Reference documentation for deal.II version Git 3e8fd02 2017-09-22 11:37:14 +0200
Classes | Public Member Functions | Private Member Functions | Friends | List of all members
PETScWrappers::SparseMatrix Class Reference

#include <deal.II/lac/petsc_sparse_matrix.h>

Inheritance diagram for PETScWrappers::SparseMatrix:
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Classes

struct  Traits
 

Public Member Functions

 SparseMatrix ()
 
 SparseMatrix (const size_type m, const size_type n, const size_type n_nonzero_per_row, const bool is_symmetric=false)
 
 SparseMatrix (const size_type m, const size_type n, const std::vector< size_type > &row_lengths, const bool is_symmetric=false)
 
template<typename SparsityPatternType >
 SparseMatrix (const SparsityPatternType &sparsity_pattern, const bool preset_nonzero_locations=true)
 
SparseMatrixoperator= (const double d)
 
void reinit (const size_type m, const size_type n, const size_type n_nonzero_per_row, const bool is_symmetric=false)
 
void reinit (const size_type m, const size_type n, const std::vector< size_type > &row_lengths, const bool is_symmetric=false)
 
template<typename SparsityPatternType >
void reinit (const SparsityPatternType &sparsity_pattern, const bool preset_nonzero_locations=true)
 
virtual const MPI_Comm & get_mpi_communicator () const
 
size_t m () const
 
size_t n () const
 
- Public Member Functions inherited from PETScWrappers::MatrixBase
 MatrixBase ()
 
virtual ~MatrixBase ()
 
MatrixBaseoperator= (const value_type d)
 
void clear ()
 
void set (const size_type i, const size_type j, const PetscScalar value)
 
void set (const std::vector< size_type > &indices, const FullMatrix< PetscScalar > &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< PetscScalar > &full_matrix, const bool elide_zero_values=false)
 
void set (const size_type row, const std::vector< size_type > &col_indices, const std::vector< PetscScalar > &values, const bool elide_zero_values=false)
 
void set (const size_type row, const size_type n_cols, const size_type *col_indices, const PetscScalar *values, const bool elide_zero_values=false)
 
void add (const size_type i, const size_type j, const PetscScalar value)
 
void add (const std::vector< size_type > &indices, const FullMatrix< PetscScalar > &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< PetscScalar > &full_matrix, const bool elide_zero_values=true)
 
void add (const size_type row, const std::vector< size_type > &col_indices, const std::vector< PetscScalar > &values, const bool elide_zero_values=true)
 
void add (const size_type row, const size_type n_cols, const size_type *col_indices, const PetscScalar *values, const bool elide_zero_values=true, const bool col_indices_are_sorted=false)
 
void clear_row (const size_type row, const PetscScalar new_diag_value=0)
 
void clear_rows (const std::vector< size_type > &rows, const PetscScalar new_diag_value=0)
 
void compress (const VectorOperation::values operation)
 
PetscScalar operator() (const size_type i, const size_type j) const
 
PetscScalar el (const size_type i, const size_type j) const
 
PetscScalar diag_element (const size_type i) const
 
size_type m () const
 
size_type n () const
 
size_type 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
 
size_type row_length (const size_type row) const
 
PetscReal l1_norm () const
 
PetscReal linfty_norm () const
 
PetscReal frobenius_norm () const
 
PetscScalar matrix_norm_square (const VectorBase &v) const
 
PetscScalar matrix_scalar_product (const VectorBase &u, const VectorBase &v) const
 
PetscScalar trace () const
 
MatrixBaseoperator*= (const PetscScalar factor)
 
MatrixBaseoperator/= (const PetscScalar factor)
 
MatrixBaseadd (const PetscScalar factor, const MatrixBase &other)
 
MatrixBaseadd (const MatrixBase &other, const PetscScalar factor) 1
 
void vmult (VectorBase &dst, const VectorBase &src) const
 
void Tvmult (VectorBase &dst, const VectorBase &src) const
 
void vmult_add (VectorBase &dst, const VectorBase &src) const
 
void Tvmult_add (VectorBase &dst, const VectorBase &src) const
 
PetscScalar residual (VectorBase &dst, const VectorBase &x, const VectorBase &b) const
 
const_iterator begin () const
 
const_iterator end () const
 
const_iterator begin (const size_type r) const
 
const_iterator end (const size_type r) const
 
 operator Mat () const
 
void transpose ()
 
PetscBool is_symmetric (const double tolerance=1.e-12)
 
PetscBool is_hermitian (const double tolerance=1.e-12)
 
void write_ascii (const PetscViewerFormat format=PETSC_VIEWER_DEFAULT)
 
void print (std::ostream &out, const bool alternative_output=false) const
 
std::size_t memory_consumption () const
 
- Public Member Functions inherited from Subscriptor
 Subscriptor ()
 
 Subscriptor (const Subscriptor &)
 
 Subscriptor (Subscriptor &&)
 
virtual ~Subscriptor ()
 
Subscriptoroperator= (const Subscriptor &)
 
Subscriptoroperator= (Subscriptor &&)
 
void subscribe (const char *identifier=nullptr) const
 
void unsubscribe (const char *identifier=nullptr) const
 
unsigned int n_subscriptions () const
 
void list_subscribers () const
 
template<class Archive >
void serialize (Archive &ar, const unsigned int version)
 

Private Member Functions

 SparseMatrix (const SparseMatrix &)=delete
 
SparseMatrixoperator= (const SparseMatrix &)=delete
 
void do_reinit (const size_type m, const size_type n, const size_type n_nonzero_per_row, const bool is_symmetric=false)
 
void do_reinit (const size_type m, const size_type n, const std::vector< size_type > &row_lengths, const bool is_symmetric=false)
 
template<typename SparsityPatternType >
void do_reinit (const SparsityPatternType &sparsity_pattern, const bool preset_nonzero_locations)
 

Friends

class BlockMatrixBase< SparseMatrix >
 

Additional Inherited Members

- Public Types inherited from PETScWrappers::MatrixBase
typedef MatrixIterators::const_iterator const_iterator
 
typedef types::global_dof_index size_type
 
typedef PetscScalar value_type
 
- Static Public Member Functions inherited from PETScWrappers::MatrixBase
static::ExceptionBase & ExcSourceEqualsDestination ()
 
static::ExceptionBase & ExcWrongMode (int arg1, int arg2)
 
- Static Public Member Functions inherited from Subscriptor
static::ExceptionBase & ExcInUse (int arg1, char *arg2, std::string &arg3)
 
static::ExceptionBase & ExcNoSubscriber (char *arg1, char *arg2)
 
- Protected Member Functions inherited from PETScWrappers::MatrixBase
void prepare_action (const VectorOperation::values new_action)
 
void assert_is_compressed ()
 
void prepare_add ()
 
void prepare_set ()
 
- Protected Attributes inherited from PETScWrappers::MatrixBase
Mat matrix
 
VectorOperation::values last_action
 

Detailed Description

Implementation of a sequential sparse matrix class based on PETSc. All the functionality is actually in the base class, except for the calls to generate a sequential sparse matrix. This is possible since PETSc only works on an abstract matrix type and internally distributes to functions that do the actual work depending on the actual matrix type (much like using virtual functions). Only the functions creating a matrix of specific type differ, and are implemented in this particular class.

Author
Wolfgang Bangerth, 2004

Definition at line 49 of file petsc_sparse_matrix.h.

Constructor & Destructor Documentation

SparseMatrix< number >::SparseMatrix ( )

Default constructor. Create an empty matrix.

Definition at line 31 of file petsc_sparse_matrix.cc.

SparseMatrix< number >::SparseMatrix ( const size_type  m,
const size_type  n,
const size_type  n_nonzero_per_row,
const bool  is_symmetric = false 
)

Create a sparse matrix of dimensions m times n, with an initial guess of n_nonzero_per_row nonzero elements per row. PETSc is able to cope with the situation that more than this number of elements is later allocated for a row, but this involves copying data, and is thus expensive.

The is_symmetric flag determines whether we should tell PETSc that the matrix is going to be symmetric (as indicated by the call MatSetOption(mat, MAT_SYMMETRIC). Note that the PETSc documentation states that one cannot form an ILU decomposition of a matrix for which this flag has been set to true, only an ICC. The default value of this flag is false.

Definition at line 41 of file petsc_sparse_matrix.cc.

SparseMatrix< number >::SparseMatrix ( const size_type  m,
const size_type  n,
const std::vector< size_type > &  row_lengths,
const bool  is_symmetric = false 
)

Initialize a rectangular matrix with m rows and n columns. The maximal number of nonzero entries for each row separately is given by the row_lengths array.

Just as for the other constructors: PETSc is able to cope with the situation that more than this number of elements is later allocated for a row, but this involves copying data, and is thus expensive.

The is_symmetric flag determines whether we should tell PETSc that the matrix is going to be symmetric (as indicated by the call MatSetOption(mat, MAT_SYMMETRIC). Note that the PETSc documentation states that one cannot form an ILU decomposition of a matrix for which this flag has been set to true, only an ICC. The default value of this flag is false.

Definition at line 51 of file petsc_sparse_matrix.cc.

template<typename SparsityPatternType >
SparseMatrix< SparsityPatternType >::SparseMatrix ( const SparsityPatternType &  sparsity_pattern,
const bool  preset_nonzero_locations = true 
)
explicit

Initialize a sparse matrix using the given sparsity pattern.

Note that PETSc can be very slow if you do not provide it with a good estimate of the lengths of rows. Using the present function is a very efficient way to do this, as it uses the exact number of nonzero entries for each row of the matrix by using the given sparsity pattern argument. If the preset_nonzero_locations flag is true, this function in addition not only sets the correct row sizes up front, but also pre-allocated the correct nonzero entries in the matrix.

PETsc allows to later add additional nonzero entries to a matrix, by simply writing to these elements. However, this will then lead to additional memory allocations which are very inefficient and will greatly slow down your program. It is therefore significantly more efficient to get memory allocation right from the start.

Definition at line 63 of file petsc_sparse_matrix.cc.

PETScWrappers::SparseMatrix::SparseMatrix ( const SparseMatrix )
privatedelete

Purposefully not implemented

Member Function Documentation

SparseMatrix & SparseMatrix< number >::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 keep the sparsity pattern previously used.

Definition at line 72 of file petsc_sparse_matrix.cc.

void SparseMatrix< number >::reinit ( const size_type  m,
const size_type  n,
const size_type  n_nonzero_per_row,
const bool  is_symmetric = false 
)

Throw away the present matrix and generate one that has the same properties as if it were created by the constructor of this class with the same argument list as the present function.

Definition at line 81 of file petsc_sparse_matrix.cc.

void SparseMatrix< number >::reinit ( const size_type  m,
const size_type  n,
const std::vector< size_type > &  row_lengths,
const bool  is_symmetric = false 
)

Throw away the present matrix and generate one that has the same properties as if it were created by the constructor of this class with the same argument list as the present function.

Definition at line 97 of file petsc_sparse_matrix.cc.

template<typename SparsityPatternType >
void SparseMatrix< SparsityPatternType >::reinit ( const SparsityPatternType &  sparsity_pattern,
const bool  preset_nonzero_locations = true 
)

Initialize a sparse matrix using the given sparsity pattern.

Note that PETSc can be very slow if you do not provide it with a good estimate of the lengths of rows. Using the present function is a very efficient way to do this, as it uses the exact number of nonzero entries for each row of the matrix by using the given sparsity pattern argument. If the preset_nonzero_locations flag is true, this function in addition not only sets the correct row sizes up front, but also pre-allocated the correct nonzero entries in the matrix.

PETsc allows to later add additional nonzero entries to a matrix, by simply writing to these elements. However, this will then lead to additional memory allocations which are very inefficient and will greatly slow down your program. It is therefore significantly more efficient to get memory allocation right from the start.

Despite the fact that it would seem to be an obvious win, setting the preset_nonzero_locations flag to true doesn't seem to accelerate program. Rather on the contrary, it seems to be able to slow down entire programs somewhat. This is surprising, since we can use efficient function calls into PETSc that allow to create multiple entries at once; nevertheless, given the fact that it is inefficient, the respective flag has a default value equal to false.

Definition at line 115 of file petsc_sparse_matrix.cc.

const MPI_Comm & SparseMatrix< number >::get_mpi_communicator ( ) const
virtual

Return a reference to the MPI communicator object in use with this matrix. Since this is a sequential matrix, it returns the MPI_COMM_SELF communicator.

Implements PETScWrappers::MatrixBase.

Definition at line 129 of file petsc_sparse_matrix.cc.

size_t SparseMatrix< number >::m ( ) const

Return the number of rows of this matrix.

Definition at line 246 of file petsc_sparse_matrix.cc.

size_t SparseMatrix< number >::n ( ) const

Return the number of coloumns of this matrix.

Definition at line 256 of file petsc_sparse_matrix.cc.

SparseMatrix& PETScWrappers::SparseMatrix::operator= ( const SparseMatrix )
privatedelete

Purposefully not implemented

void SparseMatrix< number >::do_reinit ( const size_type  m,
const size_type  n,
const size_type  n_nonzero_per_row,
const bool  is_symmetric = false 
)
private

Do the actual work for the respective reinit() function and the matching constructor, i.e. create a matrix. Getting rid of the previous matrix is left to the caller.

Definition at line 140 of file petsc_sparse_matrix.cc.

void SparseMatrix< number >::do_reinit ( const size_type  m,
const size_type  n,
const std::vector< size_type > &  row_lengths,
const bool  is_symmetric = false 
)
private

Same as previous function.

Definition at line 163 of file petsc_sparse_matrix.cc.

template<typename SparsityPatternType >
void SparseMatrix< SparsityPatternType >::do_reinit ( const SparsityPatternType &  sparsity_pattern,
const bool  preset_nonzero_locations 
)
private

Same as previous function.

Definition at line 197 of file petsc_sparse_matrix.cc.

Friends And Related Function Documentation

friend class BlockMatrixBase< SparseMatrix >
friend

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

Definition at line 251 of file petsc_sparse_matrix.h.


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