische Mathematik)

TrilinosScalar TrilinosWrappers::SparseMatrix::frobenius_norm ( ) const

Return the frobenius norm of the matrix, i.e. the square root of the sum of squares of all entries in the matrix.

const Epetra_CrsMatrix& TrilinosWrappers::SparseMatrix::trilinos_matrix ( ) const

Return a const reference to the underlying Trilinos Epetra_CrsMatrix data.

const Epetra_CrsGraph& TrilinosWrappers::SparseMatrix::trilinos_sparsity_pattern ( ) const

Return a const reference to the underlying Trilinos Epetra_CrsGraph data that stores the sparsity pattern of the matrix.

const Epetra_Map& TrilinosWrappers::SparseMatrix::domain_partitioner ( ) const

Return a const reference to the underlying Trilinos Epetra_Map that sets the partitioning of the domain space of this matrix, i.e., the partitioning of the vectors this matrix has to be multiplied with.

const Epetra_Map& TrilinosWrappers::SparseMatrix::range_partitioner ( ) const

Return a const reference to the underlying Trilinos Epetra_Map that sets the partitioning of the range space of this matrix, i.e., the partitioning of the vectors that are result from matrix-vector products.

const Epetra_Map& TrilinosWrappers::SparseMatrix::row_partitioner ( ) const

Return a const reference to the underlying Trilinos Epetra_Map that sets the partitioning of the matrix rows. Equal to the partitioning of the range.

const Epetra_Map& TrilinosWrappers::SparseMatrix::col_partitioner ( ) const

Return a const reference to the underlying Trilinos Epetra_Map that sets the partitioning of the matrix columns. This is in general not equal to the partitioner Epetra_Map for the domain because of overlap in the matrix.

const_iterator TrilinosWrappers::SparseMatrix::begin ( ) const

STL-like iterator with the first entry.

const_iterator TrilinosWrappers::SparseMatrix::end ( ) const

Final iterator.

const_iterator TrilinosWrappers::SparseMatrix::begin ( const size_type  r) const

STL-like iterator with the first entry of row r.

Note that if the given row is empty, i.e. does not contain any nonzero entries, then the iterator returned by this function equals end(r). Note also that the iterator may not be dereferencable in that case.

const_iterator TrilinosWrappers::SparseMatrix::end ( const size_type  r) const

Final iterator of row r. It points to the first element past the end of line r, or past the end of the entire sparsity pattern.

Note that the end iterator is not necessarily dereferencable. This is in particular the case if it is the end iterator for the last row of a matrix.

iterator TrilinosWrappers::SparseMatrix::begin ( )

STL-like iterator with the first entry.

iterator TrilinosWrappers::SparseMatrix::end ( )

Final iterator.

iterator TrilinosWrappers::SparseMatrix::begin ( const size_type  r)

STL-like iterator with the first entry of row r.

Note that if the given row is empty, i.e. does not contain any nonzero entries, then the iterator returned by this function equals end(r). Note also that the iterator may not be dereferencable in that case.

iterator TrilinosWrappers::SparseMatrix::end ( const size_type  r)

Final iterator of row r. It points to the first element past the end of line r, or past the end of the entire sparsity pattern.

Note that the end iterator is not necessarily dereferencable. This is in particular the case if it is the end iterator for the last row of a matrix.

void TrilinosWrappers::SparseMatrix::write_ascii ( )

Abstract Trilinos object that helps view in ASCII other Trilinos objects. Currently this function is not implemented. TODO: Not implemented.

void TrilinosWrappers::SparseMatrix::print ( std::ostream &  out,
const bool  write_extended_trilinos_info = false 
) const

Print the matrix to the given stream, using the format (line,col) value, i.e. one nonzero entry of the matrix per line. The optional flag outputs the sparsity pattern in Trilinos style, where the data is sorted according to the processor number when printed to the stream, as well as a summary of the matrix like the global size.

void TrilinosWrappers::SparseMatrix::prepare_add ( )
protected

For some matrix storage formats, in particular for the PETSc distributed blockmatrices, set and add operations on individual elements can not be freely mixed. Rather, one has to synchronize operations when one wants to switch from setting elements to adding to elements. BlockMatrixBase automatically synchronizes the access by calling this helper function for each block. This function ensures that the matrix is in a state that allows adding elements; if it previously already was in this state, the function does nothing.

void TrilinosWrappers::SparseMatrix::prepare_set ( )
protected

Same as prepare_add() but prepare the matrix for setting elements if the representation of elements in this class requires such an operation.

Friends And Related Function Documentation

friend class BlockMatrixBase< SparseMatrix >
friend

To allow calling protected prepare_add() and prepare_set().

Definition at line 2550 of file trilinos_sparse_matrix.h.

Member Data Documentation

std_cxx1x::shared_ptr<Epetra_Map> TrilinosWrappers::SparseMatrix::column_space_map
private

Pointer to the user-supplied Epetra Trilinos mapping of the matrix columns that assigns parts of the matrix to the individual processes.

Definition at line 2501 of file trilinos_sparse_matrix.h.

std_cxx1x::shared_ptr<Epetra_FECrsMatrix> TrilinosWrappers::SparseMatrix::matrix
private

A sparse matrix object in Trilinos to be used for finite element based problems which allows for assembling into non-local elements. The actual type, a sparse matrix, is set in the constructor.

Definition at line 2513 of file trilinos_sparse_matrix.h.

Epetra_CombineMode TrilinosWrappers::SparseMatrix::last_action
private

Trilinos doesn't allow to mix additions to matrix entries and overwriting them (to make synchronisation of parallel computations simpler). The way we do it is to, for each access operation, store whether it is an insertion or an addition. If the previous one was of different type, then we first have to flush the Trilinos buffers; otherwise, we can simply go on. Luckily, Trilinos has an object for this which does already all the parallel communications in such a case, so we simply use their model, which stores whether the last operation was an addition or an insertion.

Definition at line 2536 of file trilinos_sparse_matrix.h.

bool TrilinosWrappers::SparseMatrix::compressed
private

A boolean variable to hold information on whether the vector is compressed or not.

Definition at line 2543 of file trilinos_sparse_matrix.h.


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